Ab initio simulations of bond breaking in sulfur crosslinked isoprene oligomer units

NASA Astrophysics Data System (ADS)

Gehrke, Sascha; Alznauer, Hans Tobias; Karimi-Varzaneh, Hossein Ali; Becker, Jörg August

2017-12-01

Sulfur crosslinked polyisoprene (rubber) is used in important material components for a number of technical tasks (e.g., in tires and sealings). If mechanical stress, like tension or shear, is applied on these material components, the sulfur crosslinks suffer from homolytic bond breaking. In this work, we have simulated the bond breaking mechanism of sulfur crosslinks between polyisoprene chains using Car-Parrinello molecular dynamic simulations and investigated the maximum forces which can be resisted by the crosslinks. Small model systems with crosslinks formed by chains of N = 1 to N = 6 sulfur atoms have been simulated with the slow growth-technique, known from the literature. The maximum force can be thereby determined from the calculated energies as a function of strain (elongation). The stability of the crosslink under strain is quantified in terms of the maximum force that can be resisted by the system before the crosslink breaks. As shown by our simulations, this maximum force decreases with the sulfur crosslink length N in a step like manner. Our findings indicate that in bridges with N = 1, 2, and 3 sulfur atoms predominantly, carbon-sulfur bonds break, while in crosslinks with N > 3, the breaking of a sulfur-sulfur bond is the dominant failure mechanism. The results are explained within a simple chemical bond model, which describes how the delocalization of the electrons in the generated radicals can lower their electronic energy and decrease the activation barriers. It is described which of the double bonds in the isoprene units are involved in the mechanochemistry of crosslinked rubber.

Exothermic Bond Breaking: A Persistent Misconception

ERIC Educational Resources Information Center

Galley, William C.

2004-01-01

The misconceptions regarding the nature of ATP hydrolysis and bond breaking are discussed. The students' knowledge in this area is quantitatively measured by a survey of over 600 biochemistry and physiology students.

Site-Specific Imaging of Elemental Steps in Dehydration of Diols on TiO 2(110)

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

Acharya, Danda P.; Yoon, Yeohoon; Li, Zhenjun

2013-11-26

The conversion of diols on partially reduced TiO 2(110) at low coverage was studied using variable-temperature scanning tunneling microscopy, temperature programmed desorption and density functional theory calculations. We find, that below ~230 K, ethane-1,2-diol and propane-1,3-diol molecules adsorb predominantly on five-fold coordinated Ti5c atoms. The dynamic equilibrium between molecularly bound and dissociated species resulting from O-H bond scission and reformation is observed. As the diols start to diffuse on the Ti5c rows above ~230 K, they dissociate irreversibly upon encountering bridging oxygen (O b) vacancy (VO’s) defects. Two dissociation pathways, one via O-H and the other via C-O bond scissionmore » leading to identical surface intermediates, hydroxyalkoxy, O b-(CH 2)n-OH (n = 2, 3) and bridging hydroxyl, HO b, are seen. For O-H bond scission, the O b-(CH 2)n-OH is found on the position of the original VO, while for C-O scission it is found on the adjacent Ob site. Theoretical calculations suggest that the observed mixture of C-O/O-H bond breaking processes are a result of the steric factors enforced upon the diols by the second OH group that is bound to a Ti5c site. At room temperature, rich dissociation/reformation dynamics of the second, Ti5c-bound O-H leads to the formation of dioxo, Ob-(CH 2)n-OTi, species. Above ~400 K, both O b-(CH 2)n-OH and Ob-(CH 2)n-OTi species convert into a new intermediate, that is centered on Ob row. Combined experimental and theoretical evidence shows that this intermediate is most likely a new dioxo, O b-(CH 2) 2-Ob, species. Further annealing leads to sequential C-Ob bond cleavage and alkene desorption above ~ 500 K. Simulations find that the sequential C-O bond breaking process follows a homolytic diradical pathway with the first C-O bond breaking event accompanied by a non-adiabatic electron transfer within the TiO 2(110) substrate.« less

Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins.

PubMed

Das, A K; Meuwly, M

2016-01-01

Following chemical reactions in atomistic detail is one of the most challenging aspects of current computational approaches to chemistry. In this chapter the application of adiabatic reactive MD (ARMD) and its multistate version (MS-ARMD) are discussed. Both methods allow to study bond-breaking and bond-forming processes in chemical and biological processes. Particular emphasis is put on practical aspects for applying the methods to investigate the dynamics of chemical reactions. The chapter closes with an outlook of possible generalizations of the methods discussed. © 2016 Elsevier Inc. All rights reserved.

Nanoscopic length scale dependence of hydrogen bonded molecular associates’ dynamics in methanol

PubMed Central

Bertrand, C. E.; Self, J. L.; Copley, J. R. D.; Faraone, A.

2017-01-01

In a recent paper [C. E. Bertrand et al., J. Chem. Phys. 145, 014502 (2016)], we have shown that the collective dynamics of methanol shows a fast relaxation process related to the standard density-fluctuation heat mode and a slow non-Fickian mode originating from the hydrogen bonded molecular associates. Here we report on the length scale dependence of this slow relaxation process. Using quasielastic neutron scattering and molecular dynamics simulations, we show that the dynamics of the slow process is affected by the structuring of the associates, which is accessible through polarized neutron diffraction experiments. Using a series of partially deuterated samples, the dynamics of the associates is investigated and is found to have a similar time scale to the lifetime of hydrogen bonding in the system. Both the structural relaxation and the dynamics of the associates are thermally activated by the breaking of hydrogen bonding. PMID:28527447

The effects of low salt concentrations on the mechanism of adhesion between two pieces of pork semimembranosus muscle following tumbling and cooking.

PubMed

Bombrun, Laure; Gatellier, Philippe; Carlier, Martine; Kondjoyan, Alain

2014-01-01

The aim of this research was to gain deeper insight into the effect of salt content on the adhesion between pieces of semimembranosus pork muscle bound by a tumbling exudate gel. Hydrophobic site number, free thiol and carbonyl content were measured in tumbling exudate and meat protein to evaluate the protein-protein interactions involved in the adhesion process. Proteins were far more oxidized in exudate than in meat, and under our experimental conditions, salt content increased protein bonding in the exudate but not in the meat. Breaking stress increased between non-salted meat and 0.8%-salted meat but did not depend on the protein physicochemical properties of the tumbling exudate. Modifying the meat surface by tumbling alone, tumbling and salting, or scarification had no effect on breaking stress. It is suggested that the break between the meat pieces occurred between the tumbling exudate and the meat surface due to weaker chemical bonds at this location. © 2013.

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

Manolopoulou, Marika; Guo, Qing; Malito, Enrico

Insulin is a hormone vital for glucose homeostasis, and insulin-degrading enzyme (IDE) plays a key role in its clearance. IDE exhibits a remarkable specificity to degrade insulin without breaking the disulfide bonds that hold the insulin A and B chains together. Using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry to obtain high mass accuracy, and electron capture dissociation (ECD) to selectively break the disulfide bonds in gas phase fragmentation, we determined the cleavage sites and composition of human insulin fragments generated by human IDE. Our time-dependent analysis of IDE-digested insulin fragments reveals that IDE is highly processive in itsmore » initial cleavage at the middle of both the insulin A and B chains. This ensures that IDE effectively splits insulin into inactive N- and C-terminal halves without breaking the disulfide bonds. To understand the molecular basis of the recognition and unfolding of insulin by IDE, we determined a 2.6-A resolution insulin-bound IDE structure. Our structure reveals that IDE forms an enclosed catalytic chamber that completely engulfs and intimately interacts with a partially unfolded insulin molecule. This structure also highlights how the unique size, shape, charge distribution, and exosite of the IDE catalytic chamber contribute to its high affinity ( approximately 100 nm) for insulin. In addition, this structure shows how IDE utilizes the interaction of its exosite with the N terminus of the insulin A chain as well as other properties of the catalytic chamber to guide the unfolding of insulin and allowing for the processive cleavages.« less

Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin

PubMed Central

Kontur, Wayne S.; Bingman, Craig A.; Olmsted, Charles N.; Wassarman, Douglas R.; Ulbrich, Arne; Gall, Daniel L.; Smith, Robert W.; Yusko, Larissa M.; Fox, Brian G.; Noguera, Daniel R.; Coon, Joshua J.; Donohue, Timothy J.

2018-01-01

As a major component of plant cell walls, lignin is a potential renewable source of valuable chemicals. Several sphingomonad bacteria have been identified that can break the β-aryl ether bond connecting most phenylpropanoid units of the lignin heteropolymer. Here, we tested three sphingomonads predicted to be capable of breaking the β-aryl ether bond of the dimeric aromatic compound guaiacylglycerol-β-guaiacyl ether (GGE) and found that Novosphingobium aromaticivorans metabolizes GGE at one of the fastest rates thus far reported. After the ether bond of racemic GGE is broken by replacement with a thioether bond involving glutathione, the glutathione moiety must be removed from the resulting two stereoisomers of the phenylpropanoid conjugate β-glutathionyl-γ-hydroxypropiovanillone (GS-HPV). We found that the Nu-class glutathione S-transferase NaGSTNu is the only enzyme needed to remove glutathione from both (R)- and (S)-GS-HPV in N. aromaticivorans. We solved the crystal structure of NaGSTNu and used molecular modeling to propose a mechanism for the glutathione lyase (deglutathionylation) reaction in which an enzyme-stabilized glutathione thiolate attacks the thioether bond of GS-HPV, and the reaction proceeds through an enzyme-stabilized enolate intermediate. Three residues implicated in the proposed mechanism (Thr51, Tyr166, and Tyr224) were found to be critical for the lyase reaction. We also found that Nu-class GSTs from Sphingobium sp. SYK-6 (which can also break the β-aryl ether bond) and Escherichia coli (which cannot break the β-aryl ether bond) can also cleave (R)- and (S)-GS-HPV, suggesting that glutathione lyase activity may be common throughout this widespread but largely uncharacterized class of glutathione S-transferases. PMID:29449375

Electrochemical removal of hydrogen atoms in Mg-doped GaN epitaxial layers

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

Lee, June Key, E-mail: junekey@jnu.ac.kr, E-mail: hskim7@jbnu.ac.kr; Hyeon, Gil Yong; Tawfik, Wael Z.

2015-05-14

Hydrogen atoms inside of an Mg-doped GaN epitaxial layer were effectively removed by the electrochemical potentiostatic activation (EPA) method. The role of hydrogen was investigated in terms of the device performance of light-emitting diodes (LEDs). The effect of the main process parameters for EPA such as solution type, voltage, and time was studied and optimized for application to LED fabrication. In optimized conditions, the light output of 385-nm LEDs was improved by about 26% at 30 mA, which was caused by the reduction of the hydrogen concentration by ∼35%. Further removal of hydrogen seems to be involved in the breaking ofmore » Ga-H bonds that passivate the nitrogen vacancies. An EPA process with high voltage breaks not only Mg-H bonds that generate hole carriers but also Ga-H bonds that generate electron carriers, thus causing compensation that impedes the practical increase of hole concentration, regardless of the drastic removal of hydrogen atoms. A decrease in hydrogen concentration affects the current-voltage characteristics, reducing the reverse current by about one order and altering the forward current behavior in the low voltage region.« less

Electrochemical removal of hydrogen atoms in Mg-doped GaN epitaxial layers

NASA Astrophysics Data System (ADS)

Lee, June Key; Hyeon, Gil Yong; Tawfik, Wael Z.; Choi, Hee Seok; Ryu, Sang-Wan; Jeong, Tak; Jung, Eunjin; Kim, Hyunsoo

2015-05-01

Hydrogen atoms inside of an Mg-doped GaN epitaxial layer were effectively removed by the electrochemical potentiostatic activation (EPA) method. The role of hydrogen was investigated in terms of the device performance of light-emitting diodes (LEDs). The effect of the main process parameters for EPA such as solution type, voltage, and time was studied and optimized for application to LED fabrication. In optimized conditions, the light output of 385-nm LEDs was improved by about 26% at 30 mA, which was caused by the reduction of the hydrogen concentration by ˜35%. Further removal of hydrogen seems to be involved in the breaking of Ga-H bonds that passivate the nitrogen vacancies. An EPA process with high voltage breaks not only Mg-H bonds that generate hole carriers but also Ga-H bonds that generate electron carriers, thus causing compensation that impedes the practical increase of hole concentration, regardless of the drastic removal of hydrogen atoms. A decrease in hydrogen concentration affects the current-voltage characteristics, reducing the reverse current by about one order and altering the forward current behavior in the low voltage region.

Ultrasonic friction power during Al wire wedge-wedge bonding

NASA Astrophysics Data System (ADS)

Shah, A.; Gaul, H.; Schneider-Ramelow, M.; Reichl, H.; Mayer, M.; Zhou, Y.

2009-07-01

Al wire bonding, also called ultrasonic wedge-wedge bonding, is a microwelding process used extensively in the microelectronics industry for interconnections to integrated circuits. The bonding wire used is a 25μm diameter AlSi1 wire. A friction power model is used to derive the ultrasonic friction power during Al wire bonding. Auxiliary measurements include the current delivered to the ultrasonic transducer, the vibration amplitude of the bonding tool tip in free air, and the ultrasonic force acting on the bonding pad during the bond process. The ultrasonic force measurement is like a signature of the bond as it allows for a detailed insight into mechanisms during various phases of the process. It is measured using piezoresistive force microsensors integrated close to the Al bonding pad (Al-Al process) on a custom made test chip. A clear break-off in the force signal is observed, which is followed by a relatively constant force for a short duration. A large second harmonic content is observed, describing a nonsymmetric deviation of the signal wave form from the sinusoidal shape. This deviation might be due to the reduced geometrical symmetry of the wedge tool. For bonds made with typical process parameters, several characteristic values used in the friction power model are determined. The ultrasonic compliance of the bonding system is 2.66μm/N. A typical maximum value of the relative interfacial amplitude of ultrasonic friction is at least 222nm. The maximum interfacial friction power is at least 11.5mW, which is only about 4.8% of the total electrical power delivered to the ultrasonic generator.

A Role-Play to Illustrate the Energy Changes Occurring in an Exothermic Reaction.

ERIC Educational Resources Information Center

Tyas, Toby; Cabot, John

1999-01-01

Describes a role-play activity designed to help students understand the energy changes involved in an exothermic reaction by modeling the concepts of bond-breaking takes in energy, activation energy, temperature rise, and bond breaking gives out energy. (WRM)

Molecular dynamics of acetamide based ionic deep eutectic solvents

NASA Astrophysics Data System (ADS)

Srinivasan, H.; Dubey, P. S.; Sharma, V. K.; Biswas, R.; Mitra, S.; Mukhopadhyay, R.

2018-04-01

Deep eutectic solvents are multi-component mixtures that have freezing point lower than their individual components. Mixture of acetamide+ lithium nitrate in the molar ratio 78:22 and acetamide+ lithium perchlorate in the molar ratio 81:19 are found to form deep eutectic solvents with melting point lower than the room temperature. It is known that the depression in freezing point is due to the hydrogen bond breaking ability of anions in the system. Quasielastic neutron scattering experiments on these systems were carried out to study the dynamics of acetamide molecules which may be influenced by this hydrogen bond breaking phenomena. The motion of acetamide molecules is modeled using jump diffusion mechanism to demonstrate continuous breaking and reforming hydrogen bonds in the solvent. Using the jump diffusion model, it is inferred that the jump lengths of acetamide molecules are better approximated by a Gaussian distribution. The shorter residence time of acetamide in presence of perchlorate ions suggest that the perchlorate ions have a higher hydrogen bond breaking ability compared to nitrate ions.

Towards a Molecular Movie: Real Time Observation of Hydrogen Bond Breaking by Transient 2D-IR Spectroscopy in a Cyclic Peptide

NASA Astrophysics Data System (ADS)

Kolano, Christoph; Helbing, Jan; Sander, Wolfram; Hamm, Peter

Transient two-dimensional infrared spectroscopy (T2D-IR) has been used to observe in real time the non-equilibrium structural dynamics of intramolecular hydrogen bond breaking in a small cyclic disulfide-bridged peptide.

Rate Kinetics and Molecular Dynamics of the Structural Transitions in Amyloidogenic Proteins

NASA Astrophysics Data System (ADS)

Steckmann, Timothy M.

Amyloid fibril aggregation is associated with several horrific diseases such as Alzheimer's, Creutzfeld-Jacob, diabetes, Parkinson's and others. The process of amyloid aggregation involves forming myriad different metastable intermediate aggregates. Amyloid fibrils are composed of proteins that originate in an innocuous alpha-helix or random-coil structure. The alpha-helices convert their structure to beta-strands that aggregate into beta-sheets, and then into protofibrils, and ultimately into fully formed amyloid fibrils. On the basis of experimental data, I have developed a mathematical model for the kinetics of the reaction pathways and determined rate parameters for peptide secondary structural conversion and aggregation during the entire fibrillogenesis process from random coil to fibrils, including the molecular species that accelerate the conversions. The specific steps of the model and the rate constants that are determined by fitting to experimental data provide insight on the molecular species involved in the fibril formation process. To better understand the molecular basis of the protein structural transitions and aggregation, I report on molecular dynamics (MD) computational studies on the formation of amyloid protofibrillar structures in the small model protein ccbeta, which undergoes many of the structural transitions of the larger, naturally occurring amyloid forming proteins. Two different structural transition processes involving hydrogen bonds are observed for aggregation into fibrils: the breaking of intrachain hydrogen bonds to allow beta-hairpin proteins to straighten, and the subsequent formation of interchain hydrogen bonds during aggregation into amyloid fibrils. For my MD simulations, I found that the temperature dependence of these two different structural transition processes results in the existence of a temperature window that the ccbeta protein experiences during the process of forming protofibrillar structures. Both the mathematical modeling of the kinetics and the MD simulations show that molecular structural heterogeneity is a major factor in the process. The MD simulations also show that intrachain and interchain hydrogen bonds breaking and forming is strongly correlated to the process of amyloid formation.

Composite adhesive bonds reinforced with microparticle filler based on egg shell waste

NASA Astrophysics Data System (ADS)

Müller, Miroslav; Valášek, Petr

2018-05-01

A research on composite adhesive bonds reinforced with waste from hen eggs processing, i.e. egg shell waste (ESW) is based on an assumption of the utilization of agricultural/food production waste. The aim of the research is to gain new pieces of knowledge about the material utilization of ESW, i.e. to evaluate possibilities of the use of various concentrations of ESW microparticles smaller than 100 µm based on hen egg shells as the filler in a structural resin used for a creation of adhesive bonds from bearing metal elements. An adhesive bond strength, an elongation at break and a fracture surface were evaluated within the research on adhesive bonds. The experiment results proved the efficiency of ESW filler in the area of composite adhesive bonds. The adhesive bond strength was increased up of more than 17 % by adding 40 wt.% of ESW microparticles.

What holds paper together: Nanometre scale exploration of bonding between paper fibres

PubMed Central

Schmied, Franz J.; Teichert, Christian; Kappel, Lisbeth; Hirn, Ulrich; Bauer, Wolfgang; Schennach, Robert

2013-01-01

Paper, a man-made material that has been used for hundreds of years, is a network of natural cellulosic fibres. To a large extent, it is the strength of bonding between these individual fibres that controls the strength of paper. Using atomic force microscopy, we explore here the mechanical properties of individual fibre-fibre bonds on the nanometre scale. A single fibre-fibre bond is loaded with a calibrated cantilever statically and dynamically until the bond breaks. Besides the calculation of the total energy input, time dependent processes such as creep and relaxation are studied. Through the nanometre scale investigation of the formerly bonded area, we show that fibrils or fibril bundles play a crucial role in fibre-fibre bonding because they act as bridging elements. With this knowledge, new fabrication routes can be deduced to increase the strength of an ancient product that is in fact an overlooked high-tech material. PMID:23969946

A study on an unusual SN2 mechanism in the methylation of benzyne through nickel-complexation.

PubMed

Hatakeyama, Makoto; Sakamoto, Yuki; Ogata, Koji; Sumida, Yuto; Sumida, Tomoe; Hosoya, Takamitsu; Nakamura, Shinichiro

2017-10-11

In this study, three reaction mechanisms of a benzyne-nickel (Ni) complex ([Ni(C 6 H 4 )(dcpe)]) with iodomethane during the methylation process were investigated, namely (a) S N 2 reaction of the benzyne-Ni complex with iodomethane, (b) concerted σ-bond metathesis during the bond breaking/forming processes, and (c) oxidative addition of iodomethane to the Ni-center and the subsequent reductive elimination process. DFT calculations revealed that the reaction barrier of the S N 2 reaction is slightly lower than those of the other mechanisms. The results of orbital analyses suggest that [Ni(C 6 H 4 )(dcpe)] forms a metallacycle structure between benzyne and the Ni II (3d 8 ) center instead of the η 2 -structure with the Ni 0 (3d 10 ) center. The metallacycle structures became inappropriate as the intermediates of oxidative addition in the formation of the Ni II -Me bond, avoiding further oxidation to the high-valent Ni IV . The high free energy along σ-bond metathesis was generated from the steric hindrance, thus invoking methylation and Ni-I bond formation concertedly.

Method for the addition of vulcanized waste rubber to virgin rubber products

DOEpatents

Romine, Robert A.; Snowden-Swan, Lesley J.

1997-01-01

The invention is a method of using enzymes from thiophyllic microbes for selectively breaking the sulfur rubber cross-link bonds in vulcanized rubber. The process is halted at the sulfoxide or sulfone step so that a devulcanized layer is reactive with virgin rubber.

Method for the addition of vulcanized waste rubber to virgin rubber products

DOEpatents

Romine, R.A.; Snowden-Swan, L.J.

1997-01-28

The invention is a method of using enzymes from thiophyllic microbes for selectively breaking the sulfur rubber cross-link bonds in vulcanized rubber. The process is halted at the sulfoxide or sulfone step so that a devulcanized layer is reactive with virgin rubber. 8 figs.

Hydration dynamics of a lipid membrane: Hydrogen bond networks and lipid-lipid associations

NASA Astrophysics Data System (ADS)

Srivastava, Abhinav; Debnath, Ananya

2018-03-01

Dynamics of hydration layers of a dimyristoylphosphatidylcholine (DMPC) bilayer are investigated using an all atom molecular dynamics simulation. Based upon the geometric criteria, continuously residing interface water molecules which form hydrogen bonds solely among themselves and then concertedly hydrogen bonded to carbonyl, phosphate, and glycerol head groups of DMPC are identified. The interface water hydrogen bonded to lipids shows slower relaxation rates for translational and rotational dynamics compared to that of the bulk water and is found to follow sub-diffusive and non-diffusive behaviors, respectively. The mean square displacements and the reorientational auto-correlation functions are slowest for the interfacial waters hydrogen bonded to the carbonyl oxygen since these are buried deep in the hydrophobic core among all interfacial water studied. The intermittent hydrogen bond auto-correlation functions are calculated, which allows breaking and reformations of the hydrogen bonds. The auto-correlation functions for interfacial hydrogen bonded networks develop humps during a transition from cage-like motion to eventual power law behavior of t-3/2. The asymptotic t-3/2 behavior indicates translational diffusion dictated dynamics during hydrogen bond breaking and formation irrespective of the nature of the chemical confinement. Employing reactive flux correlation analysis, the forward rate constant of hydrogen bond breaking and formation is calculated which is used to obtain Gibbs energy of activation of the hydrogen bond breaking. The relaxation rates of the networks buried in the hydrophobic core are slower than the networks near the lipid-water interface which is again slower than bulk due to the higher Gibbs energy of activation. Since hydrogen bond breakage follows a translational diffusion dictated mechanism, chemically confined hydrogen bond networks need an activation energy to diffuse through water depleted hydrophobic environments. Our calculations reveal that the slow relaxation rates of interfacial waters in the vicinity of lipids are originated from the chemical confinement of concerted hydrogen bond networks. The analysis suggests that the networks in the hydration layer of membranes dynamically facilitate the water mediated lipid-lipid associations which can provide insights on the thermodynamic stability of soft interfaces relevant to biological systems in the future.

Predicting Trigger Bonds in Explosive Materials through Wiberg Bond Index Analysis.

PubMed

Harper, Lenora K; Shoaf, Ashley L; Bayse, Craig A

2015-12-21

Understanding the explosive decomposition pathways of high-energy-density materials (HEDMs) is important for developing compounds with improved properties. Rapid reaction rates make the detonation mechanisms of HEDMs difficult to understand, so computational tools are used to predict trigger bonds-weak bonds that break, leading to detonation. Wiberg bond indices (WBIs) have been used to compare bond densities in HEDMs to reference molecules to provide a relative scale for the bond strength to predict the activated bonds most likely to break to trigger an explosion. This analysis confirms that X-NO2 (X=N,C,O) bonds are trigger linkages in common HEDMs such as TNT, RDX and PETN, consistent with previous experimental and theoretical studies. Calculations on a small test set of substituted tetrazoles show that the assignment of the trigger bond depends upon the functionality of the material and that the relative weakening of the bond correlates with experimental impact sensitivities. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biomolecular structure manipulation using tailored electromagnetic radiation: a proof of concept on a simplified model of the active site of bacterial DNA topoisomerase.

PubMed

Jarukanont, Daungruthai; Coimbra, João T S; Bauerhenne, Bernd; Fernandes, Pedro A; Patel, Shekhar; Ramos, Maria J; Garcia, Martin E

2014-10-21

We report on the viability of breaking selected bonds in biological systems using tailored electromagnetic radiation. We first demonstrate, by performing large-scale simulations, that pulsed electric fields cannot produce selective bond breaking. Then, we present a theoretical framework for describing selective energy concentration on particular bonds of biomolecules upon application of tailored electromagnetic radiation. The theory is based on the mapping of biomolecules to a set of coupled harmonic oscillators and on optimal control schemes to describe optimization of temporal shape, the phase and polarization of the external radiation. We have applied this theory to demonstrate the possibility of selective bond breaking in the active site of bacterial DNA topoisomerase. For this purpose, we have focused on a model that was built based on a case study. Results are given as a proof of concept.

Nonlinear electronic stopping power of channeled slow light ions in ZnSe: Evidence of energy loss caused by formation and breaking of chemical bond

NASA Astrophysics Data System (ADS)

Li, Chang-kai; Wang, Feng; Gao, Cong-Zhang; Liao, Bin; Ouyang, Xiao-ping; Zhang, Feng-Shou

2018-07-01

Electronic stopping power of helium ions in a semiconductor material ZnSe has been investigated through non-adiabatic dynamics simulations at energies of a few keV under channeling condition. The stopping power is predicted to be proportional to velocity for the trajectory along middle axis of a 〈 1 1 0 〉 channel, as expected for the linear response theory accounts for election-hole pair creation. While for the off-center channeling trajectory, a counterintuitive of electronic stopping power versus velocity is observed. Our study, presented herein, finds a non-trivial connection between charge transfer and the force experienced by the projectile. Charge transfer can produce, throughout the collision process, additional force by continuously forming and breaking instantaneous chemical bonds between the projectile and the neighboring host atoms.

The Relaxation of Vicinal (001) with ZigZag [110] Steps

NASA Astrophysics Data System (ADS)

Hawkins, Micah; Hamouda, Ajmi Bh; González-Cabrera, Diego Luis; Einstein, Theodore L.

2012-02-01

This talk presents a kinetic Monte Carlo study of the relaxation dynamics of [110] steps on a vicinal (001) simple cubic surface. This system is interesting because [110] steps have different elementary excitation energetics and favor step diffusion more than close-packed [100] steps. In this talk we show how this leads to relaxation dynamics showing greater fluctuations on a shorter time scale for [110] steps as well as 2-bond breaking processes being rate determining in contrast to 3-bond breaking processes for [100] steps. The existence of a steady state is shown via the convergence of terrace width distributions at times much longer than the relaxation time. In this time regime excellent fits to the modified generalized Wigner distribution (as well as to the Berry-Robnik model when steps can overlap) were obtained. Also, step-position correlation function data show diffusion-limited increase for small distances along the step as well as greater average step displacement for zigzag steps compared to straight steps for somewhat longer distances along the step. Work supported by NSF-MRSEC Grant DMR 05-20471 as well as a DOE-CMCSN Grant.

Adhesive bonding and performance testing of bonded wood products

Treesearch

Charles R. Frihart

2005-01-01

Despite the importance of durable wood bonds, the factors that lead to durability are not well understood, and the internal forces exerted upon the bondline are often overlooked. Durability requires that the bonded assembly resist dimensional changes of wood with fluctuation of wood moisture levels. Both bonding and bond breaking steps need to be understood at cellular...

Covalent bond force profile and cleavage in a single polymer chain

NASA Astrophysics Data System (ADS)

Garnier, Lionel; Gauthier-Manuel, Bernard; van der Vegte, Eric W.; Snijders, Jaap; Hadziioannou, Georges

2000-08-01

We present here the measurement of the single-polymer entropic elasticity and the single covalent bond force profile, probed with two types of atomic force microscopes (AFM) on a synthetic polymer molecule: polymethacrylic acid in water. The conventional AFM allowed us to distinguish two types of interactions present in this system when doing force spectroscopic measurements: the first interaction is associated with adsorption sites of the polymer chains onto a bare gold surface, the second interaction is directly correlated to the rupture process of a single covalent bond. All these bridging interactions allowed us to stretch the single polymer chain and to determine the various factors playing a role in the elasticity of these molecules. To obtain a closer insight into the bond rupture process, we moved to a force sensor stable in position when measuring attractive forces. By optimizing the polymer length so as to fulfill the elastic stability conditions, we were able for the first time to map out the entire force profile associated with the cleavage of a single covalent bond. Experimental data coupled with molecular quantum mechanical calculations strongly suggest that the breaking bond is located at one end of the polymer chain.

Unravelling the reaction mechanism of matrix metalloproteinase 3 using QM/MM calculations

NASA Astrophysics Data System (ADS)

Feliciano, Gustavo Troiano; da Silva, Antônio José Roque

2015-07-01

The matrix metalloproteinase family (MMP) constitutes a family of zinc (Zn) proteases that catalyze the breaking of peptide bonds in proteins. These enzymes are very promising drug targets, since they are involved in remodeling and degradation of the extracellular matrix, which is a key process required for cancer metastasis, and thus, their reaction mechanism has been an area of intensive research. Early proposal based on acid base catalyzed hydrolysis, suggested that a conserved zinc bound water molecule acted as the nucleophile attacking the peptide bond carbon, after being activated by essential glutamate. The possibility of a direct nucleophilic attack by the enzyme, performed by the glutamate was also suggested. These are the key yet unsolved issues about MMP reaction mechanism. In the present work, we used hybrid quantum/classical calculations to analyze the structure and energetics of different possible hydrolysis reaction paths. The results support a water mediated mechanism, where both the nucleophile water molecule and the carbonyl oxygen of the scissile peptide bond are coordinated to zinc in the reactive configuration, while the essential glutamate acts as the base accepting the proton from the nucleophilic water. Formation of the carbon-oxygen bond and breaking of carbon-nitrogen bond were found to be concerted events, with a computed barrier of 14.8 kcal/mol. Substrate polarization was found to be important for the observed reaction mechanism, and a substantial change in the metal coordination environment was observed, particularly, regarding the zinc-histidine coordination.

Method of processing materials using an inductively coupled plasma

DOEpatents

Hull, D.E.; Bieniewski, T.M.

1987-04-13

A method of processing materials. The invention enables ultrafine, ultrapure powders to be formed from solid ingots in a gas free environment. A plasma is formed directly from an ingot which insures purity. The vaporized material is expanded through a nozzle and the resultant powder settles on a cold surface. An inductively coupled plasma may also be used to process waste chemicals. Noxious chemicals are directed through a series of plasma tubes, breaking molecular bonds and resulting in relatively harmless atomic constituents. 3 figs.

Bimetallic catalysis for C–C and C–X coupling reactions

PubMed Central

Pye, Dominic R.

2017-01-01

Bimetallic catalysis represents an alternative paradigm for coupling chemistry that complements the more traditional single-site catalysis approach. In this perspective, recent advances in bimetallic systems for catalytic C–C and C–X coupling reactions are reviewed. Behavior which complements that of established single-site catalysts is highlighted. Two major reaction classes are covered. First, generation of catalytic amounts of organometallic species of e.g. Cu, Au, or Ni capable of transmetallation to a Pd co-catalyst (or other traditional cross-coupling catalyst) has allowed important new C–C coupling technologies to emerge. Second, catalytic transformations involving binuclear bond-breaking and/or bond-forming steps, in some cases involving metal–metal bonds, represent a frontier area for C–C and C–X coupling processes.

Nonholonomic Hamiltonian Method for Molecular Dynamics Simulations of Reacting Shocks

NASA Astrophysics Data System (ADS)

Fahrenthold, Eric; Bass, Joseph

2015-06-01

Conventional molecular dynamics simulations of reacting shocks employ a holonomic Hamiltonian formulation: the breaking and forming of covalent bonds is described by potential functions. In general these potential functions: (a) are algebraically complex, (b) must satisfy strict smoothness requirements, and (c) contain many fitted parameters. In recent research the authors have developed a new noholonomic formulation of reacting molecular dynamics. In this formulation bond orders are determined by rate equations and the bonding-debonding process need not be described by differentiable functions. This simplifies the representation of complex chemistry and reduces the number of fitted model parameters. Example applications of the method show molecular level shock to detonation simulations in nitromethane and RDX. Research supported by the Defense Threat Reduction Agency.

Role of step stiffness and kinks in the relaxation of vicinal (001) with zigzag [110] steps

NASA Astrophysics Data System (ADS)

Mahjoub, B.; Hamouda, Ajmi BH.; Einstein, TL.

2017-08-01

We present a kinetic Monte Carlo study of the relaxation dynamics and steady state configurations of 〈110〉 steps on a vicinal (001) simple cubic surface. This system is interesting because 〈110〉 (fully kinked) steps have different elementary excitation energetics and favor step diffusion more than 〈100〉 (nominally straight) steps. In this study we show how this leads to different relaxation dynamics as well as to different steady state configurations, including that 2-bond breaking processes are rate determining for 〈110〉 steps in contrast to 3-bond breaking processes for 〈100〉-steps found in previous work [Surface Sci. 602, 3569 (2008)]. The analysis of the terrace-width distribution (TWD) shows a significant role of kink-generation-annihilation processes during the relaxation of steps: the kinetic of relaxation, toward the steady state, is much faster in the case of 〈110〉-zigzag steps, with a higher standard deviation of the TWD, in agreement with a decrease of step stiffness due to orientation. We conclude that smaller step stiffness leads inexorably to faster step dynamics towards the steady state. The step-edge anisotropy slows the relaxation of steps and increases the strength of step-step effective interactions.

Ethylene glycol revisited: Molecular dynamics simulations and visualization of the liquid and its hydrogen-bond network☆

PubMed Central

Kaiser, Alexander; Ismailova, Oksana; Koskela, Antti; Huber, Stefan E.; Ritter, Marcel; Cosenza, Biagio; Benger, Werner; Nazmutdinov, Renat; Probst, Michael

2014-01-01

Molecular dynamics simulations of liquid ethylene glycol described by the OPLS-AA force field were performed to gain insight into its hydrogen-bond structure. We use the population correlation function as a statistical measure for the hydrogen-bond lifetime. In an attempt to understand the complicated hydrogen-bonding, we developed new molecular visualization tools within the Vish Visualization shell and used it to visualize the life of each individual hydrogen-bond. With this tool hydrogen-bond formation and breaking as well as clustering and chain formation in hydrogen-bonded liquids can be observed directly. Liquid ethylene glycol at room temperature does not show significant clustering or chain building. The hydrogen-bonds break often due to the rotational and vibrational motions of the molecules leading to an H-bond half-life time of approximately 1.5 ps. However, most of the H-bonds are reformed again so that after 50 ps only 40% of these H-bonds are irreversibly broken due to diffusional motion. This hydrogen-bond half-life time due to diffusional motion is 80.3 ps. The work was preceded by a careful check of various OPLS-based force fields used in the literature. It was found that they lead to quite different angular and H-bond distributions. PMID:24748697

Bonding of glass with femtosecond laser pulses at high repetition rates

NASA Astrophysics Data System (ADS)

Richter, S.; Döring, S.; Tünnermann, A.; Nolte, S.

2011-05-01

We report on the welding of fused silica with ultrashort laser pulses at high repetition rates. Femtosecond laser pulses were focused at the interface of two optically contacted fused silica samples. Due to the nonlinear absorption in the focal volume and heat accumulation of successive pulses, the laser acts as a localized heat source at the focus position. Here, we analyze the influence of the laser and processing parameters on the amount of molten material. Moreover, we determine the achievable breaking stress by a three point bending test. With optimized parameters up to 75% of the breaking stress of the bulk material have been obtained.

Microwave-enhanced chemical processes

DOEpatents

Varma, Ravi

1990-01-01

A process for disposal of toxic wastes including chlorinated hydrocarbons, comprising, establishing a bed of non-metallic particulates having a high dielectric loss factor. Effecting intimate contact of the particulates and the toxic wastes at a temperature in excess of about 400.degree. C. in the presence of microwave radiation for a time sufficient to break the hydrocarbon chlorine bonds and provide detoxification values in excess of 80 and further detoxifying the bed followed by additional disposal of toxic wastes.

Fast Rotational Diffusion of Water Molecules in a 2D Hydrogen Bond Network at Cryogenic Temperatures

NASA Astrophysics Data System (ADS)

Prisk, T. R.; Hoffmann, C.; Kolesnikov, A. I.; Mamontov, E.; Podlesnyak, A. A.; Wang, X.; Kent, P. R. C.; Anovitz, L. M.

2018-05-01

Individual water molecules or small clusters of water molecules contained within microporous minerals present an extreme case of confinement where the local structure of hydrogen bond networks are dramatically altered from bulk water. In the zinc silicate hemimorphite, the water molecules form a two-dimensional hydrogen bond network with hydroxyl groups in the crystal framework. Here, we present a combined experimental and theoretical study of the structure and dynamics of water molecules within this network. The water molecules undergo a continuous phase transition in their orientational configuration analogous to a two-dimensional Ising model. The incoherent dynamic structure factor reveals two thermally activated relaxation processes, one on a subpicosecond timescale and another on a 10-100 ps timescale, between 70 and 130 K. The slow process is an in-plane reorientation of the water molecule involving the breaking of hydrogen bonds with a framework that, despite the low temperatures involved, is analogous to rotational diffusion of water molecules in the bulk liquid. The fast process is a localized motion of the water molecule with no apparent analogs among known bulk or confined phases of water.

Fast Rotational Diffusion of Water Molecules in a 2D Hydrogen Bond Network at Cryogenic Temperatures

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

Prisk, Timothy; Hoffmann, Christina; Kolesnikov, Alexander I.

Individual water molecules or small clusters of water molecules contained within microporous minerals present an extreme case of confinement where the local structure of hydrogen bond networks are dramatically altered from bulk water. In the zinc silicate hemimorphite, the water molecules form a two-dimensional hydrogen bond network with hydroxyl groups in the crystal framework. Here in this paper, we present a combined experimental and theoretical study of the structure and dynamics of water molecules within this network. The water molecules undergo a continuous phase transition in their orientational configuration analogous to a two-dimensional Ising model. The incoherent dynamic structure factormore » reveals two thermally activated relaxation processes, one on a subpicosecond timescale and another on a 10–100 ps timescale, between 70 and 130 K. The slow process is an in-plane reorientation of the water molecule involving the breaking of hydrogen bonds with a framework that, despite the low temperatures involved, is analogous to rotational diffusion of water molecules in the bulk liquid. The fast process is a localized motion of the water molecule with no apparent analogs among known bulk or confined phases of water.« less

Fast Rotational Diffusion of Water Molecules in a 2D Hydrogen Bond Network at Cryogenic Temperatures

DOE PAGES

Prisk, Timothy; Hoffmann, Christina; Kolesnikov, Alexander I.; ...

2018-05-09

Individual water molecules or small clusters of water molecules contained within microporous minerals present an extreme case of confinement where the local structure of hydrogen bond networks are dramatically altered from bulk water. In the zinc silicate hemimorphite, the water molecules form a two-dimensional hydrogen bond network with hydroxyl groups in the crystal framework. Here in this paper, we present a combined experimental and theoretical study of the structure and dynamics of water molecules within this network. The water molecules undergo a continuous phase transition in their orientational configuration analogous to a two-dimensional Ising model. The incoherent dynamic structure factormore » reveals two thermally activated relaxation processes, one on a subpicosecond timescale and another on a 10–100 ps timescale, between 70 and 130 K. The slow process is an in-plane reorientation of the water molecule involving the breaking of hydrogen bonds with a framework that, despite the low temperatures involved, is analogous to rotational diffusion of water molecules in the bulk liquid. The fast process is a localized motion of the water molecule with no apparent analogs among known bulk or confined phases of water.« less

Low-intensity lasers, modern filling materials, and bonding systems influence on mineral metabolism of hard dental tissues

NASA Astrophysics Data System (ADS)

Kunin, Anatoly A.; Yesaulenko, I. E.; Zoibelmann, M.; Pankova, Svetlana N.; Ippolitov, Yu. A.; Oleinik, Olga I.; Popova, T. A.; Koretskaya, I. V.; Shumilovitch, Bogdan R.; Podolskaya, Elana E.

2001-10-01

One of the main reasons of low quality filling is breaking Ca-P balance in hard tissues. Our research was done with the purpose of studying the influence of low intensity lasers, diodic radiation, the newest filling and bonding systems on the processes of mineral metabolism in hard dental tissues while filling a tooth. 250 patients having caries and its compli-cations were examined and treated. Our complex research included: visual and instrumental examination, finding out the level of oral cavity hygiene, acid enamel biopsy, scanning electronic microscopy and X-ray spectrum microanalysis. Filling processes may produce a negative effect on mineral metabolism of hard dental tissues the latter is less pronounced when applying fluoride-containing filling materials with bonding systems. It has also been found that bonding dentin and enamel systems are designed for both a better filling adhesion (i.e. mechanical adhesion) and migration of useful microelements present in them by their sinking into hard dental tissues (i.e. chemical adhesion). Our research showed a positive influence of low intensity laser and diodic beams accompanying the use of modern filling and bonding systems on mineral metabolism of hard dental tissues.

Role of intramolecular hydrogen bonding in the excited-state intramolecular double proton transfer (ESIDPT) of calix[4]arene: A TDDFT study

NASA Astrophysics Data System (ADS)

Wang, Se; Wang, Zhuang; Hao, Ce

2016-01-01

The time-dependent density functional theory (TDDFT) method was performed to investigate the excited-state intramolecular double proton transfer (ESIDPT) reaction of calix[4] arene (C4A) and the role of the intramolecular hydrogen bonds in the ESIDPT process. The geometries of C4A in the ground state and excited states (S1, S2 and T1) were optimized. Four intramolecular hydrogen bonds formed in the C4A are strengthened or weakened in the S2 and T1 states compared to those in the ground state. Interestingly, upon excitation to the S1 state of C4A, two protons H1 and H2 transfer along the two intramolecular hydrogen bonds O1-H1···O2 and O2-H2···O3, while the other two protons do not transfer. The ESIDPT reaction breaks the primary symmetry of C4A in the ground state. The potential energy curves of proton transfer demonstrate that the ESIDPT process follows the stepwise mechanism but not the concerted mechanism. Findings indicate that intramolecular hydrogen bonding is critical to the ESIDPT reactions in intramolecular hydrogen-bonded systems.

Hydrogen bond breaking in aqueous solutions near the critical point

USGS Publications Warehouse

Mayanovic, Robert A.; Anderson, Alan J.; Bassett, William A.; Chou, I.-Ming

2001-01-01

The nature of water-anion bonding is examined using X-ray absorption fine structure spectroscopy on a 1mZnBr2/6m NaBr aqueous solution, to near critical conditions. Analyses show that upon heating the solution from 25??C to 500??C, a 63% reduction of waters occurs in the solvation shell of ZnBr42-, which is the predominant complex at all pressure-temperature conditions investigated. A similar reduction in the hydration shell of waters in the Br- aqua ion was found. Our results indicate that the water-anion and water-water bond breaking mechanisms occurring at high temperatures are essentially the same. This is consistent with the hydration waters being weakly hydrogen bonded to halide anions in electrolyte solutions. ?? 2001 Elsevier Science B.V.

Nature's Mechanisms for Tough, Self-healing Polymers and Polymer Adhesives

NASA Astrophysics Data System (ADS)

Hansma, Paul

2007-03-01

Spider silk^2 and the natural polymer adhesives in abalone shells^3 and bone^4,5 can give us insights into nature's mechanisms for tough, self-healing polymers and polymer adhesives. The natural polymer adhesives in biomaterials have been optimized by evolution. An optimized polymer adhesive has five characteristics. 1) It holds together the strong elements of the composite. 2) It yields just before the strong elements would otherwise break. 3) It dissipates large amounts of energy as it yields. 4) It self heals after it yields. 5) It takes just a few percent by weight. Both natural polymer adhesives and silk rely on sacrificial bonds and hidden length for toughness and self-healing.^6 A relatively large energy, of order 100eV, is required to stretch a polymer molecule after a weak bond, a sacrificial bond, breaks and liberates hidden length, which was previously hidden, typically in a loop or folded domain, from whatever was stretching the polymer. The bond is called sacrificial if it breaks at forces well below the forces that could otherwise break the polymer backbone, typically greater than 1nN. In many biological cases, the breaking of sacrificial bonds has been found to be reversible, thereby also providing a ``self-healing'' property to the material.^2-4 Individual polymer adhesive molecules based on sacrificial bonds and hidden length can supply forces of order 300pN over distances of 100s of nanometers. Model calculations show that a few percent by weight of adhesives based on these principles could be optimized adhesives for high performance composite materials including nanotube and graphene sheet composites. ^2N. Becker, E. Oroudjev, S. Mutz et al., Nature Materials 2 (4), 278 (2003). ^3B. L. Smith, T. E. Schaffer, M. Viani et al., Nature 399 (6738), 761 (1999). ^4J. B. Thompson, J. H. Kindt, B. Drake et al., Nature 414 (6865), 773 (2001). ^5G. E. Fantner, T. Hassenkam, J. H. Kindt et al., Nature Materials 4, 612 (2005). ^6G. E. Fantner, E. Oroudjev, G. Schitter et al., Biophysical Journal 90 (4), 1411 (2006).

Insight into conformational changes of a single α-helix peptide molecule through stiffness measurements

NASA Astrophysics Data System (ADS)

Kageshima, Masami; Lantz, Mark A.; Jarvis, Suzanne P.; Tokumoto, Hiroshi; Takeda, Seiji; Ptak, Arkadiusz; Nakamura, Chikashi; Miyake, Jun

2001-07-01

Stiffness variations during the conformational change of a single α-helix polylysine peptide molecule were measured in a liquid environment using atomic force microscopy (AFM) with magnetic cantilever modulation. At the initial stage of the stretching process the stiffness decreased due to the breaking of hydrogen bonds and then increased due to the stretching of the helix backbone. These changes were reversible on reversal of the stretching motion. Below p K, the stiffness did not show increase on reversal, indicating that the reforming of hydrogen bonds did not take place. Conformational changes in the molecule were examined via these changes in stiffness.

Microwave-enhanced chemical processes

DOEpatents

Varma, R.

1990-06-19

A process is disclosed for the disposal of toxic wastes including chlorinated hydrocarbons, comprising, establishing a bed of non-metallic particulates having a high dielectric loss factor. Intimate contact of the particulates and the toxic wastes at a temperature in excess of about 400 C in the presence of microwave radiation for a time sufficient breaks the hydrocarbon chlorine bonds. Detoxification values in excess of 80 are provided and further detoxification of the bed is followed by additional disposal of toxic wastes. 1 figure.

New method for calculations of nanostructure kinetic stability at high temperature

NASA Astrophysics Data System (ADS)

Fedorov, A. S.; Kuzubov, A. A.; Visotin, M. A.; Tomilin, F. N.

2017-10-01

A new universal method is developed for determination of nanostructure kinetic stability (KS) at high temperatures, when nanostructures can be destroyed by chemical bonds breaking due to atom thermal vibrations. The method is based on calculation of probability for any bond in the structure to stretch more than a limit value Lmax, when the bond breaks. Assuming the number of vibrations is very large and all of them are independent, using the central limit theorem, an expression for the probability of a given bond elongation up to Lmax is derived in order to determine the KS. It is shown that this expression leads to the effective Arrhenius formula, but unlike the standard transition state theory it allows one to find the contributions of different vibrations to a chemical bond cleavage. To determine the KS, only calculation of frequencies and eigenvectors of vibrational modes in the groundstate of the nanostructure is needed, while the transition states need not be found. The suggested method was tested on calculating KS of bonds in some alkanes, octene isomers and narrow graphene nanoribbons of different types and widths at the temperature T=1200 K. The probability of breaking of the C-C bond in the center of these hydrocarbons is found to be significantly higher than at the ends of the molecules. It is also shown that the KS of the octene isomers decreases when the double C˭C bond is moved to the end of the molecule, which agrees well with the experimental data. The KS of the narrowest graphene nanoribbons of different types varies by 1-2 orders of magnitude depending on the width and structure, while all of them are by several orders of magnitude less stable at high temperature than the hydrocarbons and benzene.

Direct observation of ligand transfer and bond formation in cytochrome c oxidase by using mid-infrared chirped-pulse upconversion

PubMed Central

Treuffet, Johanne; Kubarych, Kevin J.; Lambry, Jean-Christophe; Pilet, Eric; Masson, Jean-Baptiste; Martin, Jean-Louis; Vos, Marten H.; Joffre, Manuel; Alexandrou, Antigoni

2007-01-01

We have implemented the recently demonstrated technique of chirped-pulse upconversion of midinfrared femtosecond pulses into the visible in a visible pump–midinfrared probe experiment for high-resolution, high-sensitivity measurements over a broad spectral range. We have succeeded in time-resolving the CO ligand transfer process from the heme Fe to the neighboring CuB atom in the bimetallic active site of mammalian cytochrome c oxidase, which was known to proceed in <1 ps, using the full CO vibrational signature of Fe–CO bond breaking and CuB–CO bond formation. Our differential transmission results show a delayed onset of the appearance of the CuB-bound species (200 fs), followed by a 450-fs exponential rise. Trajectories calculated by using molecular-dynamics simulations with a Morse potential for the CuB–C interaction display a similar behavior. Both experimental and calculated data strongly suggest a ballistic contribution to the transfer process. PMID:17895387

Unexpected mechanochemical complexity in the mechanistic scenarios of disulfide bond reduction in alkaline solution

NASA Astrophysics Data System (ADS)

Dopieralski, Przemyslaw; Ribas-Arino, Jordi; Anjukandi, Padmesh; Krupicka, Martin; Marx, Dominik

2017-02-01

The reduction of disulfides has a broad importance in chemistry, biochemistry and materials science, particularly those methods that use mechanochemical activation. Here we show, using isotensional simulations, that strikingly different mechanisms govern disulfide cleavage depending on the external force. Desolvation and resolvation processes are found to be crucial, as they have a direct impact on activation free energies. The preferred pathway at moderate forces, a bimolecular SN2 attack of OH- at sulfur, competes with unimolecular C-S bond rupture at about 2 nN, and the latter even becomes barrierless at greater applied forces. Moreover, our study unveils a surprisingly rich reactivity scenario that also includes the transformation of concerted SN2 reactions into pure bond-breaking processes at specific forces. Given that these forces are easily reached in experiments, these insights will fundamentally change our understanding of mechanochemical activation in general, which is now expected to be considerably more intricate than previously thought.

Hydrogen bonding in hydrates with one acetic acid molecule.

PubMed

Pu, Liang; Sun, Yueming; Zhang, Zhibing

2010-10-14

Hydrogen bonding (H-bond) interaction significantly influences the separation of acetic acid (HAc) from the HAc/H(2)O mixtures, especially the dilute solution, in distillation processes. It has been examined from the HAc mono-, di-, tri-, and tetrahydrates by analyzing the structures, binding energies, and infrared vibrational frequencies from quantum chemical calculations. For the first coordinate shell the 6-membered head-on ring is surely the most favorable structure because it has (1) the most favorable H-bonding parameters, (2) almost the largest binding energy per H-bond, (3) the biggest wavenumber shifts, and (4) the highest ring distribution (the AIMD simulations). Moreover, the comparison of the calculations with the experiments (the X-ray scattering data and IR frequencies) suggests that the possible structures in dilute aqueous solution are those involving two or more coordinate shells. The H-bonding in these water-surrounded HAc hydrates are the origin of the low-efficiency problem of isolating HAc from the dilute HAc/H(2)O mixtures. It is apparently a tougher work to break the H-bonds among HAc and the surrounded H(2)O molecules with respect to the case of more concentrated solutions, where the dominant structures are HAc or H(2)O aggregates.

Effects of defects on thermal decomposition of HMX via ReaxFF molecular dynamics simulations.

PubMed

Zhou, Ting-Ting; Huang, Feng-Lei

2011-01-20

Effects of molecular vacancies on the decomposition mechanisms and reaction dynamics of condensed-phase β-HMX at various temperatures were studied using ReaxFF molecular dynamics simulations. Results show that three primary initial decomposition mechanisms, namely, N-NO(2) bond dissociation, HONO elimination, and concerted ring fission, exist at both high and lower temperatures. The contribution of the three mechanisms to the initial decomposition of HMX is influenced by molecular vacancies, and the effects vary with temperature. At high temperature (2500 K), molecular vacancies remarkably promote N-N bond cleavage and concerted ring breaking but hinder HONO formation. N-N bond dissociation and HONO elimination are two primary competing reaction mechanisms, and the former is dominant in the initial decomposition. Concerted ring breaking of condensed-phase HMX is not favored at high temperature. At lower temperature (1500 K), the most preferential initial decomposition pathway is N-N bond dissociation followed by the formation of NO(3) (O migration), although all three mechanisms are promoted by molecular vacancies. The promotion effect on concerted ring breaking is considerable at lower temperature. Products resulting from concerted ring breaking appear in the defective system but not in the perfect crystal. The mechanism of HONO elimination is less important at lower temperature. We also estimated the reaction rate constant and activation barriers of initial decomposition with different vacancy concentrations. Molecular vacancies accelerate the decomposition of condensed-phase HMX by increasing the reaction rate constant and reducing activation barriers.

Catch-slip bonds can be dispensable for motor force regulation during skeletal muscle contraction

NASA Astrophysics Data System (ADS)

Dong, Chenling; Chen, Bin

2015-07-01

It is intriguing how multiple molecular motors can perform coordinated and synchronous functions, which is essential in various cellular processes. Recent studies on skeletal muscle might have shed light on this issue, where rather precise motor force regulation was partly attributed to the specific stochastic features of a single attached myosin motor. Though attached motors can randomly detach from actin filaments either through an adenosine triphosphate (ATP) hydrolysis cycle or through "catch-slip bond" breaking, their respective contribution in motor force regulation has not been clarified. Here, through simulating a mechanical model of sarcomere with a coupled Monte Carlo method and finite element method, we find that the stochastic features of an ATP hydrolysis cycle can be sufficient while those of catch-slip bonds can be dispensable for motor force regulation.

Dynamic Responses and Initial Decomposition under Shock Loading: A DFTB Calculation Combined with MSST Method for β-HMX with Molecular Vacancy.

PubMed

He, Zheng-Hua; Chen, Jun; Ji, Guang-Fu; Liu, Li-Min; Zhu, Wen-Jun; Wu, Qiang

2015-08-20

Despite extensive efforts on studying the decomposition mechanism of HMX under extreme condition, an intrinsic understanding of mechanical and chemical response processes, inducing the initial chemical reaction, is not yet achieved. In this work, the microscopic dynamic response and initial decomposition of β-HMX with (1 0 0) surface and molecular vacancy under shock condition, were explored by means of the self-consistent-charge density-functional tight-binding method (SCC-DFTB) in conjunction with multiscale shock technique (MSST). The evolutions of various bond lengths and charge transfers were analyzed to explore and understand the initial reaction mechanism of HMX. Our results discovered that the C-N bond close to major axes had less compression sensitivity and higher stretch activity. The charge was transferred mainly from the N-NO2 group along the minor axes and H atom to C atom during the early compression process. The first reaction of HMX primarily initiated with the fission of the molecular ring at the site of the C-N bond close to major axes. Further breaking of the molecular ring enhanced intermolecular interactions and promoted the cleavage of C-H and N-NO2 bonds. More significantly, the dynamic response behavior clearly depended on the angle between chemical bond and shock direction.

Degradation reaction of Diazo reactive black 5 dye with copper (II) sulfate catalyst in thermolysis treatment.

PubMed

Lau, Yen-Yie; Wong, Yee-Shian; Ang, Tze-Zhang; Ong, Soon-An; Lutpi, Nabilah Aminah; Ho, Li-Ngee

2018-03-01

The theme of present research demonstrates performance of copper (II) sulfate (CuSO 4 ) as catalyst in thermolysis process to treat reactive black 5 (RB 5) dye. During thermolysis without presence of catalyst, heat was converted to thermal energy to break the enthalpy of chemical structure bonding and only 31.62% of color removal. With CuSO 4 support as auxiliary agent, the thermally cleaved molecular structure was further destabilized and reacted with CuSO 4 . Copper ions functioned to delocalize the coordination of π of the lone paired electron in azo bond, C=C bond of the sp 2 carbon to form C-C of the sp 3 amorphous carbon in benzene and naphthalene. Further, the radicals of unpaired electrons were stabilized and RB 5 was thermally decomposed to methyl group. Zeta potential measurement was carried out to analyze the mechanism of RB 5 degradation and measurement at 0 mV verified the critical chemical concentration (CCC) (0.7 g/L copper (II) sulfate), as the maximum 92.30% color removal. The presence of copper (II) sulfate catalyst has remarkably increase the RB 5 dye degradation as the degradation rate constant without catalyst, k 1 is 6.5224 whereas the degradation rate constant with catalyst, k 2 is 25.6810. This revealed the correlation of conversion of thermal energy from heat to break the chemical bond strength, subsequent fragmentation of RB 5 dye molecular mediated by copper (II) sulfate catalyst. The novel framework on thermolysis degradation of molecular structure of RB 5 with respect to the bond enthalpy and interfacial intermediates decomposition with catalyst reaction were determined.

Molecular Simulations of The Formation of Gold-Molecule-Gold Junctions

NASA Astrophysics Data System (ADS)

Wang, Huachuan

2013-03-01

We perform classical molecular simulations by combining grand canonical Monte Carlo (GCMC) sampling with molecular dynamics (MD) simulation to explore the dynamic gold nanojunctions in a Alkenedithiol (ADT) solvent. With the aid of a simple driving-spring model, which can reasonably represent the long-range elasticity of the gold electrode, the spring forces are obtained during the dynamic stretching procedure. A specific multi-time-scale double reversible reference system propagator (double-RESPA) algorithm has been designed for the metal-organic complex in MD simulations to identify the detailed metal-molecule bonding geometry at metal-molecule-metal interface. We investigate the variations of bonding sites of ADT molecules on gold nanojunctions at Au (111) surface at a constant chemical potential. Simulation results show that an Au-ADT-Au interface is formed on Au nanojunctions, bond-breaking intersection is at 1-1 bond of the monatomic chain of the cross-section, instead of at the Au-S bond. Breaking force is around 1.5 nN. These are consistent with the experimental measurements.

Assessing the distinguishable cluster approximation based on the triple bond-breaking in the nitrogen molecule

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

Rishi, Varun; Perera, Ajith; Bartlett, Rodney J., E-mail: bartlett@qtp.ufl.edu

2016-03-28

Obtaining the correct potential energy curves for the dissociation of multiple bonds is a challenging problem for ab initio methods which are affected by the choice of a spin-restricted reference function. Coupled cluster (CC) methods such as CCSD (coupled cluster singles and doubles model) and CCSD(T) (CCSD + perturbative triples) correctly predict the geometry and properties at equilibrium but the process of bond dissociation, particularly when more than one bond is simultaneously broken, is much more complicated. New modifications of CC theory suggest that the deleterious role of the reference function can be diminished, provided a particular subset of termsmore » is retained in the CC equations. The Distinguishable Cluster (DC) approach of Kats and Manby [J. Chem. Phys. 139, 021102 (2013)], seemingly overcomes the deficiencies for some bond-dissociation problems and might be of use in quasi-degenerate situations in general. DC along with other approximate coupled cluster methods such as ACCD (approximate coupled cluster doubles), ACP-D45, ACP-D14, 2CC, and pCCSD(α, β) (all defined in text) falls under a category of methods that are basically obtained by the deletion of some quadratic terms in the double excitation amplitude equation for CCD/CCSD (coupled cluster doubles model/coupled cluster singles and doubles model). Here these approximate methods, particularly those based on the DC approach, are studied in detail for the nitrogen molecule bond-breaking. The N{sub 2} problem is further addressed with conventional single reference methods but based on spatial symmetry-broken restricted Hartree–Fock (HF) solutions to assess the use of these references for correlated calculations in the situation where CC methods using fully symmetry adapted SCF solutions fail. The distinguishable cluster method is generalized: 1) to different orbitals for different spins (unrestricted HF based DCD and DCSD), 2) by adding triples correction perturbatively (DCSD(T)) and iteratively (DCSDT-n), and 3) via an excited state approximation through the equation of motion (EOM) approach (EOM-DCD, EOM-DCSD). The EOM-CC method is used to identify lower-energy CC solutions to overcome singularities in the CC potential energy curves. It is also shown that UHF based CC and DC methods behave very similarly in bond-breaking of N{sub 2}, and that using spatially broken but spin preserving SCF references makes the CCSD solutions better than those for DCSD.« less

Chemisorption of 1,1-dichloroethene on the Si(1 1 1)-7 × 7 surface

NASA Astrophysics Data System (ADS)

Andersen, T. H.; Zahl, M. G.; Svenum, I.-H.; Børve, K. J.; Borg, A.; Sæthre, L. J.

2007-12-01

Chemisorption of 1,1-dichloroethene (Cl 2C dbnd CH 2) to a Si(1 1 1)-7 × 7 surface was studied by means of X-ray photoelectron spectroscopy using synchrotron radiation, recording chlorine 2p and carbon 1s spectra. For carbon 1s, spectral assignment of the chemisorbed species is based on quantum chemical calculations of chemical shifts in model compounds. The results confirm the identity of covalently bonded 1-chlorovinyl (-CCl dbnd CH 2) and vinylidene ( lbond2 C dbnd CH 2) adspecies. Upon chemisorption at room temperature it was found that about one-third of the molecules break one C-Cl bond while about two-thirds of the adsorbates break two C-Cl bonds. We do not, however, find evidence for isomerization of lbond2 C dbnd CH 2 to di-bonded vinylene (-CH dbnd CH-).

Communication: Site-selective bond excision of adenine upon electron transfer

NASA Astrophysics Data System (ADS)

Cunha, T.; Mendes, M.; Ferreira da Silva, F.; Eden, S.; García, G.; Limão-Vieira, P.

2018-01-01

This work demonstrates that selective excision of hydrogen atoms at a particular site of the DNA base adenine can be achieved in collisions with electronegative atoms by controlling the impact energy. The result is based on analysing the time-of-flight mass spectra yields of potassium collisions with a series of labeled adenine derivatives. The production of dehydrogenated parent anions is consistent with neutral H loss either from selective breaking of C-H or N-H bonds. These unprecedented results open up a new methodology in charge transfer collisions that can initiate selective reactivity as a key process in chemical reactions that are dominant in different areas of science and technology.

Modeling of Laser Material Interactions

NASA Astrophysics Data System (ADS)

Garrison, Barbara

2009-03-01

Irradiation of a substrate by laser light initiates the complex chemical and physical process of ablation where large amounts of material are removed. Ablation has been successfully used in techniques such as nanolithography and LASIK surgery, however a fundamental understanding of the process is necessary in order to further optimize and develop applications. To accurately describe the ablation phenomenon, a model must take into account the multitude of events which occur when a laser irradiates a target including electronic excitation, bond cleavage, desorption of small molecules, ongoing chemical reactions, propagation of stress waves, and bulk ejection of material. A coarse grained molecular dynamics (MD) protocol with an embedded Monte Carlo (MC) scheme has been developed which effectively addresses each of these events during the simulation. Using the simulation technique, thermal and chemical excitation channels are separately studied with a model polymethyl methacrylate system. The effects of the irradiation parameters and reaction pathways on the process dynamics are investigated. The mechanism of ablation for thermal processes is governed by a critical number of bond breaks following the deposition of energy. For the case where an absorbed photon directly causes a bond scission, ablation occurs following the rapid chemical decomposition of material. The study provides insight into the influence of thermal and chemical processes in polymethyl methacrylate and facilitates greater understanding of the complex nature of polymer ablation.

The reactions of thiophene on Mo(110) and Mo(110)-p(2×2)-S

NASA Astrophysics Data System (ADS)

Roberts, Jeffrey T.; Friend, C. M.

1987-07-01

The reactions of thiophene and 2,5-dideuterothiophene on Mo(110) and Mo(110)-p(2×2)-S have been investigated under ultrahigh vacuum conditions using temperature programmed reaction spectroscopy and Auger electron spectroscopy. Thiophene chemisorbed on Mo(110) decomposes during temperature programmed reaction to yield only gaseous dihydrogen, surface carbon, and surface sulfur. At low thiophene exposures, dihydrogen evolves from Mo(110) in a symmetric peak at 440 K. At saturation exposures, three dihydrogen peaks are detected at 360 K, at 420 K and at 565 K. Multilayers of thiophene desorb at 180 K. Temperature programmed reaction of 2,5-dideuterothiophene demonstrates that at high thiophene coverages, one of the α-C-H bonds (those nearest sulfur) breaks first. No bond breaking selectivity is observed at low thiophene exposures. The Mo(110)-p(2×2)-S surface is less active for thiophene decomposition. Thiophene adsorbed on Mo(110)-p(2×2)-S to low coverages decomposes to surface carbon surface sulfur, and hydrogen at 430 K. At reaction saturation, dihydrogen production is observed at 375 and 570 K. In addition, at moderate and high exposures, chemisorbed thiophene desorbs from Mo(110)-p(2×2)-S. At saturation the desorption temperature of the reversibly chemisorbed state is 215 K. Experiments with 2,5-dideuterothiophene demonstrate no surface selectivity for α-C-H bond breaking reactions on Mo(110)-p(2×2)-S. The decomposition mechanism and energetics of thiophene decomposition are proposed to be dependent on the coverage of thiophene. At low thiophene exposures, the ring is proposed to bond parallel to the surface. All C-H bonds in the parallel geometry are sterically available for activation by the surface, accounting for the lack of selectivity in C-H bond breaking. High thiophene coverages are suggested to result in perpendicularly bound thiophene which undergoes selective α-dehydrogenation to an α)-thiophenyl intermediate. The presence of sulfur leads to a high energy pathway for cleavage of C-H bonds in a thiophene derived intermediate. Carbon-hydrogen bonds survive on the surface up to temperatures of 650 K. Comparison of this study with work on Mo(100) demonstrates that the reaction of thiophene on molybdenum is relatively insensitive to the surface geometric structure.

Damage, Self-Healing, and Hysteresis in Spider Silks

PubMed Central

De Tommasi, D.; Puglisi, G.; Saccomandi, G.

2010-01-01

Abstract In this article, we propose a microstructure-based continuum model to describe the material behavior of spider silks. We suppose that the material is composed of a soft fraction with entropic elasticity and a hard, damageable fraction. The hard fraction models the presence of stiffer, crystal-rich, oriented regions and accounts for the effect of softening induced by the breaking of hydrogen bonds. To describe the observed presence of crystals with different size, composition, and orientation, this hard fraction is modeled as a distribution of materials with variable properties. The soft fraction describes the remaining regions of amorphous material and is here modeled as a wormlike chain. During stretching, we consider the effect of bond-breaking as a transition from the hard- to the soft-material phase. As we demonstrate, a crucial effect of bond-breaking that accompanies the softening of the material is an increase in contour length associated with chains unraveling. The model describes also the self-healing properties of the material by assuming partial bond reconnection upon unloading. Despite its simplicity, the proposed mechanical system reproduces the main experimental effects observed in cyclic loading of spider silks. Moreover, our approach is amenable to two- or three-dimensional extensions and may prove to be a useful tool in the field of microstructure optimization for bioinspired materials. PMID:20441758

A critical Examination of the Phenomenon of Bonding Area - Bonding Strength Interplay in Powder Tableting.

PubMed

Osei-Yeboah, Frederick; Chang, Shao-Yu; Sun, Changquan Calvin

2016-05-01

Although the bonding area (BA) and bonding strength (BS) interplay is used to explain complex tableting behaviors, it has never been experimentally proven. The purpose of this study is to unambiguously establish the distinct contributions of each by decoupling the contributions from BA and BS. To modulate BA, a Soluplus® powder was compressed into tablets at different temperatures and then broken following equilibration at 25°C. To modulate BS, tablets were equilibrated at different temperatures. To simultaneously modulate BA and BS, both powder compression and tablet breaking test were carried out at different temperatures. Lower tablet tensile strength is observed when the powder is compressed at a lower temperature but broken at 25°C. This is consistent with the increased resistance to polymer deformation at lower temperatures. When equilibrated at different temperatures, the tensile strength of tablets prepared under identical conditions increases with decreasing storage temperature, indicating that BS is higher at a lower temperature. When powder compression and tablet breaking are carried out at the same temperature, the profile with a maximum tensile strength at 4°C is observed due to the BA-BS interplay. By systematically varying temperature during tablet compression and breaking, we have experimentally demonstrated the phenomenon of BA-BS interplay in tableting.

Study of hydrogen bond polarized IR spectra of cinnamic acid crystals

NASA Astrophysics Data System (ADS)

Flakus, Henryk T.; Jabłońska, Magdalena

2004-11-01

This paper presents the results of investigation of the polarized IR spectra of cinnamic acid and of its deuterium derivative crystals. The spectra were measured by a transmission method, using polarized light, at the room temperature and at 77 K, for two different crystalline faces. Theoretical analysis of the results concerned linear dichroic effects, H/D isotopic and temperature effects, observed in the spectra of the hydrogen and of the deuterium bonds in cinnamic acid crystals, at the frequency ranges of the νO-H and the νO-D bands. The basic crystal spectral properties could be satisfactorily interpreted in a quantitative way for a centrosymmetric cyclic hydrogen bond dimer model. Such a model explains not only a two-branch structure of the νO-H and νO-D bands in crystalline spectra, but also some essential linear dichroic effects in the band frequency ranges, measured for isotopically diluted crystals. Model calculations, performed within the limits of the 'strong-coupling' model, allowed for quantitative interpretation and for understanding of the basic properties of the hydrogen bond IR spectra of cinnamic acid crystals, H/D isotopic, temperature and dichroic effects included. In the scope of our studies the mechanism of H/D isotopic 'self-organization' processes, taking place in the crystal hydrogen bond lattices, was also recognized. It was proved that for isotopically diluted crystalline samples of cinnamic acid, a non-random distribution of protons and deuterons occurs exclusively in the hydrogen bond dimers. Nevertheless, these co-operative interactions between the hydrogen bonds do not involve the adjacent hydrogen bond dimers in each unit cell. The two-branch fine structure pattern of the νO-H and νO-D bands was ascribed to the vibronic mechanism of vibrational dipole selection rule breaking in centrosymmetric hydrogen bond dimers. The observed in the spectra very high intensity of the forbidden transition sub-band in the analyzed νO-H and νO-D bands is a manifestation of an extremely effective symmetry rule breaking mechanism. It correlates with a relatively large excess electron charge on the cinnamic aid dimer carboxyl groups. This effect is a result of a partial withdrawal of the electron charge, from the conjugated π-bond systems of the styryl substituents, by the carboxyl groups. This statement has been supported by ab initio calculations.

Initial decomposition of the condensed-phase β-HMX under shock waves: molecular dynamics simulations.

PubMed

Ge, Ni-Na; Wei, Yong-Kai; Ji, Guang-Fu; Chen, Xiang-Rong; Zhao, Feng; Wei, Dong-Qing

2012-11-26

We have performed quantum-based multiscale simulations to study the initial chemical processes of condensed-phase octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) under shock wave loading. A self-consistent charge density-functional tight-binding (SCC-DFTB) method was employed. The results show that the initial decomposition of shocked HMX is triggered by the N-NO(2) bond breaking under the low velocity impact (8 km/s). As the shock velocity increases (11 km/s), the homolytic cleavage of the N-NO(2) bond is suppressed under high pressure, the C-H bond dissociation becomes the primary pathway for HMX decomposition in its early stages. It is accompanied by a five-membered ring formation and hydrogen transfer from the CH(2) group to the -NO(2) group. Our simulations suggest that the initial chemical processes of shocked HMX are dependent on the impact velocity, which gain new insights into the initial decomposition mechanism of HMX upon shock loading at the atomistic level, and have important implications for understanding and development of energetic materials.

Low energy electron induced cytosine base release in 2′-deoxycytidine-3′-monophosphate via glycosidic bond cleavage: A time-dependent wavepacket study

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

Bhaskaran, Renjith; Sarma, Manabendra, E-mail: msarma@iitg.ernet.in

2014-09-14

Low energy electron (LEE) induced cytosine base release in a selected pyrimidine nucleotide, viz., 2′-deoxycytidine-3′-monophosphate is investigated using ab initio electronic structure methods and time dependent quantum mechanical calculations. It has been noted that the cytosine base scission is comparatively difficult process than the 3′ C–O bond cleavage from the lowest π{sup *} shape resonance in energy region <1 eV. This is mainly due to the high activation energy barrier associated with the electron transfer from the π{sup *} orbital of the base to the σ{sup *} orbital of the glycosidic N–C bond. In addition, the metastable state formed aftermore » impinging LEE (0–1 eV) has very short lifetime (10 fs) which may decay in either of the two competing auto-detachment or dissociation process simultaneously. On the other hand, the selected N–C mode may cleave to form the cytosine base anion at higher energy regions (>2 eV) via tunneling of the glycosidic bond. Resonance states generated within this energy regime will exist for a duration of ∼35–55 fs. Comparison of salient features of the two dissociation events, i.e., 3′ C–O single strand break and glycosidic N–C bond cleavage in 3′-dCMPH molecule are also provided.« less

Effect of Sorbitol Plasticizer on the Structure and Properties of Melt Processed Polyvinyl Alcohol Films.

PubMed

Tian, Huafeng; Liu, Di; Yao, Yuanyuan; Ma, Songbai; Zhang, Xing; Xiang, Aimin

2017-12-01

Poly (vinyl alcohol) (PVA) possesses wide applications as food packaging materials, but is difficult to melt process for its strong inter/intra hydrogen bonding. In this work, flexible PVA films with different content of sorbitol plasticizers were prepared by melt processing with the assistance of water. And the influence of sorbitol plasticizer content on the crystallinity, optical transparency, water-retaining capability, mechanical properties, thermal stability and oxygen and water permeability were investigated. The results indicated that sorbitol dramatically improved the melt processing ability of PVA. Sorbitol could interact with PVA to form strong hydrogen bonding interactions, which would decrease the original hydrogen bonding of the matrix, resulting in the decrease of crystallinity degrees. The glass transition, melting and crystallization peak temperatures decreased with the increase of sorbitol. All the films exhibited fine optical transparency. The water retaining capability were improved with the increase of sorbitol. Especially, an increase in elongation at break and decrease in Young's modulus and tensile strength were observed indicating good plasticizing effect of sorbitol on PVA films. In addition, the PVA films prepared in this work exhibited fine barrier properties against oxygen and water, suggesting wide application potential as packaging materials. © 2017 Institute of Food Technologists®.

Single-Molecule Sensing with Nanopore Confinement: From Chemical Reactions to Biological Interactions.

PubMed

Lin, Yao; Ying, Yi-Lun; Gao, Rui; Long, Yi-Tao

2018-03-25

The nanopore can generate an electrochemical confinement for single-molecule sensing that help understand the fundamental chemical principle in nanoscale dimensions. By observing the generated ionic current, individual bond-making and bond-breaking steps, single biomolecule dynamic conformational changes and electron transfer processes that occur within pore can be monitored with high temporal and current resolution. These single-molecule studies in nanopore confinement are revealing information about the fundamental chemical and biological processes that cannot be extracted from ensemble measurements. In this Concept article, we introduce and discuss the electrochemical confinement effects on single-molecule covalent reactions, conformational dynamics of individual molecules and host-guest interactions in protein nanopores. Then, we extend the concept of nanopore confinement effects to confine electrochemical redox reactions in solid-state nanopores for developing new sensing mechanisms. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ab initio molecular dynamics of solvation effects on reactivity at electrified interfaces

DOE PAGES

Herron, Jeffrey A.; Morikawa, Yoshitada; Mavrikakis, Manos

2016-08-08

Using ab initio molecular dynamics (as implemented in periodic, self-consistent (GGA-PBE) density functional theory (DFT) we investigated the mechanism of methanol electro-oxidation on Pt(111). We investigated the role of solvation and electrode potential on the energetics of the first proton transfer step, methanol electro-oxidation to methoxy (CH 3O) or hydroxymethyl (CH 2OH). The results show that solvation weakens the adsorption of methoxy to uncharged Pt(111), while the binding energy of methanol and hydroxymethyl are not significantly affected. The free energies of activation for breaking the C-H and O-H bonds in methanol were calculated through a Blue Moon Ensemble using constrainedmore » ab initio molecular dynamics. Calculated barriers for these elementary steps on unsolvated, uncharged Pt(111) are similar to results for climbing-image nudged elastic band calculations from the literature. Solvation reduces the barrier for both C-H and O-H bond activation steps with respect to their vapor phase values, though the effect is more pronounced for C-H bond activation due to less disruption of the hydrogen-bond network. The calculated activation energy barriers show that breaking the C-H bond of methanol is more facile than the O-H bond on solvated negatively biased, or uncharged Pt(111). Furthermore, with positive bias, O-H bond activation is enhanced, becoming slightly more facile than C-H bond activation.« less

Destruction of Peptides and Nucleosides in Reactions with Low-Energy Electrons

NASA Astrophysics Data System (ADS)

Muftakhov, M. V.; Shchukin, P. V.

2018-05-01

Mass-spectrometry of negative ions is used to study dissociative electron capture by molecules of several nucleosides, simplest di- and tripeptides, and modified dipeptides. Energy domains and efficiencies of dissociative capture are determined for the objects under study, and threshold energies of several fragmentation processes are estimated. It is shown that cytidine and peptides are stable against fragmentation due to simple bond breaking at electron energies ranging from 0 to 1 eV.

Toughening elastomers with sacrificial bonds and watching them break

NASA Astrophysics Data System (ADS)

Creton, Costantino

2014-03-01

Most unfilled elastomers are relatively brittle, in particular when the average molecular weight between crosslinks is lower than the average molecular weight between entanglements. We created a new class of tough elastomers by introducing isotropically prestretched chains inside ordinary acrylic elastomers by successive swelling and polymerization steps. These new materials combine a high entanglement density with a densely crosslinked structure reaching elastic moduli of 4 MPa and fracture strength of 25 MPa. The highly prestretched chains are the minority in the material and can break in the bulk of the material before catastrophic failure occurs, increasing the toughness of the material by two orders of magnitude up to 5 kJ/m2. To investigate the details of the toughening mechanism we introduced specific sacrificial dioxetane bonds in the prestretched chains that emit light when they break. In uniaxial extension cyclic experiments, we checked that the light emission corresponded exactly and quantitatively to the energy dissipation in each cycle demonstrating that short chains break first and long chains later. We then watched crack propagation in notched samples and mapped spatially the location of bond breakage ahead of the crack tip before and during propagation. This new toughening mechanism for elastomers creates superentangled rubbers and is ideally suited to overcome the trade-off between toughness and stiffness of ordinary elastomers. We gratefully acknowledge funding from DSM Ahead

Torsional Rigidity of Single Actin Filaments and Actin-Actin Bond Breaking Force under Torsion Measured Directly by in vitro Micromanipulation

NASA Astrophysics Data System (ADS)

Tsuda, Yuri; Yasutake, Hironori; Ishijima, Akihiko; Yanagida, Toshio

1996-11-01

Knowledge of the elastic properties of actin filaments is crucial for considering its role in muscle contraction, cellular motile events, and formation of cell shape. The stiffness of actin filaments in the directions of stretching and bending has been determined. In this study, we have directly determined the torsional rigidity and breaking force of single actin filaments by measuring the rotational Brownian motion and tensile strength using optical tweezers and microneedles, respectively. Rotational angular fluctuations of filaments supplied the torsional rigidity as (8.0 ± 1.2) × 10-26 Nm2. This value is similar to that deduced from the longitudinal rigidity, assuming the actin filament to be a homogeneous rod. The breaking force of the actin-actin bond was measured while twisting a filament through various angles using microneedles. The breaking force decreased greatly under twist, e.g., from 600-320 pN when filaments were turned through 90 degrees, independent of the rotational direction. Our results indicate that an actin filament exhibits comparable flexibility in the rotational and longitudinal directions, but breaks more easily under torsional load.

On the Structure Sensitivity of Dimethyl Ether Electro-oxidation on Eight FCC Metals: A First-Principles Study

DOE PAGES

Herron, Jeffrey A.; Ferrin, Peter; Mavrikakis, Manos

2015-09-24

The electro-oxidation of dimethyl ether (DME) was investigated using periodic, self-consistent density functional theory (DFT) calculations on the (111) and (100) facets of eight fcc metals: Au, Ag, Cu, Pt, Pd, Ni, Ir, and Rh. The goal of this study is to understand the experimentally observed structure sensitivity of this reaction on Pt, and to predict trends in structure sensitivity of this reaction across the other seven metals studied. The main conclusion is that the enhanced activity of Pt(100) originates from more facile C–O bond breaking and removal of surface poisoning species, including CO and CH. When comparing C–O bondmore » breaking energetics, we do not find a universal trend where these elementary steps are always more exergonic on the (100) facet. However, we find that, at a given potential, DME can be dehydrogenated (prior to breaking the C–O bond) to a greater extent on the (100) facet. Additionally, we find that the reaction energy for C–O bond breaking in CHxOCHy-type species becomes increasingly exergonic as the species becomes increasingly dehydrogenated. Together, the more facile dehydrogenation on the (100) facets provides more favorable routes to C–O bond activation. Though we calculate a lower onset potential on Au(100), Ag(100), Cu(100), Pt(100), and Pd(100) than their respective (111) facets, the calculated onset potential for Ni(100), Ir(100), and Rh(100) are actually higher than for their respective (111) facets. Lastly, by constructing theoretical volcano plots, we conclude that Au(100), Ag(100), Cu(100), Pt(100), and Pd(100) should be more active than their respective (111) facets, while Ni(100), Rh(100), and Ir(100) will show the opposite trend.« less

THz spectra and corresponding vibrational modes of DNA base pair cocrystals and polynucleotides

NASA Astrophysics Data System (ADS)

Wang, Fang; Zhao, Dongbo; Dong, Hao; Jiang, Ling; Huang, Lin; Liu, Yunfei; Li, Shuhua

2018-07-01

The generalized energy-based fragmentation (GEBF) approach has been applied to study the THz spectra and vibrational modes of base pair cocrystals under periodic boundary conditions (denoted as PBC-GEBF). Results of vibrational mode reveal that hydrogen bonds play a pivotal role in the pairing process of base crystals, where most Nsbnd H and Csbnd H bonds stretch to some extent. We also found that hydrogen bonds of a self-made A:T cocrystal completely break in a transition from liquid to the solid state, while self-made C:G cocrystal is different and easier to form a cocrystal, as confirmed by X-ray diffraction (XRD) and terahertz (THz) spectra. Furthermore, we have studied DNA polynucleotides (in both A and B forms) found that the vibrational modes changed a lot during the process of their forming double strand. Despite the key role played by hydrogen bonds, the key contribution originates from collective motions of the main skeleton. A comparative study of the spectra of some stranded fragments suggests that different sequences or forms have similar spectra in THz band. They distinguish from each other mainly in the low-frequency regions, especially below 1 THz. This study would make great contributions to the molecular dynamics model based DNA long-chain structure simulation in the future study.

Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains

PubMed Central

Daidone, Isabella; Neuweiler, Hannes; Doose, Sören; Sauer, Markus; Smith, Jeremy C.

2010-01-01

Characterization of the length dependence of end-to-end loop-closure kinetics in unfolded polypeptide chains provides an understanding of early steps in protein folding. Here, loop-closure in poly-glycine-serine peptides is investigated by combining single-molecule fluorescence spectroscopy with molecular dynamics simulation. For chains containing more than 10 peptide bonds loop-closing rate constants on the 20–100 nanosecond time range exhibit a power-law length dependence. However, this scaling breaks down for shorter peptides, which exhibit slower kinetics arising from a perturbation induced by the dye reporter system used in the experimental setup. The loop-closure kinetics in the longer peptides is found to be determined by the formation of intra-peptide hydrogen bonds and transient β-sheet structure, that accelerate the search for contacts among residues distant in sequence relative to the case of a polypeptide chain in which hydrogen bonds cannot form. Hydrogen-bond-driven polypeptide-chain collapse in unfolded peptides under physiological conditions found here is not only consistent with hierarchical models of protein folding, that highlights the importance of secondary structure formation early in the folding process, but is also shown to speed up the search for productive folding events. PMID:20098498

Thermal decay of rhodopsin: role of hydrogen bonds in thermal isomerization of 11-cis retinal in the binding site and hydrolysis of protonated Schiff base.

PubMed

Liu, Jian; Liu, Monica Yun; Nguyen, Jennifer B; Bhagat, Aditi; Mooney, Victoria; Yan, Elsa C Y

2009-07-01

Although thermal stability of the G protein-coupled receptor rhodopsin is directly related to its extremely low dark noise level and has recently generated considerable interest, the chemistry behind the thermal decay process of rhodopsin has remained unclear. Using UV-vis spectroscopy and HPLC analysis, we have demonstrated that the thermal decay of rhodopsin involves both hydrolysis of the protonated Schiff base and thermal isomerization of 11-cis to all-trans retinal. Examining the unfolding of rhodopsin by circular dichroism spectroscopy and measuring the rate of thermal isomerization of 11-cis retinal in solution, we conclude that the observed thermal isomerization of 11-cis to all-trans retinal happens when 11-cis retinal is in the binding pocket of rhodopsin. Furthermore, we demonstrate that solvent deuterium isotope effects are involved in the thermal decay process by decreasing the rates of thermal isomerization and hydrolysis, suggesting that the rate-determining step of these processes involves breaking hydrogen bonds. These results provide insight into understanding the critical role of an extensive hydrogen-bonding network on stabilizing the inactive state of rhodopsin and contribute to our current understanding of the low dark noise level of rhodopsin, which enables this specialized protein to function as an extremely sensitive biological light detector. Because similar hydrogen-bonding networks have also been suggested by structural analysis of two other GPCRs, beta1 and beta2 adrenergic receptors, our results could reveal a general role of hydrogen bonds in facilitating GPCR function.

Application of Density Functional Theory to Systems Containing Metal Atoms

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.

2006-01-01

The accuracy of density functional theory (DFT) for problems involving metal atoms is considered. The DFT results are compared with experiment as well as results obtained using the coupled cluster approach. The comparisons include geometries, frequencies, and bond energies. The systems considered include MO2, M(OH)+n, MNO+, and MCO+2. The DFT works well for frequencies and geometries, even in case with symmetry breaking; however, some examples have been found where the symmetry breaking is quite severe and the DFT methods do not work well. The calculation of bond energies is more difficult and examples of successes as well as failures of DFT will be given.

CH 3NO 2 decomposition/isomerization mechanism and product branching ratios: An ab initio chemical kinetic study

NASA Astrophysics Data System (ADS)

Zhu, R. S.; Lin, M. C.

2009-08-01

The low-lying energy pathways for the decomposition/isomerization of nitromethane (NM) have been investigated using different molecular orbital methods. Our results show that in addition to the commonly known CH 3 + NO 2 products formed by direct C-N bond breaking and the trans-CH 3ONO formed by nitro-nitrite isomerization, NM can also isomerize to cis-CH 3ONO via a very loose transition state (TS) lying 59.2 kcal/mol above CH 3NO 2 or 0.6 kcal/mol below the CH 3 + NO 2 asymptote predicted at the UCCSD(T)/CBS level of theory. Kinetic results indicate that in the energy range of 59 ± 1 kcal/mol, production of CH 3O + NO is dominant, whereas above the C-N bond breaking threshold, the formation of CH 3 + NO 2 sharply increases and becomes dominant. The k( E) values predicted at different energies clearly indicate that CH 3O + NO could be detected in an infrared multi-photon dissociation study, whereas in UV dissociation experiments with energies high above the C-N bond breaking threshold the CH 3 + NO 2 products are generated predominantly.

DNA denaturation through a model of the partition points on a one-dimensional lattice

NASA Astrophysics Data System (ADS)

Mejdani, R.; Huseini, H.

1994-08-01

We have shown that by using a model of the partition points gas on a one-dimensional lattice, we can study, besides the saturation curves obtained before for the enzyme kinetics, also the denaturation process, i.e. the breaking of the hydrogen bonds connecting the two strands, under treatment by heat of DNA. We think that this model, as a very simple model and mathematically transparent, can be advantageous for pedagogic goals or other theoretical investigations in chemistry or modern biology.

The Chemical Structure and Acid Deterioration of Paper.

ERIC Educational Resources Information Center

Hollinger, William K., Jr.

1984-01-01

Describes the chemical structure of paper, including subatomic particles, atoms and molecules, and the forces that bond atoms into molecules, molecules into chains, chains into sheets, and sheets into layers. Acid is defined, and the deleterious role of acid in breaking the forces that bond atoms into molecules is detailed. (EJS)

Observed mechanism for the breakup of small bundles of cellulose Iα and Iβ in ionic liquids from molecular dynamics simulations.

PubMed

Rabideau, Brooks D; Agarwal, Animesh; Ismail, Ahmed E

2013-04-04

Explicit, all-atom molecular dynamics simulations are used to study the breakup of small bundles of cellulose Iα and Iβ in the ionic liquids [BMIM]Cl, [EMIM]Ac, and [DMIM]DMP. In all cases, significant breakup of the bundles is observed with the initial breakup following a common underlying mechanism. Anions bind strongly to the hydroxyl groups of the exterior strands of the bundle, forming negatively charged complexes. Binding also weakens the intrastrand hydrogen bonds present in the cellulose strands, providing greater strand flexibility. Cations then intercalate between the individual strands, likely due to charge imbalances, providing the bulk to push the individual moieties apart and initiating the separation. The peeling of an individual strand from the main bundle is observed in [EMIM]Ac with an analysis of its hydrogen bonds with other strands showing that the chain detaches glucan by glucan from the main bundle in discrete, rapid events. Further analysis shows that the intrastrand hydrogen bonds of each glucan tend to break for a sustained period of time before the interstrand hydrogen bonds break and strand detachment occurs. Examination of similar nonpeeling strands shows that, without this intrastrand hydrogen bond breakage, the structural rigidity of the individual unit can hinder its peeling despite interstrand hydrogen bond breakage.

STUDY BY AES AND EELS OF InP, InSb, InPO4 AND InxGa1-xAs SUBMITTED TO ELECTRON IRRADIATION

NASA Astrophysics Data System (ADS)

Ghaffour, M.; Abdellaoui, A.; Bouslama, M.; Ouerdane, A.; Al-Douri, Y.

2012-02-01

The surface of materials plays an important role in their technological applications. In the interest to study the stability of materials and their behavior, we irradiate them by the electrons by using the electron spectroscopy such as the Auger electron spectroscopy (AES) and the electron energy loss spectroscopy (EELS). These methods have proved their good sensitivity to study material surfaces. In this paper, we give some results about the effect of the electron beam irradiating the compounds InP, InSb, InPO4 and InxGa1-xAs. The III-V semiconductors InP and InSb seem to be sensitive to the electron irradiation. This breaks the chemical bonds between the element III and V which leads to an oxidation process at the surface. The AES and EELS spectroscopy are also used to characterize the oxide InPO4 whose thickness is about 10 Å grown on the substrate InP(100). The irradiation of the system InPO4/InP(100) by the electron beam of 5 keV energy leads to a structural change of the surface, so that there is breaking of chemical bonds between indium and phosphorus (In-P) and formation of new oxide other than InPO4. In this study we show an important result concerning the effect of the electron beam on the compound InxGa1-xAs by varying the parameter x to obtain In0.2Ga0.8As and In0.53Ga0.47As. It appears that the electron beam affects In0.2Ga0.8As too much in comparison with In0.53Ga0.47As. In the case of the irradiation of In0.2Ga0.8As, there is breaking of chemical bonds between indium and GaAs leading to formation of indium oxide associated to GaAs.

Macrophages lift off surface-bound bacteria using a filopodium-lamellipodium hook-and-shovel mechanism.

PubMed

Möller, Jens; Lühmann, Tessa; Chabria, Mamta; Hall, Heike; Vogel, Viola

2013-10-07

To clear pathogens from host tissues or biomaterial surfaces, phagocytes have to break the adhesive bacteria-substrate interactions. Here we analysed the mechanobiological process that enables macrophages to lift-off and phagocytose surface-bound Escherichia coli (E. coli). In this opsonin-independent process, macrophage filopodia hold on to the E. coli fimbriae long enough to induce a local protrusion of a lamellipodium. Specific contacts between the macrophage and E. coli are formed via the glycoprotein CD48 on filopodia and the adhesin FimH on type 1 fimbriae (hook). We show that bacterial detachment from surfaces occurrs after a lamellipodium has protruded underneath the bacterium (shovel), thereby breaking the multiple bacterium-surface interactions. After lift-off, the bacterium is engulfed by a phagocytic cup. Force activated catch bonds enable the long-term survival of the filopodium-fimbrium interactions while soluble mannose inhibitors and CD48 antibodies suppress the contact formation and thereby inhibit subsequent E. coli phagocytosis.

Macrophages lift off surface-bound bacteria using a filopodium-lamellipodium hook-and-shovel mechanism

PubMed Central

Möller, Jens; Lühmann, Tessa; Chabria, Mamta; Hall, Heike; Vogel, Viola

2013-01-01

To clear pathogens from host tissues or biomaterial surfaces, phagocytes have to break the adhesive bacteria-substrate interactions. Here we analysed the mechanobiological process that enables macrophages to lift-off and phagocytose surface-bound Escherichia coli (E. coli). In this opsonin-independent process, macrophage filopodia hold on to the E. coli fimbriae long enough to induce a local protrusion of a lamellipodium. Specific contacts between the macrophage and E. coli are formed via the glycoprotein CD48 on filopodia and the adhesin FimH on type 1 fimbriae (hook). We show that bacterial detachment from surfaces occurrs after a lamellipodium has protruded underneath the bacterium (shovel), thereby breaking the multiple bacterium-surface interactions. After lift-off, the bacterium is engulfed by a phagocytic cup. Force activated catch bonds enable the long-term survival of the filopodium-fimbrium interactions while soluble mannose inhibitors and CD48 antibodies suppress the contact formation and thereby inhibit subsequent E. coli phagocytosis. PMID:24097079

Platinum-catalyzed hydrolysis etching of SiC in water: A density functional theory study

NASA Astrophysics Data System (ADS)

Van Bui, Pho; Toh, Daisetsu; Isohashi, Ai; Matsuyama, Satoshi; Inagaki, Kouji; Sano, Yasuhisa; Yamauchi, Kazuto; Morikawa, Yoshitada

2018-05-01

A comprehensive study of the physicochemical interactions and the reaction mechanism of SiC etching with water by Pt catalysts can reveal key details about the surface treatment and catalytic phenomena at interfaces. Therefore, density functional theory simulations were performed to study the kinetics of Pt-assisted water dissociation and breaking of a Si–C bond compared to the HF-assisted mechanism. These calculations carefully considered the elastic and chemical interaction energies at the Pt–SiC interface, activation barriers of Si–C bond dissociation, and the catalytic role of Pt. It was found that the Pt-catalyzed etching of SiC in water is initiated via hydrolysis reactions that break the topmost Si–C bonds. The activation barrier strongly depends on the elastic and chemical interactions. However, chemical interactions are a dominant factor and mainly contribute to the lowering of the activation barrier, resulting in an increased rate of reaction.

Creep test observation of viscoelastic failure of edible fats

NASA Astrophysics Data System (ADS)

Vithanage, C. R.; Grimson, M. J.; Smith, B. G.; Wills, P. R.

2011-03-01

A rheological creep test was used to investigate the viscoelastic failure of five edible fats. Butter, spreadable blend and spread were selected as edible fats because they belong to three different groups according to the Codex Alimentarius. Creep curves were analysed according to the Burger model. Results were fitted to a Weibull distribution representing the strain-dependent lifetime of putative fibres in the material. The Weibull shape and scale (lifetime) parameters were estimated for each substance. A comparison of the rheometric measurements of edible fats demonstrated a clear difference between the three different groups. Taken together the results indicate that butter has a lower threshold for mechanical failure than spreadable blend and spread. The observed behaviour of edible fats can be interpreted using a model in which there are two types of bonds between fat crystals; primary bonds that are strong and break irreversibly, and secondary bonds, which are weaker but break and reform reversibly.

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

PubMed

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

2013-04-05

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

The development of methods of analysis of documents on the basis of the methods of Raman spectroscopy and fluorescence analysis

NASA Astrophysics Data System (ADS)

Gorshkova, Kseniia O.; Tumkin, Ilya I.; Kirillova, Elizaveta O.; Panov, Maxim S.; Kochemirovsky, Vladimir A.

2017-05-01

The investigation of natural aging of writing inks printed on paper using Raman spectroscopy was performed. Based on the obtained dependencies of the Raman peak intensities ratios on the exposure time, the dye degradation model was proposed. It was suggested that there are several competing bond breaking and bond forming reactions corresponding to the characteristic vibration frequencies of the dye molecule that simultaneously occur during ink aging process. Also we propose a methodology based on the study of the optical properties of paper, particularly changes in the fluorescence of optical brighteners included in its composition as well as the paper reflectivity using spectrophotometric methods. These results can be implemented to develop the novel and promising method of criminology.

Molecular excitonic seesaws.

PubMed

Wilhelm, Philipp; Schedlbauer, Jakob; Hinderer, Florian; Hennen, Daniel; Höger, Sigurd; Vogelsang, Jan; Lupton, John M

2018-04-17

The breaking of molecular symmetry through photoexcitation is a ubiquitous but rather elusive process, which, for example, controls the microscopic efficiency of light harvesting in molecular aggregates. A molecular excitation within a π-conjugated segment will self-localize due to strong coupling to molecular vibrations, locally changing bond alternation in a process which is fundamentally nondeterministic. Probing such symmetry breaking usually relies on polarization-resolved fluorescence, which is most powerful on the level of single molecules. Here, we explore symmetry breaking by designing a large, asymmetric acceptor-donor-acceptor (A 1 -D-A 2 ) complex 10 nm in length, where excitation energy can flow from the donor, a π-conjugated oligomer, to either one of the two boron-dipyrromethene (bodipy) dye acceptors of different color. Fluorescence correlation spectroscopy (FCS) reveals a nondeterministic switching between the energy-transfer pathways from the oligomer to the two acceptor groups on the submillisecond timescale. We conclude that excitation energy transfer, and light harvesting in general, are fundamentally nondeterministic processes, which can be strongly perturbed by external stimuli. A simple demonstration of the relation between exciton localization within the extended π-system and energy transfer to the endcap is given by considering the selectivity of endcap emission through the polarization of the excitation light in triads with bent oligomer backbones. Bending leads to increased localization so that the molecule acquires bichromophoric characteristics in terms of its fluorescence photon statistics.

Dimethyl ether electro-oxidation on platinum surfaces

DOE PAGES

Roling, Luke T.; Herron, Jeffrey A.; Budiman, Winny; ...

2016-02-27

A first-principles density functional theory study was performed in this paper to elucidate the mechanism of dimethyl ether electro-oxidation on three low-index platinum surfaces (Pt(111), Pt(100), and Pt(211)). The goal of this study is to provide a fundamental explanation for the high activity observed experimentally on Pt(100) compared to Pt(111) and stepped surfaces. We determine that the enhanced activity of Pt(100) stems from more facile C–O bond breaking kinetics, as well as from easier removal of CO as a surface poison through activation of water. In general, the C–O bond (in CH xOCH y) becomes easier to break as dimethylmore » ether is dehydrogenated to a greater extent. In contrast, dehydrogenation becomes more difficult as more hydrogen atoms are removed. We perform two analyses of probable reaction pathways, which both identify CHOC and CO as the key reaction intermediates on these Pt surfaces. We show that the reaction mechanism on each surface is dependent on the cell operating potential, as increasing the potential facilitates C–H bond scission, in turn promoting the formation of intermediates for which C–O scission is more facile. We additionally demonstrate that CO oxidation determines the high overpotential required for electro-oxidation on Pt surfaces. Finally, at practical operating potentials (~0.60 V RHE), we determine that C–O bond breaking is most likely the most difficult step on all three Pt surfaces studied.« less

Double-stage nematic bond ordering above double stripe magnetism: Application to BaTi 2 Sb 2 O

DOE PAGES

Zhang, G.; Glasbrenner, J. K.; Flint, R.; ...

2017-05-01

Spin-driven nemore » maticity, or the breaking of the point-group symmetry of the lattice without long-range magnetic order, is clearly quite important in iron-based superconductors. From a symmetry point of view, nematic order can be described as a coherent locking of spin fluctuations in two interpenetrating Néel sublattices with ensuing nearest-neighbor bond order and an absence of static magnetism. In this paper, we argue that the low-temperature state of the recently discovered superconductor BaTi 2 Sb 2 O is a strong candidate for a more exotic form of spin-driven nematic order, in which fluctuations occurring in four Néel sublattices promote both nearest- and next-nearest-neighbor bond order. We develop a low-energy field theory of this state and show that it can have, as a function of temperature, up to two separate bond-order phase transitions, namely, one that breaks rotation symmetry and one that breaks reflection and translation symmetries of the lattice. The resulting state has an orthorhombic lattice distortion, an intra-unit-cell charge density wave, and no long-range magnetic order, all consistent with reported measurements of the low-temperature phase of BaTi 2 Sb 2 O . Finally, we then use density functional theory calculations to extract exchange parameters to confirm that the model is applicable to BaTi 2 Sb 2 O .« less

Double-stage nematic bond ordering above double stripe magnetism: Application to BaTi 2 Sb 2 O

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

Zhang, G.; Glasbrenner, J. K.; Flint, R.

Spin-driven nemore » maticity, or the breaking of the point-group symmetry of the lattice without long-range magnetic order, is clearly quite important in iron-based superconductors. From a symmetry point of view, nematic order can be described as a coherent locking of spin fluctuations in two interpenetrating Néel sublattices with ensuing nearest-neighbor bond order and an absence of static magnetism. In this paper, we argue that the low-temperature state of the recently discovered superconductor BaTi 2 Sb 2 O is a strong candidate for a more exotic form of spin-driven nematic order, in which fluctuations occurring in four Néel sublattices promote both nearest- and next-nearest-neighbor bond order. We develop a low-energy field theory of this state and show that it can have, as a function of temperature, up to two separate bond-order phase transitions, namely, one that breaks rotation symmetry and one that breaks reflection and translation symmetries of the lattice. The resulting state has an orthorhombic lattice distortion, an intra-unit-cell charge density wave, and no long-range magnetic order, all consistent with reported measurements of the low-temperature phase of BaTi 2 Sb 2 O . Finally, we then use density functional theory calculations to extract exchange parameters to confirm that the model is applicable to BaTi 2 Sb 2 O .« less

Anisotropic mechanoresponse of energetic crystallites: a quantum molecular dynamics study of nano-collision

NASA Astrophysics Data System (ADS)

Li, Ying; Kalia, Rajiv K.; Misawa, Masaaki; Nakano, Aiichiro; Nomura, Ken-Ichi; Shimamura, Kohei; Shimojo, Fuyuki; Vashishta, Priya

2016-05-01

At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision was found to originate from the twisting and bending to breaking of nitro-groups mediated by strong intra-layer hydrogen bonds. This causes the closing of the electronic energy gap due to an inverse Jahn-Teller effect. On the other hand, the insensitive collisions normal to multilayers are accomplished by more delocalized molecular deformations mediated by inter-layer interactions. Our nano-collision studies provide a much needed atomistic understanding for the rational design of insensitive energetic nanomaterials and the detonation synthesis of novel nanomaterials.At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision was found to originate from the twisting and bending to breaking of nitro-groups mediated by strong intra-layer hydrogen bonds. This causes the closing of the electronic energy gap due to an inverse Jahn-Teller effect. On the other hand, the insensitive collisions normal to multilayers are accomplished by more delocalized molecular deformations mediated by inter-layer interactions. Our nano-collision studies provide a much needed atomistic understanding for the rational design of insensitive energetic nanomaterials and the detonation synthesis of novel nanomaterials. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr08769d

Application of Density Functional Theory to Systems Containing Metal Atoms

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Arnold, James O. (Technical Monitor)

1997-01-01

The accuracy of density functional theory (DFT) for problems involving metal atoms is considered. The DFT results are compared with experiment as well as results obtained using the coupled cluster approach. The comparisons include geometries, frequencies, and bond energies. The systems considered include MO2, M(OH)+(sub n), MNO+, and MCO+(sub 2). The DFT works well for frequencies and geometries, even in cases with symmetry breaking; however, some examples have been found where the symmetry breaking is quite severe and the DFT methods do not work well. The calculation of bond energies is more difficult and examples of the successes as well as failures of DFT will be given.

THz spectra and corresponding vibrational modes of DNA base pair cocrystals and polynucleotides.

PubMed

Wang, Fang; Zhao, Dongbo; Dong, Hao; Jiang, Ling; Huang, Lin; Liu, Yunfei; Li, Shuhua

2018-07-05

The generalized energy-based fragmentation (GEBF) approach has been applied to study the THz spectra and vibrational modes of base pair cocrystals under periodic boundary conditions (denoted as PBC-GEBF). Results of vibrational mode reveal that hydrogen bonds play a pivotal role in the pairing process of base crystals, where most NH and CH bonds stretch to some extent. We also found that hydrogen bonds of a self-made A:T cocrystal completely break in a transition from liquid to the solid state, while self-made C:G cocrystal is different and easier to form a cocrystal, as confirmed by X-ray diffraction (XRD) and terahertz (THz) spectra. Furthermore, we have studied DNA polynucleotides (in both A and B forms) found that the vibrational modes changed a lot during the process of their forming double strand. Despite the key role played by hydrogen bonds, the key contribution originates from collective motions of the main skeleton. A comparative study of the spectra of some stranded fragments suggests that different sequences or forms have similar spectra in THz band. They distinguish from each other mainly in the low-frequency regions, especially below 1 THz. This study would make great contributions to the molecular dynamics model based DNA long-chain structure simulation in the future study. Copyright © 2018 Elsevier B.V. All rights reserved.

Nucleation, Growth, Annealing, and Coagulation of Refractory Oxides and Metals: Recent Experimental Progress and Applications to Astrophysical Systems

NASA Technical Reports Server (NTRS)

Nuth, J. A.; Rietmeijer, F. J. M.; Hallenbeck, S. L.; Withey, P. A.

1999-01-01

Starting with cooling, refractory vapors diluted in significant quantities of H and He there are four processes that most natural systems will undergo: nucleation, growth, annealing, and coagulation. Nucleation is the processes by which the first stable refractory nuclei form in the vapor. These are the seeds onto which the remaining vapors will condense during the growth stage. Solids of any composition will try to arrange themselves into the least energetic configuration, provided that there is sufficient energy available to support such processes as diffusion and the breaking of chemical bonds. There is a significant activation energy associated with the annealing process in refractory solids due to the relatively high energy of the chemical bonds in solids. The grains formed in most cosmochemical systems are extremely small and often tightly coupled to the gas. Because of their small physical cross sections coagulation may be a very slow process unless there is another driving force involved in addition to normal Brownian motion. In what follows we will briefly cover each of these four stages for refractory oxide and metal grains, although in inverse order.

Distinct hydroxy-radical-induced damage of 3'-uridine monophosphate in RNA: a theoretical study.

PubMed

Zhang, Ru bo; Eriksson, Leif A

2009-01-01

RNA strand scission and base release in 3'-uridine monophosphate (UMP), induced by OH radical addition to uracil, is studied at the DFT B3LYP/6-31+G(d,p) level in the gas phase and in solution. In particular, the mechanism of hydrogen-atom transfer subsequent to radical formation, from C2' on the sugar to the C6 site on the base, is explored. The barriers of (C2'-)H2'(a) abstraction by the C6 radical site range from 11.2 to 20.0 kcal mol(-1) in the gas phase and 14.1 to 21.0 kcal mol(-1) in aqueous solution, indicating that the local surrounding governs the hydrogen-abstraction reaction in a stereoselective way. The calculated N1-C1' (N1-glycosidic bond) and beta-phosphate bond strengths show that homolytic and heterolytic bond-breaking processes are largely favored in each case, respectively. The barrier for beta-phosphate bond rupture is approximately 3.2-4.0 kcal mol(-1) and is preferred by 8-12 kcal mol(-1) over N1-glycosidic bond cleavage in both the gas phase and solution. The beta-phosphate bond-rupture reactions are exothermal in the gas phase and solution, whereas N1-C1' bond-rupture reactions require both solvation and thermal corrections at 298 K to be energetically favored. The presence of the ribose 2'-OH group and its formation of low-barrier hydrogen bonds with oxygen atoms of the 3'-phosphate linkage are highly important for hydrogen transfer and the subsequent bond-breakage reactions.

Breaking the limits of structural and mechanical imaging of the heterogeneous structure of coal macerals

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

Collins, L.; Tselev, A.; Jesse, S.

The correlation between local mechanical (elasto-plastic) and structural (composition) properties of coal presents significant fundamental and practical interest for coal processing and the development of rheological models of coal to coke transformations and for advancing novel approaches. Here, we explore the relationship between the local structural, chemical composition and mechanical properties of coal using a combination of confocal micro-Raman imaging and band excitation atomic force acoustic microscopy (BE-AFAM) for a bituminous coal. This allows high resolution imaging (10s of nm) of mechanical properties of the heterogeneous (banded) architecture of coal and correlating them to the optical gap, average crystallite size,more » the bond-bending disorder of sp2 aromatic double bonds and the defect density. This methodology hence allows the structural and mechanical properties of coal components (lithotypes, microlithotypes, and macerals) to be understood, and related to local chemical structure, potentially allowing for knowledge-based modelling and optimization of coal utilization processes.« less

Plasma-deposited amorphous silicon carbide films for micromachined fluidic channels

NASA Astrophysics Data System (ADS)

Wuu, Dong-Sing; Horng, Ray-Hua; Chan, Chia-Chi; Lee, Yih-Shing

1999-04-01

The stress properties of the a-SiC:H films on Si by plasma-enhanced chemical vapor deposition (PECVD) are investigated. It is found that the stability of the a-SiC:H films relates to Si-H bonds breaking and changes the stress toward tensile. No evident reduction in the content of Si-H bonds after thermal cycles was found in the carbon-rich samples. Moreover, a new method to fabricate microchannels by through-hole etching with subsequent planarization is proposed. The process is based on etching out the deep grooves through a perforated a-SiC:H membrane, where poly-Si is used as a sacrificial layer to define the channel structure, followed by PECVD sealing the SiC:H membrane. In order to improve the etching performance, the agitated KOH etch is performed at low temperatures (<50°C). The process technology is demonstrated on the fabrication of microfluidic channels with the low-stress (<0.1 GPa) a-SiC:H membranes.

Analysis of splicing complexes on native gels.

PubMed

Ares, Manuel

2013-10-01

Splicing requires a complex set of ATP-dependent macromolecular associations that lead to the rearrangement of just a few covalent bonds in the pre-mRNA substrate. Seeing only the covalent bonds breaking and forming is seeing only a very small part of the process. Analysis of native splicing complexes into which the radiolabeled substrate has been assembled, but not necessarily completely reacted, has provided a good understanding of the process. This protocol describes a gel method for detecting and analyzing yeast splicing complexes formed in vitro on a radiolabeled pre-mRNA substrate. Complexes formed during the splicing reaction are quenched by dilution and addition of an excess of RNA, which is thought to strip nonspecifically bound proteins from the labeled substrate RNA. After loading on a low-percentage, low-cross-linking ratio composite agarose-acrylamide gel (in 10% glycerol), labeled bands are detected. These can be extracted and shown to contain small nuclear RNAs (snRNAs) and partly reacted pre-mRNA.

Study of variation grain size in desulfurization process of calcined petroleum coke

NASA Astrophysics Data System (ADS)

Pintowantoro, Sungging; Setiawan, Muhammad Arif; Abdul, Fakhreza

2018-04-01

Indonesia is a country with abundant natural resources, such as mineral mining and petroleum. In petroleum processing, crude oil can be processed into a source of fuel energy such as gasoline, diesel, oil, petroleum coke, and others. One of crude oil potentials in Indonesia is petroleum coke. Petroleum coke is a product from oil refining process. Sulfur reducing process in calcined petroleum cokes can be done by desulfurization process. The industries which have potential to become petroleum coke processing consumers are industries of aluminum smelting (anode, graphite block, carbon mortar), iron riser, calcined coke, foundry coke, etc. Sulfur reducing process in calcined petroleum coke can be done by thermal desulfurization process with alkaline substance NaOH. Desulfurization of petroleum coke process can be done in two ways, which are thermal desulfurization and hydrodesulphurization. This study aims to determine the effect of various grain size on sulfur, carbon, and chemical bond which contained by calcined petroleum coke. The raw material use calcined petroleum coke with 0.653% sulfur content. The grain size that used in this research is 50 mesh, then varied to 20 mesh and 100 mesh for each desulfurization process. Desulfurization are tested by ICP, UV-VIS, and FTIR to determine levels of sulfur, carbon, chemical bonding and sulfur dissolved water which contained in the residual washing of calcined petroleum coke. From various grain size that mentioned before, the optimal value is on 100 mesh grain size, where the sulfur content in petroleum coke is 0.24% and carbon content reaches the highest level of 97.8%. Meanwhile for grain size 100 mesh in the desulfurization process is enough to break the chemical bonds of organic sulfur in petroleum coke.

New insights into the mechanism of interaction between CO2 and polymers from thermodynamic parameters obtained by in situ ATR-FTIR spectroscopy.

PubMed

Gabrienko, Anton A; Ewing, Andrew V; Chibiryaev, Andrey M; Agafontsev, Alexander M; Dubkov, Konstantin A; Kazarian, Sergei G

2016-03-07

This work reports new physical insights of the thermodynamic parameters and mechanisms of possible interactions occurring in polymers subjected to high-pressure CO2. ATR-FTIR spectroscopy has been used in situ to determine the thermodynamic parameters of the intermolecular interactions between CO2 and different functional groups of the polymers capable of specific interactions with sorbed CO2 molecules. Based on the measured ATR-FTIR spectra of the polymer samples subjected to high-pressure CO2 (30 bar) at different temperatures (300-340 K), it was possible to characterize polymer-polymer and CO2-polymer interactions. Particularly, the enthalpy and entropy of the formation of the specific non-covalent complexes between CO2 and the hydroxy (-OH), carbonyl (C[double bond, length as m-dash]O) and hydroxyimino ([double bond, length as m-dash]N-OH) functional groups of the polymer samples have been measured. Furthermore, the obtained spectroscopic results have provided an opportunity for the structure of these complexes to be proposed. An interesting phenomenon regarding the behavior of CO2/polymer systems has also been observed. It has been found that only for the polyketone, the value of enthalpy was negative indicating an exothermic process during the formation of the CO2-polymer non-covalent complexes. Conversely, for the polyoxime and polyalcohol samples there is a positive enthalpy determined. This is a result of the initial polymer-polymer interactions requiring more energy to break than is released during the formation of the CO2-polymer complex. The effect of increasing temperature to facilitate the breaking of the polymer-polymer interactions has also been observed. Hence, a mechanism for the formation of CO2-polymer complexes was suggested based on these results, which occurs via a two-step process: (1) the breaking of the existing polymer-polymer interactions followed by (2) the formation of new CO2-polymer non-covalent interactions.

Development and application of contamination technology for MSFC managed space systems

NASA Technical Reports Server (NTRS)

1993-01-01

The second annual report on the development and application of contamination technology for MSFC managed space systems covering the period from 10 Dec. 1992 to 10 Dec. 1993 is presented. During this time period, studies were concluded which proved that in-process corrosion protection is not required during Redesigned Solid Rocket Motor (RSRM) case processing. Also completed were a series of tests evaluating the effects of environmental exposure and contamination on 2219-T87 aluminum (Space Shuttle External Tank) OSEE response and bonding properties. Correlations were developed between OSEE response, contamination type/level, and primer adhesion. The results showed that the wet tape and water break free tests currently employed during ET processing may not detect bond affecting levels of some potential contaminants; however, the contaminants were detected with OSEE analysis. Finally, exposure/contamination studies were initiated with HP9-4-30 steel. HP9-4-30 was selected for evaluation because it represents a class of metals commom to MSFC managed space flight systems which are less prone to oxidation than D6AC steel or aluminum.

Development and application of contamination technology for MSFC managed space systems

NASA Astrophysics Data System (ADS)

The second annual report on the development and application of contamination technology for MSFC managed space systems covering the period from 10 Dec. 1992 to 10 Dec. 1993 is presented. During this time period, studies were concluded which proved that in-process corrosion protection is not required during Redesigned Solid Rocket Motor (RSRM) case processing. Also completed were a series of tests evaluating the effects of environmental exposure and contamination on 2219-T87 aluminum (Space Shuttle External Tank) OSEE response and bonding properties. Correlations were developed between OSEE response, contamination type/level, and primer adhesion. The results showed that the wet tape and water break free tests currently employed during ET processing may not detect bond affecting levels of some potential contaminants; however, the contaminants were detected with OSEE analysis. Finally, exposure/contamination studies were initiated with HP9-4-30 steel. HP9-4-30 was selected for evaluation because it represents a class of metals commom to MSFC managed space flight systems which are less prone to oxidation than D6AC steel or aluminum.

Plasmonic Spherical Heterodimers: Reversal of Optical Binding Force Based on the Forced Breaking of Symmetry.

PubMed

Mahdy, M R C; Danesh, Md; Zhang, Tianhang; Ding, Weiqiang; Rivy, Hamim Mahmud; Chowdhury, Ariful Bari; Mehmood, M Q

2018-02-16

The stimulating connection between the reversal of near-field plasmonic binding force and the role of symmetry-breaking has not been investigated comprehensively in the literature. In this work, the symmetry of spherical plasmonic heterodimer-setup is broken forcefully by shining the light from a specific side of the set-up instead of impinging it from the top. We demonstrate that for the forced symmetry-broken spherical heterodimer-configurations: reversal of lateral and longitudinal near-field binding force follow completely distinct mechanisms. Interestingly, the reversal of longitudinal binding force can be easily controlled either by changing the direction of light propagation or by varying their relative orientation. This simple process of controlling binding force may open a novel generic way of optical manipulation even with the heterodimers of other shapes. Though it is commonly believed that the reversal of near-field plasmonic binding force should naturally occur for the presence of bonding and anti-bonding modes or at least for the Fano resonance (and plasmonic forces mostly arise from the surface force), our study based on Lorentz-force dynamics suggests notably opposite proposals for the aforementioned cases. Observations in this article can be very useful for improved sensors, particle clustering and aggregation.

Understanding cation ordering and oxygen vacancy site preference in Ba3CaNb2O9 from first-principles

NASA Astrophysics Data System (ADS)

Ding, Hepeng; Virkar, Anil; Liu, Feng

2014-03-01

We investigate the physical mechanism underlying the formation of the B-site cation ordering and the oxygen vacancy site selection in Ba3CaNb2O9 using density functional theory calculations. We found that either cation site exchange or oxygen vacancy formation induces negligible lattice strain. This implies that the ionic radius plays an insignificant role in governing these two processes. Furthermore, the electrostatic interactions are found dominant in the ordering of mixed valence species on one or more sites, the ionic bond strength is identified as the dominant force in governing both the 1:2 B-site cation ordering along the <111>direction and the oxygen vacancy site preference in Ba3CaNb2O9. Specifically, the cation ordering can be rationalized by the increased mixing bonding energy of the Ca-O-Nb bonds over the Ca-O-Ca and Nb-O-Nb bonds, i.e., 1/2(Ca-O-Ca + Nb-O-Nb)

Carbon-14 decay as a source of non-canonical bases in DNA.

PubMed

Sassi, Michel; Carter, Damien J; Uberuaga, Blas P; Stanek, Chris R; Marks, Nigel A

2014-01-01

Significant experimental effort has been applied to study radioactive beta-decay in biological systems. Atomic-scale knowledge of this transmutation process is lacking due to the absence of computer simulations. Carbon-14 is an important beta-emitter, being ubiquitous in the environment and an intrinsic part of the genetic code. Over a lifetime, around 50 billion (14)C decays occur within human DNA. We apply ab initio molecular dynamics to quantify (14)C-induced bond rupture in a variety of organic molecules, including DNA base pairs. We show that double bonds and ring structures confer radiation resistance. These features, present in the canonical bases of the DNA, enhance their resistance to (14)C-induced bond-breaking. In contrast, the sugar group of the DNA and RNA backbone is vulnerable to single-strand breaking. We also show that Carbon-14 decay provides a mechanism for creating mutagenic wobble-type mispairs. The observation that DNA has a resistance to natural radioactivity has not previously been recognized. We show that (14)C decay can be a source for generating non-canonical bases. Our findings raise questions such as how the genetic apparatus deals with the appearance of an extra nitrogen in the canonical bases. It is not obvious whether or not the DNA repair mechanism detects this modification nor how DNA replication is affected by a non-canonical nucleobase. Accordingly, (14)C may prove to be a source of genetic alteration that is impossible to avoid due to the universal presence of radiocarbon in the environment. © 2013.

19 CFR 122.135 - When airline has in-bond liquor storeroom.

Code of Federal Regulations, 2010 CFR

2010-04-01

...; DEPARTMENT OF THE TREASURY AIR COMMERCE REGULATIONS Aircraft Liquor Kits § 122.135 When airline has in-bond liquor storeroom. (a) Restocking. Liquor kits on board an aircraft landing at an airport where the... director: (1) A list of names of all airline employees authorized to break Customs seals on liquor kits in...

19 CFR 122.135 - When airline has in-bond liquor storeroom.

Code of Federal Regulations, 2013 CFR

2013-04-01

...; DEPARTMENT OF THE TREASURY AIR COMMERCE REGULATIONS Aircraft Liquor Kits § 122.135 When airline has in-bond liquor storeroom. (a) Restocking. Liquor kits on board an aircraft landing at an airport where the... director: (1) A list of names of all airline employees authorized to break Customs seals on liquor kits in...

19 CFR 122.135 - When airline has in-bond liquor storeroom.

Code of Federal Regulations, 2012 CFR

2012-04-01

...; DEPARTMENT OF THE TREASURY AIR COMMERCE REGULATIONS Aircraft Liquor Kits § 122.135 When airline has in-bond liquor storeroom. (a) Restocking. Liquor kits on board an aircraft landing at an airport where the... director: (1) A list of names of all airline employees authorized to break Customs seals on liquor kits in...

19 CFR 122.135 - When airline has in-bond liquor storeroom.

Code of Federal Regulations, 2014 CFR

2014-04-01

...; DEPARTMENT OF THE TREASURY AIR COMMERCE REGULATIONS Aircraft Liquor Kits § 122.135 When airline has in-bond liquor storeroom. (a) Restocking. Liquor kits on board an aircraft landing at an airport where the... director: (1) A list of names of all airline employees authorized to break Customs seals on liquor kits in...

19 CFR 122.135 - When airline has in-bond liquor storeroom.

Code of Federal Regulations, 2011 CFR

2011-04-01

...; DEPARTMENT OF THE TREASURY AIR COMMERCE REGULATIONS Aircraft Liquor Kits § 122.135 When airline has in-bond liquor storeroom. (a) Restocking. Liquor kits on board an aircraft landing at an airport where the... director: (1) A list of names of all airline employees authorized to break Customs seals on liquor kits in...

Discrete-Element bonded-particle Sea Ice model DESIgn, version 1.3a - model description and implementation

NASA Astrophysics Data System (ADS)

Herman, Agnieszka

2016-04-01

This paper presents theoretical foundations, numerical implementation and examples of application of the two-dimensional Discrete-Element bonded-particle Sea Ice model - DESIgn. In the model, sea ice is represented as an assemblage of objects of two types: disk-shaped "grains" and semi-elastic bonds connecting them. Grains move on the sea surface under the influence of forces from the atmosphere and the ocean, as well as interactions with surrounding grains through direct contact (Hertzian contact mechanics) and/or through bonds. The model has an experimental option of taking into account quasi-three-dimensional effects related to the space- and time-varying curvature of the sea surface, thus enabling simulation of ice breaking due to stresses resulting from bending moments associated with surface waves. Examples of the model's application to simple sea ice deformation and breaking problems are presented, with an analysis of the influence of the basic model parameters ("microscopic" properties of grains and bonds) on the large-scale response of the modeled material. The model is written as a toolbox suitable for usage with the open-source numerical library LIGGGHTS. The code, together with full technical documentation and example input files, is freely available with this paper and on the Internet.

Binding of dinitrogen to an iron-sulfur-carbon site

NASA Astrophysics Data System (ADS)

Čorić, Ilija; Mercado, Brandon Q.; Bill, Eckhard; Vinyard, David J.; Holland, Patrick L.

2015-10-01

Nitrogenases are the enzymes by which certain microorganisms convert atmospheric dinitrogen (N2) to ammonia, thereby providing essential nitrogen atoms for higher organisms. The most common nitrogenases reduce atmospheric N2 at the FeMo cofactor, a sulfur-rich iron-molybdenum cluster (FeMoco). The central iron sites that are coordinated to sulfur and carbon atoms in FeMoco have been proposed to be the substrate binding sites, on the basis of kinetic and spectroscopic studies. In the resting state, the central iron sites each have bonds to three sulfur atoms and one carbon atom. Addition of electrons to the resting state causes the FeMoco to react with N2, but the geometry and bonding environment of N2-bound species remain unknown. Here we describe a synthetic complex with a sulfur-rich coordination sphere that, upon reduction, breaks an Fe-S bond and binds N2. The product is the first synthetic Fe-N2 complex in which iron has bonds to sulfur and carbon atoms, providing a model for N2 coordination in the FeMoco. Our results demonstrate that breaking an Fe-S bond is a chemically reasonable route to N2 binding in the FeMoco, and show structural and spectroscopic details for weakened N2 on a sulfur-rich iron site.

Adhesion, friction and micromechanical properties of ceramics

NASA Technical Reports Server (NTRS)

Miyoshi, Kazuhisa

1988-01-01

The adhesion, friction, and micromechanical properties of ceramics, both in monolithic and coating form, are reviewed. Ceramics are examined in contact with themselves, other harder materials, and metals. For the simplicity of discussion, the tribological properties of concern in the processes are separated into two parts. The first part discusses the pull-off force (adhesion) and the shear force required to break the interfacial junctions between contacting surfaces. The role of chemical bonding in adhesion and friction, and the effects of surface contaminant films and temperature on tribological response with respect to adhesion and friction are discussed. The second part deals with abrasion of ceramics. Elastic, plastic, and fracture behavior of ceramics in solid state contact is discussed. The scratch technique of determining the critical load needed to fracture interfacial adhesive bonds of ceramic deposited on substrates is also addressed.

Carrier-envelope phase dependence of the directional fragmentation and hydrogen migration in toluene in few-cycle laser fields.

PubMed

Li, Hui; Kling, Nora G; Förg, Benjamin; Stierle, Johannes; Kessel, Alexander; Trushin, Sergei A; Kling, Matthias F; Kaziannis, Spyros

2016-07-01

The dissociative ionization of toluene initiated by a few-cycle laser pulse as a function of the carrier envelope phase (CEP) is investigated using single-shot velocity map imaging. Several ionic fragments, CH3 (+), H2 (+), and H3 (+), originating from multiply charged toluene ions present a CEP-dependent directional emission. The formation of H2 (+) and H3 (+) involves breaking C-H bonds and forming new bonds between the hydrogen atoms within the transient structure of the multiply charged precursor. We observe appreciable intensity-dependent CEP-offsets. The experimental data are interpreted with a mechanism that involves laser-induced coupling of vibrational states, which has been found to play a role in the CEP-control of molecular processes in hydrocarbon molecules, and appears to be of general importance for such complex molecules.

Cells having cathodes containing polycarbon disulfide materials

DOEpatents

Okamoto, Yoshi; Skotheim, Terje A.; Lee, Hung S.

1995-08-15

The present invention relates to an electric current producing cell which contains an anode, a cathode having as a cathode-active material one or more carbon-sulfur compounds of the formula (CS.sub.x).sub.n, in which x takes values from 1.2 to 2.3 and n is greater or equal to 2, and where the redox process does not involve polymerization and de-polymerization by forming and breaking S--S bonds in the polymer backbone. The cell also contains an electrolyte which is chemically inert with respect to the anode and the cathode.

No effects of intermittent 50 Hz EMF on cytoplasmic free calcium and on the mitochondrial membrane potential in human diploid fibroblasts.

PubMed

Pilger, Alexander; Ivancsits, Sabine; Diem, Elisabeth; Steffens, Melanie; Kolb, Hans-Albert; Rüdiger, Hugo W

2004-09-01

The recently described increase in DNA strand breaks of cultured human diploid fibroblasts after intermittent exposure to extremely-low-frequency electromagnetic fields (ELF-EMF) of more than about 70 microT ELF-EMF is difficult to explain by a direct induction of covalent bond disruption. Therefore the hypothesis has been tested that ELF-EMF-induced DNA strand breaks might be mediated by cellular processes that cause alteration of the intracellular concentration of free calcium ([Ca2+]i) and/or the membrane potential (DeltaPsi(m)). [Ca2+]i was determined by the ratiometric fura-2 technique. Changes in DeltaPsi(m) were assessed by using the potential-dependent lipophilic cationic probe JC-1. Human fibroblasts were exposed to intermittent ELF-EMF (50 Hz, 1000 microT). Although exposure of fiboblasts to ELF-EMF resulted in a highly significant increase in DNA strand breaks as determined by the comet assay, no effect on JC-1 fluorescence emission or on [Ca2+]i has been observed when comparing exposed with sham-exposed cells. Therefore, it is suggested that ELF-EMF-induced DNA strand breaks are unlikely to be caused by intracellular changes that affect [Ca2+]i and/or DeltaPsi(m).

Photocatalytic mechanism of high-activity anatase TiO2 with exposed (001) facets from molecular-atomic scale: HRTEM and Raman studies

NASA Astrophysics Data System (ADS)

Wu, Jun; Shi, Chentian; Zhang, Yupeng; Fu, Qiang; Pan, Chunxu

2017-12-01

Anatase TiO2 with a variant percentage of exposed (001) facets was prepared under hydrothermal processes by adjusting the volume of HF, and the photocatalytic mechanism was studied from atomic-molecular scale by HRTEM and Raman spectroscopy. It was revealed that: 1) From HRTEM observations, the surface of original TiO2 with exposed (001) facets was clean without impurity, and the crystal lattice was clear and completed; however, when mixed with methylene blue (MB) solution, there were many 1 nm molecular absorbed at the surface of TiO2; after the photocatalytic experiment, MB molecules disappeared and the TiO2 lattice image became fuzzy. 2) The broken path of the MB chemical bond was obtained by Raman spectroscopy, i.e., after the irradiation of the light, the vibrational mode of C-N-C disappeared due to the chemical bond breakage, and the groups containing C-N bond and carbon rings were gradually decomposed. Accordingly, we propose that the driving force for breaking the chemical bond and the disappearance of groups is from the surface lattice distortion of TiO2 during photocatalyzation.

Effects of Atomic-Scale Structure on the Fracture Properties of Amorphous Carbon - Carbon Nanotube Composites

NASA Technical Reports Server (NTRS)

Jensen, Benjamin D.; Wise, Kristopher E.; Odegard, Gregory M.

2015-01-01

The fracture of carbon materials is a complex process, the understanding of which is critical to the development of next generation high performance materials. While quantum mechanical (QM) calculations are the most accurate way to model fracture, the fracture behavior of many carbon-based composite engineering materials, such as carbon nanotube (CNT) composites, is a multi-scale process that occurs on time and length scales beyond the practical limitations of QM methods. The Reax Force Field (ReaxFF) is capable of predicting mechanical properties involving strong deformation, bond breaking and bond formation in the classical molecular dynamics framework. This has been achieved by adding to the potential energy function a bond-order term that varies continuously with distance. The use of an empirical bond order potential, such as ReaxFF, enables the simulation of failure in molecular systems that are several orders of magnitude larger than would be possible in QM techniques. In this work, the fracture behavior of an amorphous carbon (AC) matrix reinforced with CNTs was modeled using molecular dynamics with the ReaxFF reactive forcefield. Care was taken to select the appropriate simulation parameters, which can be different from those required when using traditional fixed-bond force fields. The effect of CNT arrangement was investigated with three systems: a single-wall nanotube (SWNT) array, a multi-wall nanotube (MWNT) array, and a SWNT bundle system. For each arrangement, covalent bonds are added between the CNTs and AC, with crosslink fractions ranging from 0-25% of the interfacial CNT atoms. The SWNT and MWNT array systems represent ideal cases with evenly spaced CNTs; the SWNT bundle system represents a more realistic case because, in practice, van der Waals interactions lead to the agglomeration of CNTs into bundles. The simulation results will serve as guidance in setting experimental processing conditions to optimize the mechanical properties of CNT composites.

Study of molecular carbon-hydrogen bond dissociation during shock compression

NASA Astrophysics Data System (ADS)

Hammel, Ben; Hawreliak, James

2017-06-01

Advancements in theory and experiment show that chemical interactions in warm dense mixtures play a non-negligible role in the high-temperature and high-pressure properties of a molecular compound. For example, recent work on polystyrene has observed features suggestive of molecular dissociation - non-linear ``kinks'' are evident in the material's Hugoniot, consistent with CH bond breaking. The assumption used in linear mixing models, that species are chemically inert, breaks down in warm dense mixtures. At the Institute for Shock Physics, we are developing the necessary capabilities to perform high-repetition-rate experiments needed to map out chemical-reaction features along a material's Hugoniot. Initially, we plan to benchmark our work to the data taken by Barrios et al., by reproducing the observed kink in the polystyrene Hugoniot. We then extend this capability to explore polypropylene, CH2, where we expect to observe multiple kink features - representative of the disassociation of multiple CH bonds. Work supported by DOE/NNSA, DOE/SC-OFES and Murdock Charitable Trust.

Microstructural and Mechanical Properties of Hot Roll Bonded Titanium Alloy/Low Carbon Steel Plate

NASA Astrophysics Data System (ADS)

Yu, Chao; Qi, Zi-chen; Yu, Hui; Xu, Cheng; Xiao, Hong

2018-03-01

In this paper, a titanium alloy and low carbon steel were bonded via hot rolling in a vacuum, and the effect of roll bonding temperature and reduction ratio on the microstructural and mechanical properties of the plate was studied. When the bonding temperature was between 850 and 1050 °C, the shear strength of the interface increased with an increasing reduction ratio from 18 to 70%. At a bonding temperature of 950 °C and at a rolling reduction ratio of 70%, the best bonding strength was obtained, and a shear fracture occurred on the low carbon steel matrix. At 1050 °C, brittle compounds, i.e., TiC, FeTi, and Fe2Ti, formed at the interface, which decreased the bonding strength. The large reduction ratio can break up compounds at the interface and extrude fresh metal for bonding, thereby increasing the bonding strength.

Inverse-Micelle-Encapsulated Water-Enabled Bond Breaking of Dialkyl Diselenide/Disulfide: A Critical Step for Synthesizing High- Quality Gold Nanoparticles

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

Zaluzhna, Oksana; Li, Ying; Allison, Thomas C.

2012-10-09

Inverse-micelle-encapsulated water formed in the two-phase Brust-Schiffrin method (BSM) synthesis of Au nanoparticles (NPs) is identified as essential for dialkyl diselenide/disulfide to react with the Au(III) complex in which the Se-Se/S-S bond is broken, leading to formation of higher-quality Au NPs.

Time resolved infrared studies of C-H bond activation by organometallics

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

Asplund, M.C.

This work describes how step-scan Fourier Transform Infrared spectroscopy and visible and near infrared ultrafast lasers have been applied to the study of the photochemical activation of C-H bonds in organometallic systems, which allow for the selective breaking of C-H bonds in alkanes. The author has established the photochemical mechanism of C-H activation by Tp{sup *}Rh(CO){sub 2}(Tp{sup *} = HB-Pz{sup *}{sub 3}, Pz = 3,5-dimethylpyrazolyl) in alkane solution. The initially formed monocarbonyl forms a weak solvent complex, which undergoes a change in Tp{sup *} ligand connectivity. The final C-H bond breaking step occurs at different time scales depending on themore » structure of the alkane. In linear solvents, the time scale is <50 ns and cyclic alkanes is {approximately}200 ps. The reactivity of the Tp{sup *}Rh(CO){sub 2} system has also been studied in aromatic solvents. Here the reaction proceeds through two different pathways, with very different time scales. The first proceeds in a manner analogous to alkanes and takes <50 ns. The second proceeds through a Rh-C-C complex, and takes place on a time scale of 1.8 {micro}s.« less

Cooperative structural transitions in amyloid-like aggregation

NASA Astrophysics Data System (ADS)

Steckmann, Timothy; Bhandari, Yuba R.; Chapagain, Prem P.; Gerstman, Bernard S.

2017-04-01

Amyloid fibril aggregation is associated with several horrific diseases such as Alzheimer's, Creutzfeld-Jacob, diabetes, Parkinson's, and others. Although proteins that undergo aggregation vary widely in their primary structure, they all produce a cross-β motif with the proteins in β-strand conformations perpendicular to the fibril axis. The process of amyloid aggregation involves forming myriad different metastable intermediate aggregates. To better understand the molecular basis of the protein structural transitions and aggregation, we report on molecular dynamics (MD) computational studies on the formation of amyloid protofibrillar structures in the small model protein ccβ, which undergoes many of the structural transitions of the larger, naturally occurring amyloid forming proteins. Two different structural transition processes involving hydrogen bonds are observed for aggregation into fibrils: the breaking of intrachain hydrogen bonds to allow β-hairpin proteins to straighten, and the subsequent formation of interchain H-bonds during aggregation into amyloid fibrils. For our MD simulations, we found that the temperature dependence of these two different structural transition processes results in the existence of a temperature window that the ccβ protein experiences during the process of forming protofibrillar structures. This temperature dependence allows us to investigate the dynamics on a molecular level. We report on the thermodynamics and cooperativity of the transformations. The structural transitions that occurred in a specific temperature window for ccβ in our investigations may also occur in other amyloid forming proteins but with biochemical parameters controlling the dynamics rather than temperature.

Controlled formation of cyclopentane hydrate suspensions via capillary-driven jet break-up

NASA Astrophysics Data System (ADS)

Geri, Michela; McKinley, Gareth

2017-11-01

Clathrate hydrates are crystalline compounds that form when a lattice of hydrogen-bonded water molecules is filled by guest molecules sequestered from an adjacent gas or liquid phase. Being able to rapidly produce and transport synthetic hydrates is of great interest given their significant potential as a clean energy source and safe option for hydrogen storage. We propose a new method to rapidly produce cyclopentane hydrate suspensions at ambient pressure with tunable particle size distribution by taking advantage of the Rayleigh-Plateau instability to form a mono-disperse stream of droplets during the controlled break-up of a water jet. The droplets are immediately frozen into ice particles through immersion in a subcooled reservoir and converted into hydrates with a dramatic reduction in the nucleation induction time. By measuring the evolution of the rheological properties with time, we monitor the process of hydrates formation via surface crystallization and agglomeration with different droplet size distributions. This new method enables us to gain new insights into hydrate formation and transport which was previously hindered by uncontrolled droplet formation and hydrate nucleation processes. MITei Chevron Fellowship.

Recyclable cross-linked anion exchange membrane for alkaline fuel cell application

NASA Astrophysics Data System (ADS)

Hou, Jianqiu; Liu, Yazhi; Ge, Qianqian; Yang, Zhengjin; Wu, Liang; Xu, Tongwen

2018-01-01

Cross-linking can effectively solve the conductivity-swelling dilemma in anion exchange membranes (AEMs) but will generate solid wastes. To address this, we developed an AEM cross-linked via disulfide bonds, bearing quaternary ammonium groups, which can be easily recycled. The membrane (RC-QPPO) with IEC of 1.78 mmol g-1, when cross-linked, showed enhanced mechanical properties and good hydroxide conductivity (24.6 mS cm-1 at 30 °C). Even at higher IEC value (2.13 mmol g-1), it still has low water uptake, low swelling ratio and delivers a peak power density of 150 mW cm-2 at 65 °C. Exploiting the formation of disulfide bonds from -SH groups, the membrane can be readily cross-linked in alkaline condition and recycled by reversibly breaking disulfide bonds with dithiothreitol (DTT). The recycled membrane solution can be directly utilized to cast a brand-new AEM. By washing away the residual DTT with water and exposure to air, it can be cross-linked again and this process is repeatable. During the recycling and cross-linking processes, the membrane showed a slight IEC decrease of 5% due to functional group degradation. The strategy presented here is promising in enhancing AEM properties and reducing the impact of artificial polymers on the environment.

Contact and Length Dependent Effects in Single-Molecule Electronics

NASA Astrophysics Data System (ADS)

Hines, Thomas

Understanding charge transport in single molecules covalently bonded to electrodes is a fundamental goal in the field of molecular electronics. In the past decade, it has become possible to measure charge transport on the single-molecule level using the STM break junction method. Measurements on the single-molecule level shed light on charge transport phenomena which would otherwise be obfuscated by ensemble measurements of groups of molecules. This thesis will discuss three projects carried out using STM break junction. In the first project, the transition between two different charge transport mechanisms is reported in a set of molecular wires. The shortest wires show highly length dependent and temperature invariant conductance behavior, whereas the longer wires show weakly length dependent and temperature dependent behavior. This trend is consistent with a model whereby conduction occurs by coherent tunneling in the shortest wires and by incoherent hopping in the longer wires. Measurements are supported with calculations and the evolution of the molecular junction during the pulling process is investigated. The second project reports controlling the formation of single-molecule junctions by means of electrochemically reducing two axial-diazonium terminal groups on a molecule, thereby producing direct Au-C covalent bonds in-situ between the molecule and gold electrodes. Step length analysis shows that the molecular junction is significantly more stable, and can be pulled over a longer distance than a comparable junction created with amine anchoring bonds. The stability of the junction is explained by the calculated lower binding energy associated with the direct Au-C bond compared with the Au-N bond. Finally, the third project investigates the role that molecular conformation plays in the conductance of oligothiophene single-molecule junctions. Ethyl substituted oligothiophenes were measured and found to exhibit temperature dependent conductance and transition voltage for molecules with between two and six repeat units. While the molecule with only one repeat unit shows temperature invariant behavior. Density functional theory calculations show that at higher temperatures the oligomers with multiple repeat units assume a more planar conformation, which increases the conjugation length and decreases the effective energy barrier of the junction.

Photophysics and Photochemistry

ERIC Educational Resources Information Center

Letokhov, V. S.

1977-01-01

Discusses recent progress in using tunable lasers to selectively separate substances at the atomic and molecular level. Emphasizes biological applications, such as selective excitation and breaking of hydrogen bonds in DNA. (MLH)

Photo-reduction on the rupture of disulfide bonds and the related protein assembling

NASA Astrophysics Data System (ADS)

Wang, Wei

It has been found that many proteins can self-assemble into nanoscale assemblies when they unfold or partially unfold under harsh conditions, such as low pH, high temperature, or the presence of denaturants, and so on. These nanoscale assemblies can have some applications such as the drug-delivery systems (DDSs). Here we report a study that a very physical way, the UV illumination, can be used to facilitate the formation of protein fibrils and nanoparticles under native conditions by breaking disulfide bonds in some disulfide-containing proteins. By controlling the intensity of UV light and the illumination time, we realized the preparation of self-assembly nanoparticles which encapsulate the anticancer drug doxorubicin (DOX) and can be used as the DDS for inhibiting the growth of tumor. The formation of fibrillary assemblies was also observed. The rupture of disulfide bonds through photo-reduction process due to the effect of tryptophan and tyrosine was studied, and the physical mechanism of the assembling of the related disulfide-containing proteins was also discussed. We thank the financial support from NSF of China and the 973 project.

Hydrogen tunneling links protein dynamics to enzyme catalysis.

PubMed

Klinman, Judith P; Kohen, Amnon

2013-01-01

The relationship between protein dynamics and function is a subject of considerable contemporary interest. Although protein motions are frequently observed during ligand binding and release steps, the contribution of protein motions to the catalysis of bond making/breaking processes is more difficult to probe and verify. Here, we show how the quantum mechanical hydrogen tunneling associated with enzymatic C-H bond cleavage provides a unique window into the necessity of protein dynamics for achieving optimal catalysis. Experimental findings support a hierarchy of thermodynamically equilibrated motions that control the H-donor and -acceptor distance and active-site electrostatics, creating an ensemble of conformations suitable for H-tunneling. A possible extension of this view to methyl transfer and other catalyzed reactions is also presented. The impact of understanding these dynamics on the conceptual framework for enzyme activity, inhibitor/drug design, and biomimetic catalyst design is likely to be substantial.

Hydrogen Tunneling Links Protein Dynamics to Enzyme Catalysis

PubMed Central

Klinman, Judith P.; Kohen, Amnon

2014-01-01

The relationship between protein dynamics and function is a subject of considerable contemporary interest. Although protein motions are frequently observed during ligand binding and release steps, the contribution of protein motions to the catalysis of bond making/breaking processes is more difficult to probe and verify. Here, we show how the quantum mechanical hydrogen tunneling associated with enzymatic C–H bond cleavage provides a unique window into the necessity of protein dynamics for achieving optimal catalysis. Experimental findings support a hierarchy of thermodynamically equilibrated motions that control the H-donor and -acceptor distance and active-site electrostatics, creating an ensemble of conformations suitable for H-tunneling. A possible extension of this view to methyl transfer and other catalyzed reactions is also presented. The impact of understanding these dynamics on the conceptual framework for enzyme activity, inhibitor/drug design, and biomimetic catalyst design is likely to be substantial. PMID:23746260

Redox and Lewis acid-base activities through an electronegativity-hardness landscape diagram.

PubMed

Das, Ranjita; Vigneresse, Jean-Louis; Chattaraj, Pratim Kumar

2013-11-01

Chemistry is the science of bond making and bond breaking which requires redistribution of electron density among the reactant partners. Accordingly acid-base and redox reactions form cardinal components in all branches of chemistry, e.g., inorganic, organic, physical or biochemistry. That is the reason it forms an integral part of the undergraduate curriculum all throughout the globe. In an electronegativity (χ)- hardness (η) landscape diagram the diagonal χ = η line separates reducing agents from oxidizing agents as well as Lewis acids from Lewis bases. While electronegativity is related to the degree of electron transfer between two reactants, hardness is related to the resistance to that process. Accordingly the electronegativities of oxidizing agents/Lewis acids are generally greater than the corresponding hardness values and the reverse is true for reducing agents/Lewis bases. Electrophiles and nucleophiles are also expected to follow similar trends.

Breaking the icosahedra in boron carbide

PubMed Central

Xie, Kelvin Y.; An, Qi; Sato, Takanori; Breen, Andrew J.; Ringer, Simon P.; Goddard, William A.; Cairney, Julie M.; Hemker, Kevin J.

2016-01-01

Findings of laser-assisted atom probe tomography experiments on boron carbide elucidate an approach for characterizing the atomic structure and interatomic bonding of molecules associated with extraordinary structural stability. The discovery of crystallographic planes in these boron carbide datasets substantiates that crystallinity is maintained to the point of field evaporation, and characterization of individual ionization events gives unexpected evidence of the destruction of individual icosahedra. Statistical analyses of the ions created during the field evaporation process have been used to deduce relative atomic bond strengths and show that the icosahedra in boron carbide are not as stable as anticipated. Combined with quantum mechanics simulations, this result provides insight into the structural instability and amorphization of boron carbide. The temporal, spatial, and compositional information provided by atom probe tomography makes it a unique platform for elucidating the relative stability and interactions of primary building blocks in hierarchically crystalline materials. PMID:27790982

Carrier-envelope phase dependence of the directional fragmentation and hydrogen migration in toluene in few-cycle laser fields

PubMed Central

Li, Hui; Kling, Nora G.; Förg, Benjamin; Stierle, Johannes; Kessel, Alexander; Trushin, Sergei A.; Kling, Matthias F.; Kaziannis, Spyros

2016-01-01

The dissociative ionization of toluene initiated by a few-cycle laser pulse as a function of the carrier envelope phase (CEP) is investigated using single-shot velocity map imaging. Several ionic fragments, CH3+, H2+, and H3+, originating from multiply charged toluene ions present a CEP-dependent directional emission. The formation of H2+ and H3+ involves breaking C-H bonds and forming new bonds between the hydrogen atoms within the transient structure of the multiply charged precursor. We observe appreciable intensity-dependent CEP-offsets. The experimental data are interpreted with a mechanism that involves laser-induced coupling of vibrational states, which has been found to play a role in the CEP-control of molecular processes in hydrocarbon molecules, and appears to be of general importance for such complex molecules. PMID:26958589

Altering intra- to inter-molecular hydrogen bonding by dimethylsulfoxide: A TDDFT study of charge transfer for coumarin 343

NASA Astrophysics Data System (ADS)

Liu, Xiaochun; Yin, Hang; Li, Hui; Shi, Ying

2017-04-01

DFT and TDDFT methods were carried out to investigate the influences of intramolecular and intermolecular hydrogen bonding on excited state charge transfer for coumarin 343 (C343). Intramolecular hydrogen bonding is formed between carboxylic acid group and carbonyl group in C343 monomer. However, in dimethylsulfoxide (DMSO) solution, DMSO 'opens up' the intramolecular hydrogen bonding and forms solute-solvent intermolecular hydrogen bonded C343-DMSO complex. Analysis of frontier molecular orbitals reveals that intramolecular charge transfer (ICT) occurs in the first excited state both for C343 monomer and complex. The results of optimized geometric structures indicate that the intramolecular hydrogen bonding interaction is strengthened while the intermolecular hydrogen bonding is weakened in excited state, which is confirmed again by monitoring the shifts of characteristic peaks of infrared spectra. We demonstrated that DMSO solvent can not only break the intramolecular hydrogen bonding to form intermolecular hydrogen bonding with C343 but also alter the mechanism of excited state hydrogen bonding strengthening.

Optical and Chemical Characterization of Polyimide in a GEO-like Environment

NASA Astrophysics Data System (ADS)

Engelhart, D.; Plis, E.; Ferguson, D.; Cooper, R.; Hoffmann, R.

2016-09-01

Ground- and space-based optical observations of space objects rely on knowledge about how spacecraft materials interact with light. However, this is not a static property. Each material's optical fingerprint changes continuously throughout a spacecraft's orbital lifetime. These changes in optical signature occur because energetic particles break bonds within a material and new bonds subsequently form. The newly formed bonds can be identical to the original bonds or different, resulting in a new material. The chemical bonds comprising the material dictate which wavelengths of light are absorbed. Understanding the processes of material damage and recovery individually will allow development of a predictive model for materials' optical properties as a function of exposure to the space environment. In order to characterize the properties, we have exposed samples of polyimide to high energy electrons comparable to those found in a geostationary earth orbit in order to simulate damage on orbit. The resultant changes in the material's optical fingerprint were then characterized in the wavelength range of 0.2 to 25 microns. The chemical modifications to the material that result in these optical changes have also been identified. After initial electron-induced damage, the rate and mechanism of material recovery have been monitored and found to be extremely sensitive to the exposure of the damaged material to air. The implications of that fact and experimental progress toward complete in vacuo characterization will be discussed.

CN-110

EPA Pesticide Factsheets

Technical product bulletin: this surface washing agent for oil spill cleanups breaks the physical bond between the oil and the object to be cleaned (e.g., shoreline). Also use for herding or corralling a slick.

Cells having cathodes containing polycarbon disulfide materials

DOEpatents

Okamoto, Y.; Skotheim, T.A.; Lee, H.S.

1995-08-15

The present invention relates to an electric current producing cell which contains an anode, a cathode having as a cathode-active material one or more carbon-sulfur compounds of the formula (CS{sub x}){sub n}, in which x takes values from 1.2 to 2.3 and n is greater or equal to 2, and where the redox process does not involve polymerization and de-polymerization by forming and breaking S--S bonds in the polymer backbone. The cell also contains an electrolyte which is chemically inert with respect to the anode and the cathode. 5 figs.

Chemistry of acetylene on platinum (111) and (100) surfaces

PubMed Central

Muetterties, E. L.; Tasi, M.-C.; Kelemen, S. R.

1981-01-01

An ultra-high vacuum experimental study of acetylene chemisorption on Pt(111) and Pt(100) and of the reaction of hydrogen with the acetylene adsorbate has established distinguishing features of carbon-hydrogen bond breaking and making processes as a function of pressure, temperature, and surface crystallography. The rates for both processes are substantially higher on the Pt(100) surface. Net acetylene-hydrogen processes, in the temperature range of 20°C to ≈130°C, are distinctly different on the two surfaces: on Pt(100) the net reaction is hydrogen exchange (1H-2H exchange) and on Pt(111) the only detectable reaction is hydrogenation. Stereochemical differences in the acetylene adsorbate structure are considered to be a contributing factor to the differences in acetylene chemistry on these two surfaces. Images PMID:16593110

Benchmarking all-atom simulations using hydrogen exchange

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

Skinner, John J.; Yu, Wookyung; Gichana, Elizabeth K.

We are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517–520] using long-time molecular dynamics (MD) simulations. Our results indicate that modern force fields can reproduce the energy surface near the native structure. In this paper, to test how well the force fields recapitulate the other regions of the energy surface, MD trajectories for a variant of protein G are compared with data from site-resolved hydrogen exchange (HX) and other biophysical measurements. Because HX monitors the breaking of individual H-bonds, this experimental technique identifies the stability andmore » H-bond content of excited states, thus enabling quantitative comparison with the simulations. Contrary to experimental findings of a cooperative, all-or-none unfolding process, the simulated denatured state ensemble, on average, is highly collapsed with some transient or persistent native 2° structure. The MD trajectories of this protein G variant and other small proteins exhibit excessive intramolecular H-bonding even for the most expanded conformations, suggesting that the force fields require improvements in describing H-bonding and backbone hydration. Finally and moreover, these comparisons provide a general protocol for validating the ability of simulations to accurately capture rare structural fluctuations.« less

Benchmarking all-atom simulations using hydrogen exchange

DOE PAGES

Skinner, John J.; Yu, Wookyung; Gichana, Elizabeth K.; ...

2014-10-27

We are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517–520] using long-time molecular dynamics (MD) simulations. Our results indicate that modern force fields can reproduce the energy surface near the native structure. In this paper, to test how well the force fields recapitulate the other regions of the energy surface, MD trajectories for a variant of protein G are compared with data from site-resolved hydrogen exchange (HX) and other biophysical measurements. Because HX monitors the breaking of individual H-bonds, this experimental technique identifies the stability andmore » H-bond content of excited states, thus enabling quantitative comparison with the simulations. Contrary to experimental findings of a cooperative, all-or-none unfolding process, the simulated denatured state ensemble, on average, is highly collapsed with some transient or persistent native 2° structure. The MD trajectories of this protein G variant and other small proteins exhibit excessive intramolecular H-bonding even for the most expanded conformations, suggesting that the force fields require improvements in describing H-bonding and backbone hydration. Finally and moreover, these comparisons provide a general protocol for validating the ability of simulations to accurately capture rare structural fluctuations.« less

Ethylene Glycol Adsorption and Reaction over CeOX(111) Thin Films

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

Mullins, David R; Chen, Tsung-Liang

2011-01-01

This study reports the interaction of ethylene glycol with well-ordered CeO{sub x}(111) thin film surfaces. Ethylene glycol initially adsorbs on fully oxidized CeO{sub 2}(111) and reduced CeO{sub 2-x}(111) through the formation of one C-O-Ce bond and then forms a second alkoxy bond after annealing. On fully oxidized CeO{sub 2}(111) both recombination of ethylene glycol and water desorption occur at low temperature leaving stable -OCH{sub 2}CH{sub 2}O- (ethylenedioxy) intermediates and oxygen vacancies on the surface. This ethylenedioxy intermediate goes through C-C bond scission to produce formate species which then react to produce CO and CO{sub 2}. The formation of water resultsmore » in the reduction of the ceria. On a reduced CeO{sub 2-x}(111) surface the reaction selectivity shifts toward a dehydration process. The ethylenedioxy intermediate decomposes by breaking a C-O bond and converts into an enolate species. Similar to the reaction of acetaldehyde on reduced CeO{sub 2-x}(111), the enolate reacts to produce acetaldehyde, acetylene, and ethylene. The loss of O from ethylene glycol leads to a small amount of oxidation of the reduced ceria.« less

Ethylene Glycol Adsorption and Reaction over CeOX(111) Thin Films

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

T Chen; D Mullins

2011-12-31

This study reports the interaction of ethylene glycol with well-ordered CeO{sub x}(111) thin film surfaces. Ethylene glycol initially adsorbs on fully oxidized CeO{sub 2}(111) and reduced CeO{sub 2-x}(111) through the formation of one C-O-Ce bond and then forms a second alkoxy bond after annealing. On fully oxidized CeO{sub 2}(111) both recombination of ethylene glycol and water desorption occur at low temperature leaving stable -OCH{sub 2}CH{sub 2}O- (ethylenedioxy) intermediates and oxygen vacancies on the surface. This ethylenedioxy intermediate goes through C-C bond scission to produce formate species which then react to produce CO and CO{sub 2}. The formation of water resultsmore » in the reduction of the ceria. On a reduced CeO{sub 2-x}(111) surface the reaction selectivity shifts toward a dehydration process. The ethylenedioxy intermediate decomposes by breaking a C-O bond and converts into an enolate species. Similar to the reaction of acetaldehyde on reduced CeO{sub 2-x}(111), the enolate reacts to produce acetaldehyde, acetylene, and ethylene. The loss of O from ethylene glycol leads to a small amount of oxidation of the reduced ceria.« less

Students' reasoning about "high-energy bonds" and ATP: A vision of interdisciplinary education

NASA Astrophysics Data System (ADS)

Dreyfus, Benjamin W.; Sawtelle, Vashti; Turpen, Chandra; Gouvea, Julia; Redish, Edward F.

2014-06-01

As interdisciplinary courses are developed, instructors and researchers have to grapple with questions of how students should make connections across disciplines. We explore the issue of interdisciplinary reconciliation (IDR): how students reconcile seemingly contradictory ideas from different disciplines. While IDR has elements in common with other frameworks for the reconciliation of ideas across contexts, it differs in that each disciplinary idea is considered canonically correct within its own discipline. The setting for the research is an introductory physics course for biology majors that seeks to build greater interdisciplinary coherence and therefore includes biologically relevant topics such as adenosine triphosphate (ATP) and chemical bond energy. In our case-study data, students grapple with the apparent contradiction between the energy released when the phosphate bond in ATP is broken and the idea that an energy input is required to break a bond. We see students justifying context-dependent modeling choices, showing nuance in articulating how system choices may be related to disciplinary problems of interest. This represents a desired end point of IDR, in which students can build coherent connections between concepts from different disciplines while understanding each concept in its own disciplinary context. Our case study also illustrates elements of the instructional environment that play roles in the process of IDR.

Ring-breaking electron attachment to uracil: following bond dissociations via evolving resonances.

PubMed

Gianturco, Franco A; Sebastianelli, F; Lucchese, R R; Baccarelli, I; Sanna, N

2008-05-07

Calculations are carried out at various distinct energies to obtain both elastic cross sections and S-matrix resonance indicators (poles) from a quantum treatment of the electron scattering from gas-phase uracil. The low-energy region confirms the presence of pi(*) resonances as revealed by earlier calculations and experiments which are compared with the present findings. They turn out to be little affected by bond deformation, while the transient negative ions (TNIs) associated with sigma(*) resonances in the higher energy region ( approximately 8 eV) indeed show that ring deformations which allow vibrational redistribution of the excess electron energy into the molecular target strongly affect these shape resonances: They therefore evolve along different dissociative pathways and stabilize different fragment anions. The calculations further show that the occurrence of conical intersections between sigma(*) and pi(*)-type potential energy surfaces (real parts) is a very likely mechanism responsible for energy transfers between different TNIs. The excess electron wavefunctions for such scattering states, once mapped over the molecular space, provide nanoscopic reasons for the selective breaking of different bonds in the ring region.

Can Internal Conversion BE Controlled by Mode-Specific Vibrational Excitation in Polyatomic Molecules

NASA Astrophysics Data System (ADS)

Portnov, Alexander; Epshtein, Michael; Bar, Ilana

2017-06-01

Nonadiabatic processes, dominated by dynamic passage of reactive fluxes through conical intersections (CIs) are considered to be appealing means for manipulating reaction paths. One approach that is considered to be effective in controlling the course of dissociation processes is the selective excitation of vibrational modes containing a considerable component of motion. Here, we have chosen to study the predissociation of the model test molecule, methylamine and its deuterated isotopologues, excited to well-characterized quantum states on the first excited electronic state, S_{1}, by following the N-H(D) bond fission dynamics through sensitive H(D) photofragment probing. The branching ratios between slow and fast H(D) photofragments, the internal energies of their counter radical photofragments and the anisotropy parameters for fast H photofragments, confirm correlated anomalies for predissociation initiated from specific rovibronic states, reflecting the existence of a dynamic resonance in each molecule. This resonance strongly depends on the energy of the initially excited rovibronic states, the evolving vibrational mode on the repulsive S_{1} part during N-H(D) bond elongation, and the manipulated passage through the CI that leads to radicals excited with C-N-H(D) bending and preferential perpendicular bond breaking, relative to the photolyzing laser polarization, in molecules containing the NH_{2} group. The indicated resonance plays an important role in the bifurcation dynamics at the CI and can be foreseen to exist in other photoinitiated processes and to control their outcome.

Conformational equilibrium in supramolecular chemistry: Dibutyltriuret case.

PubMed

Mroczyńska, Karina; Kaczorowska, Małgorzata; Kolehmainen, Erkki; Grubecki, Ireneusz; Pietrzak, Marek; Ośmiałowski, Borys

2015-01-01

The association of substituted benzoates and naphthyridine dianions was used to study the complexation of dibutyltriuret. The title molecule is the simplest molecule able to form two intramolecular hydrogen bonds. The naphthyridine salt was used to break two intramolecular hydrogen bonds at a time while with the use of substituted benzoates the systematic approach to study association was achieved. Both, titrations and variable temperature measurements shed the light on the importance of conformational equilibrium and its influence on association in solution. Moreover, the associates were observed by mass spectrometry. The DFT-based computations for complexes and single bond rotational barriers supports experimental data and helps understanding the properties of multiply hydrogen bonded complexes.

reaxFF Reactive Force Field for Disulfide Mechanochemistry, Fitted to Multireference ab Initio Data.

PubMed

Müller, Julian; Hartke, Bernd

2016-08-09

Mechanochemistry, in particular in the form of single-molecule atomic force microscopy experiments, is difficult to model theoretically, for two reasons: Covalent bond breaking is not captured accurately by single-determinant, single-reference quantum chemistry methods, and experimental times of milliseconds or longer are hard to simulate with any approach. Reactive force fields have the potential to alleviate both problems, as demonstrated in this work: Using nondeterministic global parameter optimization by evolutionary algorithms, we have fitted a reaxFF force field to high-level multireference ab initio data for disulfides. The resulting force field can be used to reliably model large, multifunctional mechanochemistry units with disulfide bonds as designed breaking points. Explorative calculations show that a significant part of the time scale gap between AFM experiments and dynamical simulations can be bridged with this approach.

Single-photon Coulomb explosion of methanol using broad bandwidth ultrafast EUV pulses.

PubMed

Luzon, Itamar; Jagtap, Krishna; Livshits, Ester; Lioubashevski, Oleg; Baer, Roi; Strasser, Daniel

2017-05-31

Single-photon Coulomb explosion of methanol is instigated using the broad bandwidth pulse achieved through high-order harmonics generation. Using 3D coincidence fragment imaging of one molecule at a time, the kinetic energy release (KER) and angular distributions of the products are measured in different Coulomb explosion (CE) channels. Two-body CE channels breaking either the C-O or the C-H bonds are described as well as a proton migration channel forming H 2 O + , which is shown to exhibit higher KER. The results are compared to intense-field Coulomb explosion measurements in the literature. The interpretation of broad bandwidth single-photon CE data is discussed and supported by ab initio calculations of the predominant C-O bond breaking CE channel. We discuss the importance of these findings for achieving time resolved imaging of ultrafast dynamics.

Supramolecular Systems and Chemical Reactions in Single-Molecule Break Junctions.

PubMed

Li, Xiaohui; Hu, Duan; Tan, Zhibing; Bai, Jie; Xiao, Zongyuan; Yang, Yang; Shi, Jia; Hong, Wenjing

2017-04-01

The major challenges of molecular electronics are the understanding and manipulation of the electron transport through the single-molecule junction. With the single-molecule break junction techniques, including scanning tunneling microscope break junction technique and mechanically controllable break junction technique, the charge transport through various single-molecule and supramolecular junctions has been studied during the dynamic fabrication and continuous characterization of molecular junctions. This review starts from the charge transport characterization of supramolecular junctions through a variety of noncovalent interactions, such as hydrogen bond, π-π interaction, and electrostatic force. We further review the recent progress in constructing highly conductive molecular junctions via chemical reactions, the response of molecular junctions to external stimuli, as well as the application of break junction techniques in controlling and monitoring chemical reactions in situ. We suggest that beyond the measurement of single molecular conductance, the single-molecule break junction techniques provide a promising access to study molecular assembly and chemical reactions at the single-molecule scale.

The Electronic Flux in Chemical Reactions. Insights on the Mechanism of the Maillard Reaction

NASA Astrophysics Data System (ADS)

Flores, Patricio; Gutiérrez-Oliva, Soledad; Herrera, Bárbara; Silva, Eduardo; Toro-Labbé, Alejandro

2007-11-01

The electronic transfer that occurs during a chemical process is analysed in term of a new concept, the electronic flux, that allows characterizing the regions along the reaction coordinate where electron transfer is actually taking place. The electron flux is quantified through the variation of the electronic chemical potential with respect to the reaction coordinate and is used, together with the reaction force, to shed light on reaction mechanism of the Schiff base formation in the Maillard reaction. By partitioning the reaction coordinate in regions in which different process might be taking place, electronic reordering associated to polarization and transfer has been identified and found to be localized at specific transition state regions where most bond forming and breaking occur.

Observation of Spontaneous C=C Bond Breaking in the Reaction between Atomic Boron and Ethylene in Solid Neon.

PubMed

Jian, Jiwen; Lin, Hailu; Luo, Mingbiao; Chen, Mohua; Zhou, Mingfei

2016-07-11

A ground-state boron atom inserts into the C=C bond of ethylene to spontaneously form the allene-like compound H2 CBCH2 on annealing in solid neon. This compound can further isomerize to the propyne-like HCBCH3 isomer under UV light excitation. The observation of this unique spontaneous C=C bond insertion reaction is consistent with theoretical predictions that the reaction is thermodynamically exothermic and kinetically facile. This work demonstrates that the stronger C=C bond, rather than the less inert C-H bond, can be broken to form organoboron species from the reaction of a boron atom with ethylene even at cryogenic temperatures. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quenched bond randomness: Superfluidity in porous media and the strong violation of universality

NASA Astrophysics Data System (ADS)

Falicov, Alexis; Berker, A. Nihat

1997-04-01

The effects of quenched bond randomness are most readily studied with superfluidity immersed in a porous medium. A lattice model for3He-4He mixtures and incomplete4He fillings in aerogel yields the signature effect of bond randomness, namely the conversion of symmetry-breaking first-order phase transitions into second-order phase transitions, the λ-line reaching zero temperature, and the elimination of non-symmetry-breaking first-order phase transitions. The model recognizes the importance of the connected nature of aerogel randomness and thereby yields superfluidity at very low4He concentrations, a phase separation entirely within the superfluid phase, and the order-parameter contrast between mixtures and incomplete fillings, all in agreement with experiments. The special properties of the helium mixture/aerogel system are distinctly linked to the aerogel properties of connectivity, randomness, and tenuousness, via the additional study of a regularized “jungle-gym” aerogel. Renormalization-group calculations indicate that a strong violation of the empirical universality principle of critical phenomena occurs under quenched bond randomness. It is argued that helium/aerogel critical properties reflect this violation and further experiments are suggested. Renormalization-group analysis also shows that, adjoiningly to the strong universality violation (which hinges on the occurrence or non-occurrence of asymptotic strong coupling—strong randomness under rescaling), there is a new “hyperuniversality” at phase transitions with asymptotic strong coupling—strong randomness behavior, for example assigning the same critical exponents to random- bond tricriticality and random- field criticality.

Effect and origin of the structure of hyperbranched polysiloxane on the surface and integrated performances of grafted Kevlar fibers

NASA Astrophysics Data System (ADS)

Zhang, Hongrui; Yuan, Li; Liang, Guozheng; Gu, Aijuan

2014-11-01

Four hyperbranched polysiloxanes (HPSis) with different molecular weights and concentration ratios of double bonds to epoxy groups (1:6.5-1:0.7) were synthesized and characterized. Each HPSi was facilely grafted onto surfaces of Kevlar fibers (KFs) to develop novel modified fibers (HPSi-g-KFs). The structures and integrated properties of HPSi-g-KFs as well as the origin behind were systematically investigated. Results show that HPSi-g-KFs have much rougher surface morphologies, and their surface free energies are as high as about 1.7 times that of KFs, showing greatly improved wettability. Besides, HPSi-g-KFs have excellent UV resistance after 168 h UV irradiation, the retentions of tenacity, energy to break, modulus and break extension are as high as 92, 86, 95 and 96%, respectively, while those of KFs are 66-85%. In addition, compared with KFs, HPSi-g-KFs have higher tensile tenacity and energy to break with similar modulus and break extension, much better thermal stability and flame retardancy. The nature of HPSi has different influence on different property of fibers, the HPSi with smaller molecular weight and more epoxy groups is beneficial to prepare HPSi-g-KFs with better wettability, while that with larger molecular weight and more double bonds tends to prepare HPSi-g-KF with better flame retardancy and UV resistance.

Hydrogenated amorphous silicon formation by flux control and hydrogen effects on the growth mechanism

NASA Astrophysics Data System (ADS)

Toyoda, H.; Sugai, H.; Kato, K.; Yoshida, A.; Okuda, T.

1986-06-01

The composition of particle flux to deposit hydrogenated amorphous silicon films in a glow discharge is controlled by a combined electrostatic-magnetic deflection technique. As a result, the films are formed firstly without hydrogen ion flux, secondly by neutral flux only, and thirdly by all species fluxes. Comparison of these films reveals the significant role of hydrogen in the surface reactions. Hydrogen breaks the Si-Si bond, decreases the sticking probability of the Si atom, and replaces the SiH bond by a SiH2 bond to increase the hydrogen content of the films.

Differences and Comparisons of the Properties and Reactivities of Iron(III)–hydroperoxo Complexes with Saturated Coordination Sphere

PubMed Central

Faponle, Abayomi S; Quesne, Matthew G; Sastri, Chivukula V; Banse, Frédéric; de Visser, Sam P

2015-01-01

Heme and nonheme monoxygenases and dioxygenases catalyze important oxygen atom transfer reactions to substrates in the body. It is now well established that the cytochrome P450 enzymes react through the formation of a high-valent iron(IV)–oxo heme cation radical. Its precursor in the catalytic cycle, the iron(III)–hydroperoxo complex, was tested for catalytic activity and found to be a sluggish oxidant of hydroxylation, epoxidation and sulfoxidation reactions. In a recent twist of events, evidence has emerged of several nonheme iron(III)–hydroperoxo complexes that appear to react with substrates via oxygen atom transfer processes. Although it was not clear from these studies whether the iron(III)–hydroperoxo reacted directly with substrates or that an initial O–O bond cleavage preceded the reaction. Clearly, the catalytic activity of heme and nonheme iron(III)–hydroperoxo complexes is substantially different, but the origins of this are still poorly understood and warrant a detailed analysis. In this work, an extensive computational analysis of aromatic hydroxylation by biomimetic nonheme and heme iron systems is presented, starting from an iron(III)–hydroperoxo complex with pentadentate ligand system (L52). Direct C–O bond formation by an iron(III)–hydroperoxo complex is investigated, as well as the initial heterolytic and homolytic bond cleavage of the hydroperoxo group. The calculations show that [(L52)FeIII(OOH)]2+ should be able to initiate an aromatic hydroxylation process, although a low-energy homolytic cleavage pathway is only slightly higher in energy. A detailed valence bond and thermochemical analysis rationalizes the differences in chemical reactivity of heme and nonheme iron(III)–hydroperoxo and show that the main reason for this particular nonheme complex to be reactive comes from the fact that they homolytically split the O–O bond, whereas a heterolytic O–O bond breaking in heme iron(III)–hydroperoxo is found. PMID:25399782

Molecular dynamics simulation, ab initio calculation, and size-selected anion photoelectron spectroscopy study of initial hydration processes of calcium chloride.

PubMed

He, Zhili; Feng, Gang; Yang, Bin; Yang, Lijiang; Liu, Cheng-Wen; Xu, Hong-Guang; Xu, Xi-Ling; Zheng, Wei-Jun; Gao, Yi Qin

2018-06-14

To understand the initial hydration processes of CaCl 2 , we performed molecular simulations employing the force field based on the theory of electronic continuum correction with rescaling. Integrated tempering sampling molecular dynamics were combined with ab initio calculations to overcome the sampling challenge in cluster structure search and refinement. The calculated vertical detachment energies of CaCl 2 (H 2 O) n - (n = 0-8) were compared with the values obtained from photoelectron spectra, and consistency was found between the experiment and computation. Separation of the Cl-Ca ion pair is investigated in CaCl 2 (H 2 O) n - anions, where the first Ca-Cl ionic bond required 4 water molecules, and both Ca-Cl bonds are broken when the number of water molecules is larger than 7. For neutral CaCl 2 (H 2 O) n clusters, breaking of the first Ca-Cl bond starts at n = 5, and 8 water molecules are not enough to separate the two ion pairs. Comparing with the observations on magnesium chloride, it shows that separating one ion pair in CaCl 2 (H 2 O) n requires fewer water molecules than those for MgCl 2 (H 2 O) n . Coincidentally, the solubility of calcium chloride is higher than that of magnesium chloride in bulk solutions.

Molecular dynamics simulation, ab initio calculation, and size-selected anion photoelectron spectroscopy study of initial hydration processes of calcium chloride

NASA Astrophysics Data System (ADS)

He, Zhili; Feng, Gang; Yang, Bin; Yang, Lijiang; Liu, Cheng-Wen; Xu, Hong-Guang; Xu, Xi-Ling; Zheng, Wei-Jun; Gao, Yi Qin

2018-06-01

To understand the initial hydration processes of CaCl2, we performed molecular simulations employing the force field based on the theory of electronic continuum correction with rescaling. Integrated tempering sampling molecular dynamics were combined with ab initio calculations to overcome the sampling challenge in cluster structure search and refinement. The calculated vertical detachment energies of CaCl2(H2O)n- (n = 0-8) were compared with the values obtained from photoelectron spectra, and consistency was found between the experiment and computation. Separation of the Cl—Ca ion pair is investigated in CaCl2(H2O)n- anions, where the first Ca—Cl ionic bond required 4 water molecules, and both Ca—Cl bonds are broken when the number of water molecules is larger than 7. For neutral CaCl2(H2O)n clusters, breaking of the first Ca—Cl bond starts at n = 5, and 8 water molecules are not enough to separate the two ion pairs. Comparing with the observations on magnesium chloride, it shows that separating one ion pair in CaCl2(H2O)n requires fewer water molecules than those for MgCl2(H2O)n. Coincidentally, the solubility of calcium chloride is higher than that of magnesium chloride in bulk solutions.

Hydrogen bond disruption in DNA base pairs from (14)C transmutation.

PubMed

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.

How does huperzine A enter and leave the binding gorge of acetylcholinesterase? Steered molecular dynamics simulations.

PubMed

Xu, Yechun; Shen, Jianhua; Luo, Xiaomin; Silman, Israel; Sussman, Joel L; Chen, Kaixian; Jiang, Hualiang

2003-09-17

The entering and leaving processes of Huperzine A (HupA) binding with the long active-site gorge of Torpedo californica acetylcholinesterase (TcAChE) have been investigated by using steered molecular dynamics simulations. The analysis of the force required along the pathway shows that it is easier for HupA to bind to the active site of AChE than to disassociate from it, which for the first time interprets at the atomic level the previous experimental result that unbinding process of HupA is much slower than its binding process to AChE. The direct hydrogen bonds, water bridges, and hydrophobic interactions were analyzed during two steered molecular dynamics (SMD) simulations. Break of the direct hydrogen bond needs a great pulling force. The steric hindrance of bottleneck might be the most important factor to produce the maximal rupture force for HupA to leave the binding site but it has a little effect on the binding process of HupA with AChE. Residue Asp72 forms a lot of water bridges with HupA leaving and entering the AChE binding gorge, acting as a clamp to take out HupA from or put HupA into the active site. The flip of the peptide bond between Gly117 and Gly118 has been detected during both the conventional MD and SMD simulations. The simulation results indicate that this flip phenomenon could be an intrinsic property of AChE and the Gly117-Gly118 peptide bond in both HupA bound and unbound AChE structures tends to adopt the native enzyme structure. At last, in a vacuum the rupture force is increased up to 1500 pN while in water solution the greatest rupture force is about 800 pN, which means water molecules in the binding gorge act as lubricant to facilitate HupA entering or leaving the binding gorge.

TDDFT investigation of excitation of water tetramer under femtosecond laser pulse irradiation

NASA Astrophysics Data System (ADS)

Wang, Zhiping; Xu, Xuefen; Zhang, Fengshou; Qian, Chaoyi

2018-04-01

We study the static properties of water tetramer in ground state, the optical absorption spectra and ultrafast nonadiabatic dynamical response of water tetramer to short and intense laser pulses with different intensities by a real-space, real-time implementation of time-dependent density functional theory coupled to molecular dynamics (TDDFT-MD) nonadiabatically. The calculated results are in good agreement with available values in literature. Four typical irradiated scenarios of water tetramer in laser field, which are “normal vibration,” “break and reorganization,” “fragmentation and new formation” and “pure fragmentation”, are explored by discussing the ionization, the bond lengths of OH bonds and hydrogen bonds and the kinetic energy of ions. The dynamic simulation shows that the reaction channel of water tetramer can really be controlled by choosing appropriate laser parameters referring to the optical absorption spectra and hydrogen ions play an important role in the reaction channel. Furthermore, it is found that the laser intensity affects the kinetic energy of ejected protons more than that of the remaining fragments and all dynamic processes are somehow directly related to the velocity of departing protons.

The effect of aromatization on the isotopic compositions of hydrocarbons during early diagenesis

NASA Technical Reports Server (NTRS)

Freeman, K. H.; Boreham, C. J.; Summons, R. E.; Hayes, J. M.

1994-01-01

Polycyclic aromatic hydrocarbons with varying degrees of aromatization were isolated from the Eocene Messel Shale (Rheingraben, Germany). The high abundances of these compounds and their structural resemblances to cyclic triterpenoid lipids are consistent with derivation from microbial rather than thermal processes. Compounds structurally related to oleanane contain from five to nine double bonds; those within a series of aromatized hopanoids contain from three to nine. All are products of diagenetic reactions that remove hydrogen or methyl groups, and, in several cases, break carbon-carbon bonds to open rings. Aromatized products are on average depleted in 13C relative to possible precursors by l.2% (range: l.5% enrichment to 4% depletion, n = 9). The dependence of 13C content on the number of double bonds is not, however, statistically significant and it must be concluded that there is no strong evidence for isotopic fractionation accompanying diagenetic aromatization. Isotopic differences between series (structures related to ursane, des-A-ursane, des-A-lupane, des-A-arborane, and possibly, des-A-gammacerane are present) are much greater, indicating that 13C contents are controlled primarily by source effects. Fractionations due to chromatographic isotope effects during HPLC ranged from 0.1 to 2.8%.

Visualizing the near-field coupling and interference of bonding and anti-bonding modes in infrared dimer nanoantennas.

PubMed

Alonso-González, Pablo; Albella, Pablo; Golmar, Federico; Arzubiaga, Libe; Casanova, Félix; Hueso, Luis E; Aizpurua, Javier; Hillenbrand, Rainer

2013-01-14

We directly visualize and identify the capacitive coupling of infrared dimer antennas in the near field by employing scattering-type scanning near-field optical microscopy (s-SNOM). The coupling is identified by (i) resolving the strongly enhanced nano-localized near fields in the antenna gap and by (ii) tracing the red shift of the dimer resonance when compared to the resonance of the single antenna constituents. Furthermore, by modifying the illumination geometry we break the symmetry, providing a means to excite both the bonding and the "dark" anti-bonding modes. By spectrally matching both modes, their interference yields an enhancement or suppression of the near fields at specific locations, which could be useful in nanoscale coherent control applications.

Modeling tabular icebergs submerged in the ocean

NASA Astrophysics Data System (ADS)

Stern, A. A.; Adcroft, A.; Sergienko, O.; Marques, G.

2017-08-01

Large tabular icebergs calved from Antarctic ice shelves have long lifetimes (due to their large size), during which they drift across large distances, altering ambient ocean circulation, bottom-water formation, sea-ice formation, and biological primary productivity in the icebergs' vicinity. However, despite their importance, the current generation of ocean circulation models usually do not represent large tabular icebergs. In this study, we develop a novel framework to model large tabular icebergs submerged in the ocean. In this framework, tabular icebergs are represented by pressure-exerting Lagrangian elements that drift in the ocean. The elements are held together and interact with each other via bonds. A breaking of these bonds allows the model to emulate calving events (i.e., detachment of a tabular iceberg from an ice shelf) and tabular icebergs breaking up into smaller pieces. Idealized simulations of a calving tabular iceberg, its drift, and its breakup demonstrate capabilities of the developed framework.

STM/STS Study of the Sb (111) Surface

NASA Astrophysics Data System (ADS)

Chekmazov, S. V.; Bozhko, S. I.; Smirnov, A. A.; Ionov, A. M.; Kapustin, A. A.

An Sb crystal is a Peierls insulator. Formation of double layers in the Sb structure is due to the shift of atomic planes (111) next but one along the C3 axis. Atomic layers inside the double layer are connected by covalent bonds. The interaction between double layers is determined mainly by Van der Waals forces. The cleave of an Sb single crystal used to be via break of Van der Waals bonds. However, using scanning tunneling microscopy (STM) and spectroscopy (STS) we demonstrated that apart from islands equal in thickness to the double layer, steps of one atomic layer in height also exist on the cleaved Sb (111) surface. Formation of "unpaired" (111) planes on the surface leads to a local break of conditions of Peierls transition. STS experiment reveals higher local density of states (LDOS) measured for "unpaired" (111) planes in comparison with those for the double layer.

Differential scanning calorimetric study of the binding between native DNA and its primary water of hydration.

NASA Astrophysics Data System (ADS)

Marlowe, R. L.; Lukan, A. M.; Lee, S. A.; Anthony, L.; Rupprecht, A.

1996-03-01

Differential scanning calorimetry was used to measure the binding strength between calf-thymus DNA and its primary water of hydration. The specific heat of wet-spun films was found to have a broad endothermic transition near 80 ^oC and a sharp exothermic transition near 250 ^oC. The broad transition is believed to be mainly due to the breaking of the bonds of the strongly bound water of hydration. This transition was found to be reversible, as expected. Kissinger analysis indicates that the activation barrier for breaking the bonds of these water molecules is about 0.6 eV. The sharp transition appeared to be an indication of a thermal decomposition of the DNA. Samples taken above this transition lost mass, showed evidence of having melted, and had turned black in color. This transition is irreversible.

Laser-driven localization of collective CO vibrations in metal-carbonyl complexes

NASA Astrophysics Data System (ADS)

Lisaj, Mateusz; Kühn, Oliver

2014-11-01

Using the example of a cobalt dicarbonyl complex it is shown that two perpendicular linearly polarized IR laser pulses can be used to trigger an excitation of the delocalized CO stretching modes, which corresponds to an alternating localization of the vibration within one CO bond. The switching time for localization in either of the two bonds is determined by the energy gap between the symmetric and asymmetric fundamental transition frequencies. The phase of the oscillation between the two local bond excitations can be tuned by the relative phase of the two pulses. The extend of control of bond localization is limited by the anharmonicity of the potential energy surfaces leading to wave packet dispersion. This prevents such a simple pulse scheme from being used for laser-driven bond breaking in the considered example.

The effects of surface polarity and dangling bonds on the electronic properties of MoS2 on SiO2

NASA Astrophysics Data System (ADS)

Sung, Ha-Jun; Choe, Duk-Hyun; Chang, Kee Joo

2015-03-01

MoS2 has recently attracted much attention due to its intriguing physical phenomena and possible applications for the next generation electronic devices. In pristine monolayer MoS2, strong spin-orbit coupling and inversion symmetry breaking allow for an effective coupling between the spin and valley degrees of freedom, inducing valley polarization at the K valleys. However, the spin-valley coupling disappears in bilayer MoS2 because the inversion symmetry is restored. In this work, we investigate the effects of surface polarity and dangling bonds on the electronic properties of MoS2 on α-quartz SiO2 through first-principles calculations. In monolayer MoS2, a transition can take place from the direct-gap to indirect-gap semiconductor in the presence of O dangling bonds. In bilayer MoS2, O dangling bonds induce dipole fields across the interface and thus break the inversion symmetry, resulting in the valley polarization, similar to that of pristine monolayer MoS2. Based on the results, we discuss the origin of the valley polarization observed in MoS2 deposited on SiO2 This work was supported by National Research Foundation of Korea (NRF) under Grant No. NRF-2005-0093845 and by Samsung Science and Technology Foundation under Grant No. SSTFBA1401-08.

Fabrication and properties of polyvinyl alcohol/starch blend films: Effect of composition and humidity.

PubMed

Tian, Huafeng; Yan, Jiaan; Rajulu, A Varada; Xiang, Aimin; Luo, Xiaogang

2017-03-01

In this work, starch/polyvinyl alcohol (PVA) blend films with different compositions were prepared by melt processing. The effect of the composition and relative humidity (RH) on the structure and properties of the resulting blends were investigated. OH groups on starch and PVA formed hydrogen bonding interactions, which could improve the compatibility of the two components. With the increase of starch, the degree of crystallinity of PVA component decreased. The fracture surface of the blend films exhibited rough surface, suggesting the tough fracture. With the increase of starch, the water uptake at equilibrium decreased. With the increase of RH, the water uptake at equilibrium of the resulting blends increased. The tensile strength, elongation at break and Young's modulus decreased with increasing content of starch. However, at 50% starch content, the flexibility of the blend films was still high, with the elongation at break more than 1000% and tensile strength of 9MPa, which was superior to the commonly LDPE package films. The tensile strength and Young's modulus decreased with the increase of RH, while the elongation at break was enhanced dramatically, indicating the improved flexibility. Therefore, these kinds of blend films exhibited wide application potentials as packaging materials. Copyright © 2016 Elsevier B.V. All rights reserved.

Direct computation of general chemical energy differences: Application to ionization potentials, excitation, and bond energies.

PubMed

Beste, A; Harrison, R J; Yanai, T

2006-08-21

Chemists are mainly interested in energy differences. In contrast, most quantum chemical methods yield the total energy which is a large number compared to the difference and has therefore to be computed to a higher relative precision than would be necessary for the difference alone. Hence, it is desirable to compute energy differences directly, thereby avoiding the precision problem. Whenever it is possible to find a parameter which transforms smoothly from an initial to a final state, the energy difference can be obtained by integrating the energy derivative with respect to that parameter (cf. thermodynamic integration or adiabatic connection methods). If the dependence on the parameter is predominantly linear, accurate results can be obtained by single-point integration. In density functional theory and Hartree-Fock, we applied the formalism to ionization potentials, excitation energies, and chemical bond breaking. Example calculations for ionization potentials and excitation energies showed that accurate results could be obtained with a linear estimate. For breaking bonds, we introduce a nongeometrical parameter which gradually turns the interaction between two fragments of a molecule on. The interaction changes the potentials used to determine the orbitals as well as the constraint on the orbitals to be orthogonal.

Gas-Phase Chemistry of Arylimido-Functionalized Hexamolybdates [Mo6O19]2-

NASA Astrophysics Data System (ADS)

Cao, Jie; Wang, QianQian; Liu, Chang; An, ShuQi

2018-04-01

The gas-phase fragmentations of a series of arylimido derivatives of hexamolybdate [Mo6O18(NC6H5-n R n )]2- (2-10, where R = CH3, i-C3H7, OCH3, NO2; n = 1 or 2) versus the parent species [Mo6O19]2- (1) were systematically studied using electrospray tandem mass spectrometry (ESI). Fragmentation of 1 generates two molybdate fragments only, [Mo3O10]2- and [Mo4O13]2-, whereas decomposition of 2-10 went through two dissociation pathways in which path A generates a variety of molybdate fragments via breaking the Mo-N bond followed by the cleavages of the multiple Mo-O bonds, whereas path B produces a range of molybdate fragments with arylimido group via breaking the multiple Mo-O bonds on POM framework. Moreover, the presences of mixed-oxidation-state molybdate fragments are characteristic for the fragmentation. The gas-phase stability order obtained by energy-variable collision-induced dissociation (CID) experiment reveals that 2-10 are generally less stable than 1 and substitution on the benzene ring exerts a considerable effect on the stabilization of the hybrid clusters. [Figure not available: see fulltext.

Substantial Cd-Cd Bonding in Ca6PtCd11: A Condensed Intermetallic Phase Built of Pentagonal Cd7 and Rectangular Cd4/2Pt Pyramids

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

Gulo, Fakhili; Samal, Saroj L.; Corbett, John D.

The new trail-breaking compound Ca6PtCd11 has been synthesized and its structural and bonding properties investigated. This unusual phase features an unprecedented degree of cadmium aggregation, including linear chains, novel Cd7 PBP aggregates, and edge-shared chains of PtCd4/2 square pyramids. Manifestations of this chemistry elsewhere has evidently been precluded in earlier work by the inclusion of larger amounts of the strong d-metal bonding Au or Pt. Under the right conditions Cd seems quite effective as an open s,p-band metal.

Laser spectroscopic visualization of hydrogen bond motions in liquid water

NASA Astrophysics Data System (ADS)

Bratos, S.; Leicknam, J.-Cl.; Pommeret, S.; Gallot, G.

2004-12-01

Ultrafast pump-probe experiments are described permitting a visualization of molecular motions in diluted HDO/D 2O solutions. The experiments were realized in the mid-infrared spectral region with a time resolution of 150 fs. They were interpreted by a careful theoretical analysis, based on the correlation function approach of statistical mechanics. Combining experiment and theory, stretching motions of the OH⋯O bonds as well as HDO rotations were 'filmed' in real time. It was found that molecular rotations are the principal agent of hydrogen bond breaking and making in water. Recent literatures covering the subject, including molecular dynamics simulations, are reviewed in detail.

Etching of enamel for direct bonding with a thulium fiber laser

NASA Astrophysics Data System (ADS)

Kabaş Sarp, Ayşe S.; Gülsoy, Murat

2011-03-01

Background: Laser etching of enamel for direct bonding can decrease the risk of surface enamel loss and demineralization which are the adverse effects of acid etching technique. However, in excess of +5.5°C can cause irreversible pulpal responses. In this study, a 1940- nm Thulium Fiber Laser in CW mode was used for laser etching. Aim: Determination of the suitable Laser parameters of enamel surface etching for direct bonding of ceramic brackets and keeping that intrapulpal temperature changes below the threshold value. Material and Method: Polycrystalline ceramic orthodontic brackets were bonded on bovine teeth by using 2 different kinds of etching techniques: Acid and Laser Etching. In addition to these 3 etched groups, there was also a group which was bonded without etching. Brackets were debonded with a material testing machine. Breaking time and the load at the breaking point were measured. Intrapulpal temperature changes were recorded by a K-type Thermocouple. For all laser groups, intrapulpal temperature rise was below the threshold value of 5.5°C. Results and Conclusion: Acid-etched group ( 11.73 MPa) significantly required more debonding force than 3- second- irradiated ( 5.03 MPa) and non-etched groups ( 3.4 MPa) but the results of acid etched group and 4- second- irradiated group (7.5 MPa) showed no significant difference. Moreover, 4- second irradiated group was over the minimum acceptable value for clinical use. Also, 3- second lasing caused a significant reduction in time according to acid-etch group. As a result, 1940- nm laser irradiation is a promising method for laser etching.

Quenched bond randomness: Superfluidity in porous media and the strong violation of universality

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

Falicov, A.; Berker, A.N.

1997-04-01

The effects of quenched bond randomness are most readily studied with superfluidity immersed in a porous medium. A lattice model for {sup 3}He-{sup 4}He mixtures and incomplete {sup 4}He fillings in aerogel yields the signature effect of bond randomness, namely the conversion of symmetry-breaking first-order phase transitions into second-order phase transitions, the A-line reaching zero temperature, and the elimination of non-symmetry-breaking first-order phase transitions. The model recognizes the importance of the connected nature of aerogel randomness and thereby yields superfluidity at very low {sup 4}He concentrations, a phase separation entirely within the superfluid phase, and the order-parameter contrast between mixturesmore » and incomplete fillings, all in agreement with experiments. The special properties of the helium mixture/aerogel system are distinctly linked to the aerogel properties of connectivity, randomness, and tenuousness, via the additional study of a regularized {open_quote}jungle-gym{close_quotes} aerogel. Renormalization-group calculations indicate that a strong violation of the empirical universality principle of critical phenomena occurs under quenched bond randomness. It is argued that helium/aerogel critical properties reflect this violation and further experiments are suggested. Renormalization-group analysis also shows that, adjoiningly to the strong universality violation (which hinges on the occurrence or non-occurrence of asymptotic strong coupling-strong randomness under resealing), there is a new {open_quotes}hyperuniversality{close_quotes} at phase transitions with asymptotic strong coupling-strong randomness behavior, for example assigning the same critical exponents to random-bond tricriticality and random-field criticality.« less

Organic Solar Cells: Degradation Processes and Approaches to Enhance Performance

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

Fungura, Fadzai

2016-12-17

Intrinsic photodegradation of organic solar cells, theoretically attributed to C-H bond rearrangement/breaking, remains a key commercialization barrier. This work presents, via dark electron paramagnetic resonance (EPR), the first experimental evidence for metastable C dangling bonds (DBs) (g=2.0029±0.0004) formed by blue/UV irradiation of polymer:fullerene blend films in nitrogen. The DB density increased with irradiation and decreased ~4 fold after 2 weeks in the dark. The dark EPR also showed increased densities of other spin-active sites in photodegraded polymer, fullerene, and polymer:fullerene blend films, consistent with broad electronic measurements of fundamental properties, including defect/gap state densities. The EPR enabled identification of defectmore » states, whether in the polymer, fullerene, or at the donor/acceptor (D/A) interface. Importantly, the EPR results indicate that the DBs are at the D/A interface, as they were present only in the blend films. The role of polarons in interface DB formation is also discussed.« less

Organic synthesis provides opportunities to transform drug discovery

NASA Astrophysics Data System (ADS)

Blakemore, David C.; Castro, Luis; Churcher, Ian; Rees, David C.; Thomas, Andrew W.; Wilson, David M.; Wood, Anthony

2018-04-01

Despite decades of ground-breaking research in academia, organic synthesis is still a rate-limiting factor in drug-discovery projects. Here we present some current challenges in synthetic organic chemistry from the perspective of the pharmaceutical industry and highlight problematic steps that, if overcome, would find extensive application in the discovery of transformational medicines. Significant synthesis challenges arise from the fact that drug molecules typically contain amines and N-heterocycles, as well as unprotected polar groups. There is also a need for new reactions that enable non-traditional disconnections, more C-H bond activation and late-stage functionalization, as well as stereoselectively substituted aliphatic heterocyclic ring synthesis, C-X or C-C bond formation. We also emphasize that syntheses compatible with biomacromolecules will find increasing use, while new technologies such as machine-assisted approaches and artificial intelligence for synthesis planning have the potential to dramatically accelerate the drug-discovery process. We believe that increasing collaboration between academic and industrial chemists is crucial to address the challenges outlined here.

Atomic structure and potential energy of β-Si3N4/diamond interface in the process of detachment: A first-principles study

NASA Astrophysics Data System (ADS)

Chen, Naichao; Chen, Yingchao; Ai, Jun; Li, Cheng; He, Ping; Ren, Jianxing; Zhu, Quanjun

2018-03-01

Peeling is regarded as a main technique barrier for the application of coating. Many factors affects the peeling of coating. Among them, the interfacial properties between coating and substrate plays a vital role. In this work, the β-Si3N4/diamond interface is conducted as the sample to study the changes in atomic structure and potential energy in the process of detachment by the first-principles calculations. The β-Si3N4/diamond (2 × 2) crystal unit is used as the calculated model. The detachment is simulated by moving up β-Si3N4 far from diamond by the 0.1 Å of each step. The results show that in the beginning of detachment, the bonds in the interface keep a constant length, rather than extension like spring. When the distance between β-Si3N4 and diamond reaches a certain distance, the interfacial bonds would suddenly break, and the elongated β-Si3N4 resumes its original statues indicating that the interface between two surfaces may exist a threshold value to control the peeling. When the external force is less than this threshold value, the peeling of coating would not occur. However, once the external force is greater than this one, the peeling would immediately present. The interface presents the brittle failure in the process of detachment, which is in good agreement with the experimental observation. Meanwhile, the different physical properties between van der Waals and quantum effects lead to the transient status in the process of detachment, where although the interfacial bonds are broken, the adhesive strength is still strong due to its low negative adsorption energy.

Break the bonds of emotional eating

MedlinePlus

... evidence for a new perspective on weight-related shame. Appetite . 2012;59(2):570-575. PMID: 22810015 www.ncbi.nlm.nih.gov/pubmed/22810015 . Cornil Y, Chandon P. From fan to fat? Vicarious losing increases unhealthy eating, but self-affirmation ...

Self-healing and thermoreversible rubber from supramolecular assembly.

PubMed

Cordier, Philippe; Tournilhac, François; Soulié-Ziakovic, Corinne; Leibler, Ludwik

2008-02-21

Rubbers exhibit enormous extensibility up to several hundred per cent, compared with a few per cent for ordinary solids, and have the ability to recover their original shape and dimensions on release of stress. Rubber elasticity is a property of macromolecules that are either covalently cross-linked or connected in a network by physical associations such as small glassy or crystalline domains, ionic aggregates or multiple hydrogen bonds. Covalent cross-links or strong physical associations prevent flow and creep. Here we design and synthesize molecules that associate together to form both chains and cross-links via hydrogen bonds. The system shows recoverable extensibility up to several hundred per cent and little creep under load. In striking contrast to conventional cross-linked or thermoreversible rubbers made of macromolecules, these systems, when broken or cut, can be simply repaired by bringing together fractured surfaces to self-heal at room temperature. Repaired samples recuperate their enormous extensibility. The process of breaking and healing can be repeated many times. These materials can be easily processed, re-used and recycled. Their unique self-repairing properties, the simplicity of their synthesis, their availability from renewable resources and the low cost of raw ingredients (fatty acids and urea) bode well for future applications.

Unique Bond Breaking in Crystalline Phase Change Materials and the Quest for Metavalent Bonding.

PubMed

Zhu, Min; Cojocaru-Mirédin, Oana; Mio, Antonio M; Keutgen, Jens; Küpers, Michael; Yu, Yuan; Cho, Ju-Young; Dronskowski, Richard; Wuttig, Matthias

2018-05-01

Laser-assisted field evaporation is studied in a large number of compounds, including amorphous and crystalline phase change materials employing atom probe tomography. This study reveals significant differences in field evaporation between amorphous and crystalline phase change materials. High probabilities for multiple events with more than a single ion detected per laser pulse are only found for crystalline phase change materials. The specifics of this unusual field evaporation are unlike any other mechanism shown previously to lead to high probabilities of multiple events. On the contrary, amorphous phase change materials as well as other covalently bonded compounds and metals possess much lower probabilities for multiple events. Hence, laser-assisted field evaporation in amorphous and crystalline phase change materials reveals striking differences in bond rupture. This is indicative for pronounced differences in bonding. These findings imply that the bonding mechanism in crystalline phase change materials differs substantially from conventional bonding mechanisms such as metallic, ionic, and covalent bonding. Instead, the data reported here confirm a recently developed conjecture, namely that metavalent bonding is a novel bonding mechanism besides those mentioned previously. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Thermal Expansion Behavior in TcO2. Toward Breaking the Tc-Tc Bond.

PubMed

Reynolds, Emily; Zhang, Zhaoming; Avdeev, Maxim; Thorogood, Gordon J; Poineau, Frederic; Czerwinski, Kenneth R; Kimpton, Justin A; Kennedy, Brendan J

2017-08-07

The structure of TcO 2 between 25 and 1000 °C has been determined in situ using X-ray powder diffraction methods and is found to remain monoclinic in space group P2 1 /c. Thermal expansion in TcO 2 is highly anisotropic, with negative thermal expansion of the b axis observed above 700 °C. This is the result of an anomalous expansion along the a axis that is a consequence of weakening of the Tc-Tc bonds.

Role of Secondary Low-Energy Electrons in the Concomitant Chemoradiation Therapy of Cancer

NASA Astrophysics Data System (ADS)

Zheng, Yi; Hunting, Darel J.; Ayotte, Patrick; Sanche, Léon

2008-05-01

Solid films of DNA with and without the chemotherapeutic agent cisplatin bonded to guanine were bombarded with electrons of 1, 10, 100, and 60 000 eV causing single and double strand breaks. In the presence of cisplatin this damage was increased by factors varying from 1.3 to 4.4 owing to an increase in bond dissociation triggered by the formation of transient anions. This mechanism may lie at the basis of the efficiency of concomitant cisplatin-radiation therapy.

Dynamics and mechanism of UV-damaged DNA repair in indole-thymine dimer adduct: molecular origin of low repair quantum efficiency.

PubMed

Guo, Xunmin; Liu, Zheyun; Song, Qinhua; Wang, Lijuan; Zhong, Dongping

2015-02-26

Many biomimetic chemical systems for repair of UV-damaged DNA showed very low repair efficiency, and the molecular origin is still unknown. Here, we report our systematic characterization of the repair dynamics of a model compound of indole-thymine dimer adduct in three solvents with different polarity. By resolving all elementary steps including three electron-transfer processes and two bond-breaking and bond-formation dynamics with femtosecond resolution, we observed the slow electron injection in 580 ps in water, 4 ns in acetonitrile, and 1.38 ns in dioxane, the fast back electron transfer without repair in 120, 150, and 180 ps, and the slow bond splitting in 550 ps, 1.9 ns, and 4.5 ns, respectively. The dimer bond cleavage is clearly accelerated by the solvent polarity. By comparing with the biological repair machine photolyase with a slow back electron transfer (2.4 ns) and a fast bond cleavage (90 ps), the low repair efficiency in the biomimetic system is mainly determined by the fast back electron transfer and slow bond breakage. We also found that the model system exists in a dynamic heterogeneous C-clamped conformation, leading to a stretched dynamic behavior. In water, we even identified another stacked form with ultrafast cyclic electron transfer, significantly reducing the repair efficiency. Thus, the comparison of the repair efficiency in different solvents is complicated and should be cautious, and only the dynamics by resolving all elementary steps can finally determine the total repair efficiency. Finally, we use the Marcus electron-transfer theory to analyze all electron-transfer reactions and rationalize all observed electron-transfer dynamics.

A DFT investigation of a bulky biomimetic model catalyzing the 5'-outer ring deiodination of thyroxine.

PubMed

Fortino, Mariagrazia; Marino, Tiziana; Russo, Nino; Sicilia, Emilia

2016-12-01

This paper illustrates the outcomes of a density functional theory investigation aimed at unraveling mechanistic aspects of the 5'-outer ring deiodination process of thyroxine (T4) assisted by the sterically protected organoselenol compound BpqSeH. BpqSeH, which was previously synthesized and tested for its deiodinase activity, is able to afford the active hormone 3,5,3'-tetraiodothyronine (T3) by selective outer-ring deiodination of T4, and to protect the SeH moiety inside the nano-sized molecular cavity from further reactivity, allowing its isolation and characterization. Calculations were also performed including an imidazole ring that, mimicking a His residue in the active site of the original enzyme, plays an crucial role in deprotonating the selenol moiety. Both the suggested enol/keto tautomerization and the previously proven formation of an intermediate whose main characteristic is the presence of a Se⋯I⋯C halogen bond, were examined along the pathway leading to 5'-outer ring deiodination. The calculated potential energy surface showed that neither the pathway encompassing enol/keto tautomerism nor the formation of a halogen bond paving the way to C-I bond breaking and chalcogen-I bond forming is viable. The exergonic formation of the final selenenyl iodide product confirms the stabilization effect of the molecular cavity. Graphical Abstract Computed free energy profile describing the 5'-outer deiodination of thyroxine assisted by the steric hindered organoselenol BpqSH compound. The molecular electrostatic potential map reoported for the INT1 intermediate shows the non-covalent Se-I interaction, due to the attraction between charges of opposite sign, that weakens the C-I bond and prepares the formation of the new Se-I bond.

Breaking the Illiteracy Bonds.

ERIC Educational Resources Information Center

Taylor, Susan Champlin

1988-01-01

Describes current research being done on literacy and discusses reasons behind the varied estimates of adult literacy rates. Presents several case studies of adults who are currently or have been in reading programs, particularly older adults. Describes the work of major literacy education providers. (CH)

Facile preparation of porous carbon from coffee bean waste using low temperature solvothermal method

NASA Astrophysics Data System (ADS)

Baroroh, L. A. Al; Fitria, D.; Amal, M. I.; Wismogroho, A. S.; Widayatno, W. B.

2018-03-01

In this study, porous carbon made from coffee bean waste (CBW) was carbonized at 500 °C, 600 °C, and 700 °C to find effective temperature. It is verified from the IR spectrum that carbonization process at certain temperature can effectively break cellulose bonding and make aromatics functional group while preserving its carbon structure. The TG-DTA curve shows four stages of decomposition process and confirms most effective carbonization temperature. Activation process of as-carbonized CBW was carried out using solvothermal method in KOH and NH4OH steam environment at 200 °C with variation of 30%, 40%, and 50% solvothermal volume. Scanning electron micrographs reveals significant increase of porosity on the carbon surface and differences of structural pores between the variations. The results show the possible potential of utilizing low temperature-solvothermal method for nanoporous carbon material.

Water dissociation in a radio-frequency electromagnetic field with ex situ electrodes—decomposition of perfluorooctanoic acid and tetrahydrofuran

NASA Astrophysics Data System (ADS)

Schneider, Jens; Holzer, Frank; Kraus, Markus; Kopinke, Frank-Dieter; Roland, Ulf

2016-10-01

The application of radio waves with a frequency of 13.56 MHz on electrolyte solutions in a capillary reactor led to the formation of reactive hydrogen and oxygen species and finally to molecular oxygen and hydrogen. This process of water splitting can be principally used for the elimination of hazardous chemicals in water. Two compounds, namely perfluorooctanoic acid (PFOA) and tetrahydrofuran, were converted using this process. Their main decomposition products were highly volatile and therefore transferred to a gas phase, where they could be identified by GC-MS analyses. It is remarkable that the chemical reactions could benefit from both the oxidizing and reducing species formed in the plasma process, which takes place in gas bubbles saturated with water vapor. The breaking of C-C and C-F bonds was proven in the case of PFOA, probably initiated by electron impacts and radical reactions.

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

USGS Publications Warehouse

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

2004-01-01

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

Electronic excited state paths of Stone-Wales rearrangement in pyrene: roles of conical intersections.

PubMed

Yamazaki, Kaoru; Niitsu, Naoyuki; Nakamura, Kosuke; Kanno, Manabu; Kono, Hirohiko

2012-11-26

We investigated the reaction paths of Stone-Wales rearrangement (SWR), i.e., π/2 rotation of two carbon atoms with respect to the midpoint of the bond, in graphene and carbon nanotube quantum chemically. Our particular attention is focused on the roles of electronic excitations and conical intersections (CIs) in the reaction mechanism. We used pyrene as a model system. The reaction paths were determined by constructing potential energy surfaces at the MS-CASPT2//SA-CASSCF level of theory. We found that there are no CIs involved in SWR when both of C-C bond cleavage and formation occur simultaneously (concerted mechanism). In contrast, for the reaction path with stepwise cleavage and formation of C-C bonds, C-C bond breaking and making processes proceed through two CIs. When SWR starts from the ground (S(0)) state, the concerted and stepwise paths have an equivalent reaction barrier ΔE(‡) (9.5-9.6 eV). For the reaction path starting from excited states, only the stepwise mechanism is energetically preferable. This path contains a nonadabatic transition between the S(1) and S(0) states via a CI associated with the first stage of C-C bond cleavage and has ΔE(‡) as large as in the S(0) paths. We confirmed that the main active molecular orbitals and electron configurations for the low-lying electronic states of larger nanocarbons are the same as those in pyrene. This result suggests the importance of the nonadiabatic transitions through CIs in the photochemical reactions in large nanocarbons.

Salt-Assisted Ultrasonicated De-Aggregation and Advanced Redox Electrochemistry of Detonation Nanodiamond

PubMed Central

Gupta, Sanju; Evans, Brendan; Henson, Alex; Carrizosa, Sara B.

2017-01-01

Nanodiamond particles form agglomerates in the dry powder state and this poses limitation to the accessibility of their diamond-like core thus dramatically impacting their technological advancement. In this work, we report de-agglomeration of nanodiamond (ND) by using a facile technique namely, salt-assisted ultrasonic de-agglomeration (SAUD). Utilizing ultrasound energy and ionic salts (sodium chloride and sodium acetate), SAUD is expected to break apart thermally treated nanodiamond aggregates (~50–100 nm) and produce an aqueous slurry of de-aggregated stable colloidal nanodiamond dispersions by virtue of ionic interactions and electrostatic stabilization. Moreover, the SAUD technique neither has toxic chemicals nor is it difficult to remove impurities and therefore the isolated nanodiamonds produced are exceptionally suited for engineered nanocarbon for mechanical (composites, lubricants) and biomedical (bio-labeling, biosensing, bioimaging, theranostic) applications. We characterized the microscopic structure using complementary techniques including transmission electron microscopy combined with selected-area electron diffraction, optical and vibrational spectroscopy. We immobilized SAUD produced NDs on boron-doped diamond electrodes to investigate fundamental electrochemical properties. They included surface potential (or Fermi energy level), carrier density and mapping electrochemical (re)activity using advanced scanning electrochemical microscopy in the presence of a redox-active probe, with the aim of understanding the surface redox chemistry and the interfacial process of isolated nanodiamond particles as opposed to aggregated and untreated nanoparticles. The experimental findings are discussed in terms of stable colloids, quantum confinement and predominantly surface effects, defect sites (sp2–bonded C and unsaturated bonds), inner core (sp3–bonded C)/outer shell (sp2–bonded C) structure, and surface functionality. Moreover, the surface electronic states give rise to midgap states which serve as electron donors (or acceptors) depending upon the bonding (or antibonding). These are important as electroanalytical platforms for various electrocatalytic processes. PMID:29125547

Polymer mechanochemistry: Up another rung

NASA Astrophysics Data System (ADS)

Craig, Stephen L.

2017-12-01

The use of mechanical force to break and build chemical bonds in polymers can enable transformations that cannot be conducted using stimuli such as light and heat. Now, an insulating polymer has been mechanically unzipped to create a semiconducting polymer with extended regions of conjugation.

Breaking the Status Quo: Information and the Future Force

DTIC Science & Technology

2012-03-12

Bonds. Hollywood rolled out Movietone news releases before every cinema offering, and stalwarts such as Frank Capra produced films destined to stir...report commissioned by the French Joint Forces Centre for Concept Development, Doctrine, and Experimentation – recommended that France adopt this

Brittle-to-ductile transition of lithiated silicon electrodes: Crazing to stable nanopore growth.

PubMed

Wang, Haoran; Wang, Xueju; Xia, Shuman; Chew, Huck Beng

2015-09-14

Using first principle calculations, we uncover the underlying mechanisms explaining the brittle-to-ductile transition of LixSi electrodes in lithium ion batteries with increasing Li content. We show that plasticity initiates at x = ∼ 0.5 with the formation of a craze-like network of nanopores separated by Si-Si bonds, while subsequent failure is still brittle-like with the breaking of Si-Si bonds. Transition to ductile behavior occurs at x ⩾ 1 due to the increased density of highly stretchable Li-Li bonds, which delays nanopore formation and stabilizes nanopore growth. Collapse of the nanopores during unloading of the LixSi alloys leads to significant strain recovery.

Conformations and charge distributions of diazocyclopropanes

NASA Astrophysics Data System (ADS)

Borges, Itamar, Jr.

Three diazo-substituted cyclopropane compounds, which have been suggested as new potential high energy compounds, were studied employing the B3LYP-DFT/6-31G(d,p) method. Geometries were optimized. Distributed multipole analysis, computed from the B3LYP-DFT/6-31G(d,p) density matrix, was used to describe the details of the molecular charge distribution of the three molecules. It was verified that electron withdrawing from the C ring atoms and charge build-up on the N atoms bonded to the ring increased with the number of diazo groups. These effects were related to increased sensitivity to impact and easiness of C bond N bond breaking in the three compounds.

Density functional study of the adsorption of aspirin on the hydroxylated (0 0 1) α-quartz surface

NASA Astrophysics Data System (ADS)

Abbasi, A.; Nadimi, E.; Plänitz, P.; Radehaus, C.

2009-08-01

In this study the adsorption geometry of aspirin molecule on a hydroxylated (0 0 1) α-quartz surface has been investigated using DFT calculations. The optimized adsorption geometry indicates that both, adsorbed molecule and substrate are strongly deformed. Strong hydrogen bonding between aspirin and surface hydroxyls, leads to the breaking of the original hydroxyl-hydroxyl hydrogen bonds (Hydrogenbridges) on the surface. In this case new hydrogen bonds on the hydroxylated (0 0 1) α-quartz surface appear which significantly differ from those at the clean surface. The 1.11 eV adsorption energy reveals that the interaction of aspirin with α-quartz is an exothermic chemical interaction.

Selective bond breaking mediated by state specific vibrational excitation in model HOD molecule through optimized femtosecond IR pulse: a simulated annealing based approach.

PubMed

Shandilya, Bhavesh K; Sen, Shrabani; Sahoo, Tapas; Talukder, Srijeeta; Chaudhury, Pinaki; Adhikari, Satrajit

2013-07-21

The selective control of O-H/O-D bond dissociation in reduced dimensionality model of HOD molecule has been explored through IR+UV femtosecond pulses. The IR pulse has been optimized using simulated annealing stochastic approach to maximize population of a desired low quanta vibrational state. Since those vibrational wavefunctions of the ground electronic states are preferentially localized either along the O-H or O-D mode, the femtosecond UV pulse is used only to transfer vibrationally excited molecule to the repulsive upper surface to cleave specific bond, O-H or O-D. While transferring from the ground electronic state to the repulsive one, the optimization of the UV pulse is not necessarily required except specific case. The results so obtained are analyzed with respect to time integrated flux along with contours of time evolution of probability density on excited potential energy surface. After preferential excitation from [line]0, 0> ([line]m, n> stands for the state having m and n quanta of excitations in O-H and O-D mode, respectively) vibrational level of the ground electronic state to its specific low quanta vibrational state ([line]1, 0> or [line]0, 1> or [line]2, 0> or [line]0, 2>) by using optimized IR pulse, the dissociation of O-D or O-H bond through the excited potential energy surface by UV laser pulse appears quite high namely, 88% (O-H ; [line]1, 0>) or 58% (O-D ; [line]0, 1>) or 85% (O-H ; [line]2, 0>) or 59% (O-D ; [line]0, 2>). Such selectivity of the bond breaking by UV pulse (if required, optimized) together with optimized IR one is encouraging compared to the normal pulses.

Role of water in aging of human butyrylcholinesterase inhibited by echothiophate: the crystal structure suggests two alternative mechanisms of aging.

PubMed

Nachon, Florian; Asojo, Oluwatoyin A; Borgstahl, Gloria E O; Masson, Patrick; Lockridge, Oksana

2005-02-01

Organophosphorus poisons (OP) bind covalently to the active-site serine of cholinesterases. The inhibited enzyme can usually be reactivated with powerful nucleophiles such as oximes. However, the covalently bound OP can undergo a suicide reaction (termed aging) yielding nonreactivatable enzyme. In human butyrylcholinesterase (hBChE), aging involves the residues His438 and Glu197 that are proximal to the active-site serine (Ser198). The mechanism of aging is known in detail for the nerve gases soman, sarin, and tabun as well as the pesticide metabolite isomalathion. Aging of soman- and sarin-inhibited acetylcholinesterase occurs by C-O bond cleavage, whereas that of tabun- and isomalathion-inhibited acetylcholinesterase occurs by P-N and P-S bond cleavage, respectively. In this work, the crystal structures of hBChE inhibited by the ophthalmic reagents echothiophate (nonaged and aged) and diisopropylfluorophosphate (aged) were solved and refined to 2.1, 2.25, and 2.2 A resolution, respectively. No appreciable shift in the position of the catalytic triad histidine was observed between the aged and nonaged conjugates of hBChE. This absence of shift contrasts with the aged and nonaged crystal structures of Torpedo californica acetylcholinesterase inhibited by the nerve agent VX. The nonaged hBChE structure shows one water molecule interacting with Glu197 and the catalytic triad histidine (His438). Interestingly, this water molecule is ideally positioned to promote aging by two mechanisms: breaking either a C-O bond or a P-O bond. Pesticides and certain stereoisomers of nerve agents are expected to undergo aging by breaking the P-O bond.

Degree of Mechanochemical Devulcanization of Model Styrene-Butadiene Rubber Compounds Containing Different Amount of Poly-, Di- and Monosulphidic Bonds

NASA Astrophysics Data System (ADS)

Sangari, Samra; Anita, Hill; Dumitru, Pavel

2004-03-01

There have been significant attempts to devulcanize waste elastomers to facilitate reusing these valuable resources in applications requiring the unique properties of rubber. The difficulty in recycling of elastomers has traditionally been with devulcanizing the elastomer without comprising its properties due to degradation of main chains. This research aimed to devulcanize model styrene-butadiene rubber (SBR) compounds, which had various amounts of poly-, di- and monosulfidic crosslinks using a mechanochemical process. Three model compounds were prepared using SBR using a laboratory two-roll mill. They were then vulcanized in a compression molding press at 140r C. The prepared vulcanized compounds were then ground and devulcanized in an internal mixer using a chemical mixture at a constant rotor speed and temperature. The crosslink density of the compounds before and after the devulcanization was calculated using volume-swelling measurements. The obtained data was used to establish the correlation between crosslink density of the compounds and the degree of devulcanization. The results showed that mechanochemical devulcanization caused a significant decrease in the crosslink density of the compounds by breaking the sulfidic linkages. The break up of polysulfidic crosslinks was predominant, meaning that mechanochemical process selectively affected different types of crosslinks.

IR spectroscopy as a source of data on bond strengths

NASA Astrophysics Data System (ADS)

Finkelshtein, E. I.; Shamsiev, R. S.

2018-02-01

The aim of this work is the estimation of double bond strength, namely Cdbnd O bonds in ketones and aldehydes and Cdbnd C bonds in various compounds. By the breaking of these bonds one or both fragments formed are carbenes, for which experimental data on the enthalpies of formation (ΔHf298) are scarce. Thus for the estimation of ΔHf298 of the corresponding carbenes, the empirical equations were proposed based on different approximations. In addition, a quantum chemical calculations of the ΔHf298 values of carbenes were performed, and the data obtained were compared with experimental values and the results of earlier calculations. Equations for the calculation of Cdbnd O bond strengths of different ketones and aldehydes from the corresponding stretching frequencies ν(Cdbnd O) were derived. Using the proposed equations, the strengths of Cdbnd O bonds of 25 ketones and 12 conjugated aldehydes, as well as Cdbnd C bonds of 13 hydrocarbons and 7 conjugated aldehydes were estimated for the first time. Linear correlations of Cdbnd C and Cdbnd O bond strengths with the bond lengths were established, and the equations permitting the estimation of the double bond strengths and lengths with acceptable accuracy were obtained. Also, the strength of central Cdbnd C bond of stilbene was calculated for the first time. The uncertainty of the strengths of double bonds obtained may be regarded as accurate ±10-15 kJ/mol.

Stepwise mechanism and H2O-assisted hydrolysis in atomic layer deposition of SiO2 without a catalyst.

PubMed

Fang, Guo-Yong; Xu, Li-Na; Wang, Lai-Guo; Cao, Yan-Qiang; Wu, Di; Li, Ai-Dong

2015-01-01

Atomic layer deposition (ALD) is a powerful deposition technique for constructing uniform, conformal, and ultrathin films in microelectronics, photovoltaics, catalysis, energy storage, and conversion. The possible pathways for silicon dioxide (SiO2) ALD using silicon tetrachloride (SiCl4) and water (H2O) without a catalyst have been investigated by means of density functional theory calculations. The results show that the SiCl4 half-reaction is a rate-determining step of SiO2 ALD. It may proceed through a stepwise pathway, first forming a Si-O bond and then breaking Si-Cl/O-H bonds and forming a H-Cl bond. The H2O half-reaction may undergo hydrolysis and condensation processes, which are similar to conventional SiO2 chemical vapor deposition (CVD). In the H2O half-reaction, there are massive H2O molecules adsorbed on the surface, which can result in H2O-assisted hydrolysis of the Cl-terminated surface and accelerate the H2O half-reaction. These findings may be used to improve methods for the preparation of SiO2 ALD and H2O-based ALD of other oxides, such as Al2O3, TiO2, ZrO2, and HfO2.

Stepwise mechanism and H2O-assisted hydrolysis in atomic layer deposition of SiO2 without a catalyst

NASA Astrophysics Data System (ADS)

Fang, Guo-Yong; Xu, Li-Na; Wang, Lai-Guo; Cao, Yan-Qiang; Wu, Di; Li, Ai-Dong

2015-02-01

Atomic layer deposition (ALD) is a powerful deposition technique for constructing uniform, conformal, and ultrathin films in microelectronics, photovoltaics, catalysis, energy storage, and conversion. The possible pathways for silicon dioxide (SiO2) ALD using silicon tetrachloride (SiCl4) and water (H2O) without a catalyst have been investigated by means of density functional theory calculations. The results show that the SiCl4 half-reaction is a rate-determining step of SiO2 ALD. It may proceed through a stepwise pathway, first forming a Si-O bond and then breaking Si-Cl/O-H bonds and forming a H-Cl bond. The H2O half-reaction may undergo hydrolysis and condensation processes, which are similar to conventional SiO2 chemical vapor deposition (CVD). In the H2O half-reaction, there are massive H2O molecules adsorbed on the surface, which can result in H2O-assisted hydrolysis of the Cl-terminated surface and accelerate the H2O half-reaction. These findings may be used to improve methods for the preparation of SiO2 ALD and H2O-based ALD of other oxides, such as Al2O3, TiO2, ZrO2, and HfO2.

An algorithm to locate optimal bond breaking points on a potential energy surface for applications in mechanochemistry and catalysis.

PubMed

Bofill, Josep Maria; Ribas-Ariño, Jordi; García, Sergio Pablo; Quapp, Wolfgang

2017-10-21

The reaction path of a mechanically induced chemical transformation changes under stress. It is well established that the force-induced structural changes of minima and saddle points, i.e., the movement of the stationary points on the original or stress-free potential energy surface, can be described by a Newton Trajectory (NT). Given a reactive molecular system, a well-fitted pulling direction, and a sufficiently large value of the force, the minimum configuration of the reactant and the saddle point configuration of a transition state collapse at a point on the corresponding NT trajectory. This point is called barrier breakdown point or bond breaking point (BBP). The Hessian matrix at the BBP has a zero eigenvector which coincides with the gradient. It indicates which force (both in magnitude and direction) should be applied to the system to induce the reaction in a barrierless process. Within the manifold of BBPs, there exist optimal BBPs which indicate what is the optimal pulling direction and what is the minimal magnitude of the force to be applied for a given mechanochemical transformation. Since these special points are very important in the context of mechanochemistry and catalysis, it is crucial to develop efficient algorithms for their location. Here, we propose a Gauss-Newton algorithm that is based on the minimization of a positively defined function (the so-called σ-function). The behavior and efficiency of the new algorithm are shown for 2D test functions and for a real chemical example.

Organic Synthesis Using Microwaves and Supported Reagents

EPA Science Inventory

In the electromagnetic radiation region, microwaves (0.3GHz-300GHz) lie between radiowave (Rf) and infrared (IR) frequencies with relatively large wavelengths (1 mm-1 m). Microwaves, non-ionizing radiation incapable of breaking bonds, are a form of energy that manifest as heat t...

X-ray targeted bond or compound destruction

DOEpatents

Pravica, Sr., Michael G.

2016-11-01

This document provides methods, systems, and devices for inducing a decomposition reaction by directing x-rays towards a location including a particular compound. The x-rays can have an irradiation energy that corresponds to a bond distance of a bond in the particular compound in order to break that bond and induce a decomposition of that particular compound. In some cases, the particular compound is a hazardous substance or part of a hazardous substance. In some cases, the particular compound is delivered to a desired location in an organism and x-rays induce a decomposition reaction that creates a therapeutic substance (e.g., a toxin that kills cancer cells) in the location of the organism. In some cases, the particular compound decomposes to produce a reactant in a reactor apparatus (e.g., fuel cell or semiconductor fabricator).

A crossover in anisotropic nanomechanochemistry of van der Waals crystals

NASA Astrophysics Data System (ADS)

Shimamura, Kohei; Misawa, Masaaki; Li, Ying; Kalia, Rajiv K.; Nakano, Aiichiro; Shimojo, Fuyuki; Vashishta, Priya

2015-12-01

In nanoscale mechanochemistry, mechanical forces selectively break covalent bonds to essentially control chemical reactions. An archetype is anisotropic detonation of layered energetic molecular crystals bonded by van der Waals (vdW) interactions. Here, quantum molecular dynamics simulations reveal a crossover of anisotropic nanomechanochemistry of vdW crystal. Within 10-13 s from the passage of shock front, lateral collision produces NO2 via twisting and bending of nitro-groups and the resulting inverse Jahn-Teller effect, which is mediated by strong intra-layer hydrogen bonds. Subsequently, as we transition from heterogeneous to homogeneous mechanochemical regimes around 10-12 s, shock normal to multilayers becomes more reactive, producing H2O assisted by inter-layer N-N bond formation. These time-resolved results provide much needed atomistic understanding of nanomechanochemistry that underlies a wider range of technologies.

Vanderbilt free-electron-laser project in biomedical and materials research. Annual report, 1 February 1987-31 January 1988

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

Haglund, R.F.; Tolk, N.H.

The Medical Free Electron Laser Program was awarded to develop, construct and operate a free-electron laser facility dedicated to biomedical and materials studies, with particular emphases on: fundamental studies of absorption and localization of electromagnetic energy on and near material surfaces, especially through electronic and other selective, non-statistical processes; non-thermal photon-materials interactions (e.g., electronic bond-breaking or vibrational energy transfer) in physical and biological materials as well as in long-wavelength biopolymer dynamics; development of FEL-based methods to study drug action and to characterize biomolecular properties and metabolic processes in biomembranes; clinical applications in otolaryngology, neurosurgery, ophthalmology and radiology stressing the usemore » of the laser for selective laser-tissue, laser-cellular and laser-molecule interactions in both therapeutic and diagnostic modalities.« less

Oxygen plasma etching of graphene: A first-principles dynamical inspection of the reaction mechanisms and related activation barriers

NASA Astrophysics Data System (ADS)

Koizumi, Kenichi; Boero, Mauro; Shigeta, Yasuteru; Oshiyama, Atsushi; Dept. of Applied Physics Team; Institute of Physics and Chemistry of Strasbourg (IPCMS) Collaboration; Department Of Materials Engineering Science Collaboration

2013-03-01

Oxygen plasma etching is a crucial step in the fabrication of electronic circuits and has recently received a renovated interest in view of the realization of carbon-based nanodevices. In an attempt at unraveling the atomic-scale details and to provide guidelines for the control of the etching processes mechanisms, we inspected the possible reaction pathways via reactive first principles simulations. These processes involve breaking and formation of several chemical bonds and are characterized by different free-energy barriers. Free-energy sampling techniques (metadynamics and blue moon), used to enhance the standard Car-Parrinello molecular dynamics, provide us a detailed microscopic picture of the etching of graphene surfaces and a comprehensive scenario of the activation barriers involved in the various steps. MEXT, Japan - contract N. 22104005

Dissolution of lignin in green urea aqueous solution

NASA Astrophysics Data System (ADS)

Wang, Jingyu; Li, Ying; Qiu, Xueqing; Liu, Di; Yang, Dongjie; Liu, Weifeng; Qian, Yong

2017-12-01

The dissolution problem is the main obstacle for the value-added modification and depolymerization of industrial lignin. Here, a green urea aqueous solution for complete dissolution of various lignin is presented and the dissolution mechanism is analyzed by AFM, DLS and NMR. The results show that the molecular interaction of lignin decreases from 32.3 mN/m in pure water to 11.3 mN/m in urea aqueous solution. The immobility of 1H NMR spectra and the shift of 17O NMR spectra of urea in different lignin/urea solutions indicate that the oxygen of carbonyl in urea and the hydrogen of hydroxyl in lignin form new hydrogen bonds and break the original hydrogen bonds among lignin molecules. The shift of 1H NMR spectra of lignin and the decrease of interactions in model compound polystyrene indicate that urea also breaks the π-π interactions between aromatic rings of lignin. Lignin dissolved in urea aqueous has good antioxidant activity and it can scavenge at least 63% free radicals in 16 min.

Bond-breaking mechanism of vitreous silica densification by IR femtosecond laser pulses

NASA Astrophysics Data System (ADS)

Shcheblanov, Nikita S.; Povarnitsyn, Mikhail E.

2016-04-01

The densification of the vitreous silica (v-SiO2) due to laser irradiation appears reasonable to cause the change in refractive index. In this letter, the v-SiO2 densification under IR femtosecond laser irradiation is studied within molecular-dynamics simulation. The single- and multi-pulse interactions are explored numerically with an account of the bond-breaking mechanism. By analyzing the network at nanoscale, the nature of v-SiO2 densification is assigned to the reduction of major ring fractions of six- and seven-membered rings to minor fractions of three- and four-membered rings (related to D 2 and D 1 Raman signatures, respectively). The athermal behavior of v-SiO2 densification is disclosed at different degrees of ionization for both the single- and multi-pulse cases at sub-threshold regimes. The good agreement between calculated and measured D2 defect line and Si-O-Si angle changes argues in favor of the found mechanism.

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

Nash, Connor P.; Farberow, Carrie A.; Hensley, Jesse E.

Temperature programmed reaction (TPRxn) is a simple yet powerful tool for screening solid catalyst performance at a variety of conditions. A TPRxn system includes a reactor, furnace, gas and vapor sources, flow control, instrumentation to quantify reaction products (e.g., gas chromatograph), and instrumentation to monitor the reaction in real time (e.g., mass spectrometer). Here, we apply the TPRxn methodology to study molybdenum carbide catalysts for the deoxygenation of acetic acid, an important reaction among many in the upgrading/stabilization of biomass pyrolysis vapors. TPRxn is used to evaluate catalyst activity and selectivity and to test hypothetical reaction pathways (e.g., decarbonylation, ketonization,more » and hydrogenation). Furthermore, the results of the TPRxn study of acetic acid deoxygenation show that molybdenum carbide is an active catalyst for this reaction at temperatures above ca. 300 °C and that the reaction favors deoxygenation (i.e., C-O bond-breaking) products at temperatures below ca. 400 °C and decarbonylation (i.e., C-C bond-breaking) products at temperatures above ca. 400 °C.« less

Preparation and Testing of Plant Seed Meal-based Wood Adhesives

PubMed Central

He, Zhongqi; Chapital, Dorselyn C.

2015-01-01

Recently, the interest in plant seed meal-based products as wood adhesives has steadily increased, as these plant raw materials are considered renewable and environment-friendly. These natural products may serve as alternatives to petroleum-based adhesives to ease environmental and sustainability concerns. This work demonstrates the preparation and testing of the plant seed-based wood adhesives using cottonseed and soy meal as raw materials. In addition to untreated meals, water washed meals and protein isolates are prepared and tested. Adhesive slurries are prepared by mixing a freeze-dried meal product with deionized water (3:25 w/w) for 2 hr. Each adhesive preparation is applied to one end of 2 wood veneer strips using a brush. The tacky adhesive coated areas of the wood veneer strips are lapped and glued by hot-pressing. Adhesive strength is reported as the shear strength of the bonded wood specimen at break. Water resistance of the adhesives is measured by the change in shear strength of the bonded wood specimens at break after water soaking. This protocol allows one to assess plant seed-based agricultural products as suitable candidates for substitution of synthetic-based wood adhesives. Adjustments to the adhesive formulation with or without additives and bonding conditions could optimize their adhesive properties for various practical applications. PMID:25867092

Preparation and testing of plant seed meal-based wood adhesives.

PubMed

He, Zhongqi; Chapital, Dorselyn C

2015-03-05

Recently, the interest in plant seed meal-based products as wood adhesives has steadily increased, as these plant raw materials are considered renewable and environment-friendly. These natural products may serve as alternatives to petroleum-based adhesives to ease environmental and sustainability concerns. This work demonstrates the preparation and testing of the plant seed-based wood adhesives using cottonseed and soy meal as raw materials. In addition to untreated meals, water washed meals and protein isolates are prepared and tested. Adhesive slurries are prepared by mixing a freeze-dried meal product with deionized water (3:25 w/w) for 2 hr. Each adhesive preparation is applied to one end of 2 wood veneer strips using a brush. The tacky adhesive coated areas of the wood veneer strips are lapped and glued by hot-pressing. Adhesive strength is reported as the shear strength of the bonded wood specimen at break. Water resistance of the adhesives is measured by the change in shear strength of the bonded wood specimens at break after water soaking. This protocol allows one to assess plant seed-based agricultural products as suitable candidates for substitution of synthetic-based wood adhesives. Adjustments to the adhesive formulation with or without additives and bonding conditions could optimize their adhesive properties for various practical applications.

Real-time observation of the dehydrogenation processes of methanol on clean Ru(001) and Ru(001)-p(2×2) O surfaces by a temperature-programmed electron-stimulated desorption ion angular distribution/time-of-flight system

NASA Astrophysics Data System (ADS)

Sasaki, Takehiko; Itai, Yuichiro; Iwasawa, Yasuhiro

1999-12-01

Decomposition processes of methanol on clean and oxygen-precovered Ru(001) surfaces have been visualized in real time with a temperature-programmed (TP) electron-stimulated desorption ion angular distribution (ESDIAD)/time-of-flight (TOF) system. The mass of desorbed ions during temperature-programmed surface processes was identified by TOF measurements. In the case of methanol (CH 3OD) adsorption on Ru(001)-p(2×2)-O, a halo pattern of H + from the methyl group of methoxy species was observed at 100-200 K, followed by a broad pattern from the methyl group at 230-250 K and by a near-center pattern from O + ions originating from adsorbed CO above 300 K. The halo pattern is attributed to a perpendicular conformation of the CO bond axis of the methoxy species, leading to off-normal CH bond scission. On the other hand, methanol adsorbed on clean Ru(001) did not give any halo pattern but a broad pattern was observed along the surface normal, indicating that the conformation of the methoxy species is not ordered on the clean surface. Comparison between the ESDIAD images of the oxygen-precovered surface and the clean surface suggests that the precovered oxygen adatoms induce ordering of the methoxy species. Real-time ESDIAD measurements revealed that the oxygen atoms at the Ru(001)-p(2×2)-O surface have a positive effect on selective dehydrogenation of the methoxy species to CO+H 2 and a blocking effect on CO bond breaking of the methoxy species.

Accurate bond energies of hydrocarbons from complete basis set extrapolated multi-reference singles and doubles configuration interaction.

PubMed

Oyeyemi, Victor B; Pavone, Michele; Carter, Emily A

2011-12-09

Quantum chemistry has become one of the most reliable tools for characterizing the thermochemical underpinnings of reactions, such as bond dissociation energies (BDEs). The accurate prediction of these particular properties (BDEs) are challenging for ab initio methods based on perturbative corrections or coupled cluster expansions of the single-determinant Hartree-Fock wave function: the processes of bond breaking and forming are inherently multi-configurational and require an accurate description of non-dynamical electron correlation. To this end, we present a systematic ab initio approach for computing BDEs that is based on three components: 1) multi-reference single and double excitation configuration interaction (MRSDCI) for the electronic energies; 2) a two-parameter scheme for extrapolating MRSDCI energies to the complete basis set limit; and 3) DFT-B3LYP calculations of minimum-energy structures and vibrational frequencies to account for zero point energy and thermal corrections. We validated our methodology against a set of reliable experimental BDE values of CC and CH bonds of hydrocarbons. The goal of chemical accuracy is achieved, on average, without applying any empirical corrections to the MRSDCI electronic energies. We then use this composite scheme to make predictions of BDEs in a large number of hydrocarbon molecules for which there are no experimental data, so as to provide needed thermochemical estimates for fuel molecules. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evaluation of coal-related model compounds using a tandem mass spectrometry.

PubMed

Li, Guo-Sheng; Dong, Xueming; Fan, Xing; You, Chun-Yan; Wu, Ge; Zhao, Yun-Peng; Lu, Yao; Wei, Xian-Yong; Ma, Feng-Yun

2018-05-08

Gas chromotography/mass spectrometry (GC/MS) is a routine and basic instrumental method for the analysis of complex coal conversion products in chemical industry. To further enhance practical potentials of GC/MS in chemical industry, a tandem MS method for the selection of ion pair applied in monitoring coal conversions was established by using GC/quadrupole time-of-flight MS (GC/Q-TOF MS). The corresponding fragmentation pathways were explored and suitable ion pairs were screened. Fourteen coal-related model compounds (CRMCs) were analyzed using a GC/Q-TOF MS with different collision induced dissociation (CID) energies (5-20 eV). The fragmentation pathways can offer a better understanding of chemical bond breaking, hydrogen transfer, rearrangement reactions and elimination of neutral fragments for CRMCs during the CID process. The precursor ions of aromatic hydrocarbons without alkyl chain were hard to fragment with a CID energy of 20 eV. But aromatic hydrocarbons with branched chains were prone to fragment via the loss of alkyl chains and further fragmented through ring-open reactions. Compared to C alk -C ar bond, C ar -C ar bond was hard to fragment duo to its high bond dissociation energy. The existence of heteroatoms facilitated fragmentation that was conducive to screening ion pair. The CID technique of GC/Q-TOF MS will contribute to the studies on the organic composition of coals and building monitoring methods for coal conversions via fragmentation and ion pair selection. This article is protected by copyright. All rights reserved.

Electron transfer dynamics of bistable single-molecule junctions.

PubMed

Danilov, Andrey V; Kubatkin, Sergey E; Kafanov, Sergey G; Flensberg, Karsten; Bjørnholm, Thomas

2006-10-01

We present transport measurements of single-molecule junctions bridged by a molecule with three benzene rings connected by two double bonds and with thiol end-groups that allow chemical binding to gold electrodes. The I-V curves show switching behavior between two distinct states. By statistical analysis of the switching events, we show that a 300 meV mode mediates the transition between the two states. We propose that breaking and reformation of a S-H bond in the contact zone between molecule and electrode explains the observed bistability.

Rupture luminescence from natural fibers

NASA Astrophysics Data System (ADS)

Li, W.; Haneman, D.

1999-12-01

Fibers of cotton and wool, and samples of paper, have been ruptured in tension in vacuum and in air, and give detectable luminescence in the visible range. All have a common emission peak at around 2.0 eV, which is ascribed to the deexcitation of states excited by the rupture of organic chain molecule bonds. Rubber bands give stronger emission in air, but no emission in vacuum, suggesting the material breaks only at weak interchain bonds. Mohair, cat, and horse hair also give emission in air. The phenomena reveal effects that would occur widely in nature.

Micromechanical Aspects of Hydraulic Fracturing Processes

NASA Astrophysics Data System (ADS)

Galindo-torres, S. A.; Behraftar, S.; Scheuermann, A.; Li, L.; Williams, D.

2014-12-01

A micromechanical model is developed to simulate the hydraulic fracturing process. The model comprises two key components. Firstly, the solid matrix, assumed as a rock mass with pre-fabricated cracks, is represented by an array of bonded particles simulated by the Discrete Element Model (DEM)[1]. The interaction is ruled by the spheropolyhedra method, which was introduced by the authors previously and has been shown to realistically represent many of the features found in fracturing and communition processes. The second component is the fluid, which is modelled by the Lattice Boltzmann Method (LBM). It was recently coupled with the spheropolyhedra by the authors and validated. An advantage of this coupled LBM-DEM model is the control of many of the parameters of the fracturing fluid, such as its viscosity and the injection rate. To the best of the authors' knowledge this is the first application of such a coupled scheme for studying hydraulic fracturing[2]. In this first implementation, results are presented for a two-dimensional situation. Fig. 1 shows one snapshot of the LBM-DEM coupled simulation for the hydraulic fracturing where the elements with broken bonds can be identified and the fracture geometry quantified. The simulation involves a variation of the underground stress, particularly the difference between the two principal components of the stress tensor, to explore the effect on the fracture path. A second study focuses on the fluid viscosity to examine the effect of the time scales of different injection plans on the fracture geometry. The developed tool and the presented results have important implications for future studies of the hydraulic fracturing process and technology. references 1. Galindo-Torres, S.A., et al., Breaking processes in three-dimensional bonded granular materials with general shapes. Computer Physics Communications, 2012. 183(2): p. 266-277. 2. Galindo-Torres, S.A., A coupled Discrete Element Lattice Boltzmann Method for the simulation of fluid-solid interaction with particles of general shapes. Computer Methods in Applied Mechanics and Engineering, 2013. 265(0): p. 107-119.

The How and Why of Chemical Reactions

ERIC Educational Resources Information Center

Schubert, Leo

1970-01-01

Presents a discussion of some of the fundamental concepts in thermodynamics and quantum mechanics including entropy, enthalpy, free energy, the partition function, chemical kinetics, transition state theory, the making and breaking of chemical bonds, electronegativity, ion sizes, intermolecular energies and of their role in explaining the nature…

Fluxless Bonding Processes Using Silver-Indium System for High Temperature Electronics and Silver Flip-Chip Interconnect Technology

NASA Astrophysics Data System (ADS)

Wu, Yuan-Yun

In this dissertation, fluxless silver (Ag)-indium (In) binary system bonding and Ag solid-state bonding are used between different bonded pairs which have large thermal expansion coefficient (CTE) mismatch and flip-chip interconnect bonding application. In contrast to the conventional soldering process, fluxless bonding technique eliminates contamination and reliability problems caused by flux to fabricate high quality joints. There are two section are reported. In the first section, the reactions of Ag-In binary system are presented. In the second section, the high melting temperature, thermal and electrical conductivity joint materials bonding by either Ag-In binary system bonding or solid-state bonding processes for different bonded pairs and flip-chip application are designed, developed, and reported. Our group have studied Ag-In system for several years and developed the bonding processes successfully. However, the detailed reactions of Ag and In were seldom studied. To design a proper bonding structure, it is necessary to understand the reaction between Ag and In. The systematic experiments were performed to investigate these reactions. A 40 um Ag layer was electroplated on copper (Cu) substrates, followed by indium layers of 1, 3, 5, 10, and 15 um, respectively. The samples were annealed at 180 °C in 0.1 torr vacuum. For samples with In thickness less than 5 mum, the joint compositions are Ag2In only (1 um) or AgIn2, Ag2In, and Ag solid solution (Ag) after annealing. No indium is identified. For 10 and 15 um thick In samples, In covers almost over the entire sample surface after annealing. Later, an Ag layer was annealed at 450 °C for 3 hours to grow Ag grains, followed by plating 10 um In and annealing at 180 °C. By annealing Ag before plating In, more In is kept in the structure during annealing at 180 °C. Based on above results, for those designs with In thinner than 5 um, the Ag layer needs to be annealed, prior to In plating in order to make a successful bonding. In this section, we further studied the Ag-In bonding and solid-state bonding for different bonded pairs and flip-chip application. For the silicon (Si) and aluminum (Al) pair, Al has been used as the material for interconnect pads on the ICs. However, its high CTE (23 x 10-6/°C) and non-solderable property limit its applications in electronic products. To overcome these problems, a fluxless Ag-In bonding was developed. Al was deposited Cr/Cu layer on the surface by E-beam evaporator to make it solderable. 15 um of Ag and 8 um of In were sequentially plated on the Al substrates and 15 um of Ag was on Si chips with Cr/Au coating layer. The bonding was performed at 180 °C in 0.1 torr vacuum. The joint consists of Ag/(Ag)/Ag2In/(Ag)/Ag. The joint can achieve a solidus temperature of beyond 600 °C. From shear test results, the shear strengths far exceed the requirement in MIL-STD-883H. Al is not considered as a favorable substrate material because it is not solderable and has a high CTE. The new method presented in this thesis seems to have surmounted these two challenges. Since Ag2In is weak inside the joint in Ag-In system, an annealed process was used to convert the joints into Ag solid solution (Ag) to increase the joint strength and ductility. Two copper (Cu) substrates were bonded at 180 °C without flux. Bonding samples were annealed at 200 °C for 1,000 hours (first design) and at 250 °C for 350 hours (second design), respectively. Scanning electron microscope with energy dispersive X-ray (EDX) analysis results indicate that the joint of the first design is an alloy of mostly (Ag) with micron-size Ag2In and Ag3In regions, and that of second design has converted to a single (Ag) phase. Shear test results show that the breaking forces far exceed the requirement in MIL-STD-883H. The joint solidus temperatures are 600 °C and 800 °C for the first and second designs, respectively. The research results have shown that high-strength and high temperature joints can be manufactured using fluxless low temperature processes with the Ag-In system and are valuable in developing high temperature package. (Abstract shortened by UMI.).

A Vibrational Spectral Maker for Probing the Hydrogen-Bonding Status of Protonated Asp and Glu Residues

PubMed Central

Nie, Beining; Stutzman, Jerrod; Xie, Aihua

2005-01-01

Hydrogen bonding is a fundamental element in protein structure and function. Breaking a single hydrogen bond may impair the stability of a protein. We report an infrared vibrational spectral marker for probing the hydrogen-bond number for buried, protonated Asp or Glu residues in proteins. Ab initio computational studies were performed on hydrogen-bonding interactions of a COOH group with a variety of side-chain model compounds of polar and charged amino acids in vacuum using density function theory. For hydrogen-bonding interactions with polar side-chain groups, our results show a strong correlation between the C=O stretching frequency and the hydrogen bond number of a COOH group: ∼1759–1776 cm−1 for zero, ∼1733–1749 cm−1 for one, and 1703–1710 cm−1 for two hydrogen bonds. Experimental evidence for this correlation will be discussed. In addition, we show an approximate linear correlation between the C=O stretching frequency and the hydrogen-bond strength. We propose that a two-dimensional infrared spectroscopy, C=O stretching versus O-H stretching, may be employed to identify the specific type of hydrogen-bonding interaction. This vibrational spectral marker for hydrogen-bonding interaction is expected to enhance the power of time-resolved Fourier transform infrared spectroscopy for structural characterization of functionally important intermediates of proteins. PMID:15653739

Conceptual DFT analysis of the fragility spectra of atoms along the minimum energy reaction coordinate.

PubMed

Ordon, Piotr; Komorowski, Ludwik; Jedrzejewski, Mateusz

2017-10-07

Theoretical justification has been provided to the method for monitoring the sequence of chemical bonds' rearrangement along a reaction path, by tracing the evolution of the diagonal elements of the Hessian matrix. Relations between the divergences of Hellman-Feynman forces and the energy and electron density derivatives have been demonstrated. By the proof presented on the grounds of the conceptual density functional theory formalism, the spectral amplitude observed on the atomic fragility spectra [L. Komorowski et al., Phys. Chem. Chem. Phys. 18, 32658 (2016)] reflects selectively the electron density modifications in bonds of an atom. In fact the spectral peaks for an atom reveal changes of the electron density occurring with bonds creation, breaking, or varying with the reaction progress.

Conceptual DFT analysis of the fragility spectra of atoms along the minimum energy reaction coordinate

NASA Astrophysics Data System (ADS)

Ordon, Piotr; Komorowski, Ludwik; Jedrzejewski, Mateusz

2017-10-01

Theoretical justification has been provided to the method for monitoring the sequence of chemical bonds' rearrangement along a reaction path, by tracing the evolution of the diagonal elements of the Hessian matrix. Relations between the divergences of Hellman-Feynman forces and the energy and electron density derivatives have been demonstrated. By the proof presented on the grounds of the conceptual density functional theory formalism, the spectral amplitude observed on the atomic fragility spectra [L. Komorowski et al., Phys. Chem. Chem. Phys. 18, 32658 (2016)] reflects selectively the electron density modifications in bonds of an atom. In fact the spectral peaks for an atom reveal changes of the electron density occurring with bonds creation, breaking, or varying with the reaction progress.

Highly Reactive Scandium Phosphinoalkylidene Complex: C-H and H-H Bonds Activation.

PubMed

Mao, Weiqing; Xiang, Li; Alvarez Lamsfus, Carlos; Maron, Laurent; Leng, Xuebing; Chen, Yaofeng

2017-01-25

The first scandium phosphinoalkylidene complex was synthesized and structurally characterized. The complex has the shortest Sc-C bond lengths reported to date (2.089(3) Å). DFT calculations reveal the presence of a three center π interaction in the complex. This scandium phosphinoalkylidene complex undergoes intermolecular C-H bond activation of pyridine, 4-dimethylamino pyridine and 1,3-dimethylpyrazole at room temperature. Furthermore, the complex rapidly activates H 2 under mild conditions. DFT calculations also demonstrate that the C-H activation of 1,3-dimethylpyrazole is selective for thermodynamic reasons and the relatively slow reaction is due to the need of fully breaking the chelating effect of the phosphino group to undergo the reaction whereas this is not the case for H 2 .

Can nature's design be improved upon? High strength, transparent nacre-like nanocomposites with double network of sacrificial cross links.

PubMed

Podsiadlo, Paul; Kaushik, Amit K; Shim, Bong Sup; Agarwal, Ashish; Tang, Zhiyong; Waas, Anthony M; Arruda, Ellen M; Kotov, Nicholas A

2008-11-20

The preparation of a high-strength and highly transparent nacre-like nanocomposite via layer-by-layer assembly technique from poly(vinyl alcohol) (PVA) and Na+-montmorillonite clay nanosheets is reported in this article. We show that a high density of weak bonding interactions between the polymer and the clay particles: hydrogen, dipole-induced dipole, and van der Waals undergoing break-reform deformations, can lead to high strength nanocomposites: sigmaUTS approximately 150 MPa and E' approximately 13 GPa. Further introduction of ionic bonds into the polymeric matrix creates a double network of sacrificial bonds which dramatically increases the mechanical properties: sigmaUTS approximately 320 MPa and E' approximately 60 GPa.

Structural singularities in Ge(x)Te(100-x) films.

PubMed

Piarristeguy, A A; Micoulaut, M; Escalier, R; Jóvári, P; Kaban, I; van Eijk, J; Luckas, J; Ravindren, S; Boolchand, P; Pradel, A

2015-08-21

Structural and calorimetric investigation of Ge(x)Te(100-x) films over wide range of concentration 10 < x < 50 led to evidence two structural singularities at x ∼ 22 at. % and x ∼ 33-35 at. %. Analysis of bond distribution, bond variability, and glass thermal stability led to conclude to the origin of the first singularity being the flexible/rigid transition proposed in the framework of rigidity model and the origin of the second one being the disappearance of the undercooled region resulting in amorphous materials with statistical distributions of bonds. While the first singularity signs the onset of the Ge-Ge homopolar bonds, the second is related to compositions where enhanced Ge-Ge correlations at intermediate lengthscales (7.7 Å) are observed. These two threshold compositions correspond to recently reported resistance drift threshold compositions, an important support for models pointing the breaking of homopolar Ge-Ge bonds as the main phenomenon behind the ageing of phase change materials.

Bond rupture between colloidal particles with a depletion interaction

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

Whitaker, Kathryn A.; Furst, Eric M., E-mail: furst@udel.edu

The force required to break the bonds of a depletion gel is measured by dynamically loading pairs of colloidal particles suspended in a solution of a nonadsorbing polymer. Sterically stabilized poly(methyl methacrylate) colloids that are 2.7 μm diameter are brought into contact in a solvent mixture of cyclohexane-cyclohexyl bromide and polystyrene polymer depletant. The particle pairs are subject to a tensile load at a constant loading rate over many approach-retraction cycles. The stochastic nature of the thermal rupture events results in a distribution of bond rupture forces with an average magnitude and variance that increases with increasing depletant concentration. The measuredmore » force distribution is described by the flux of particle pairs sampling the energy barrier of the bond interaction potential based on the Asakura–Oosawa depletion model. A transition state model demonstrates the significance of lubrication hydrodynamic interactions and the effect of the applied loading rate on the rupture force of bonds in a depletion gel.« less

Automated Construction of Molecular Active Spaces from Atomic Valence Orbitals.

PubMed

Sayfutyarova, Elvira R; Sun, Qiming; Chan, Garnet Kin-Lic; Knizia, Gerald

2017-09-12

We introduce the atomic valence active space (AVAS), a simple and well-defined automated technique for constructing active orbital spaces for use in multiconfiguration and multireference (MR) electronic structure calculations. Concretely, the technique constructs active molecular orbitals capable of describing all relevant electronic configurations emerging from a targeted set of atomic valence orbitals (e.g., the metal d orbitals in a coordination complex). This is achieved via a linear transformation of the occupied and unoccupied orbital spaces from an easily obtainable single-reference wave function (such as from a Hartree-Fock or Kohn-Sham calculations) based on projectors to targeted atomic valence orbitals. We discuss the premises, theory, and implementation of the idea, and several of its variations are tested. To investigate the performance and accuracy, we calculate the excitation energies for various transition-metal complexes in typical application scenarios. Additionally, we follow the homolytic bond breaking process of a Fenton reaction along its reaction coordinate. While the described AVAS technique is not a universal solution to the active space problem, its premises are fulfilled in many application scenarios of transition-metal chemistry and bond dissociation processes. In these cases the technique makes MR calculations easier to execute, easier to reproduce by any user, and simplifies the determination of the appropriate size of the active space required for accurate results.

Bond-equilibrium theory of liquid Se-Te alloys. II. Effect of singly attached ring molecules

NASA Astrophysics Data System (ADS)

Cutler, Melvin; Bez, Wolfgang G.

1981-06-01

A statistical-mechanical theory for bond equilibrium of chain polymers containing threefold (3F) and onefold (1F) bond defects is extended to include the effects of free ring molecules and ring molecules attached to chains by a single 3F atom. Positively charged singly attached rings are shown to play a key role in bond equilibrium in liquid Sex Te1-x by permitting the formation of ion pairs in which both constituents are effectively chain terminators, thus decreasing the average polymer size. The theory is applied to explain the behavior of the paramagnetic susceptibility, χp, and electronic transport as affected by the Fermi energy EF. It is found that the increase in χp with the concentration of Te is primarily the result of the smaller energy for breaking Te bonds. In addition, attached rings play an important role in determining the effect of temperature on χp. At x<~0.5, the concentrations of both free and attached rings becomes small at high T because of the high concentration of bond defects.

Single Molecule Junctions: A Laboratory for Chemistry, Mechanics and Bond Rupture

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

Hybertsen M. S.

Simultaneous measurement [1] of junction conductance and sustained force in single molecule junctions bridging metal electrodes provides a powerful tool in the quantitative study of the character of molecule-metal bonds. In this talk I will discuss three topics. First, I will describe chemical trends in link bond strength based on experiments and Density Functional Theory based calculations. Second, I will focus on the specific case of pyridine-linked junctions. Bond rupture from the high conductance junction structure shows a requires a force that exceeds the rupture force of gold point contacts and clearly indicates the role of additional forces, beyond themore » specific N-Au donor acceptor bond. DFT-D2 calculations with empirical addition of dispersion interactions illustrates the interplay between the donor-acceptor bonding and the non-specific van der Waals interactions between the pyridine rings and Au asperities. Third, I will describe recent efforts to characterize the diversity of junction structures realized in break-junction experiments with suitable models for the potential surfaces that are observed. [1] Venkataraman Group, Columbia University.« less

Aging pathways for organophosphate-inhibited human butyrylcholinesterase, including novel pathways for isomalathion, resolved by mass spectrometry.

PubMed

Li, He; Schopfer, Lawrence M; Nachon, Florian; Froment, Marie-Thérèse; Masson, Patrick; Lockridge, Oksana

2007-11-01

Some organophosphorus compounds are toxic because they inhibit acetylcholinesterase (AChE) by phosphylation of the active site serine, forming a stable conjugate: Ser-O-P(O)-(Y)-(XR) (where X can be O, N, or S and Y can be methyl, OR, or SR). The inhibited enzyme can undergo an aging process, during which the X-R moiety is dealkylated by breaking either the P-X or the X-R bond depending on the specific compound, leading to a nonreactivatable enzyme. Aging mechanisms have been studied primarily using AChE. However, some recent studies have indicated that organophosphate-inhibited butyrylcholinesterase (BChE) may age through an alternative pathway. Our work utilized matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry to study the aging mechanism of human BChE inhibited by dichlorvos, echothiophate, diisopropylfluorophosphate (DFP), isomalathion, soman, sarin, cyclohexyl sarin, VX, and VR. Inhibited BChE was aged in the presence of H2O18 to allow incorporation of (18)O, if cleavage was at the P-X bond. Tryptic-peptide organophosphate conjugates were identified through peptide mass mapping. Our results showed no aging of VX- and VR-treated BChE at 25 degrees C, pH 7.0. However, BChE inhibited by dichlorvos, echothiophate, DFP, soman, sarin, and cyclohexyl sarin aged exclusively through O-C bond cleavage, i.e., the classical X-R scission pathway. In contrast, isomalathion aged through both X-R and P-X pathways; the main aged product resulted from P-S bond cleavage and a minor product resulted from O-C and/or S-C bond cleavage.

Non-thermal damage to lead tungstate induced by intense short-wavelength laser radiation (Conference Presentation)

NASA Astrophysics Data System (ADS)

Vozda, Vojtech; Boháček, Pavel; Burian, Tomáš; Chalupský, Jaromir; Hájková, Vera; Juha, Libor; Vyšín, Ludek; Gaudin, Jérôme; Heimann, Philip A.; Hau-Riege, Stefan P.; Jurek, Marek; Klinger, Dorota; Krzywinski, Jacek; Messerschmidt, Marc; Moeller, Stefan P.; Nagler, Robert; Pelka, Jerzy B.; Rowen, Michael; Schlotter, William F.; Swiggers, Michele L.; Sinn, Harald; Sobierajski, Ryszard; Tiedtke, Kai; Toleikis, Sven; Tschentscher, Thomas; Turner, Joshua J.; Wabnitz, Hubertus; Nelson, Art J.; Kozlova, Maria V.; Vinko, Sam M.; Whitcher, Thomas; Dzelzainis, Thomas; Renner, Oldrich; Saksl, Karel; Fäustlin, Roland R.; Khorsand, Ali R.; Fajardo, Marta; Iwan, Bianca S.; Andreasson, Jakob; Hajdu, Janos; Timneanu, Nicusor; Wark, Justin S.; Riley, David; Lee, Richard W.; Nagasono, Mitsuru; Yabashi, Makina

2017-05-01

Interaction of short-wavelength free-electron laser (FEL) beams with matter is undoubtedly a subject to extensive investigation in last decade. During the interaction various exotic states of matter, such as warm dense matter, may exist for a split second. Prior to irreversible damage or ablative removal of the target material, complicated electronic processes at the atomic level occur. As energetic photons impact the target, electrons from inner atomic shells are almost instantly photo-ionized, which may, in some special cases, cause bond weakening, even breaking of the covalent bonds, subsequently result to so-called non-thermal melting. The subject of our research is ablative damage to lead tungstate (PbWO4) induced by focused short-wavelength FEL pulses at different photon energies. Post-mortem analysis of complex damage patterns using the Raman spectroscopy, atomic-force (AFM) and Nomarski (DIC) microscopy confirms an existence of non-thermal melting induced by high-energy photons in the ionic monocrystalline target. Results obtained at Linac Coherent Light Source (LCLS), Free-electron in Hamburg (FLASH), and SPring-8 Compact SASE Source (SCSS) are presented in this Paper.

Sputtered carbon as a corrosion barrier for x-ray detector windows

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

Rowley, Joseph; Pei, Lei; Davis, Robert C., E-mail: davis@byu.edu

Sputtered amorphous carbon thin films were explored as corrosion resistant coatings on aluminum thin films to be incorporated into x-ray detector windows. The requirements for this application include high corrosion resistance, low intrinsic stress, high strains at failure, and high x-ray transmission. Low temperature sputtering was used because of its compatibility with the rest of the window fabrication process. Corrosion resistance was tested by exposure of carbon coated and uncoated Al thin films to humidity. Substrate curvature and bulge testing measurements were used to determine intrinsic stress and ultimate strain at failure. The composition and bonding of the carbon filmsmore » were further characterized by electron energy loss spectroscopy, Raman spectroscopy, and carbon, hydrogen, and nitrogen elemental analyses. Samples had low compressive stress (down to.08 GPa), a high strain at failure (3%), and a low fraction of sp{sup 3} carbon–carbon bonds (less than 5%). The high breaking strain and excellent x-ray transmission of these sputtered carbon films indicate that they will work well as corrosion barriers in this application.« less

A robust, highly stretchable supramolecular polymer conductive hydrogel with self-healability and thermo-processability

NASA Astrophysics Data System (ADS)

Wu, Qian; Wei, Junjie; Xu, Bing; Liu, Xinhua; Wang, Hongbo; Wang, Wei; Wang, Qigang; Liu, Wenguang

2017-01-01

Dual amide hydrogen bond crosslinked and strengthened high strength supramolecular polymer conductive hydrogels were fabricated by simply in situ doping poly (N-acryloyl glycinamide-co-2-acrylamide-2-methylpropanesulfonic) (PNAGA-PAMPS) hydrogels with PEDOT/PSS. The nonswellable conductive hydrogels in PBS demonstrated high mechanical performances—0.22-0.58 MPa tensile strength, 1.02-7.62 MPa compressive strength, and 817-1709% breaking strain. The doping of PEDOT/PSS could significantly improve the specific conductivities of the hydrogels. Cyclic heating and cooling could lead to reversible sol-gel transition and self-healability due to the dynamic breakup and reconstruction of hydrogen bonds. The mending hydrogels recovered not only the mechanical properties, but also conductivities very well. These supramolecular conductive hydrogels could be designed into arbitrary shapes with 3D printing technique, and further, printable electrode can be obtained by blending activated charcoal powder with PNAGA-PAMPS/PEDOT/PSS hydrogel under melting state. The fabricated supercapacitor via the conducting hydrogel electrodes possessed high capacitive performances. These cytocompatible conductive hydrogels have a great potential to be used as electro-active and electrical biomaterials.

Reaction mechanisms and kinetics of the elimination processes of 2-chloroethylsilane and derivatives: A DFT study using CTST, RRKM, and BET theories

NASA Astrophysics Data System (ADS)

Shiroudi, Abolfazl; Zahedi, Ehsan; Oliaey, Ahmad Reza; Deleuze, Michael S.

2017-03-01

The thermal decomposition kinetics of 2-chloroethylsilane and derivatives in the gas phase has been studied computationally using density functional theory, along with various exchange-correlation functionals (UM06-2x and ωB97XD) and the aug-cc-pVTZ basis set. The calculated energy profile has been supplemented with calculations of kinetic rate constants under atmospheric pressure and in the fall-off regime, using transition state theory (TST) and statistical Rice-Ramsperger-Kassel-Marcus (RRKM) theory. Activation energies and rate constants obtained using the UM06-2x/aug-cc-pVTZ approach are in good agreement with the experimental data. The decomposition of 2-chloroethyltriethylsilane species into the related products [C2H4 + Et3SiCl] is characterized by 6 successive structural stability domains associated to the sequence of catastrophes C8H19SiCl: 6-C†FCC†[FF]-0: C6H15SiCl + C2H4. Breaking of Si-C bonds and formation of Si-Cl bonds occur in the vicinity of the transition state.

Symmetry Breaking in the Supramolecular Gels of an Achiral Gelator Exclusively Driven by π-π Stacking.

PubMed

Shen, Zhaocun; Jiang, Yuqian; Wang, Tianyu; Liu, Minghua

2015-12-30

Supramolecular symmetry breaking, in which chiral assemblies with imbalanced right- and left-handedness emerge from achiral molecular building blocks, has been achieved in the organogels of a C3-symmetric molecule only via π-π stacking. Specifically, an achiral C3-symmetric benzene-1,3,5-tricarboxylate substituted with methyl cinnamate through ester bond was found to form organogels in various organic solvents. More interestingly, when gels formed in cyclohexane, symmetry breaking occurred; i.e., optically active organogels together with the helical nanofibers with predominant handedness were obtained. Furthermore, the stochastically appeared imbalanced helicity could be driven to desired handedness by utilizing slight chiral solvents such as (R)- or (S)-terpinen-4-ol. Remarkably, the handedness of supramolecular assemblies thus formed could be kept even when the chiral solvents were removed. For the first time, we show that symmetry breaking can occur in supramolecular gel system driven exclusively through π-π stacking.

Superconductivity as a Synchronous Spatial Alternation of Valence Bonds.

DTIC Science & Technology

1987-04-01

approach. 9 This is likely to be the case in three-dimensions as well. As pair breaking excitations ( magnons ) can be formed at essentially no energy...cost (remember the form of the magnon dispersion curve of 1-D Heisenberg model), superconductivity cannot be achieved. In principle, these metals can be

Reciprocating Generosity

ERIC Educational Resources Information Center

Hernandez, Juan Avila

2009-01-01

Years before she became editor for the "Tribal College Journal" (TCJ), Marjane Ambler had already demonstrated her dedication and generosity to the Tribal College Movement. Ambler arranged for some of the royalty payments from the sale of her first book, "Breaking the Iron Bonds: Indian Control of Energy Development" (University of Kansas, 1990)…

Specialisation in Building of Third World Science and Education

NASA Astrophysics Data System (ADS)

Salam, Abdus

"To those people in the huts and villages of half the globe, struggling to break the bonds of mass misery, we pledge our best efforts to help them help themselves for whatever period is required, … not because we seek their votes, but because it is right…

Chain Ends and the Ultimate Tensile Strength of Polyethylene Fibers

NASA Astrophysics Data System (ADS)

O'Connor, Thomas C.; Robbins, Mark O.

Determining the tensile yield mechanisms of oriented polymer fibers remains a challenging problem in polymer mechanics. By maximizing the alignment and crystallinity of polyethylene (PE) fibers, tensile strengths σ ~ 6 - 7 GPa have been achieved. While impressive, first-principal calculations predict carbon backbone bonds would allow strengths four times higher (σ ~ 20 GPa) before breaking. The reduction in strength is caused by crystal defects like chain ends, which allow fibers to yield by chain slip in addition to bond breaking. We use large scale molecular dynamics (MD) simulations to determine the tensile yield mechanism of orthorhombic PE crystals with finite chains spanning 102 -104 carbons in length. The yield stress σy saturates for long chains at ~ 6 . 3 GPa, agreeing well with experiments. Chains do not break but always yield by slip, after nucleation of 1D dislocations at chain ends. Dislocations are accurately described by a Frenkel-Kontorova model, parametrized by the mechanical properties of an ideal crystal. We compute a dislocation core size ξ = 25 . 24 Å and determine the high and low strain rate limits of σy. Our results suggest characterizing such 1D dislocations is an efficient method for predicting fiber strength. This research was performed within the Center for Materials in Extreme Dynamic Environments (CMEDE) under the Hopkins Extreme Materials Institute at Johns Hopkins University. Financial support was provided by Grant W911NF-12-2-0022.

Aeroacoustic Duster

NASA Technical Reports Server (NTRS)

Marshall, Jeffrey S. (Inventor); Chen, Di (Inventor); Vachon, Nicholas Mario (Inventor); Hitt, Darren (Inventor); Wu, Junru (Inventor)

2014-01-01

The aero-acoustic duster invention disclosed herein provides for high particle removal rate from surfaces with low energy expenditure relative to competing vacuum-based devices. The device removes particulate matter from a surface using a two-step process: 1. Acoustic radiation is used to break the adhesive bonds between dust and the surface, forcing particles into a mode where they continuously bounce up and down on the surface; and, 2. A bounded vortex is generated over the surface, with suction in the vortex center and jets for blowing air along the periphery. The jets are tilted in the tangential direction to induce vortex motion within the suction region. The vortex is said to be bounded because streamlines originating in the downward jets are entrained back into the central vortex.

High conductance values in π-folded molecular junctions

NASA Astrophysics Data System (ADS)

Carini, Marco; Ruiz, Marta P.; Usabiaga, Imanol; Fernández, José A.; Cocinero, Emilio J.; Melle-Franco, Manuel; Diez-Perez, Ismael; Mateo-Alonso, Aurelio

2017-05-01

Folding processes play a crucial role in the development of function in biomacromolecules. Recreating this feature on synthetic systems would not only allow understanding and reproducing biological functions but also developing new functions. This has inspired the development of conformationally ordered synthetic oligomers known as foldamers. Herein, a new family of foldamers, consisting of an increasing number of anthracene units that adopt a folded sigmoidal conformation by a combination of intramolecular hydrogen bonds and aromatic interactions, is reported. Such folding process opens up an efficient through-space charge transport channel across the interacting anthracene moieties. In fact, single-molecule conductance measurements carried out on this series of foldamers, using the scanning tunnelling microscopy-based break-junction technique, reveal exceptionally high conductance values in the order of 10-1 G0 and a low length decay constant of 0.02 Å-1 that exceed the values observed in molecular junctions that make use of through-space charge transport pathways.

Nanoscale multireference quantum chemistry: full configuration interaction on graphical processing units.

PubMed

Fales, B Scott; Levine, Benjamin G

2015-10-13

Methods based on a full configuration interaction (FCI) expansion in an active space of orbitals are widely used for modeling chemical phenomena such as bond breaking, multiply excited states, and conical intersections in small-to-medium-sized molecules, but these phenomena occur in systems of all sizes. To scale such calculations up to the nanoscale, we have developed an implementation of FCI in which electron repulsion integral transformation and several of the more expensive steps in σ vector formation are performed on graphical processing unit (GPU) hardware. When applied to a 1.7 × 1.4 × 1.4 nm silicon nanoparticle (Si72H64) described with the polarized, all-electron 6-31G** basis set, our implementation can solve for the ground state of the 16-active-electron/16-active-orbital CASCI Hamiltonian (more than 100,000,000 configurations) in 39 min on a single NVidia K40 GPU.

Aminosilanization nanoadhesive layer for nanoelectric circuits with porous ultralow dielectric film.

PubMed

Zhao, Zhongkai; He, Yongyong; Yang, Haifang; Qu, Xinping; Lu, Xinchun; Luo, Jianbin

2013-07-10

An ultrathin layer is investigated for its potential application of replacing conventional diffusion barriers and promoting interface adhesion for nanoelectric circuits with porous ultralow dielectrics. The porous ultralow dielectric (k ≈ 2.5) substrate is silanized by 3-aminopropyltrimethoxysilane (APTMS) to form the nanoadhesive layer by performing oxygen plasma modification and tailoring the silanization conditions appropriately. The high primary amine content is obtained in favor of strong interaction between amino groups and copper. And the results of leakage current measurements of metal-oxide-semiconductor capacitor structure demonstrate that the aminosilanization nanoadhesive layer can block copper diffusion effectively and guarantee the performance of devices. Furthermore, the results of four-point bending tests indicate that the nanoadhesive layer with monolayer structure can provide the satisfactory interface toughness up to 6.7 ± 0.5 J/m(2) for Cu/ultralow-k interface. Additionally, an annealing-enhanced interface toughness effect occurs because of the formation of Cu-N bonding and siloxane bridges below 500 °C. However, the interface is weakened on account of the oxidization of amines and copper as well as the breaking of Cu-N bonding above 500 °C. It is also found that APTMS nanoadhesive layer with multilayer structure provides relatively low interface toughness compared with monolayer structure, which is mainly correlated to the breaking of interlayer hydrogen bonding.

Of cuts and cracks: data analytics on constrained graphs for early prediction of failure in cementitious materials

NASA Astrophysics Data System (ADS)

Kahagalage, Sanath; Tordesillas, Antoinette; Nitka, Michał; Tejchman, Jacek

2017-06-01

Using data from discrete element simulations, we develop a data analytics approach using network flow theory to study force transmission and failure in a `dog-bone' concrete specimen submitted to uniaxial tension. With this approach, we establish the extent to which the bottlenecks, i.e., a subset of contacts that impedes flow and are prone to becoming overloaded, can predict the location of the ultimate macro-crack. At the heart of this analysis is a capacity function that quantifies, in relative terms, the maximum force that can be transmitted through the different contacts or edges in the network. Here we set this function to be solely governed by the size of the contact area between the deformable spherical grains. During all the initial stages of the loading history, when no bonds are broken, we find the bottlenecks coincide consistently with, and therefore predict, the location of the crack that later forms in the failure regime after peak force. When bonds do start to break, they are spread throughout the specimen: in, near, and far from, the bottlenecks. In one stage leading up to peak force, bonds collectively break in the lower portion of the specimen, momentarily shifting the bottlenecks to this location. Just before and around peak force, however, the bottlenecks return to their original location and remain there until the macro-crack emerges right along the bottlenecks.

Theoretical evidence for unexpected O-rich phases at corners of MgO surfaces

NASA Astrophysics Data System (ADS)

Bhattacharya, Saswata; Berger, Daniel; Reuter, Karsten; Ghiringhelli, Luca M.; Levchenko, Sergey V.

2017-12-01

Realistic oxide materials are often semiconductors, in particular at elevated temperatures, and their surfaces contain undercoordinated atoms at structural defects such as steps and corners. Using hybrid density-functional theory and ab initio atomistic thermodynamics, we investigate the interplay of bond-making, bond-breaking, and charge-carrier trapping at the corner defects at the (100) surface of a p -doped MgO in thermodynamic equilibrium with an O2 atmosphere. We show that by manipulating the coordination of surface atoms, one can drastically change and even reverse the order of stability of reduced versus oxidized surface sites.

Stability Limits and Dynamics of Nonaxisymmetric Liquid Bridges

NASA Technical Reports Server (NTRS)

Alexander, J. Iwan D.

1998-01-01

Theoretical and experimental investigation of the stability of nonaxisymmetric and nonaxisymmetric bridges contained between equal and unequal radii disks as a function of Bond and Weber number with emphasis on the transition from unstable axisymmetric to stable nonaxisymmetric shapes. Numerical analysis of the stability of nonaxisymmetric bridges for various orientations of the gravity vector for equal and unequal disks. Experimental and theoretical investigation of large (nonaxisymmetric) oscillations and breaking of liquid bridges. This project involves both experimental and theoretical work. Static and dynamic experiments are conducted in a Plateau tank which makes a range of static Bond numbers accessible.

An Inherited Efficiencies Model of Non-Genomic Evolution

NASA Technical Reports Server (NTRS)

New, Michael H.; Pohorille, Andrew

1999-01-01

A model for the evolution of biological systems in the absence of a nucleic acid-like genome is proposed and applied to model the earliest living organisms -- protocells composed of membrane encapsulated peptides. Assuming that the peptides can make and break bonds between amino acids, and bonds in non-functional peptides are more likely to be destroyed than in functional peptides, it is demonstrated that the catalytic capabilities of the system as a whole can increase. This increase is defined to be non-genomic evolution. The relationship between the proposed mechanism for evolution and recent experiments on self-replicating peptides is discussed.

Evaluation of DSS-14 pedestal-review of top surface repair procedures

NASA Technical Reports Server (NTRS)

Oesterle, R. G.; Musser, D. W.; Salse, E. A. B.

1983-01-01

Proposed repair procedures for the top surface of the pedestal supporting the hydrostatic bearing runner for the 64m Antenna are presented. These procedures included: (1) removal of existing grout and concrete to approximately 8 in. below original concrete surface using a presplitting technique with expansive cement followed by secondary breaking; (2) preparation of exposed concrete surface including an epoxy bonding agent; and (3) replacement of material removed with 8 in. of new concrete surface including an epoxy bonding agent; and (4) replacement of material removed with 8 in. of new concrete and 4 in. of new grout.

Topological Qubits from Valence Bond Solids

NASA Astrophysics Data System (ADS)

Wang, Dong-Sheng; Affleck, Ian; Raussendorf, Robert

2018-05-01

Topological qubits based on S U (N )-symmetric valence-bond solid models are constructed. A logical topological qubit is the ground subspace with twofold degeneracy, which is due to the spontaneous breaking of a global parity symmetry. A logical Z rotation by an angle 2 π /N , for any integer N >2 , is provided by a global twist operation, which is of a topological nature and protected by the energy gap. A general concatenation scheme with standard quantum error-correction codes is also proposed, which can lead to better codes. Generic error-correction properties of symmetry-protected topological order are also demonstrated.

Why soft UV-A damages DNA: An optical micromanipulation study

NASA Astrophysics Data System (ADS)

Rapp, A.; Greulich, K. O.

2013-09-01

Optical micromanipulation studies have solved a puzzle on DNA damage and repair. Such knowledge is crucial for understanding cancer and ageing. So far it was not understood, why the soft UV component of sunlight, UV-A, causes the dangerous DNA double strand breaks. The energy of UV-A photons is below 4 eV per photon, too low to directly cleave the corresponding chemical bonds in DNA. This is occasionally used to claim that artificial sunbeds, which mainly use UV-A, would not impose a risk on health. UV-A is only sufficient for induction of single strand breaks. The essential new observation is that, when on the opposite strand there is another single strand break at a distance of up to 20 base pairs. These two breaks will be converted into a break of the whole double strand with all its known consequences for cancer and ageing. However, in natural sun the effect is counteracted. Simultaneous red light illumination reduces UV induced DNA damages to 1/3. Since sunlight has a red component, skin tanning with natural sun is not as risky as might appear at a first glance.

Single-strand breakage of DNA in UV-irradiated uvrA, uvrB, and uvrC mutants of Escherichia coli.

PubMed Central

Tang, M S; Ross, L

1985-01-01

We transduced the uvrA6, uvrB5, uvrC34, and uvrC56 markers from the original mutagenized strains into an HF4714 background. Although in the original mutagenized strains uvrA6 cells are more UV sensitive than uvrB5 and uvrC34 cells, in the new background no significant difference in UV sensitivity is observed among uvrA6, uvrB5, and uvrC34 cells. No DNA single-strand breaks are detected in UV-irradiated uvrA6 or uvrB5 cells, whereas in contrast a significant number of single-strand breaks are detected in both UV-irradiated uvrC34 and uvrC56 cells. The number of single-strand breaks in these cells reaches a plateau at 20-J/m2 irradiation. Since these single-strand breaks can be detected by both alkaline sucrose and neutral formamide-sucrose gradient sedimentation, we concluded that the single-strand breaks observed in UV-irradiated uvrC cells are due to phosphodiester bond interruptions in DNA and are not due to apurinic/apyrimidinic sites. PMID:3882671

Superhard BC(3) in cubic diamond structure.

PubMed

Zhang, Miao; Liu, Hanyu; Li, Quan; Gao, Bo; Wang, Yanchao; Li, Hongdong; Chen, Changfeng; Ma, Yanming

2015-01-09

We solve the crystal structure of recently synthesized cubic BC(3) using an unbiased swarm structure search, which identifies a highly symmetric BC(3) phase in the cubic diamond structure (d-BC(3)) that contains a distinct B-B bonding network along the body diagonals of a large 64-atom unit cell. Simulated x-ray diffraction and Raman peaks of d-BC(3) are in excellent agreement with experimental data. Calculated stress-strain relations of d-BC(3) demonstrate its intrinsic superhard nature and reveal intriguing sequential bond-breaking modes that produce superior ductility and extended elasticity, which are unique among superhard solids. The present results establish the first boron carbide in the cubic diamond structure with remarkable properties, and these new findings also provide insights for exploring other covalent solids with complex bonding configurations.

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

Mei, Donghai; Lebarbier, Vanessa M.; Rousseau, Roger

In a combined experimental and first-principles density functional theory (DFT) study, benzene steam reforming (BSR) over MgAl 2O 4 supported Rh and Ir catalysts was investigated. Experimentally, it has been found that both highly dispersed Rh and Ir clusters (1-2 nm) on the MgAl 2O 4 spinel support are stable during the BSR in the temperature range of 700-850°C. Compared to the Ir/MgAl 2O 4 catalyst, the Rh/MgAl 2O 4 catalyst is more active with higher benzene turnover frequency and conversion. At typical steam conditions with the steam-to-carbon ratio > 12, the benzene conversion is only a weak function ofmore » the H 2O concentration in the feed. This suggests that the initial benzene decomposition step rather than the benzene adsorption is most likely the rate-determined step in BSR over supported Rh and Ir catalysts. In order to understand the differences between the two catalysts, we followed with a comparative DFT study of initial benzene decomposition pathways over two representative model systems for each supported metal (Rh and Ir) catalysts. A periodic terrace (111) surface and an amorphous 50-atom metal cluster with a diameter of 1.0 nm were used to represent the two supported model catalysts under low and high dispersion conditions. Our DFT results show that the decreasing catalyst particle size enhances the benzene decomposition on supported Rh catalysts by lowering both C-C and C-H bond scission. The activation barriers of the C-C and the C-H bond scission decrease from 1.60 and 1.61 eV on the Rh(111) surface to 1.34 and 1.26 eV on the Rh50 cluster. For supported Ir catalysts, the decreasing particle size only affects the C-C scission. The activation barrier of the C-C scission of benzene decreases from 1.60 eV on the Ir(111) surface to 1.35 eV on the Ir50 cluster while the barriers of the C-H scission are practically the same. The experimentally measured higher BSR activity on the supported highly dispersed Rh catalyst can be rationalized by the thermodynamic limitation for the very first C-C bond scission of benzene on the small Ir50 catalyst. The C-C bond scission of benzene on the small Ir50 catalyst is highly endothermic although the barrier is competitive with the barriers of both the C-C and the C-H bond-breakings on the small Rh50 catalyst. The calculations also imply that, for the supported Rh catalysts the C-C and C-H bond scissions are competitive, independently of the Rh cluster sizes. After the initial dissociation step via either the C-C or the C-H bond scission, the C-H bond breaking seems to be more favorable rather than the C-C bond breaking on the larger Rh terrace surface. This work was financially supported by the United States Department of Energy’s Office of Biomass Program’s. Computing time was granted by a user project at the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.« less

Voltage-induced Interface Reconstruction and Electrical Instability of the Ferromagnet-Semiconductor Device.

PubMed

Chang, Shu-Jui; Chang, Po-Chun; Lin, Wen-Chin; Lo, Shao-Hua; Chang, Liang-Chun; Lee, Shang-Fan; Tseng, Yuan-Chieh

2017-03-23

Using x-ray magnetic spectroscopy with in-situ electrical characterizations, we investigated the effects of external voltage on the spin-electronic and transport properties at the interface of a Fe/ZnO device. Layer-, element-, and spin-resolved information of the device was obtained by cross-tuning of the x-ray mode and photon energy, when voltage was applied. At the early stage of the operation, the device exhibited a low-resistance state featuring robust Fe-O bonds. However, the Fe-O bonds were broken with increasing voltage. Breaking of the Fe-O bonds caused the formation of oxygen vacancies and resulted in a high-resistance state. Such interface reconstruction was coupled to a charge-transfer effect via Fe-O hybridization, which suppressed/enhanced the magnetization/coercivity of Fe electronically. Nevertheless, the interface became stabilized with the metallic phase if the device was continuously polarized. During this stage, the spin-polarization of Fe was enhanced whereas the coercivity was lowered by voltage, but changes of both characteristics were reversible. This stage is desirable for spintronic device applications, owing to a different voltage-induced electronic transition compared to the first stage. The study enabled a straightforward detection of the spin-electronic state at the ferromagnet-semiconductor interface in relation to the transport and reversal properties during operation process of the device.

Flow-induced detachment of red blood cells adhering to surfaces by specific antigen-antibody bonds.

PubMed

Xia, Z; Goldsmith, H L; van de Ven, T G

1994-04-01

Fixed spherical swollen human red blood cells of blood type B adhering on a glass surface through antigen-antibody bonds to monoclonal mouse antihuman IgM, adsorbed or covalently linked on the surface, were detached by known hydrodynamic forces created in an impinging jet. The dynamic process of detachment of the specifically bound cells was recorded and analyzed. The fraction of adherent cells remaining on the surface decreased with increasing hydrodynamic force. For an IgM coverage of 0.26%, a tangential force on the order of 100 pN was able to detach almost all of the cells from the surface within 20 min. After a given time of exposure to hydrodynamic force, the fraction of adherent cells remaining increased with time, reflecting an increase in adhesion strength. The characteristic time for effective aging was approximately 4 h. Results from experiments in which the adsorbed antibody molecules were immobilized through covalent coupling and from evanescent wave light scattering of adherent cells, imply that deformation of red cells at the contact area was the principal cause for aging, rather than local clustering of the antibody through surface diffusion. Experiments with latex beads specifically bound to red blood cells suggest that, instead of breaking the antigen-antibody bonds, antigen molecules were extracted from the cell membrane during detachment.

Bonding, Bridging, and Boundary Breaking: The Civic Lessons of High School Student Activities

ERIC Educational Resources Information Center

Shelly, Bryan

2011-01-01

This article presents evidence designed to expand scholarly knowledge of how high school co-curricular activities generate the positive effects previous scholarship has found. Studies of empowerment across various fields identify a sense of autonomy, self-belief, self-expression, the ability to work together with diverse others, and a critical…

19 CFR 146.8 - Seals, authority of operator to break and affix.

Code of Federal Regulations, 2012 CFR

2012-04-01

...; DEPARTMENT OF THE TREASURY (CONTINUED) FOREIGN TRADE ZONES General Provisions § 146.8 Seals, authority of... intermodal container containing merchandise approved for admission to the zone upon its arrival at the zone... entry, withdrawal, or other approval document has been obtained for movement in-bond from the zone. The...

19 CFR 146.8 - Seals, authority of operator to break and affix.

Code of Federal Regulations, 2011 CFR

2011-04-01

...; DEPARTMENT OF THE TREASURY (CONTINUED) FOREIGN TRADE ZONES General Provisions § 146.8 Seals, authority of... intermodal container containing merchandise approved for admission to the zone upon its arrival at the zone... entry, withdrawal, or other approval document has been obtained for movement in-bond from the zone. The...

19 CFR 146.8 - Seals, authority of operator to break and affix.

Code of Federal Regulations, 2014 CFR

2014-04-01

...; DEPARTMENT OF THE TREASURY (CONTINUED) FOREIGN TRADE ZONES General Provisions § 146.8 Seals, authority of... intermodal container containing merchandise approved for admission to the zone upon its arrival at the zone... entry, withdrawal, or other approval document has been obtained for movement in-bond from the zone. The...

19 CFR 146.8 - Seals, authority of operator to break and affix.

Code of Federal Regulations, 2013 CFR

2013-04-01

...; DEPARTMENT OF THE TREASURY (CONTINUED) FOREIGN TRADE ZONES General Provisions § 146.8 Seals, authority of... intermodal container containing merchandise approved for admission to the zone upon its arrival at the zone... entry, withdrawal, or other approval document has been obtained for movement in-bond from the zone. The...

19 CFR 146.8 - Seals, authority of operator to break and affix.

Code of Federal Regulations, 2010 CFR

2010-04-01

...; DEPARTMENT OF THE TREASURY (CONTINUED) FOREIGN TRADE ZONES General Provisions § 146.8 Seals, authority of... intermodal container containing merchandise approved for admission to the zone upon its arrival at the zone... entry, withdrawal, or other approval document has been obtained for movement in-bond from the zone. The...

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

Andino, José G; Kilgore, Uriah J; Pink, Maren

Breaking of the carbon-hydrogen bond of benzene and pyridine is observed with (PNP)V(CH 2tBu) 2 (1), and in the case of benzene, the formation of an intermediate benzyne complex (C) is proposed, and indirect proof of its intermediacy is provided by identification of (PNP)V=O(η 2-C 6H 4) in combination with DFT calculations.

Reductive cleavage of the peptide bond

NASA Technical Reports Server (NTRS)

Holian, J.; Garrison, W. M.

1973-01-01

In many biological research efforts, long chain organic molecules are studied by breaking large molecules into smaller components. Cleavage technique of recent interest is the use of solvated electrons. These are formed when aqueous solutions are bombarded with gamma radiation. Solvated electron is very reactive and can reduce most any species present, even to form free radicals.

Pyrolytic sugars from cellulosic biomass.

PubMed

Kuzhiyil, Najeeb; Dalluge, Dustin; Bai, Xianglan; Kim, Kwang Ho; Brown, Robert C

2012-11-01

Depolymerization of cellulose offers the prospect of inexpensive sugars from biomass. Breaking the glycosidic bonds of cellulose to liberate glucose has usually been pursued by acid or enzymatic hydrolysis although a purely thermal depolymerization route to sugars is also possible. Fast pyrolysis of pure cellulose yields primarily the anhydrosugar levoglucosan (LG) whereas the presence of naturally occurring alkali and alkaline earth metals (AAEMs) in biomass strongly catalyzes ring-breaking reactions that favor formation of light oxygenates. Here, we show a method of significantly increasing the yield of sugars from biomass by purely thermal means through infusion of certain mineral acids (phosphoric and sulfuric acid) into the biomass to convert the AAEMs into thermally stable salts (particularly potassium sulfates and phosphates). These salts not only passivate AAEMs that normally catalyze fragmentation of pyranose rings, but also buffer the system at pH levels that favor glycosidic bond breakage. It appears that AAEM passivation contributes to 80 % of the enhancement in LG yield while the buffering effect of the acid salts contributes to the balance of the enhancement. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rotational symmetry breaking toward a string-valence bond solid phase in frustrated J1 -J2 transverse field Ising model

NASA Astrophysics Data System (ADS)

Sadrzadeh, M.; Langari, A.

2018-06-01

We study the effect of quantum fluctuations by means of a transverse magnetic field (Γ) on the highly degenerate ground state of antiferromagnetic J1 -J2 Ising model on the square lattice, at the limit J2 /J1 = 0.5 . We show that harmonic quantum fluctuations based on single spin flips can not lift such degeneracy, however an-harmonic quantum fluctuations based on multi spin cluster flip excitations lift the degeneracy toward a unique ground state with string-valence bond solid (VBS) nature. A cluster operator formalism has been implemented to incorporate an-harmonic quantum fluctuations. We show that cluster-type excitations of the model lead not only to lower the excitation energy compared with a single-spin flip but also to lift the extensive degeneracy in favor of a string-VBS state, which breaks lattice rotational symmetry with only two fold degeneracy. The tendency toward the broken symmetry state is justified by numerical exact diagonalization. Moreover, we introduce a map to find the relation between the present model on the checkerboard and square lattices.

Temperature-programmed deoxygenation of acetic acid on molybdenum carbide catalysts

DOE PAGES

Nash, Connor P.; Farberow, Carrie A.; Hensley, Jesse E.

2017-02-07

Temperature programmed reaction (TPRxn) is a simple yet powerful tool for screening solid catalyst performance at a variety of conditions. A TPRxn system includes a reactor, furnace, gas and vapor sources, flow control, instrumentation to quantify reaction products (e.g., gas chromatograph), and instrumentation to monitor the reaction in real time (e.g., mass spectrometer). Here, we apply the TPRxn methodology to study molybdenum carbide catalysts for the deoxygenation of acetic acid, an important reaction among many in the upgrading/stabilization of biomass pyrolysis vapors. TPRxn is used to evaluate catalyst activity and selectivity and to test hypothetical reaction pathways (e.g., decarbonylation, ketonization,more » and hydrogenation). Furthermore, the results of the TPRxn study of acetic acid deoxygenation show that molybdenum carbide is an active catalyst for this reaction at temperatures above ca. 300 °C and that the reaction favors deoxygenation (i.e., C-O bond-breaking) products at temperatures below ca. 400 °C and decarbonylation (i.e., C-C bond-breaking) products at temperatures above ca. 400 °C.« less

Powder fed sheared dispersal particle generator

NASA Technical Reports Server (NTRS)

Morrisette, E. L.; Bushnell, D. M. (Inventor)

1984-01-01

A particle generating system is described which is capable of breaking up agglomerations of particles and producing a cloud of uniform, submicron-sized particles at high pressure and high flow rates. This is achieved by utilizing a tubular structure which has injection microslits on is periphery to accept and disperse the desired particle feed. By suppling a carrying fluid at a pressure, of approximately twice the ambient pressure of the velocimeter's settling chamber, the microslits operate at choked flow conditions. The shearing action of this choked flow is sufficient to overcome interparticle bonding forces, thereby breaking up the agglomerates of the particles feed into individual particles.

Modeling the archetype cysteine protease reaction using dispersion corrected density functional methods in ONIOM-type hybrid QM/MM calculations; the proteolytic reaction of papain.

PubMed

Fekete, Attila; Komáromi, István

2016-12-07

A proteolytic reaction of papain with a simple peptide model substrate N-methylacetamide has been studied. Our aim was twofold: (i) we proposed a plausible reaction mechanism with the aid of potential energy surface scans and second geometrical derivatives calculated at the stationary points, and (ii) we investigated the applicability of the dispersion corrected density functional methods in comparison with the popular hybrid generalized gradient approximations (GGA) method (B3LYP) without such a correction in the QM/MM calculations for this particular problem. In the resting state of papain the ion pair and neutral forms of the Cys-His catalytic dyad have approximately the same energy and they are separated by only a small barrier. Zero point vibrational energy correction shifted this equilibrium slightly to the neutral form. On the other hand, the electrostatic solvation free energy corrections, calculated using the Poisson-Boltzmann method for the structures sampled from molecular dynamics simulation trajectories, resulted in a more stable ion-pair form. All methods we applied predicted at least a two elementary step acylation process via a zwitterionic tetrahedral intermediate. Using dispersion corrected DFT methods the thioester S-C bond formation and the proton transfer from histidine occur in the same elementary step, although not synchronously. The proton transfer lags behind (or at least does not precede) the S-C bond formation. The predicted transition state corresponds mainly to the S-C bond formation while the proton is still on the histidine Nδ atom. In contrast, the B3LYP method using larger basis sets predicts a transition state in which the S-C bond is almost fully formed and the transition state can be mainly featured by the Nδ(histidine) to N(amid) proton transfer. Considerably lower activation energy was predicted (especially by the B3LYP method) for the next amide bond breaking elementary step of acyl-enzyme formation. Deacylation appeared to be a single elementary step process in all the methods we applied.

Two Simple Models for Fracking

NASA Astrophysics Data System (ADS)

Norris, Jaren Quinn

Recent developments in fracking have enable the recovery of oil and gas from tight shale reservoirs. These developments have also made fracking one of the most controversial environmental issues in the United States. Despite the growing controversy surrounding fracking, there is relatively little publicly available research. This dissertation introduces two simple models for fracking that were developed using techniques from non-linear and statistical physics. The first model assumes that the volume of induced fractures must be equal to the volume of injected fluid. For simplicity, these fractures are assumed to form a spherically symmetric damage region around the borehole. The predicted volumes of water necessary to create a damage region with a given radius are in good agreement with reported values. The second model is a modification of invasion percolation which was previously introduced to model water flooding. The reservoir rock is represented by a regular lattice of local traps that contain oil and/or gas separated by rock barriers. The barriers are assumed to be highly heterogeneous and are assigned random strengths. Fluid is injected from a central site and the weakest rock barrier breaks allowing fluid to flow into the adjacent site. The process repeats with the weakest barrier breaking and fluid flowing to an adjacent site each time step. Extensive numerical simulations were carried out to obtain statistical properties of the growing fracture network. The network was found to be fractal with fractal dimensions differing slightly from the accepted values for traditional percolation. Additionally, the network follows Horton-Strahler and Tokunaga branching statistics which have been used to characterize river networks. As with other percolation models, the growth of the network occurs in bursts. These bursts follow a power-law size distribution similar to observed microseismic events. Reservoir stress anisotropy is incorporated into the model by assigning horizontal bonds weaker strengths on average than vertical bonds. Numerical simulations show that increasing bond strength anisotropy tends to reduce the fractal dimension of the growing fracture network, and decrease the power-law slope of the burst size distribution. Although simple, these two models are useful for making informed decisions about fracking.

Temporal heating profile influence on the immediate bond strength following laser tissue soldering.

PubMed

Rabi, Yaron; Katzir, Abraham

2010-07-01

Bonding of tissues by laser heating is considered as a future alternative to sutures and staples. Increasing the post-operative bond strength remains a challenging issue for laser tissue bonding, especially in organs that have to sustain considerable tension or pressure. In this study, we investigated the influence of different temporal heating profiles on the strength of soldered incisions. The thermal damage following each heating procedure was quantified, in order to assess the effect of each heating profile on the thermal damage. Incisions in porcine bowel tissue strips (1 cmx4 cm) were soldered, using a 44% liquid albumin mixed with indocyanine green and a temperature controlled laser (830 nm) tissue bonding system. Heating was done either with a linear or a step temporal heating profile. The incisions were bonded by soldering at three points, separated by 2 mm. Set-point temperatures of T(set) = 60, 70, 80, 90, 100, 110, 150 degrees C and dwell times of t(d) = 10, 20, 30, 40 seconds were investigated. The bond strength was measured immediately following each soldering by applying a gradually increased tension on the tissue edges until the bond break. Bonds formed by linear heating were stronger than the ones formed by step heating: at T(set) = 80 degrees C the bonds were 40% stronger and at T(set) = 90 degrees C the bonds strength was nearly doubled. The bond strength difference between the heating methods was larger as T(set) increased. Linear heating produced stronger bonds than step heating. The difference in the bond strength was more pronounced at high set-point temperatures and short dwell times. The bond strength could be increased with either higher set-point temperature or a longer dwell time.

Microscopic dynamics of water around unfolded structures of barstar at room temperature

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

Pal, Somedatta; Chakraborty, Kaushik; Khatua, Prabir

2015-02-07

The breaking of the native structure of a protein and its influences on the dynamic response of the surrounding solvent is an important issue in protein folding. In this work, we have carried out atomistic molecular dynamics simulations to unfold the protein barstar at two different temperatures (400 K and 450 K). The two unfolded forms obtained at such high temperatures are further studied at room temperature to explore the effects of nonuniform unfolding of the protein secondary structures along two different pathways on the microscopic dynamical properties of the surface water molecules. It is demonstrated that though the structuralmore » transition of the protein in general results in less restricted water motions around its segments, but there are evidences of formation of new conformational motifs upon unfolding with increasingly confined environment around them, thereby resulting in further restricted water mobility in their hydration layers. Moreover, it is noticed that the effects of nonuniform unfolding of the protein segments on the relaxation times of the protein–water (PW) and the water–water (WW) hydrogen bonds are correlated with hindered hydration water motions. However, the kinetics of breaking and reformation of such hydrogen bonds are found to be influenced differently at the interface. It is observed that while the effects of unfolding on the PW hydrogen bond kinetics seem to be minimum, but the kinetics involving the WW hydrogen bonds around the protein segments exhibit noticeably heterogeneous characteristics. We believe that this is an important observation, which can provide valuable insights on the origin of heterogeneous influence of unfolding of a protein on the microscopic properties of its hydration water.« less

Chemistry at molecular junctions: Rotation and dissociation of O2 on the Ag(110) surface induced by a scanning tunneling microscope.

PubMed

Roy, Sharani; Mujica, Vladimiro; Ratner, Mark A

2013-08-21

The scanning tunneling microscope (STM) is a fascinating tool used to perform chemical processes at the single-molecule level, including bond formation, bond breaking, and even chemical reactions. Hahn and Ho [J. Chem. Phys. 123, 214702 (2005)] performed controlled rotations and dissociations of single O2 molecules chemisorbed on the Ag(110) surface at precise bias voltages using STM. These threshold voltages were dependent on the direction of the bias voltage and the initial orientation of the chemisorbed molecule. They also observed an interesting voltage-direction-dependent and orientation-dependent pathway selectivity suggestive of mode-selective chemistry at molecular junctions, such that in one case the molecule underwent direct dissociation, whereas in the other case it underwent rotation-mediated dissociation. We present a detailed, first-principles-based theoretical study to investigate the mechanism of the tunneling-induced O2 dynamics, including the origin of the observed threshold voltages, the pathway dependence, and the rate of O2 dissociation. Results show a direct correspondence between the observed threshold voltage for a process and the activation energy for that process. The pathway selectivity arises from a competition between the voltage-modified barrier heights for rotation and dissociation, and the coupling strength of the tunneling electrons to the rotational and vibrational modes of the adsorbed molecule. Finally, we explore the "dipole" and "resonance" mechanisms of inelastic electron tunneling to elucidate the energy transfer between the tunneling electrons and chemisorbed O2.

Nuclear magnetic resonance analysis and activation energy spectrum of the irreversible structural relaxation of amorphous zirconium tungstate

NASA Astrophysics Data System (ADS)

Miotto, F.; Rech, G. L.; Turatti, A. M.; Catafesta, J.; Zorzi, J. E.; Pereira, A. S.; Perottoni, C. A.

2018-03-01

Zirconium tungstate undergoes a sequence of phase transitions from cubic (α -ZrW2O8 ) to orthorhombic (γ -ZrW2O8 ) to amorphous (a -ZrW2O8 ) upon increasing pressure at room temperature. The amorphous phase is known to undergo anomalous endothermic recrystallization into a high-temperature β -ZrW2O8 phase above 600∘C at ambient pressure (and back to α -ZrW2O8 when brought to room temperature). The endothermic recrystallization of a -ZrW2O8 is preceded by an irreversible exothermic structural relaxation. New W-O bonds are formed upon amorphization, continuing a tendency of increasing W coordination number in going from α to γ -ZrW2O8 . In fact, contrarily to α -ZrW2O8 , in which one-quarter of the oxygen atoms are bonded only to one W (terminal oxygens), previous works found no evidence of single-bonded oxygen atoms in a -ZrW2O8 . It thus could be argued that the irreversible character of the structural relaxation of a -ZrW2O8 is due to W-O bond breaking upon annealing of the amorphous phase. To test this hypothesis, x-ray diffraction, 17O magic-angle spinning NMR, Raman, and far-infrared analyses were performed on samples of amorphous zirconium tungstate previously annealed to increasingly higher temperatures, looking for any evidence of features that could be assigned to the presence of terminal oxygen atoms. No evidence of single-bonded oxygen was found before the onset of recrystallization. Furthermore, the kinetics of the structural relaxation of a -ZrW2O8 is consistent with a continuous spectrum of activation energy, spanning all the range from 1 to 2.5 eV . These findings suggest that the structural relaxation of amorphous zirconium tungstate, however irreversible, is not accompanied by W-O bond breaking, but most probably characterized by a succession of (mostly) irreversible local atomic rearrangements.

A ReaxFF-based molecular dynamics study of the mechanisms of interactions between reactive oxygen plasma species and the Candida albicans cell wall

NASA Astrophysics Data System (ADS)

Zhao, T.; Shi, L.; Zhang, Y. T.; Zou, L.; Zhang, L.

2017-10-01

Atmospheric pressure non-equilibrium plasmas have attracted significant attention and have been widely used to inactivate pathogens, yet the mechanisms underlying the interactions between plasma-generated species and bio-organisms have not been elucidated clearly. In this paper, reactive molecular dynamics simulations are employed to investigate the mechanisms of interactions between reactive oxygen plasma species (O, OH, and O2) and β-1,6-glucan (a model for the C. albicans cell wall) from a microscopic point of view. Our simulations show that O and OH species can break structurally important C-C and C-O bonds, while O2 molecules exhibit only weak, non-bonded interactions with β-1,6-glucan. Hydrogen abstraction from hydroxyl or CH groups occurs first in all bond cleavage mechanisms. This is followed by a cascade of bond cleavage and double bond formation events. These lead to the destruction of the fungal cell wall. O and OH have similar effects related to their bond cleavage mechanisms. Our simulation results provide fundamental insights into the mechanisms underlying the interactions between reactive oxygen plasma species and the fungal cell wall of C. albicans at the atomic level.

Self-Attractive Hartree Decomposition: Partitioning Electron Density into Smooth Localized Fragments.

PubMed

Zhu, Tianyu; de Silva, Piotr; Van Voorhis, Troy

2018-01-09

Chemical bonding plays a central role in the description and understanding of chemistry. Many methods have been proposed to extract information about bonding from quantum chemical calculations, the majority of them resorting to molecular orbitals as basic descriptors. Here, we present a method called self-attractive Hartree (SAH) decomposition to unravel pairs of electrons directly from the electron density, which unlike molecular orbitals is a well-defined observable that can be accessed experimentally. The key idea is to partition the density into a sum of one-electron fragments that simultaneously maximize the self-repulsion and maintain regular shapes. This leads to a set of rather unusual equations in which every electron experiences self-attractive Hartree potential in addition to an external potential common for all the electrons. The resulting symmetry breaking and localization are surprisingly consistent with chemical intuition. SAH decomposition is also shown to be effective in visualization of single/multiple bonds, lone pairs, and unusual bonds due to the smooth nature of fragment densities. Furthermore, we demonstrate that it can be used to identify specific chemical bonds in molecular complexes and provides a simple and accurate electrostatic model of hydrogen bonding.

Ultra-stiff metallic glasses through bond energy density design.

PubMed

Schnabel, Volker; Köhler, Mathias; Music, Denis; Bednarcik, Jozef; Clegg, William J; Raabe, Dierk; Schneider, Jochen M

2017-07-05

The elastic properties of crystalline metals scale with their valence electron density. Similar observations have been made for metallic glasses. However, for metallic glasses where covalent bonding predominates, such as metalloid metallic glasses, this relationship appears to break down. At present, the reasons for this are not understood. Using high energy x-ray diffraction analysis of melt spun and thin film metallic glasses combined with density functional theory based molecular dynamics simulations, we show that the physical origin of the ultrahigh stiffness in both metalloid and non-metalloid metallic glasses is best understood in terms of the bond energy density. Using the bond energy density as novel materials design criterion for ultra-stiff metallic glasses, we are able to predict a Co 33.0 Ta 3.5 B 63.5 short range ordered material by density functional theory based molecular dynamics simulations with a high bond energy density of 0.94 eV Å -3 and a bulk modulus of 263 GPa, which is 17% greater than the stiffest Co-B based metallic glasses reported in literature.

Bonding strength of alkyl-2-cyanoacrylates to bone in vitro.

PubMed

Kilpikari, J; Lapinsuo, M; Törmälä, P; Pätiälä, H; Rokkanen, P

1986-10-01

This study measured the bonding strength between alkyl-2-cyanoacrylates and bone, and examined how treatment of the bone surface with acid, and prolonged exposure to moisture, affected this strength. The initial strength of all cyanoacrylates was high (9.6-11.2 N/mm2). In long-term experiments under water, n- and i-butylcyanoacrylates lost their strength at a far slower rate than ethylcyanoacrylates. However, the butylcyanoacrylates also showed a decrease of 15% in strength after three weeks. Pretreatment of the bone surface with acid did not have a marked effect on bonding strength, although SEM investigation revealed that the acid treatment had increased the porosity of the bone surface. A study of the fracture surface proved that the adhesive film tended to loosen or break after 3 to 6 weeks under water. The decrease in the bonding strength was probably due to the degradation of the adhesive film in water which loosened mechanical bonds between the bone and adhesive. Considering clinical use it would be necessary to achieve better long-term strength.

Novel Bonding Technology for Hermetically Sealed Silicon Micropackage

NASA Astrophysics Data System (ADS)

Lee, Duck-Jung; Ju, Byeong-Kwon; Choi, Woo-Beom; Jeong, Jee-Won; Lee, Yun-Hi; Jang, Jin; Lee, Kwang-Bae; Oh, Myung-Hwan

1999-01-01

We performed glass-to-silicon bonding and fabricated a hermetically sealed silicon wafer using silicon direct bonding followed by anodic bonding (SDAB). The hydrophilized glass and silicon wafers in solution were dried and initially bonded in atmosphere as in the silicon direct bonding (SDB) process, but annealing at high temperature was not performed. Anodic bonding was subsequently carried out for the initially bonded specimens. Then the wafer pairs bonded by the SDAB method were different from those bonded by the anodic bonding process only. The effects of the bonding process on the bonded area and tensile strength were investigated as functions of bonding temperature and voltage. Using scanning electron microscopy (SEM), the cross-sectional view of the bonded interface region was observed. In order to investigate the migration of the sodium ions in the bonding process, the concentration of the bonded glass was compared with that of standard glass. The specimen bonded using the SDAB process had higher efficiency than that using the anodic bonding process only.

Modified low-temperture direct bonding method for vacuum microelectronics application

NASA Astrophysics Data System (ADS)

Ju, Byeong-Kwon; Lee, Duck-Jung; Choi, Woo-Beom; Lee, Yun-Hi; Jang, Jin; Lee, Kwang-Bae; Oh, Myung-Hwan

1997-06-01

This paper presents the process and experimental results for the improved silicon-to-glass bonding using silicon direct bonding (SDB) followed by anodic bonding. The initial bonding between glass and silicon was caused by the hydrophilic surfaces of silicon-glass ensemble using SDB method. Then the initially bonded specimen had to be strongly bonded by anodic bonding process. The effects of the bonding process parameters on the interface energy were investigated as functions of the bonding temperature and voltage. We found that the specimen which was bonded using SDB process followed by anodic bonding process had higher interface energy than one using anodic bonding process only. The main factor contributing to the higher interface energy in the glass-to-silicon assemble bonded by SDB followed by anodic bonding was investigated by secondary ion mass spectroscopy analysis.

Significant Quantum Effects in Hydrogen Activation

DOE PAGES

Kyriakou, Georgios; Davidson, Erlend R. M.; Peng, Guowen; ...

2014-03-31

Dissociation of molecular hydrogen is an important step in a wide variety of chemical, biological, and physical processes. Due to the light mass of hydrogen, it is recognized that quantum effects are often important to its reactivity. However, understanding how quantum effects impact the reactivity of hydrogen is still in its infancy. Here, we examine this issue using a well-defined Pd/Cu(111) alloy that allows the activation of hydrogen and deuterium molecules to be examined at individual Pd atom surface sites over a wide range of temperatures. Experiments comparing the uptake of hydrogen and deuterium as a function of temperature revealmore » completely different behavior of the two species. The rate of hydrogen activation increases at lower sample temperature, whereas deuterium activation slows as the temperature is lowered. Density functional theory simulations in which quantum nuclear effects are accounted for reveal that tunneling through the dissociation barrier is prevalent for H 2 up to ~190 K and for D 2 up to ~140 K. Kinetic Monte Carlo simulations indicate that the effective barrier to H 2 dissociation is so low that hydrogen uptake on the surface is limited merely by thermodynamics, whereas the D 2 dissociation process is controlled by kinetics. These data illustrate the complexity and inherent quantum nature of this ubiquitous and seemingly simple chemical process. Here, examining these effects in other systems with a similar range of approaches may uncover temperature regimes where quantum effects can be harnessed, yielding greater control of bond-breaking processes at surfaces and uncovering useful chemistries such as selective bond activation or isotope separation.« less

Force and Conductance Spectroscopy of Single Molecule Junctions

NASA Astrophysics Data System (ADS)

Frei, Michael

Investigation of mechanical properties of single molecule junctions is crucial to develop an understanding and enable control of single molecular junctions. This work presents an experimental and analytical approach that enables the statistical evaluation of force and simultaneous conductance data of metallic atomic point contacts and molecular junctions. A conductive atomic force microscope based break junction technique is developed to form single molecular junctions and collect conductance and force data simultaneously. Improvements of the optical components have been achieved through the use of a super-luminescent diode, enabling tremendous increases in force resolution. An experimental procedure to collect data for various molecular junctions has been developed and includes deposition, calibration, and analysis methods. For the statistical analysis of force, novel approaches based on two dimensional histograms and a direct force identification method are presented. The two dimensional method allows for an unbiased evaluation of force events that are identified using corresponding conductance signatures. This is not always possible however, and in these situations, the force based identification of junction rearrangement events is an attractive alternative method. This combined experimental and analytical approach is then applied to three studies: First, the impact of molecular backbones to the mechanical behavior of single molecule junctions is investigated and it is found that junctions formed with identical linkers but different backbone structure result in junctions with varying breaking forces. All molecules used show a clear molecular signature and force data can be evaluated using the 2D method. Second, the effects of the linker group used to attach molecules to gold electrodes are investigated. A study of four alkane molecules with different linkers finds a drastic difference in the evolution of donor-acceptor and covalently bonded molecules respectively. In fact, the covalent bond is found to significantly distort the metal electrode rearrangement such that junction rearrangement events can no longer be identified with a clean and well defined conductance signature. For this case, the force based identification process is used. Third, results for break junction measurements with different metals are presented. It is found that silver and palladium junctions rupture with forces different from those of gold contacts. In the case of silver experiments in ambient conditions, we can also identify oxygen impurities in the silver contact formation process, leading to force and conductance measurements of silver-oxygen structures. For the future, this work provides an experimental and analytical foundation that will enable insights into single molecule systems not previously accessible.

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

PubMed Central

Takahashi, Ohgi; Kirikoshi, Ryota; Manabe, Noriyoshi

2015-01-01

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. PMID:25588215

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

PubMed

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.

Learning probabilistic models of hydrogen bond stability from molecular dynamics simulation trajectories.

PubMed

Chikalov, Igor; Yao, Peggy; Moshkov, Mikhail; Latombe, Jean-Claude

2011-02-15

Hydrogen bonds (H-bonds) play a key role in both the formation and stabilization of protein structures. They form and break while a protein deforms, for instance during the transition from a non-functional to a functional state. The intrinsic strength of an individual H-bond has been studied from an energetic viewpoint, but energy alone may not be a very good predictor. This paper describes inductive learning methods to train protein-independent probabilistic models of H-bond stability from molecular dynamics (MD) simulation trajectories of various proteins. The training data contains 32 input attributes (predictors) that describe an H-bond and its local environment in a conformation c and the output attribute is the probability that the H-bond will be present in an arbitrary conformation of this protein achievable from c within a time duration Δ. We model dependence of the output variable on the predictors by a regression tree. Several models are built using 6 MD simulation trajectories containing over 4000 distinct H-bonds (millions of occurrences). Experimental results demonstrate that such models can predict H-bond stability quite well. They perform roughly 20% better than models based on H-bond energy alone. In addition, they can accurately identify a large fraction of the least stable H-bonds in a conformation. In most tests, about 80% of the 10% H-bonds predicted as the least stable are actually among the 10% truly least stable. The important attributes identified during the tree construction are consistent with previous findings. We use inductive learning methods to build protein-independent probabilistic models to study H-bond stability, and demonstrate that the models perform better than H-bond energy alone.

The origin of the Debye relaxation in liquid water and fitting the high frequency excess response.

PubMed

Elton, Daniel C

2017-07-19

We critically review the literature on the Debye absorption peak of liquid water and the excess response found on the high frequency side of the Debye peak. We find a lack of agreement on the microscopic phenomena underlying both of these features. To better understand the molecular origin of Debye peak we ran large scale molecular dynamics simulations and performed several different distance-dependent decompositions of the low frequency dielectric spectra, finding that it involves processes that take place on scales of 1.5-2.0 nm. We also calculated the k-dependence of the Debye relaxation, finding it to be highly dispersive. These findings are inconsistent with models that relate Debye relaxation to local processes such as the rotation/translation of molecules after H-bond breaking. We introduce the spectrumfitter Python package for fitting dielectric spectra and analyze different ways of fitting the high frequency excess, such as including one or two additional Debye peaks. We propose using the generalized Lydanne-Sachs-Teller (gLST) equation as a way of testing the physicality of model dielectric functions. Our attempts at fitting the experimental spectrum using the gLST relation as a constraint indicate that the traditional way of fitting the excess response with secondary and tertiary Debye relaxations is problematic. All of our work is consistent with the recent theory of Popov et al. (2016) that Debye relaxation is due to the migration of Bjerrum-like defects in the hydrogen bond network. Under this theory, the mechanism of Debye relaxation in liquid water is similar to the mechanism in ice, but the heterogeneity and power-law dynamics of the H-bond network in water results in excess response on the high frequency side of the peak.

Breaking the Bonds: Women School Leaders Confront the Effects of Socialization.

ERIC Educational Resources Information Center

Williamson, Ronald D.; Hudson, Martha B.

Demand for school reform continues to be characterized by a cry to adopt new leadership behaviors and change the preparation of school leaders. Once hired, new school leaders are confronted by the weight of tradition and history in their new jobs. This paper reports on an investigation of the impact of these socialization practices on new…

Breaking the Bonds of Poverty: A Motivational Profile of Selected Welfare Single Mothers Entering College.

ERIC Educational Resources Information Center

Cheng, Barbara Davis

Single mothers on welfare were recruited for a program at Trinity College of Vermont using a variety of methods: newspaper advertisements, admission office applicants, and welfare office solicitation. Eligible for the program were single mothers on welfare meeting all Trinity College entrance requirements and having an interest in and commitment…

Upper Secondary French Students, Chemical Transformations and the "Register of Models": A Cross-Sectional Study

ERIC Educational Resources Information Center

Cokelez, Aytekin; Dumon, Alain; Taber, Keith S.

2008-01-01

The purpose of this study is to identify how upper secondary school French students (Grade 10-12) interpret chemical transformation with regards to the changes within molecules and atoms, and in terms of intramolecular and/or intermolecular bond breaking. In order to identify and describe the students' assimilated knowledge, four questions were…

Electrostatically Embedded Many-Body Expansion for Neutral and Charged Metalloenzyme Model Systems.

PubMed

Kurbanov, Elbek K; Leverentz, Hannah R; Truhlar, Donald G; Amin, Elizabeth A

2012-01-10

The electrostatically embedded many-body (EE-MB) method has proven accurate for calculating cohesive and conformational energies in clusters, and it has recently been extended to obtain bond dissociation energies for metal-ligand bonds in positively charged inorganic coordination complexes. In the present paper, we present four key guidelines that maximize the accuracy and efficiency of EE-MB calculations for metal centers. Then, following these guidelines, we show that the EE-MB method can also perform well for bond dissociation energies in a variety of neutral and negatively charged inorganic coordination systems representing metalloenzyme active sites, including a model of the catalytic site of the zinc-bearing anthrax toxin lethal factor, a popular target for drug development. In particular, we find that the electrostatically embedded three-body (EE-3B) method is able to reproduce conventionally calculated bond-breaking energies in a series of pentacoordinate and hexacoordinate zinc-containing systems with an average absolute error (averaged over 25 cases) of only 0.98 kcal/mol.

Statics and dynamics of free and hydrogen-bonded OH groups at the air/water interface.

PubMed

Vila Verde, Ana; Bolhuis, Peter G; Campen, R Kramer

2012-08-09

We use classical atomistic molecular dynamics simulations of two water models (SPC/E and TIP4P/2005) to investigate the orientation and reorientation dynamics of two subpopulations of OH groups belonging to water molecules at the air/water interface at 300 K: those OH groups that donate a hydrogen bond (called "bonded") and those that do not (called "free"). Free interfacial OH groups reorient in two distinct regimes: a fast regime from 0 to 1 ps and a slow regime thereafter. Qualitatively similar behavior was reported by others for free OH groups near extended hydrophobic surfaces. In contrast, the net reorientation of bonded OH groups occurs at a rate similar to that of bulk water. This similarity in reorientation rate results from compensation of two effects: decreasing frequency of hydrogen-bond breaking/formation (i.e., hydrogen-bond exchange) and faster rotation of intact hydrogen bonds. Both changes result from the decrease in density at the air/water interface relative to the bulk. Interestingly, because of the presence of capillary waves, the slowdown of hydrogen-bond exchange is significantly smaller than that reported for water near extended hydrophobic surfaces, but it is almost identical to that reported for water near small hydrophobic solutes. In this sense water at the air/water interface has characteristics of water of hydration of both small and extended hydrophobic solutes.

Water reorientation in the hydration shells of hydrophilic and hydrophobic solutes

NASA Astrophysics Data System (ADS)

Laage, Damien; Stirnemann, Guillaume; Hynes, James T.

2010-06-01

We discuss some key aspects of our recent theoretical work on water reorientation dynamics, which is important in a wide range of phenomena, including aqueous phase chemical reactions, protein folding, and drug binding to proteins and DNA. It is shown that, contrary to the standard conception that these dynamics are diffusional, the reorientation of a water molecule occurs by sudden, large amplitude angular jumps. The mechanism involves the exchange of one hydrogen bond for another by the reorienting water, and the process can be fruitfully viewed as a chemical reaction. The results for reorientation times, which can be well described analytically, are discussed in the context of the molecular level interpretation of recent ultrafast infrared spectroscopic results, focusing on the concepts of structure making/breaking and solvent ‘icebergs’.

Laser control of electronic transitions of wave packet by using quadratically chirped pulses.

PubMed

Zou, Shiyang; Kondorskiy, Alexey; Mil'nikov, Gennady; Nakamura, Hiroki

2005-02-22

An effective scheme is proposed for the laser control of wave packet dynamics. It is demonstrated that by using specially designed quadratically chirped pulses, fast and nearly complete excitation of wave packet can be achieved without significant distortion of its shape. The parameters of the laser pulse can be estimated analytically from the Zhu-Nakamura theory of nonadiabatic transition. If the wave packet is not too narrow or not too broad, then the scheme is expected to be utilizable for multidimensional systems. The scheme is applicable to various processes such as simple electronic excitation, pump-dump, and selective bond breaking, and it is actually numerically demonstrated to work well by taking diatomic and triatomic molecules (LiH, NaK, H(2)O) as examples.

Laser control of electronic transitions of wave packet by using quadratically chirped pulses

NASA Astrophysics Data System (ADS)

Zou, Shiyang; Kondorskiy, Alexey; Mil'nikov, Gennady; Nakamura, Hiroki

2005-02-01

An effective scheme is proposed for the laser control of wave packet dynamics. It is demonstrated that by using specially designed quadratically chirped pulses, fast and nearly complete excitation of wave packet can be achieved without significant distortion of its shape. The parameters of the laser pulse can be estimated analytically from the Zhu-Nakamura theory of nonadiabatic transition. If the wave packet is not too narrow or not too broad, then the scheme is expected to be utilizable for multidimensional systems. The scheme is applicable to various processes such as simple electronic excitation, pump-dump, and selective bond breaking, and it is actually numerically demonstrated to work well by taking diatomic and triatomic molecules (LiH, NaK, H2O) as examples.

Superhard BC 3 in cubic diamond structure

DOE PAGES

Zhang, Miao; Liu, Hanyu; Li, Quan; ...

2015-01-06

We solve the crystal structure of recently synthesized cubic BC 3 using an unbiased swarm structure search, which identifies a highly symmetric BC 3 phase in the cubic diamond structure (d–BC3) that contains a distinct B-B bonding network along the body diagonals of a large 64-atom unit cell. Simulated x-ray diffraction and Raman peaks of d–BC 3 are in excellent agreement with experimental data. Calculated stress-strain relations of d–BC 3 demonstrate its intrinsic superhard nature and reveal intriguing sequential bond-breaking modes that produce superior ductility and extended elasticity, which are unique among superhard solids. Here, the present results establish themore » first boron carbide in the cubic diamond structure with remarkable properties, and these new findings also provide insights for exploring other covalent solids with complex bonding configurations.« less

Holistic quantum design of thermoelectric niobium oxynitride

NASA Astrophysics Data System (ADS)

Music, Denis; Bliem, Pascal; Hans, Marcus

2015-06-01

We have applied holistic quantum design to thermoelectric NbON (space group Pm-3m). Even though transport properties are central in designing efficient thermoelectrics, mechanical properties should also be considered to minimize their thermal fatigue during multiple heating/cooling cycles. Using density functional theory, elastic constants of NbON were predicted and validated by nanoindentation measurements on reactively sputtered thin films. Based on large bulk-to-shear modulus ratio and positive Cauchy pressure, ceramic NbON appears ductile. These unusual properties may be understood by analyzing the electronic structure. Nb-O bonding is of covalent-ionic nature with metallic contributions. Second neighbor O-N bonds exhibit covalent-ionic character. Upon shear loading, these O-N bonds break giving rise to easily shearable planes. Ductile NbON, together with large Seebeck coefficient and low thermal expansion, is promising for thermoelectric applications.

Sphalerite is a geochemical catalyst for carbon−hydrogen bond activation

PubMed Central

Shipp, Jessie A.; Gould, Ian R.; Shock, Everett L.; Williams, Lynda B.; Hartnett, Hilairy E.

2014-01-01

Reactions among minerals and organic compounds in hydrothermal systems are critical components of the Earth’s deep carbon cycle, provide energy for the deep biosphere, and may have implications for the origins of life. However, there is limited information as to how specific minerals influence the reactivity of organic compounds. Here we demonstrate mineral catalysis of the most fundamental component of an organic reaction: the breaking and making of a covalent bond. In the absence of mineral, hydrothermal reaction of cis- and trans-1,2-dimethylcyclohexane is extremely slow and generates many products. In the presence of sphalerite (ZnS), however, the reaction rate increases dramatically and one major product is formed: the corresponding stereoisomer. Isotope studies show that the sphalerite acts as a highly specific heterogeneous catalyst for activation of a single carbon−hydrogen bond in the dimethylcyclohexanes. PMID:25071186

Sphalerite is a geochemical catalyst for carbon-hydrogen bond activation.

PubMed

Shipp, Jessie A; Gould, Ian R; Shock, Everett L; Williams, Lynda B; Hartnett, Hilairy E

2014-08-12

Reactions among minerals and organic compounds in hydrothermal systems are critical components of the Earth's deep carbon cycle, provide energy for the deep biosphere, and may have implications for the origins of life. However, there is limited information as to how specific minerals influence the reactivity of organic compounds. Here we demonstrate mineral catalysis of the most fundamental component of an organic reaction: the breaking and making of a covalent bond. In the absence of mineral, hydrothermal reaction of cis- and trans-1,2-dimethylcyclohexane is extremely slow and generates many products. In the presence of sphalerite (ZnS), however, the reaction rate increases dramatically and one major product is formed: the corresponding stereoisomer. Isotope studies show that the sphalerite acts as a highly specific heterogeneous catalyst for activation of a single carbon-hydrogen bond in the dimethylcyclohexanes.

Peculiarities of electron density distribution in bismuth chalcogenides, iron pnictides, cuprates and related unconventional superconductors

NASA Astrophysics Data System (ADS)

Orlov, V. G.; Sergeev, G. S.

2018-05-01

With the aim to reveal the origin of instabilities in the electron subsystem of unconventional superconductors, such as stripes or nematic symmetry breaking, electron band structure calculations were performed for a number of bismuth chalcogenides, bismuth oxide, iron pnictides, as well as for Bi2Sr2CaCu2O8, YBa2Cu3O7 and La2CuO4. It was found that bond critical points in the electron density distribution ρ(r) of all the studied compounds were characterized by positive sign of electron density Laplacian evidencing on depletion of electron charge from the area of bond critical points. A correlation was found between the Tc and the value of electron density Laplacian in the strongest bond critical points of superconductors and related substances.

Bond-selective photoacoustic imaging by converting molecular vibration into acoustic waves

PubMed Central

Hui, Jie; Li, Rui; Phillips, Evan H.; Goergen, Craig J.; Sturek, Michael; Cheng, Ji-Xin

2016-01-01

The quantized vibration of chemical bonds provides a way of detecting specific molecules in a complex tissue environment. Unlike pure optical methods, for which imaging depth is limited to a few hundred micrometers by significant optical scattering, photoacoustic detection of vibrational absorption breaks through the optical diffusion limit by taking advantage of diffused photons and weak acoustic scattering. Key features of this method include both high scalability of imaging depth from a few millimeters to a few centimeters and chemical bond selectivity as a novel contrast mechanism for photoacoustic imaging. Its biomedical applications spans detection of white matter loss and regeneration, assessment of breast tumor margins, and diagnosis of vulnerable atherosclerotic plaques. This review provides an overview of the recent advances made in vibration-based photoacoustic imaging and various biomedical applications enabled by this new technology. PMID:27069873

Measuring the reactivity of a silicon-terminated probe

NASA Astrophysics Data System (ADS)

Sweetman, Adam; Stirling, Julian; Jarvis, Samuel Paul; Rahe, Philipp; Moriarty, Philip

2016-09-01

It is generally accepted that the exposed surfaces of silicon crystals are highly reactive due to the dangling bonds which protrude into the vacuum. However, surface reconstruction not only modifies the reactivity of bulk silicon crystals, but also plays a key role in determining the properties of silicon nanocrystals. In this study we probe the reactivity of silicon clusters at the end of a scanning probe tip by examining their interaction with closed-shell fullerene molecules. Counter to intuitive expectations, many silicon clusters do not react strongly with the fullerene cage, and we find that only specific highly oriented clusters have sufficient reactivity to break open the existing carbon-carbon bonds.

X-ray photoelectron spectroscopy and paramagnetic resonance evidence for shock-induced intramolecular bond breaking in some energetic solids

NASA Astrophysics Data System (ADS)

Owens, F. J.; Sharma, J.

1980-03-01

Solid samples of 1,3,5, trinitro 1,3,5, triazacyclohexane (RDX), trinitrotoluene (TNT), and ammonium nitrate were subjected to shock pulses of strength and duration less than the threshold to cause detonation. The recovered shocked samples were studied by x-ray photoelectron spectroscopy (XPS) and electron paramagnetic resonance (EPR). The results of these measurements indicate that the shock pulse either broke or altered the internal bonds of the molecules of the solid. The results of the shock decomposition are compared with measurements of the uv and slow thermal decomposition of these materials using the same experimental techniques.

Raman spectroscopy of femtosecond multipulse irradiation of vitreous silica: Experiment and simulation

NASA Astrophysics Data System (ADS)

Shcheblanov, N. S.; Povarnitsyn, M. E.; Mishchik, K. N.; Tanguy, A.

2018-02-01

We report an experimental and numerical study of femtosecond multipulse laser-induced densification in vitreous silica (v -SiO2 ) and its signature in Raman spectra. We compare the experimental findings to the recently developed molecular dynamics (MD) approach accounting for bond breaking due to laser irradiation, together with a dynamical matrix approach and bond polarizability model based on first-principles calculations for the estimation of Raman spectra. We observe two stages of the laser-induced densification and Raman spectrum evolution: growth during several hundreds of pulses followed by further saturation. At the medium range, the network connectivity change in v -SiO2 is expressed in reduction of the major ring fractions leading to more compacted structure. With the help of the Sen and Thorpe model, we also study the short-range order transformation and derive the interbonding Si-O-Si angle change from the Raman measurements. Experimental findings are in excellent agreement with our MD simulations and hence support a bond-breaking mechanism of laser-induced densification. Thus, our modeling explains well the laser-induced changes both in the short-range order caused by the appearance of Si coordination defects and medium-range order connected to evolution of the ring distribution. Finally, our findings disclose similarities between sheared, permanently densified, and laser-induced glass and suggest interesting future experiments in order to clarify the impact of the thermomechanical history on glasses under shear, cold and hot compression, and laser-induced densification.

A robust, highly stretchable supramolecular polymer conductive hydrogel with self-healability and thermo-processability

PubMed Central

Wu, Qian; Wei, Junjie; Xu, Bing; Liu, Xinhua; Wang, Hongbo; Wang, Wei; Wang, Qigang; Liu, Wenguang

2017-01-01

Dual amide hydrogen bond crosslinked and strengthened high strength supramolecular polymer conductive hydrogels were fabricated by simply in situ doping poly (N-acryloyl glycinamide-co-2-acrylamide-2-methylpropanesulfonic) (PNAGA-PAMPS) hydrogels with PEDOT/PSS. The nonswellable conductive hydrogels in PBS demonstrated high mechanical performances—0.22–0.58 MPa tensile strength, 1.02–7.62 MPa compressive strength, and 817–1709% breaking strain. The doping of PEDOT/PSS could significantly improve the specific conductivities of the hydrogels. Cyclic heating and cooling could lead to reversible sol-gel transition and self-healability due to the dynamic breakup and reconstruction of hydrogen bonds. The mending hydrogels recovered not only the mechanical properties, but also conductivities very well. These supramolecular conductive hydrogels could be designed into arbitrary shapes with 3D printing technique, and further, printable electrode can be obtained by blending activated charcoal powder with PNAGA-PAMPS/PEDOT/PSS hydrogel under melting state. The fabricated supercapacitor via the conducting hydrogel electrodes possessed high capacitive performances. These cytocompatible conductive hydrogels have a great potential to be used as electro-active and electrical biomaterials. PMID:28134283

Gradual collapse of nuclear wave functions regulated by frequency tuned X-ray scattering.

PubMed

Ignatova, Nina; Cruz, Vinícius V; Couto, Rafael C; Ertan, Emelie; Zimin, Andrey; Guimarães, Freddy F; Polyutov, Sergey; Ågren, Hans; Kimberg, Victor; Odelius, Michael; Gel'mukhanov, Faris

2017-03-07

As is well established, the symmetry breaking by isotope substitution in the water molecule results in localisation of the vibrations along one of the two bonds in the ground state. In this study we find that this localisation may be broken in excited electronic states. Contrary to the ground state, the stretching vibrations of HDO are delocalised in the bound core-excited state in spite of the mass difference between hydrogen and deuterium. The reason for this effect can be traced to the narrow "canyon-like" shape of the potential of the state along the symmetric stretching mode, which dominates over the localisation mass-difference effect. In contrast, the localisation of nuclear motion to one of the HDO bonds is preserved in the dissociative core-excited state . The dynamics of the delocalisation of nuclear motion in these core-excited states is studied using resonant inelastic X-ray scattering of the vibrationally excited HDO molecule. The results shed light on the process of a wave function collapse. After core-excitation into the state of HDO the initial wave packet collapses gradually, rather than instantaneously, to a single vibrational eigenstate.

Observation of the Hydrogen Migration in the Cation-Induced Fragmentation of the Pyridine Molecules.

PubMed

Wasowicz, Tomasz J; Pranszke, Bogusław

2016-02-25

The ability to selectively control chemical reactions related to biology, combustion, and catalysis has recently attracted much attention. In particular, the hydrogen atom relocation may be used to manipulate bond-breaking and new bond-forming processes and may hold promise for far-reaching applications. Thus, the hydrogen atom migration preceding fragmentation of the gas-phase pyridine molecules by the H(+), H2(+), He(+), He(2+), and O(+) impact has been studied experimentally in the energy range of 5-2000 eV using collision-induced luminescence spectroscopy. Formation of the excited NH(A(3)Π) radicals was observed among the atomic and diatomic fragments. The structure of the pyridine molecule is lacking of the NH group, therefore observation of its A(3)Π → X(3)Σ(-) emission bands is an evidence of the hydrogen atom relocation prior to the cation-induced fragmentation. The NH(A(3)Π) emission yields indicate that formation of the NH radicals depends on the type of selected projectile and can be controlled by tuning its velocity. The plausible collisional mechanisms as well as fragmentation channels for NH formation in pyridine are discussed.

Mechanisms and time-resolved dynamics for trihydrogen cation (H 3 +) formation from organic molecules in strong laser fields

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

Ekanayake, Nagitha; Nairat, Muath; Kaderiya, Balram

Strong-field laser-matter interactions often lead to exotic chemical reactions. Trihydrogen cation formation from organic molecules is one such case that requires multiple bonds to break and form. Here, we present evidence for the existence of two different reaction pathways for H 3 + formation from organic molecules irradiated by a strong-field laser. Assignment of the two pathways was accomplished through analysis of femtosecond time-resolved strong-field ionization and photoion-photoion coincidence measurements carried out on methanol isotopomers, ethylene glycol, and acetone. Ab initio molecular dynamics simulations suggest the formation occurs via two steps: the initial formation of a neutral hydrogen molecule, followedmore » by the abstraction of a proton from the remaining CHOH 2+ fragment by the roaming H 2 molecule. This reaction has similarities to the H 2+H 2 + mechanism leading to formation of H 3 + in the universe. These exotic chemical reaction mechanisms, involving roaming H 2 molecules, are found to occur in the ~100 fs timescale. Roaming molecule reactions may help to explain unlikely chemical processes, involving dissociation and formation of multiple chemical bonds, occurring under strong laser fields.« less

Mechanisms and time-resolved dynamics for trihydrogen cation (H 3 +) formation from organic molecules in strong laser fields

DOE PAGES

Ekanayake, Nagitha; Nairat, Muath; Kaderiya, Balram; ...

2017-07-05

Strong-field laser-matter interactions often lead to exotic chemical reactions. Trihydrogen cation formation from organic molecules is one such case that requires multiple bonds to break and form. Here, we present evidence for the existence of two different reaction pathways for H 3 + formation from organic molecules irradiated by a strong-field laser. Assignment of the two pathways was accomplished through analysis of femtosecond time-resolved strong-field ionization and photoion-photoion coincidence measurements carried out on methanol isotopomers, ethylene glycol, and acetone. Ab initio molecular dynamics simulations suggest the formation occurs via two steps: the initial formation of a neutral hydrogen molecule, followedmore » by the abstraction of a proton from the remaining CHOH 2+ fragment by the roaming H 2 molecule. This reaction has similarities to the H 2+H 2 + mechanism leading to formation of H 3 + in the universe. These exotic chemical reaction mechanisms, involving roaming H 2 molecules, are found to occur in the ~100 fs timescale. Roaming molecule reactions may help to explain unlikely chemical processes, involving dissociation and formation of multiple chemical bonds, occurring under strong laser fields.« less

Cosensitized Porphyrin System for High-Performance Solar Cells with TOF-SIMS Analysis.

PubMed

Wu, Wenjun; Xiang, Huaide; Fan, Wei; Wang, Jinglin; Wang, Haifeng; Hua, Xin; Wang, Zhaohui; Long, Yitao; Tian, He; Zhu, Wei-Hong

2017-05-17

To date, development of organic sensitizers has been predominately focused on light harvesting, highest occupied molecular orbital and lowest unoccupied molecular orbital energy levels, and the electron transferring process. In contrast, their adsorption mode as well as the dynamic loading behavior onto nanoporous TiO 2 is rarely considered. Herein, we have employed the time-of-flight secondary ion mass spectrometry (TOF-SIMS) to gain insight into the competitive dye adsorption mode and kinetics in the cosensitized porphyrin system. Using novel porphyrin dye FW-1 and D-A-π-A featured dye WS-5, the different bond-breaking mode in TOF-SIMS and dynamic dye-loading amount during the coadsorption process are well-compared with two different anchoring groups, such as benzoic acid and cyanoacrylic acid. With the bombardment mode in TOF-SIMS spectra, we have speculated that the cyano group grafts onto nanoporous TiO 2 as tridentate binding for the common anchoring unit of cyanoacrylic acid and confirmed it through extensive first-principles density functional theory calculation by anchoring either the carboxyl or cyano group, which shows that the cyano group can efficiently participate in the adsorption of the WS-5 molecule onto the TiO 2 nanocrystal. The grafting reinforcement interaction between the cyano group and TiO 2 in WS-5 can well-explain the rapid adsorption characteristics. A strong coordinate bond between the lone pair of electrons on the nitrogen or oxygen atom and the Lewis acid sites of TiO 2 can increase electron injection efficiencies with respect to those from the bond between the benzoic acid group and the Brønsted acid sites of the TiO 2 surface. Upon optimization of the coadsorption process with dye WS-5, the photoelectric conversion efficiency based on porphyrin dye FW-1 is increased from 6.14 to 9.72%. The study on the adsorption dynamics of organic sensitizers with TOF-SIMS analysis might provide a new venue for improvement of cosensitized solar cells.

The autumn effect: timing of physical dormancy break in seeds of two winter annual species of Geraniaceae by a stepwise process

PubMed Central

Gama-Arachchige, N. S.; Baskin, J. M.; Geneve, R. L.; Baskin, C. C.

2012-01-01

Background and Aims The involvement of two steps in the physical dormancy (PY)-breaking process previously has been demonstrated in seeds of Fabaceae and Convolvulaceae. Even though there is a claim for a moisture-controlled stepwise PY-breaking in some species of Geraniaceae, no study has evaluated the role of temperature in the PY-breaking process in this family. The aim of this study was to determine whether a temperature-controlled stepwise PY-breaking process occurs in seeds of the winter annuals Geranium carolinianum and G. dissectum. Methods Seeds of G. carolinianum and G. dissectum were stored under different temperature regimes to test the effect of storage temperature on PY-break. The role of temperature and moisture regimes in regulating PY-break was investigated by treatments simulating natural conditions. Greenhouse (non-heated) experiments on seed germination and burial experiments (outdoors) were carried out to determine the PY-breaking behaviour in the natural habitat. Key Results Irrespective of moisture conditions, sensitivity to the PY-breaking step in seeds of G. carolinianum was induced at temperatures ≥20 °C, and exposure to temperatures ≤20 °C made the sensitive seeds permeable. Sensitivity of seeds increased with time. In G. dissectum, PY-break occurred at temperatures ≥20 °C in a single step under constant wet or dry conditions and in two steps under alternate wet–dry conditions if seeds were initially kept wet. Conclusions Timing of seed germination with the onset of autumn can be explained by PY-breaking processes involving (a) two temperature-dependent steps in G. carolinianum and (b) one or two moisture-dependent step(s) along with the inability to germinate under high temperatures in G. dissectum. Geraniaceae is the third of 18 families with PY in which a two-step PY-breaking process has been demonstrated. PMID:22684684

Characterization and Modeling of the Collision Induced Dissociation Patterns of Deprotonated Glycosphingolipids: Cleavage of the Glycosidic Bond

NASA Astrophysics Data System (ADS)

Rožman, Marko

2016-01-01

Glycosphingolipid fragmentation behavior was investigated by combining results from analysis of a series of negative ion tandem mass spectra and molecular modeling. Fragmentation patterns extracted from 75 tandem mass spectra of mainly acidic glycosphingolipid species (gangliosides) suggest prominent cleavage of the glycosidic bonds with retention of the glycosidic oxygen atom by the species formed from the reducing end (B and Y ion formation). Dominant product ions arise from dissociation of sialic acids glycosidic bonds whereas product ions resulting from cleavage of other glycosidic bonds are less abundant. Potential energy surfaces and unimolecular reaction rates of several low-energy fragmentation pathways leading to cleavage of glycosidic bonds were estimated in order to explain observed dissociation patterns. Glycosidic bond cleavage in both neutral (unsubstituted glycosyl group) and acidic glycosphingolipids was the outcome of the charge-directed intramolecular nucleophilic substitution (SN2) mechanism. According to the suggested mechanism, the nucleophile in a form of carboxylate or oxyanion attacks the carbon at position one of the sugar ring, simultaneously breaking the glycosidic bond and yielding an epoxide. For gangliosides, unimolecular reaction rates suggest that dominant product ions related to the cleavage of sialic acid glycosidic bonds are formed via direct dissociation channels. On the other hand, low abundant product ions related to the dissociation of other glycosidic bonds are more likely to be the result of sequential dissociation. Although results from this study mainly contribute to the understanding of glycosphingolipid fragmentation chemistry, some mechanistic findings regarding cleavage of the glycosidic bond may be applicable to other glycoconjugates.

Ab Initio Molecular Dynamics Studies on Substitution vs. Electron Transfer Reactions of Substituted Ketyl Radical Anions with Chloroalkanes: How Do the Two Products Form in a Borderline Mechanism?

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

Yamataka, H.; Aida, Misako; Dupuis, Michel

We present a qualitative analysis, based on ab initio molecular dynamics (MD) calculations, of the SN2/ET mechanistic spectrum for three reactions: (1) HC(CN)=O.- + CH3Cl, (2) HC(CN)=O.- + (CH3)2CHCl, and (3) H2C=O.- + CH3Cl, passing through their SN2-like transition states. The finite temperature (298 K) direct-MD simulations indicate that the trajectories for reaction 1 appear to have a propensity towards SN2 products, the propensity for trajectories for reaction 2 seems to be towards ET products, whereas trajectories for reaction 3 appear to show no particular propensity towards either ET or SN2 products. The mechanistic diversity is consistent with the electronmore » donating ability of the ketyl species and steric bulkiness of chloroalkanes. We find that the trajectories have characteristics that reflect strongly the types of process (SN2 trajectories in reactions 1 and 3 vs. ET trajectories in reactions 2 and 3). Trajectories that lead to SN2 products are simple with C-C bond formation and C-Cl bond breaking essentially completed within 50 fs. By contrast, trajectories leading to ET products are more complex with a sudden electron reorganization taking place within 15 - 30 fs and the major bonding changes and electron and spin reorganizations completed after 250 fs.« less

Breaking Bonds, Actualizing Possibility: Schools as Community Hubs of Social Justice

ERIC Educational Resources Information Center

Williams-Boyd, Pat

2010-01-01

One of every two children in the world lives in poverty, with no access to safe water, health services or adequate shelter to the extent that 25,000 children die every day. Thirty-seven million Americans, thirteen million of whom are children, live below the poverty level. Of the developed world, despite our wealth and sophistication, the United…

How quantum entanglement in DNA synchronizes double-strand breakage by type II restriction endonucleases.

PubMed

Kurian, P; Dunston, G; Lindesay, J

2016-02-21

Macroscopic quantum effects in living systems have been studied widely in pursuit of fundamental explanations for biological energy transport and sensing. While it is known that type II endonucleases, the largest class of restriction enzymes, induce DNA double-strand breaks by attacking phosphodiester bonds, the mechanism by which simultaneous cutting is coordinated between the catalytic centers remains unclear. We propose a quantum mechanical model for collective electronic behavior in the DNA helix, where dipole-dipole oscillations are quantized through boundary conditions imposed by the enzyme. Zero-point modes of coherent oscillations would provide the energy required for double-strand breakage. Such quanta may be preserved in the presence of thermal noise by the enzyme's displacement of water surrounding the DNA recognition sequence. The enzyme thus serves as a decoherence shield. Palindromic mirror symmetry of the enzyme-DNA complex should conserve parity, because symmetric bond-breaking ceases when the symmetry of the complex is violated or when physiological parameters are perturbed from optima. Persistent correlations in DNA across longer spatial separations-a possible signature of quantum entanglement-may be explained by such a mechanism. Copyright © 2015 Elsevier Ltd. All rights reserved.

How quantum entanglement in DNA synchronizes double-strand breakage by type II restriction endonucleases

PubMed Central

Kurian, P.; Dunston, G.; Lindesay, J.

2015-01-01

Macroscopic quantum effects in living systems have been studied widely in pursuit of fundamental explanations for biological energy transport and sensing. While it is known that type II endonucleases, the largest class of restriction enzymes, induce DNA double-strand breaks by attacking phosphodiester bonds, the mechanism by which simultaneous cutting is coordinated between the catalytic centers remains unclear. We propose a quantum mechanical model for collective electronic behavior in the DNA helix, where dipole-dipole oscillations are quantized through boundary conditions imposed by the enzyme. Zero-point modes of coherent oscillations would provide the energy required for double-strand breakage. Such quanta may be preserved in the presence of thermal noise by the enzyme’s displacement of water surrounding the DNA recognition sequence. The enzyme thus serves as a decoherence shield. Palindromic mirror symmetry of the enzyme-DNA complex should conserve parity, because symmetric bond-breaking ceases when the symmetry of the complex is violated or when physiological parameters are perturbed from optima. Persistent correlations in DNA across longer spatial separations—a possible signature of quantum entanglement—may be explained by such a mechanism. PMID:26682627

Theoretical Insights into Methane C–H Bond Activation on Alkaline Metal Oxides

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

Aljama, Hassan; Nørskov, Jens K.; Abild-Pedersen, Frank

Here, we investigate the role of alkaline metal oxides (AMO) (MgO, CaO, and SrO) in activating the C–H bond in methane. We also use Density Functional Theory (DFT) and microkinetic modeling to study the catalytic elementary steps in breaking the C–H bond in methane and creating the methyl radical, a precursor prior to creating C2 products. We also study the effects of surface geometry on the catalytic activity of AMO by examining terrace and step sites. We observe that the process of activating methane depends strongly on the structure of the AMO. When the AMO surface is doped with anmore » alkali metal, the transition state (TS) structure has a methyl radical-like behavior, where the methyl radical interacts weakly with the AMO surface. In this case, the TS energy scales with the hydrogen binding energy. On pure AMO, the TS interacts with AMO surface oxygen as well as the metal atom on the surface, and consequently the TS energy scales with the binding energy of hydrogen and methyl. We study the activity of AMO using a mean-field microkinetic model. The results indicate that terrace sites have similar catalytic activity, with the exception of MgO(100). Step sites bind hydrogen more strongly, making them more active, and this confirms previously reported experimental results. We map the catalytic activity of AMO using a volcano plot with two descriptors: the methyl and the hydrogen binding energies, with the latter being a more significant descriptor. The microkinetic model results suggest that C–H bond dissociation is not always the rate-limiting step. At weak hydrogen binding, the reaction is limited by C–H bond activation. At strong hydrogen binding, the reaction is limited due to poisoning of the active site. We found an increase in activity of AMO as the basicity increased. Finally, the developed microkinetic model allows screening for improved catalysts using simple calculations of the hydrogen binding energy.« less

Theoretical Insights into Methane C–H Bond Activation on Alkaline Metal Oxides

DOE PAGES

Aljama, Hassan; Nørskov, Jens K.; Abild-Pedersen, Frank

2017-07-17

Here, we investigate the role of alkaline metal oxides (AMO) (MgO, CaO, and SrO) in activating the C–H bond in methane. We also use Density Functional Theory (DFT) and microkinetic modeling to study the catalytic elementary steps in breaking the C–H bond in methane and creating the methyl radical, a precursor prior to creating C2 products. We also study the effects of surface geometry on the catalytic activity of AMO by examining terrace and step sites. We observe that the process of activating methane depends strongly on the structure of the AMO. When the AMO surface is doped with anmore » alkali metal, the transition state (TS) structure has a methyl radical-like behavior, where the methyl radical interacts weakly with the AMO surface. In this case, the TS energy scales with the hydrogen binding energy. On pure AMO, the TS interacts with AMO surface oxygen as well as the metal atom on the surface, and consequently the TS energy scales with the binding energy of hydrogen and methyl. We study the activity of AMO using a mean-field microkinetic model. The results indicate that terrace sites have similar catalytic activity, with the exception of MgO(100). Step sites bind hydrogen more strongly, making them more active, and this confirms previously reported experimental results. We map the catalytic activity of AMO using a volcano plot with two descriptors: the methyl and the hydrogen binding energies, with the latter being a more significant descriptor. The microkinetic model results suggest that C–H bond dissociation is not always the rate-limiting step. At weak hydrogen binding, the reaction is limited by C–H bond activation. At strong hydrogen binding, the reaction is limited due to poisoning of the active site. We found an increase in activity of AMO as the basicity increased. Finally, the developed microkinetic model allows screening for improved catalysts using simple calculations of the hydrogen binding energy.« less

Effect of phosphorylation on hydrogen-bonding interactions of the active site histidine of the phosphocarrier protein HPr of the phosphoenolpyruvate-dependent phosphotransferase system determined by sup 15 N NMR spectroscopy

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

van Dijk, A.A.; de Lange, L.C.M.; Robillard, G.T.

1990-09-04

The phosphocarrier protein HPr of the phosphoenolpyruvate-dependent sugar transport system of Escherichia coli can exist in a phosphorylated and a nonphosphorylated form. During phosphorylation, the phosphoryl group is carried on a histidine residue, His15. The hydrogen-bonding state of this histidine was examined with {sup 15}N NMR. For this purpose we selectively enriched the histidine imidazole nitrogens with {sup 15}N by supplying an E. coli histidine auxotroph with the amino acid labeled either at the N{delta}1 and N{epsilon}2 positions or at only the N{delta}1 position. {sup 15}N NMR spectra of two synthesized model compound, phosphoimidazole and phosphomethylimidazole, were also recorded. Themore » authors show that, prior to phosphorylation, the protonated His15 N{epsilon}2 is strongly hydrogen bonded, most probably to a carboxylate moiety. The H-bond should strengthen the nucleophilic character of the deprotonated N{delta}1, resulting in a good acceptor for the phosphoryl group. The hydrogen bond to the His15 N{delta}1 breaks upon phosphorylation of the residue. Implications of the H-bond structure for the mechanism of phosphorylation of HPr are discussed.« less

Processing consequences of superfluous and missing prosodic breaks in auditory sentence comprehension.

PubMed

Bögels, Sara; Schriefers, Herbert; Vonk, Wietske; Chwilla, Dorothee J; Kerkhofs, Roel

2013-11-01

This ERP study investigates whether a superfluous prosodic break (i.e., a prosodic break that does not coincide with a syntactic break) has more severe processing consequences during auditory sentence comprehension than a missing prosodic break (i.e., the absence of a prosodic break at the position of a syntactic break). Participants listened to temporarily ambiguous sentences involving a prosody-syntax match or mismatch. The disambiguation of these sentences was always lexical in nature in the present experiment. This contrasts with a related study by Pauker, Itzhak, Baum, and Steinhauer (2011), where the disambiguation was of a lexical type for missing PBs and of a prosodic type for superfluous PBs. Our results converge with those of Pauker et al. (2011): superfluous prosodic breaks lead to more severe processing problems than missing prosodic breaks. Importantly, the present results extend those of Pauker et al. (2011) showing that this holds when the disambiguation is always lexical in nature. Furthermore, our results show that the way listeners use prosody can change over the course of the experiment which bears consequences for future studies. © 2013 Elsevier Ltd. All rights reserved.

Contribution of Hydrogen Bonds to Paper Strength Properties.

PubMed

Przybysz, Piotr; Dubowik, Marcin; Kucner, Marta Anna; Przybysz, Kazimierz; Przybysz Buzała, Kamila

2016-01-01

The objective of this work was to investigate the influence of hydrogen bonds between fibres on static and dynamic strength properties of paper. A commercial bleached pinewood kraft pulp was soaked in water, refined in a PFI, and used to form paper webs in different solvents, such as water, methanol, ethanol, n-propanol and n-butanol, to determine the effect of their dipole moment on static and dynamic strength properties of resulting paper sheets. Paper which was formed in water, being the solvent of the highest dipole moment among the tested ones, showed the highest breaking length and tear resistance. When paper webs were formed in n-butanol, which was the least polar among the solvents, these parameters were reduced by around 75%. These results provide evidence of the importance of water in paper web formation and strong impact of hydrogen bonds between fibres on strength properties of paper.

Contribution of Hydrogen Bonds to Paper Strength Properties

PubMed Central

Przybysz, Piotr; Dubowik, Marcin; Kucner, Marta Anna; Przybysz, Kazimierz; Przybysz Buzała, Kamila

2016-01-01

The objective of this work was to investigate the influence of hydrogen bonds between fibres on static and dynamic strength properties of paper. A commercial bleached pinewood kraft pulp was soaked in water, refined in a PFI, and used to form paper webs in different solvents, such as water, methanol, ethanol, n-propanol and n-butanol, to determine the effect of their dipole moment on static and dynamic strength properties of resulting paper sheets. Paper which was formed in water, being the solvent of the highest dipole moment among the tested ones, showed the highest breaking length and tear resistance. When paper webs were formed in n-butanol, which was the least polar among the solvents, these parameters were reduced by around 75%. These results provide evidence of the importance of water in paper web formation and strong impact of hydrogen bonds between fibres on strength properties of paper. PMID:27228172

Probing Charge Transport through Peptide Bonds.

PubMed

Brisendine, Joseph M; Refaely-Abramson, Sivan; Liu, Zhen-Fei; Cui, Jing; Ng, Fay; Neaton, Jeffrey B; Koder, Ronald L; Venkataraman, Latha

2018-02-15

We measure the conductance of unmodified peptides at the single-molecule level using the scanning tunneling microscope-based break-junction method, utilizing the N-terminal amine group and the C-terminal carboxyl group as gold metal-binding linkers. Our conductance measurements of oligoglycine and oligoalanine backbones do not rely on peptide side-chain linkers. We compare our results with alkanes terminated asymmetrically with an amine group on one end and a carboxyl group on the other to show that peptide bonds decrease the conductance of an otherwise saturated carbon chain. Using a newly developed first-principles approach, we attribute the decrease in conductance to charge localization at the peptide bond, which reduces the energy of the frontier orbitals relative to the Fermi energy and the electronic coupling to the leads, lowering the tunneling probability. Crucially, this manifests as an increase in conductance decay of peptide backbones with increasing length when compared with alkanes.

Hugoniot curve calculation of nitromethane decomposition mixtures: A reactive force field molecular dynamics approach

NASA Astrophysics Data System (ADS)

Guo, Feng; Zhang, Hong; Hu, Hai-Quan; Cheng, Xin-Lu; Zhang, Li-Yan

2015-11-01

We investigate the Hugoniot curve, shock-particle velocity relations, and Chapman-Jouguet conditions of the hot dense system through molecular dynamics (MD) simulations. The detailed pathways from crystal nitromethane to reacted state by shock compression are simulated. The phase transition of N2 and CO mixture is found at about 10 GPa, and the main reason is that the dissociation of the C-O bond and the formation of C-C bond start at 10.0-11.0 GPa. The unreacted state simulations of nitromethane are consistent with shock Hugoniot data. The complete pathway from unreacted to reacted state is discussed. Through chemical species analysis, we find that the C-N bond breaking is the main event of the shock-induced nitromethane decomposition. Project supported by the National Natural Science Foundation of China (Grant No. 11374217) and the Shandong Provincial Natural Science Foundation, China (Grant No. ZR2014BQ008).

Evaluation of tannins interactions in grape (Vitis vinifera L.) skins.

PubMed

Rustioni, Laura; Fiori, Simone; Failla, Osvaldo

2014-09-15

Tannins have a central role in grapevine berries both for their physiological and enological implications. In the skin tissue they can be in vacuolar solution, or associated to the cell walls through weak or strong physicochemical interactions. The present work aims to separate vacuolar, non-covalently and covalently bonded tannins fractions. A specific extraction procedure was developed. A first extraction in ethanol at low temperature allowed the quantification of vacuolar tannins. An urea treatment followed by an ethanol extraction at room temperature was able to separate non-covalently bonded compounds. Finally an acid catalysis was used to break down proanthocyanidin covalent bonds. The method was validated on ripe grape samples of three cultivars, on berries developed in two sun exposure conditions. The Ethephon treatment effect was also evaluated. Beside the method development, a preliminary evaluation of the cultivar, exposition and Ethephon treatment effects are discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

Atomic-scale models of early-stage alkali depletion and SiO2-rich gel formation in bioactive glasses.

PubMed

Tilocca, Antonio

2015-01-28

Molecular dynamics simulations of Na(+)/H(+)-exchanged 45S5 Bioglass® models reveal that a large fraction of the hydroxyl groups introduced into the proton-exchanged, hydrated glass structure do not initially form covalent bonds with Si and P network formers but remain free and stabilised by the modifier metal cations, whereas substantial Si-OH and P-OH bonding is observed only at higher Na(+)/H(+) exchange levels. The strong affinity between free OH groups and modifier cations in the highly fragmented 45S5 glass structure appears to represent the main driving force for this effect. This suggests an alternative direct route for the formation of a repolymerised silica-rich gel in the early stages of the bioactive mechanism, not considered before, which does not require sequential repeated breakings of Si-O-Si bonds and silanol condensations.

Conversion of amides to esters by the nickel-catalysed activation of amide C-N bonds.

PubMed

Hie, Liana; Fine Nathel, Noah F; Shah, Tejas K; Baker, Emma L; Hong, Xin; Yang, Yun-Fang; Liu, Peng; Houk, K N; Garg, Neil K

2015-08-06

Amides are common functional groups that have been studied for more than a century. They are the key building blocks of proteins and are present in a broad range of other natural and synthetic compounds. Amides are known to be poor electrophiles, which is typically attributed to the resonance stability of the amide bond. Although amides can readily be cleaved by enzymes such as proteases, it is difficult to selectively break the carbon-nitrogen bond of an amide using synthetic chemistry. Here we demonstrate that amide carbon-nitrogen bonds can be activated and cleaved using nickel catalysts. We use this methodology to convert amides to esters, which is a challenging and underdeveloped transformation. The reaction methodology proceeds under exceptionally mild reaction conditions, and avoids the use of a large excess of an alcohol nucleophile. Density functional theory calculations provide insight into the thermodynamics and catalytic cycle of the amide-to-ester transformation. Our results provide a way to harness amide functional groups as synthetic building blocks and are expected to lead to the further use of amides in the construction of carbon-heteroatom or carbon-carbon bonds using non-precious-metal catalysis.

Failure modes of microstructured fibers with sacrificial bonds made by instability-assisted 3D printing

NASA Astrophysics Data System (ADS)

Zou, Shibo; Therriault, Daniel; Gosselin, Frederick

A simple modification by increasing the deposition height on a commercially available 3D printer makes it a mechanical sewing machine due to the fluid mechanical instability. A variety of stitches-like patterns can be produced, similar to those by the Newtonian fluid mechanical sewing machine\\x9D, but with more interesting characteristics in the additional third dimension, which creates weakly fused bonds in some patterns. With these bonds, the fabricated fibers exhibit improved toughness in uniaxial tensile test. The toughening mechanism is found to be similar to the one in spider silk - the breaking of sacrificial bonds and the releasing of hidden length contribute significant dissipated energy to the system. However, the mechanical performance of these microstructured fibers is restricted by early fiber breakage as the number of sacrificial bonds increases. Here, we seek to understand the failure mechanisms of the microstructured fibers through tensile tests and finite element simulations. Static and dynamic failure are both found to cause early fiber breakage. These findings are helpful for the design optimization of microstructured fibers with high toughness and ductility, which can find potential use in impact protection and safety-critical applications.

Ensemble cryoEM elucidates the mechanism of insulin capture and degradation by human insulin degrading enzyme

PubMed Central

Bailey, Lucas J; Tan, Yong Zi; Wei, Hui; Wang, Andrew; Farcasanu, Mara; Woods, Virgil A; McCord, Lauren A; Lee, David; Shang, Weifeng; Deprez-Poulain, Rebecca; Deprez, Benoit; Liu, David R; Koide, Akiko; Koide, Shohei; Kossiakoff, Anthony A

2018-01-01

Insulin degrading enzyme (IDE) plays key roles in degrading peptides vital in type two diabetes, Alzheimer's, inflammation, and other human diseases. However, the process through which IDE recognizes peptides that tend to form amyloid fibrils remained unsolved. We used cryoEM to understand both the apo- and insulin-bound dimeric IDE states, revealing that IDE displays a large opening between the homologous ~55 kDa N- and C-terminal halves to allow selective substrate capture based on size and charge complementarity. We also used cryoEM, X-ray crystallography, SAXS, and HDX-MS to elucidate the molecular basis of how amyloidogenic peptides stabilize the disordered IDE catalytic cleft, thereby inducing selective degradation by substrate-assisted catalysis. Furthermore, our insulin-bound IDE structures explain how IDE processively degrades insulin by stochastically cutting either chain without breaking disulfide bonds. Together, our studies provide a mechanism for how IDE selectively degrades amyloidogenic peptides and offers structural insights for developing IDE-based therapies. PMID:29596046

Anoxic photochemical oxidation of siderite generates molecular hydrogen and iron oxides

PubMed Central

Kim, J. Dongun; Yee, Nathan; Nanda, Vikas; Falkowski, Paul G.

2013-01-01

Photochemical reactions of minerals are underappreciated processes that can make or break chemical bonds. We report the photooxidation of siderite (FeCO3) by UV radiation to produce hydrogen gas and iron oxides via a two-photon reaction. The calculated quantum yield for the reaction suggests photooxidation of siderite would have been a significant source of molecular hydrogen for the first half of Earth’s history. Further, experimental results indicate this abiotic, photochemical process may have led to the formation of iron oxides under anoxic conditions. The reaction would have continued through the Archean to at least the early phases of the Great Oxidation Event, and provided a mechanism for oxidizing the atmosphere through the loss of hydrogen to space, while simultaneously providing a key reductant for microbial metabolism. We propose that the photochemistry of Earth-abundant minerals with wide band gaps would have potentially played a critical role in shaping the biogeochemical evolution of early Earth. PMID:23733945

Thermochemolysis: A New Sample Preparation Approach for the Detection of Organic Components of Complex Macromolecules in Mars Rocks via Gas Chromatography Mass Spectrometry in SAM on MSL

NASA Technical Reports Server (NTRS)

Eugenbrode, J.; Glavin, D.; Dworkin, J.; Conrad, P.; Mahaffy, P.

2011-01-01

Organic chemicals, when present in extraterrestrial samples, afford precious insight into past and modern conditions elsewhere in the Solar System . No single technology identifies all molecular components because naturally occurring molecules have different chemistries (e.g., polar vs. non-polar, low to high molecular weight) and interface with the ambient sample chemistry in a variety of modes (i.e., organics may be bonded, absorbed or trapped by minerals, liquids, gases, or other organics). More than 90% of organic matter in most natural samples on Earth and in meteorites is composed of complex macromolecules (e.g. biopolymers, complex biomolecules, humic substances, kerogen) because the processes that tend to break down organic molecules also tend towards complexation of the more recalcitrant components. Thus, methodologies that tap the molecular information contained within macromolecules may be critical to detecting extraterrestrial organic matter and assessing the sources and processes influencing its nature.

Characterization of the hydrogen-bond network of water around sucrose and trehalose: Microwave and terahertz spectroscopic study

NASA Astrophysics Data System (ADS)

Shiraga, Keiichiro; Adachi, Aya; Nakamura, Masahito; Tajima, Takuro; Ajito, Katsuhiro; Ogawa, Yuichi

2017-03-01

Modification of the water hydrogen bond network imposed by disaccharides is known to serve as a bioprotective agent in living organisms, though its comprehensive understanding is still yet to be reached. In this study, aiming to characterize the dynamical slowing down and destructuring effect of disaccharides, we performed broadband dielectric spectroscopy, ranging from 0.5 GHz to 12 THz, of sucrose and trehalose aqueous solutions. The destructuring effect was examined in two ways (the hydrogen bond fragmentation and disordering) and our result showed that both sucrose and trehalose exhibit an obvious destructuring effect with a similar strength, by fragmenting hydrogen bonds and distorting the tetrahedral-like structure of water. This observation strongly supports a chaotropic (structure-breaking) aspect of disaccharides on the water structure. At the same time, hydration water was found to exhibit slower dynamics and a greater reorientational cooperativity than bulk water because of the strengthened hydrogen bonds. These results lead to the conclusion that strong disaccharide-water hydrogen bonds structurally incompatible with native water-water bonds lead to the rigid but destructured hydrogen bond network around disaccharides. Another important finding in this study is that the greater dynamical slowing down of trehalose was found compared with that of sucrose, at variance with the destructuring effect where no solute dependent difference was observed. This discovery suggests that the exceptionally greater bioprotective impact especially of trehalose among disaccharides is mainly associated with the dynamical slowing down (rather than the destructuring effect).

Assessment of optimal control mechanism complexity by experimental landscape Hessian analysis: fragmentation of CH2BrI

NASA Astrophysics Data System (ADS)

Xing, Xi; Rey-de-Castro, Roberto; Rabitz, Herschel

2014-12-01

Optimally shaped femtosecond laser pulses can often be effectively identified in adaptive feedback quantum control experiments, but elucidating the underlying control mechanism can be a difficult task requiring significant additional analysis. We introduce landscape Hessian analysis (LHA) as a practical experimental tool to aid in elucidating control mechanism insights. This technique is applied to the dissociative ionization of CH2BrI using shaped fs laser pulses for optimization of the absolute yields of ionic fragments as well as their ratios for the competing processes of breaking the C-Br and C-I bonds. The experimental results suggest that these nominally complex problems can be reduced to a low-dimensional control space with insights into the control mechanisms. While the optimal yield for some fragments is dominated by a non-resonant intensity-driven process, the optimal generation of other fragments maa difficult task requiring significant additionaly be explained by a non-resonant process coupled to few level resonant dynamics. Theoretical analysis and modeling is consistent with the experimental observations.

Ion Transport via Structural Relaxations in Polymerized Ionic Liquids

NASA Astrophysics Data System (ADS)

Ganesan, Venkat; Mogurampelly, Santosh

We study the mechanisms underlying ion transport in poly(1-butyl-3-vinylimidazolium-hexafluorophosphate) polymer electrolytes. We consider polymer electrolytes of varying polymerized ionic liquid to ionic liquid (polyIL:IL) ratios and use atomistic molecular dynamics (MD) simulations to probe the dynamical and structural characteristics of the electrolyte. Our results reveal that anion diffusion along polymer backbone occurs primarily viathe formation and breaking of ion-pairs involving threepolymerized cationic monomers of twodifferent polymer chains. Moreover, we observe that the ionic diffusivities exhibit a direct correlation with the structural relaxation times of the ion-pairs and hydrogen bonds (H-bonds). These results provide new insights into the mechanisms underlying ion transport in polymerized ionic liquid electrolytes.

Additive-induced aggregate changes of two structurally similar dyes in aqueous solutions: A comparative photophysical study.

PubMed

Ghanadzadeh Gilani, A; Poormohammadi-Ahandani, Z; Kian, R

2018-01-15

Absorption and emission spectral characteristics of the two structurally similar phenothiazine dyes, azure B and toluidine blue, in aqueous solutions of the two sets of molecular additives (ureas and monosaccharides) were studied as a function of the dye and additive concentrations. The absorption spectra of the dyes were also studied in pure tetramethylurea with an aprotic nature. The spectral data were analyzed using DECOM Program. The dimer structure of the interacting molecules in these dyes was discussed using the exciton model. The urea class of additives was found to act as water structure-breakers over the range of studied concentration. The carbohydrate additives were found to act as water structure-breakers at low concentrations. However, the water structure breaking process may be disfavored by the additive-additive interactions at higher concentrations. It can be concluded that at low additive concentrations, the main driving force for breaking the dye association is water-additive interaction, which disrupts the water hydrogen bonds induced by the additives. However, at the high additive concentrations, the different phenomena including additive-additive and additive-dye interactions can change the structure, strength, and aggregative properties of the dyes. Finally, the urea in water induces noticeably fluorescence quenching in emission spectra of both the dyes. Copyright © 2017 Elsevier B.V. All rights reserved.

Additive-induced aggregate changes of two structurally similar dyes in aqueous solutions: A comparative photophysical study

NASA Astrophysics Data System (ADS)

Ghanadzadeh Gilani, A.; Poormohammadi-Ahandani, Z.; Kian, R.

2018-01-01

Absorption and emission spectral characteristics of the two structurally similar phenothiazine dyes, azure B and toluidine blue, in aqueous solutions of the two sets of molecular additives (ureas and monosaccharides) were studied as a function of the dye and additive concentrations. The absorption spectra of the dyes were also studied in pure tetramethylurea with an aprotic nature. The spectral data were analyzed using DECOM Program. The dimer structure of the interacting molecules in these dyes was discussed using the exciton model. The urea class of additives was found to act as water structure-breakers over the range of studied concentration. The carbohydrate additives were found to act as water structure-breakers at low concentrations. However, the water structure breaking process may be disfavored by the additive-additive interactions at higher concentrations. It can be concluded that at low additive concentrations, the main driving force for breaking the dye association is water-additive interaction, which disrupts the water hydrogen bonds induced by the additives. However, at the high additive concentrations, the different phenomena including additive-additive and additive-dye interactions can change the structure, strength, and aggregative properties of the dyes. Finally, the urea in water induces noticeably fluorescence quenching in emission spectra of both the dyes.

Split-estate negotiations: the case of coal-bed methane

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

Hayley H. Chouinard; Christina Steinhoff

Coal-bed methane is an emerging contributor to the US energy supply. Split estates, where landowners control the surface and the energy companies lease the rights to the underground gas from the federal government, often impede successful negotiations for methane extraction. We provide an extensive form representation of the dynamic game of the negotiation process for subsurface access. We then solve for a set of Nash equilibrium outcomes associated with the split estate negotiations. By examining the optimal offers we can identify methods to improve the likelihood of negotiations that do not break down and result in the gas developer resortingmore » to the use of a bond. We examine how changes in transaction costs or entitlements will affect the outcomes, and support our finds with anecdotal evidence from actual negotiations for coal-bed methane access. 55 refs.« less

Fundamental tribological properties of ion-beam-deposited boron nitride films

NASA Technical Reports Server (NTRS)

Miyoshi, Kazuhisa

1989-01-01

The adhesion, friction, and micromechanical properties of ion-beam-deposited boron nitride (BN) films are reviewed. The BN films are examined in contact with BN metals and other harder materials. For simplicity of discussion, the tribological properties of concern in the processes are separated into two parts. First, the pull-off force (adhesion) and the shear force required to break the interfacial junctions between contacting surfaces are discussed. The effects of surface films, hardness of metals, and temperature on tribological response with respect to adhesion and friction are considered. The second part deals with the abrasion of the BN films. Elastic, plastic, and fracture behavior of the BN films in solid-state contact are discussed. The scratch technique of determining the critical load needed to fracture interfacial adhesive bonds of BN films deposited on substrates is also addressed.

Fundamental tribological properties of ion-beam-deposited boron nitride films

NASA Technical Reports Server (NTRS)

Miyoshi, K.

1990-01-01

The adhesion, friction, and micromechanical properties of ion-beam-deposited boron nitride (BN) films are reviewed. The BN films are examined in contact with BN metals and other harder materials. For simplicity of discussion, the tribological properties of concern in the processes are separated into two parts. First, the pull-off force (adhesion) and the shear force required to break the interfacial junctions between contacting surfaces are discussed. The effects of surface films, hardness of metals, and temperature on tribological response with respect to adhesion and friction are considered. The second part deals with the abrasion of the BN films. Elastic, plastic, and fracture behavior of the BN films in solid-state contact are discussed. The scratch technique of determining the critical load needed to fracture interfacial adhesive bonds of BN films deposited on substrates is also addressed.

Numerical Simulation of Transient Liquid Phase Bonding under Temperature Gradient

NASA Astrophysics Data System (ADS)

Ghobadi Bigvand, Arian

Transient Liquid Phase bonding under Temperature Gradient (TG-TLP bonding) is a relatively new process of TLP diffusion bonding family for joining difficult-to-weld aerospace materials. Earlier studies have suggested that in contrast to the conventional TLP bonding process, liquid state diffusion drives joint solidification in TG-TLP bonding process. In the present work, a mass conservative numerical model that considers asymmetry in joint solidification is developed using finite element method to properly study the TG-TLP bonding process. The numerical results, which are experimentally verified, show that unlike what has been previously reported, solid state diffusion plays a major role in controlling the solidification behavior during TG-TLP bonding process. The newly developed model provides a vital tool for further elucidation of the TG-TLP bonding process.

Structures of water molecules in carbon nanotubes under electric fields

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

Winarto,; Takaiwa, Daisuke; Yamamoto, Eiji

2015-03-28

Carbon nanotubes (CNTs) are promising for water transport through membranes and for use as nano-pumps. The development of CNT-based nanofluidic devices, however, requires a better understanding of the properties of water molecules in CNTs because they can be very different from those in the bulk. Using all-atom molecular dynamics simulations, we investigate the effect of axial electric fields on the structure of water molecules in CNTs having diameters ranging from (7,7) to (10,10). The water dipole moments were aligned parallel to the electric field, which increases the density of water inside the CNTs and forms ordered ice-like structures. The electricmore » field induces the transition from liquid to ice nanotubes in a wide range of CNT diameters. Moreover, we found an increase in the lifetime of hydrogen bonds for water structures in the CNTs. Fast librational motion breaks some hydrogen bonds, but the molecular pairs do not separate and the hydrogen bonds reform. Thus, hydrogen bonds maintain the water structure in the CNTs, and the water molecules move collectively, decreasing the axial diffusion coefficient and permeation rate.« less

Interaction of a single acetophenone molecule with group III-IV elements mediated by Si(001)

NASA Astrophysics Data System (ADS)

Racis, A.; Jurczyszyn, L.; Radny, M. W.

2018-03-01

A theoretical study of an influence of the acetophenone molecule adsorbed on the Si(001) on the local chemical reactivity of silicon surface is presented. The obtained results indicate that the interaction of the molecule with silicon substrate breaks the intra-dimer π bonds in four surface silicon dimers interacting directly with adsorbed molecule. This leads to the formation of two pairs of unpaired dangling bonds at two opposite sides of the molecule. It is demonstrated that these dangling bonds increase considerably the local chemical reactivity of the silicon substrate in the vicinity of the adsorbed molecule. Consequently, it is shown that such molecule bonded with Si(001) can stabilize the position of In and Pb adatoms diffusing on silicon substrate at two sides and initiate the one-dimensional aggregation of the metallic adatoms on the Si(001) substrate anchored at both sides of the adsorbed molecule. This type of aggregation leads to the growth of chain-like atomic structures in opposite directions, pinned to adsorbed molecule and oriented perpendicular to the rows of surface silicon dimers.

How ions affect the structure of water.

PubMed

Hribar, Barbara; Southall, Noel T; Vlachy, Vojko; Dill, Ken A

2002-10-16

We model ion solvation in water. We use the MB model of water, a simple two-dimensional statistical mechanical model in which waters are represented as Lennard-Jones disks having Gaussian hydrogen-bonding arms. We introduce a charge dipole into MB waters. We perform (NPT) Monte Carlo simulations to explore how water molecules are organized around ions and around nonpolar solutes in salt solutions. The model gives good qualitative agreement with experiments, including Jones-Dole viscosity B coefficients, Samoilov and Hirata ion hydration activation energies, ion solvation thermodynamics, and Setschenow coefficients for Hofmeister series ions, which describe the salt concentration dependence of the solubilities of hydrophobic solutes. The two main ideas captured here are (1) that charge densities govern the interactions of ions with water, and (2) that a balance of forces determines water structure: electrostatics (water's dipole interacting with ions) and hydrogen bonding (water interacting with neighboring waters). Small ions (kosmotropes) have high charge densities so they cause strong electrostatic ordering of nearby waters, breaking hydrogen bonds. In contrast, large ions (chaotropes) have low charge densities, and surrounding water molecules are largely hydrogen bonded.

Silylene-Nickel Promoted Cleavage of B-O Bonds: From Catechol Borane to the Hydroborylene Ligand.

PubMed

Hadlington, Terrance J; Szilvási, Tibor; Driess, Matthias

2017-06-19

The first 16 valence electron [bis(NHC)](silylene)Ni 0 complex 1, [( TMS L)ClSi:→Ni(NHC) 2 ], bearing the acyclic amido-chlorosilylene ( TMS L)ClSi: ( TMS L=N(SiMe 3 )Dipp; Dipp=2,6-Pr i 2 C 6 H 4 ) and two NHC ligands (N-heterocyclic carbene=:C[(Pr i )NC(Me)] 2 ) was synthesized in high yield and structurally characterized. Compound 1 is capable of facile dihydrogen activation under ambient conditions to give the corresponding HSi-NiH complex 2. Most notably, 1 reacts with catechol borane to afford the unprecedented hydroborylene-coordinated (chloro)(silyl)nickel(II) complex 3, {[cat( TMS L)Si](Cl)Ni←:BH(NHC) 2 }, via the cleavage of two B-O bonds and simultaneous formation of two Si-O bonds. The mechanism for the formation of 3 was rationalized by means of DFT calculations, which highlight the powerful synergistic effects of the Si:→Ni moiety in the breaking of incredibly strong B-O bonds. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

None

In order to stop bacteria from reproducing and causing a disease like tuberculosis, researchers must first block its enzymes' ability to bind with certain molecules. A research team from Brandeis University worked with the Advanced Protein Characterization Facility at Argonne National Laboratory to define 13 different bacterial structures and uncover the mechanism by which their enzymes form and break bonds with molecules. This animation depicts how an enzyme may be inhibited using this knowledge.

When Bonds Are Broken: Family Literacy for Incarcerated Fathers and Their Children. 353 Final Report. Year Three. July 1, 1994 - June 30, 1995.

ERIC Educational Resources Information Center

Northampton Community Coll., Bethlehem, PA. Adult Literacy Div.

To break intergenerational patterns of literacy-related problems, four 10-week cycles of family literacy programming provided direct literacy and family literacy instruction for fathers incarcerated in Northampton County Prison. Participants included 10-12 fathers per cycle of 50 hours weekly in 6 hours of adult basic education, English as a…

Not Breaking Bonds on Facebook--Mixed-Methods Research on the Influence of Individuals' Need to Belong on "Unfriending" Behavior on Facebook

ERIC Educational Resources Information Center

Kramer, Nicole; Hoffmann, Laura; Eimler, Sabrina

2015-01-01

Although recent research demonstrates that people deem a considerable number of their Facebook friends dispensable, they nevertheless refrain from deleting a large number of contacts. While there are first studies on the reasons why users decide to "unfriend" contacts, there is no research on the motives for keeping social contacts even…

Effects of protonation on the hydrolysis of triphosphate in vacuum and the implications for catalysis by nucleotide hydrolyzing enzymes.

PubMed

Kiani, Farooq Ahmad; Fischer, Stefan

2016-06-29

Nucleoside triphosphate (NTP) hydrolysis is a key reaction in biology. It involves breaking two very stable bonds (one P-O bond and one O-H bond of water), in either a concurrent or a sequential way. Here, we systematically examine how protonation of the triphosphate affects the mechanism of hydrolysis. The hydrolysis reaction of methyl triphosphate in vacuum is computed with protons in various numbers and position on the three phosphate groups. Protonation is seen to have a strong catalytic effect, with the reaction mechanism depending highly on the protonation pattern. This dependence is apparently complicated, but is shown to obey a well-defined set of rules: Protonation of the α- and β-phosphate groups favors a sequential hydrolysis mechanism, whereas γ-protonation favors a concurrent mechanism, the two effects competing with each other in cases of simultaneous protonation. The rate-limiting step is always the breakup of the water molecule while it attacks the γ-phosphorus, and its barrier is lowered by γ-protonation. This step has significantly lower barriers in the sequential reactions, because the dissociated γ-metaphosphate intermediate (P γ O 3 - ) is a much better target for water attack than the un-dissociated γ-phosphate (-P γ O 4 2- ). The simple chemical logic behind these rules helps to better understand the catalytic strategy used by NTPase enzymes, as illustrated here for the catalytic pocket of myosin. A set of rules was determined that describes how protonating the phosphate groups affects the hydrolysis mechanism of methyl triphosphate: Protonation of the α- and/or β- phosphate groups promotes a sequential mechanism in which P-O bond breaking precedes the breakup of the attacking water, whereas protonation of the γ-phosphate promotes a concurrent mechanism and lowers the rate-limiting barrier of water breakup. The role played by individual protein residues in the catalytic pocket of triphosphate hydrolysing enzymes can be assigned accordingly.

Investigation of ball bond integrity for 0.8 mil (20 microns) diameter gold bonding wire on low k die in wire bonding technology

NASA Astrophysics Data System (ADS)

Kudtarkar, Santosh Anil

Microelectronics technology has been undergoing continuous scaling to accommodate customer driven demand for smaller, faster and cheaper products. This demand has been satisfied by using novel materials, design techniques and processes. This results in challenges for the chip connection technology and also the package technology. The focus of this research endeavor was restricted to wire bond interconnect technology using gold bonding wires. Wire bond technology is often regarded as a simple first level interconnection technique. In reality, however, this is a complex process that requires a thorough understanding of the interactions between the design, material and process variables, and their impact on the reliability of the bond formed during this process. This research endeavor primarily focused on low diameter, 0.8 mil thick (20 mum) diameter gold bonding wire. Within the scope of this research, the integrity of the ball bond formed by 1.0 mil (25 mum) and 0.8 mil (20 mum) diameter wires was compared. This was followed by the evaluation of bonds formed on bond pads having doped SiO2 (low k) as underlying structures. In addition, the effect of varying the percentage of the wire dopant, palladium and bonding process parameters (bonding force, bond time, ultrasonic energy) for 0.8 mil (20 mum) bonding wire was also evaluated. Finally, a degradation empirical model was developed to understand the decrease in the wire strength. This research effort helped to develop a fundamental understanding of the various factors affecting the reliability of a ball bond from a design (low diameter bonding wire), material (low k and bonding wire dopants), and process (wire bonding process parameters) perspective for a first level interconnection technique, namely wire bonding. The significance of this research endeavor was the systematic investigation of the ball bonds formed using 0.8 mil (20 microm) gold bonding wire within the wire bonding arena. This research addressed low k structures on 90 nm silicon technology, bonding wires with different percentage of doping element (palladium), and different levels of bonding process parameters. An empirical model to understand the high temperature effects for bonds formed using the low diameter wire was also developed.

High-strain-rate deformation of granular silicon carbide

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

Shih, C.J.; Meyers, M.A.; Nesterenko, V.F.

1998-07-01

Silicon carbide powders with three particle size distributions (average sizes of 0.4, 3 and 50 {micro}m) were subjected to strain-controlled, high-strain-rate deformation ({dot {var_epsilon}} {approx} 3 {times} 10{sup 4}/s) in a cylindrical geometry which imposed simultaneous compressive stresses. The experiments involved two explosive stages to (a) densify the powder and to (b) subject the densified granules to large deformation. The powder, with initial density of 33--59% of theoretical density, was densified to densities between 73 and 94% of theoretical density in the first stage. The densified powders were subjected to a global effective strain of {approx}{minus}0.27 in the second stage.more » Their response to be imposed constraints occurred through both homogeneous deformation (82--100%) and shear localization (0--18%), depending on the particle size. In the coarse powder (50 {micro}m), the shear localization process was primarily due to particle break-up (comminution) and rearrangement of the comminuted particles, through a similar mechanism to the bulk and prefractured SiC (Shih, C.J., Nesterenko, V.F. and Meyers, M.A., Journal of Applied Physics, 1998, 83, 4660). Comminution was observed in the medium powder (3 {micro}m), but was never seen in the fine powder (0.4 {micro}m). In medium and fine granular SiC, the shear localization at sufficiently high displacement (>150 {micro}m) leads to the formation of a thin layer (5--20 {micro}m) of well-bonded material. Calculated temperatures in the centers of the bands are up to 2300 C (using an assumed shear strength of 2 GPa and linear thermal softening), which explain the bonding. An analytical model is developed that correctly predicts break-up of large particles and plastic deformation of the smaller ones. It is based on the Griffith fracture criterion and Weibull distribution of strength, which quantitatively express the fact that the fracture is generated by flaws the size of which is limited by the particle size.« less

Processing Load Imposed by Line Breaks in English Temporal Wh-Questions.

PubMed

Hirotani, Masako; Terry, J Michael; Sadato, Norihiro

2016-01-01

Prosody plays an important role in online sentence processing both explicitly and implicitly. It has been shown that prosodically packaging together parts of a sentence that are interpreted together facilitates processing of the sentence. This applies not only to explicit prosody but also implicit prosody. The present work hypothesizes that a line break in a written text induces an implicit prosodic break, which, in turn, should result in a processing bias for interpreting English wh-questions. Two experiments-one self-paced reading study and one questionnaire study-are reported. Both supported the "line break" hypothesis mentioned above. The results of the self-paced reading experiment showed that unambiguous wh-questions were read faster when the location of line breaks (or frame breaks) matched the scope of a wh-phrase (main or embedded clause) than when they did not. The questionnaire tested sentences with an ambiguous wh-phrase, one that could attach either to the main or the embedded clause. These sentences were interpreted as attaching to the main clause more often than to the embedded clause when a line break appeared after the main verb, but not when it appeared after the embedded verb.

RSRM nozzle fixed housing cooldown test

NASA Technical Reports Server (NTRS)

Bolieau, D. J.

1989-01-01

Flight 5 aft segments with nozzles were exposed to -17 F temperatures while awaiting shipment to KSC in February, 1989. No records were found which show that any previous nozzles were exposed to air temperatures as low as those seen by the Flight 5 nozzles. Thermal analysis shows that the temperature of the fixed housing, and forward and aft exit cone components dropped as low as -10 F. Structural analysis of the nozzles at these low temperatures show the forward and aft exit cone adhesive bonds to have a positive margin of safety, based on a 2.0 safety factor. These analyses show the normal and shear stresses in the fixed housing bond as low values. However, the hoop and meridinal stresses were predicted to be in the 4000 psi range; the failure stress allowable of EA913NA adhesive at -7 F. If the bonds did break in directions perpendicular to the surfaces, called bond crazing, no normal bond strength would be lost. Testing was conducted in two phases, showing that no degradation to the adhesive bonds occurred while the Flight 5 nozzles were subjected to subzero temperatures. The results of these tests are documented. Phase 1 testing cooled a full-scale RSRM insulated fixed housing to -13 F, with extensive bondline inspections. Phase 2 testing cooled the witness panel adhesive tensile buttions to -13 F, with failure strengths recorded before, during, and after the cooldown.

Divorce and infidelity are associated with skewed adult sex ratios in birds.

PubMed

Liker, András; Freckleton, Robert P; Székely, Tamás

2014-04-14

Adult sex ratio (ASR) is a fundamental concept in population demography, and recent theory suggests that ASR plays a central role in social behavior, mating systems, and parental care. Unbalanced ASRs are predicted to influence pair-bond and mating behavior, since the rarer sex in the population has more potential partners to mate with than the more common sex. Here we use phylogenetic comparative analyses to test whether ASR is related to three major aspects of mating behavior: divorce, social polygamy, and pair-bond infidelity. ASR is strongly correlated with long-term pair bonds, since the divorce rate is higher in species with a female-biased sex ratio, indicating that mate change by pair members and/or breaking of pair bonds by unmated individuals is more frequent when females outnumber males. Short-term pair bonds are also associated with unbalanced ASRs: males are more commonly polygamous when females outnumber males, and conversely, females are more polygamous when males outnumber females. Furthermore, infidelity increases with male-biased ASR in socially monogamous birds, suggesting that male coercion and/or female willingness to cheat the partner are facilitated by male-biased ASR. Our results provide the first comprehensive support for the proposition that ASR influences multiple aspects of pair-bond and mating behavior in wild populations. Copyright © 2014 Elsevier Ltd. All rights reserved.

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.

PubMed

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.

Hydraulic fracturing - an attempt of DEM simulation

NASA Astrophysics Data System (ADS)

Kosmala, Alicja; Foltyn, Natalia; Klejment, Piotr; Dębski, Wojciech

2017-04-01

Hydraulic fracturing is a technique widely used in oil, gas and unconventional reservoirs exploitation in order to enable the oil/gas to flow more easily and enhance the production. It relays on pumping into a rock a special fluid under a high pressure which creates a set of microcracks which enhance porosity of the reservoir rock. In this research, attempt of simulation of such hydrofracturing process using the Discrete Element Method approach is presented. The basic assumption of this approach is that the rock can be represented as an assembly of discrete particles cemented into a rigid sample (Potyondy 2004). An existence of voids among particles simulates then a pore system which can be filled out by fracturing fluid, numerically represented by much smaller particles. Following this microscopic point of view and its numerical representation by DEM method we present primary results of numerical analysis of hydrofracturing phenomena, using the ESyS-Particle Software. In particular, we consider what is happening in distinct vicinity of the border between rock sample and fracking particles, how cracks are creating and evolving by breaking bonds between particles, how acoustic/seismic energy is releasing and so on. D.O. Potyondy, P.A. Cundall. A bonded-particle model for rock. International Journal of Rock Mechanics and Mining Sciences, 41 (2004), pp. 1329-1364.

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

PubMed

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

2012-03-02

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

Report on JANNAF panel on shotgun/relative quickness testing

NASA Technical Reports Server (NTRS)

Gould, R. A.

1980-01-01

As the need for more energetic solid propellants continues, a number of problems arises. One of these is the tendency of high energy propellants to transition from burning (deflagration) to detonation in regions where the propellant is present in small particle sizes; e.g., in case bonding areas of a motor after a rapid depressurization causes a shear zone at the bond interface as the stressed propellant and motor case relax at different rates. In an effort to determine the susceptibility of propellants to high strain rate break up (friability), and subsequent DDT, the propulsion community uses the shotgun/relative quickness test as one of a number of screening tests for new propellant formulations. Efforts to standardize test techniques and equipment are described.

Dissipation in graphene and nanotube resonators

NASA Astrophysics Data System (ADS)

Seoánez, C.; Guinea, F.; Castro Neto, A. H.

2007-09-01

Different damping mechanisms in graphene nanoresonators are studied: charges in the substrate, ohmic losses in the substrate and the graphene sheet, breaking and healing of surface bonds (Velcro effect), two level systems, attachment losses, and thermoelastic losses. We find that, for realistic structures and contrary to semiconductor resonators, dissipation is dominated by ohmic losses in the graphene layer and metallic gate. An extension of this study to carbon nanotube-based resonators is presented.

Excimer laser phototherapy for the dissolution of vascular obstruction

DOEpatents

Gruen, D.M.; Young, C.E.; Pellin, M.J.

1984-01-09

Removal of abnormal human tissue with reduced thermal damage is achieved by selecting a laser having a wavelength in the order of 290 to 400 nm, orienting a laser-transmitting glass member toward the abnormal tissue and directing the laser through the glass member at power densities, pulse rates, and times sufficient to cause multiphoton absorption and bond breaking by Coulomb repulsion rather than thermal destruction. 2 figures.

Gene delivery in conjunction with gold nanoparticle and tumor treating electric field

NASA Astrophysics Data System (ADS)

Tiwari, Pawan K.; Soo Lee, Yeon

2013-08-01

The advances in electrotherapy to treat the diseased biological cell instigate its extension in gene therapy through the delivery of gene into the nucleus. The objective of this study is to investigate the application of moderate intensity alternating electric field, also known as tumor treating electric field on a carrier system consisting of a charged gene complex conjugated to the surface of a gold nanoparticle. The gene delivery mechanism relies on the magnitude and direction of the induced electric field inside the cytoplasm in presence of carrier system. The induced electric field strength is significant in breaking the gene complex-gold nanoparticle bonding, and exerting an electric force pushing the charged gene into the nucleus. The electric force orientation is dependent on the aspect ratio (AR) of the gold nanoparticle and a relationship between them is studied via Maxwell two-dimensional (2D) finite element simulation analyzer. The development of charge density on the surface of carrier system and the required electric field strength to break the bonding are investigated utilizing the Gouy-Chapman-Grahame-Stern (GCGS) theoretical model. A carrier system having the aspect ratio of the gold nanoparticle in the range 1 < AR ≤ 5 and AR = 1 are substantial delivering cationic and anionic genes into the nucleus, respectively.

Low Earth Orbital Atomic Oxygen Interactions With Materials

NASA Technical Reports Server (NTRS)

Banks, Bruce A.; Miller, Sharon K.; deGroh, Kim K.

2004-01-01

Atomic oxygen is formed in the low Earth orbital environment (LEO) by photo dissociation of diatomic oxygen by short wavelength (< 243 nm) solar radiation which has sufficient energy to break the 5.12 eV O2 diatomic bond in an environment where the mean free path is sufficiently long ( 108 meters) that the probability of reassociation or the formation of ozone (O3) is small. As a consequence, between the altitudes of 180 and 650 km, atomic oxygen is the most abundant species. Spacecraft impact the atomic oxygen resident in LEO with sufficient energy to break hydrocarbon polymer bonds, causing oxidation and thinning of the polymers due to loss of volatile oxidation products. Mitigation techniques, such as the development of materials with improved durability to atomic oxygen attack, as well as atomic oxygen protective coatings, have been employed with varying degrees of success to improve durability of polymers in the LEO environment. Atomic oxygen can also oxidize silicones and silicone contamination to produce non-volatile silica deposits. Such contaminants are present on most LEO missions and can be a threat to performance of optical surfaces. The LEO atomic oxygen environment, its interactions with materials, results of space testing, computational modeling, mitigation techniques, and ground laboratory simulation procedures and issues are presented.

Rheology of granular materials composed of crushable particles.

PubMed

Nguyen, Duc-Hanh; Azéma, Émilien; Sornay, Philippe; Radjaï, Farhang

2018-04-11

We investigate sheared granular materials composed of crushable particles by means of contact dynamics simulations and the bonded-cell model for particle breakage. Each particle is paved by irregular cells interacting via cohesive forces. In each simulation, the ratio of the internal cohesion of particles to the confining pressure, the relative cohesion, is kept constant and the packing is subjected to biaxial shearing. The particles can break into two or more fragments when the internal cohesive forces are overcome by the action of compressive force chains between particles. The particle size distribution evolves during shear as the particles continue to break. We find that the breakage process is highly inhomogeneous both in the fragment sizes and their locations inside the packing. In particular, a number of large particles never break whereas a large number of particles are fully shattered. As a result, the packing keeps the memory of its initial particle size distribution, whereas a power-law distribution is observed for particles of intermediate size due to consecutive fragmentation events whereby the memory of the initial state is lost. Due to growing polydispersity, dense shear bands are formed inside the packings and the usual dilatant behavior is reduced or cancelled. Hence, the stress-strain curve no longer passes through a peak stress, and a progressive monotonic evolution towards a pseudo-steady state is observed instead. We find that the crushing rate is controlled by the confining pressure. We also show that the shear strength of the packing is well expressed in terms of contact anisotropies and force anisotropies. The force anisotropy increases while the contact orientation anisotropy declines for increasing internal cohesion of the particles. These two effects compensate each other so that the shear strength is nearly independent of the internal cohesion of particles.

Conversion of Amides to Esters by the Nickel-Catalyzed Activation of Amide C–N Bonds

PubMed Central

Hie, Liana; Fine Nathel, Noah F.; Shah, Tejas K.; Baker, Emma L.; Hong, Xin; Yang, Yun-Fang; Liu, Peng; Houk, K. N.; Garg, Neil K.

2015-01-01

Amides are common functional groups that have been well studied for more than a century.1 They serve as the key building blocks of proteins and are present in an broad range of other natural and synthetic compounds. Amides are known to be poor electrophiles, which is typically attributed to resonance stability of the amide bond.1,2 Whereas Nature can easily cleave amides through the action of enzymes, such as proteases,3 the ability to selectively break the C–N bond of an amide using synthetic chemistry is quite difficult. In this manuscript, we demonstrate that amide C–N bonds can be activated and cleaved using nickel catalysts. We have used this methodology to convert amides to esters, which is a challenging and underdeveloped transformation. The reaction methodology proceeds under exceptionally mild reaction conditions, and avoids the use of a large excess of an alcohol nucleophile. Density functional theory (DFT) calculations provide insight into the thermodynamics and catalytic cycle of this unusual transformation. Our results provide a new strategy to harness amide functional groups as synthons and are expected fuel the further use of amides for the construction of carbon–heteroatom or carbon–carbon bonds using non-precious metal catalysis. PMID:26200342

Mechanical measurement of hydrogen bonded host-guest systems under non-equilibrium, near-physiological conditions.

PubMed

Naranjo, Teresa; Cerrón, Fernando; Nieto-Ortega, Belén; Latorre, Alfonso; Somoza, Álvaro; Ibarra, Borja; Pérez, Emilio M

2017-09-01

Decades after the birth of supramolecular chemistry, there are many techniques to measure noncovalent interactions, such as hydrogen bonding, under equilibrium conditions. As ensembles of molecules rapidly lose coherence, we cannot extrapolate bulk data to single-molecule events under non-equilibrium conditions, more relevant to the dynamics of biological systems. We present a new method that exploits the high force resolution of optical tweezers to measure at the single molecule level the mechanical strength of a hydrogen bonded host-guest pair out of equilibrium and under near-physiological conditions. We utilize a DNA reporter to unambiguously isolate single binding events. The Hamilton receptor-cyanuric acid host-guest system is used as a test bed. The force required to dissociate the host-guest system is ∼17 pN and increases with the pulling rate as expected for a system under non-equilibrium conditions. Blocking one of the hydrogen bonding sites results in a significant decrease of the force-to-break by 1-2 pN, pointing out the ability of the method to resolve subtle changes in the mechanical strength of the binding due to the individual H-bonding components. We believe the method will prove to be a versatile tool to address important questions in supramolecular chemistry.

LAMMPS framework for dynamic bonding and an application modeling DNA

NASA Astrophysics Data System (ADS)

Svaneborg, Carsten

2012-08-01

We have extended the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to support directional bonds and dynamic bonding. The framework supports stochastic formation of new bonds, breakage of existing bonds, and conversion between bond types. Bond formation can be controlled to limit the maximal functionality of a bead with respect to various bond types. Concomitant with the bond dynamics, angular and dihedral interactions are dynamically introduced between newly connected triplets and quartets of beads, where the interaction type is determined from the local pattern of bead and bond types. When breaking bonds, all angular and dihedral interactions involving broken bonds are removed. The framework allows chemical reactions to be modeled, and use it to simulate a simplistic, coarse-grained DNA model. The resulting DNA dynamics illustrates the power of the present framework. Catalogue identifier: AEME_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEME_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public Licence No. of lines in distributed program, including test data, etc.: 2 243 491 No. of bytes in distributed program, including test data, etc.: 771 Distribution format: tar.gz Programming language: C++ Computer: Single and multiple core servers Operating system: Linux/Unix/Windows Has the code been vectorized or parallelized?: Yes. The code has been parallelized by the use of MPI directives. RAM: 1 Gb Classification: 16.11, 16.12 Nature of problem: Simulating coarse-grain models capable of chemistry e.g. DNA hybridization dynamics. Solution method: Extending LAMMPS to handle dynamic bonding and directional bonds. Unusual features: Allows bonds to be created and broken while angular and dihedral interactions are kept consistent. Additional comments: The distribution file for this program is approximately 36 Mbytes and therefore is not delivered directly when download or E-mail is requested. Instead an html file giving details of how the program can be obtained is sent. Running time: Hours to days. The examples provided in the distribution take just seconds to run.

Study on the mechanism of Si-glass-Si two step anodic bonding process

NASA Astrophysics Data System (ADS)

Hu, Lifang; Wang, Hao; Xue, Yongzhi; Shi, Fangrong; Chen, Shaoping

2018-04-01

Si-glass-Si was successfully bonded together through a two-step anodic bonding process. The bonding current in each step of the two-step bonding process was investigated, and found to be quite different. The first bonding current decreased quickly to a relatively small value, but for the second bonding step, there were two current peaks; the current first decreased, then increased, and then decreased again. The second current peak occurred earlier with higher temperature and voltage. The two-step anodic bonding process was investigated in terms of bonding current. SEM and EDS tests were conducted to investigate the interfacial structure of the Si-glass-Si samples. The two bonding interfaces were almost the same, but after an etching process, transitional layers could be found in the bonding interface and a deeper trench with a thickness of ~1.5 µm could be found in the second bonding interface. Atomic force microscopy mapping results indicated that sodium precipitated from the back of the glass, which makes the roughness of the surface become coarse. Tensile tests indicated that the fracture occurred at the glass substrate and that the bonding strength increased with the increment of bonding temperature and voltage with the maximum strength of 6.4 MPa.

Tabletop imaging of structural evolutions in chemical reactions demonstrated for the acetylene cation

NASA Astrophysics Data System (ADS)

Ibrahim, Heide; Wales, Benji; Beaulieu, Samuel; Schmidt, Bruno E.; Thiré, Nicolas; Fowe, Emmanuel P.; Bisson, Éric; Hebeisen, Christoph T.; Wanie, Vincent; Giguére, Mathieu; Kieffer, Jean-Claude; Spanner, Michael; Bandrauk, André D.; Sanderson, Joseph; Schuurman, Michael S.; Légaré, François

2014-07-01

The introduction of femto-chemistry has made it a primary goal to follow the nuclear and electronic evolution of a molecule in time and space as it undergoes a chemical reaction. Using Coulomb Explosion Imaging, we have shot the first high-resolution molecular movie of a to and fro isomerization process in the acetylene cation. So far, this kind of phenomenon could only be observed using vacuum ultraviolet light from a free-electron laser. Here we show that 266 nm ultrashort laser pulses are capable of initiating rich dynamics through multiphoton ionization. With our generally applicable tabletop approach that can be used for other small organic molecules, we have investigated two basic chemical reactions simultaneously: proton migration and C=C bond breaking, triggered by multiphoton ionization. The experimental results are in excellent agreement with the timescales and relaxation pathways predicted by new and quantitative ab initio trajectory simulations.

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

Wang, Yujie; Gong, Sha; Wang, Zhen

The thermodynamic and kinetic parameters of an RNA base pair were obtained through a long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The thermodynamic parameters were in good agreement with the nearest-neighbor model. The opening rates showed strong temperature dependence, however, the closing rates showed only weak temperature dependence. The transition path time was weakly temperature dependent and was insensitive to the energy barrier. The diffusion constant exhibited super-Arrhenius behavior. The free energy barrier of breaking a single base stack results from the enthalpy increase, ΔH, caused by the disruption ofmore » hydrogen bonding and base-stacking interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss, ΔS, caused by the restriction of torsional angles. These results suggest that a one-dimensional free energy surface is sufficient to accurately describe the dynamics of base pair opening and closing, and the dynamics are Brownian.« less

Some Applications of the Model of the Partion Points on a One Dimensional Lattice

NASA Astrophysics Data System (ADS)

Mejdani, R.; Huseini, H.

1996-02-01

We have shown that by using a model of gas of partition points on a one-dimensional lattice, we can find some results about the saturation curves for enzyme kinetics or the average domain-size, which we have obtained before by using a correlated walks' theory or a probabilistic (combinatoric) way. We have studied, using the same model and the same technique, the denaturation process, i.e., the breaking of the hydrogen bonds connecting the two strands, under treatment by heat. Also, we have discussed, without entering in details, the problem related to the spread of an infections disease and the stochastic model of partition points. We think that this model, being simple and mathematically transparent, can be advantageous for the other theoratical investigations in chemistry or modern biology. PACS NOS.: 05.50. + q; 05.70.Ce; 64.10.+h; 87.10. +e; 87.15.Rn

Biophysical behavior of Scomberoides commersonianus skin collagen.

PubMed

Kolli, Nagamalleswari; Joseph, K Thomas; Ramasami, T

2002-06-01

Some biophysical characteristics of the skin collagen from Scomberoides commersonianus were measured and compared to those of rat tail tendon. Stress-strain data indicate that the strain at break as well as the tensile strength of the fish skin without scales increased significantly. The maximum tension in case of rat skin is at least a factor of two higher than that observed in fish skin. The much lower hydrothermal isometric tension measurements observed in fish skin are attributable to a lesser number of heat stable crosslinks. Stress relaxation measurements in the fish skin indicate that more than one relaxation process may be involved in the stabilization of collagenous matrix. The observed differences in the biophysical behavior of fish skin may well arise from combination of changes in extent of hydroxylation of proline in collagen synthesis, hydrogen bond network and fibril orientation as compared to rat tail tendon.

De Novo Computational Design of Retro-Aldol Enzymes

PubMed Central

Jiang, Lin; Althoff, Eric A.; Clemente, Fernando R.; Doyle, Lindsey; Röthlisberger, Daniela; Zanghellini, Alexandre; Gallaher, Jasmine L.; Betker, Jamie L.; Tanaka, Fujie; Barbas, Carlos F.; Hilvert, Donald; Houk, Kendall N.; Stoddard, Barry L.; Baker, David

2012-01-01

The creation of enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Using new algorithms that rely on hashing techniques to construct active sites for multistep reactions, we designed retro-aldolases that use four different catalytic motifs to catalyze the breaking of a carbon-carbon bond in a nonnatural substrate. Of the 72 designs that were experimentally characterized, 32, spanning a range of protein folds, had detectable retro-aldolase activity. Designs that used an explicit water molecule to mediate proton shuffling were significantly more successful, with rate accelerations of up to four orders of magnitude and multiple turnovers, than those involving charged side-chain networks. The atomic accuracy of the design process was confirmed by the x-ray crystal structure of active designs embedded in two protein scaffolds, both of which were nearly superimposable on the design model. PMID:18323453

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

Hong, Seung Sae; Yu, Jung Ho; Lu, Di

Long-range order and phase transitions in two-dimensional (2D) systems—such as magnetism, superconductivity, and crystallinity—have been important research topics for decades. The issue of 2D crystalline order has reemerged recently, with the development of exfoliated atomic crystals. Understanding the dimensional limit of crystalline phases, with different types of bonding and synthetic techniques, is at the foundation of low-dimensional materials design. We study ultrathin membranes of SrTiO 3, an archetypal perovskite oxide with isotropic (3D) bonding. Atomically controlled membranes are released after synthesis by dissolving an underlying epitaxial layer. Although all unreleased films are initially single-crystalline, the SrTiO 3 membrane lattice collapsesmore » below a critical thickness (5 unit cells). This crossover from algebraic to exponential decay of the crystalline coherence length is analogous to the 2D topological Berezinskii-Kosterlitz-Thouless (BKT) transition. Finally, the transition is likely driven by chemical bond breaking at the 2D layer-3D bulk interface, defining an effective dimensional phase boundary for coherent crystalline lattices.« less

Imaging chiral symmetry breaking from Kekule bond order in graphene

DOE PAGES

Gutiérrez, Christopher; Kim, Cheol -Joo; Brown, Lola; ...

2016-05-23

Chirality—or ‘handedness’—is a symmetry property crucial to fields as diverse as biology, chemistry and high-energy physics. In graphene, chiral symmetry emerges naturally as a consequence of the carbon honeycomb lattice. This symmetry can be broken by interactions that couple electrons with opposite momenta in graphene. Here we directly visualize the formation of Kekulé bond order, one such phase of broken chiral symmetry, in an ultraflat graphene sheet grown epitaxially on a copper substrate. We show that its origin lies in the interactions between individual vacancies in the copper substrate that are mediated electronically by the graphene. We show that thismore » interaction causes the bonds in graphene to distort, creating a phase with broken chiral symmetry. Furthermore, the Kekulé ordering is robust at ambient temperature and atmospheric conditions, indicating that intercalated atoms may be harnessed to drive graphene and other two-dimensional materials towards electronically desirable and exotic collective phases.« less

Finite-temperature behavior of a classical spin-orbit-coupled model for YbMgGaO4 with and without bond disorder

NASA Astrophysics Data System (ADS)

Parker, Edward; Balents, Leon

2018-05-01

We present the results of finite-temperature classical Monte Carlo simulations of a strongly spin-orbit-coupled nearest-neighbor triangular-lattice model for the candidate U (1 ) quantum spin liquid YbMgGaO4 at large system sizes. We find a single continuous finite-temperature stripe-ordering transition with slowly diverging heat capacity that completely breaks the sixfold ground-state degeneracy, despite the absence of a known conformal field theory describing such a transition. We also simulate the effect of random-bond disorder in the model, and find that even weak bond disorder destroys the transition by fragmenting the system into very large domains—possibly explaining the lack of observed ordering in the real material. The Imry-Ma argument only partially explains this fragility to disorder, and we extend the argument with a physical explanation for the preservation of our system's time-reversal symmetry even under a disorder model that preserves the same symmetry.

Breaking the regioselectivity rule for acrylate insertion in the Mizoroki-Heck reaction.

PubMed

Wucher, Philipp; Caporaso, Lucia; Roesle, Philipp; Ragone, Francesco; Cavallo, Luigi; Mecking, Stefan; Göttker-Schnetmann, Inigo

2011-05-31

In modern methods for the preparation of small molecules and polymers, the insertion of substrate carbon-carbon double bonds into metal-carbon bonds is a fundamental step of paramount importance. This issue is illustrated by Mizoroki-Heck coupling as the most prominent example in organic synthesis and also by catalytic insertion polymerization. For unsymmetric substrates H(2)C = CHX the regioselectivity of insertion is decisive for the nature of the product formed. Electron-deficient olefins insert selectively in a 2,1-fashion for electronic reasons. A means for controlling this regioselectivity is lacking to date. In a combined experimental and theoretical study, we now report that, by destabilizing the transition state of 2,1-insertion via steric interactions, the regioselectivity of methyl acrylate insertion into palladium-methyl and phenyl bonds can be inverted entirely to yield the opposite "regioirregular" products in stoichiometric reactions. Insights from these experiments will aid the rational design of complexes which enable a catalytic and regioirregular Mizoroki-Heck reaction of electron-deficient olefins.

Temperature dependent polymorphism of pyrazinamide: An in situ Raman and DFT study

NASA Astrophysics Data System (ADS)

Sharma, Poornima; Nandi, Rajib; Gangopadhyay, Debraj; Singh, Anurag; Singh, Ranjan K.

2018-02-01

The α and γ polymorphs of drug pyrazinamide have been detected with the help of temperature dependent Raman spectroscopic technique. Pyrazinamide is a very useful drug used for the treatment of tuberculosis (TB) and plays a significant role in destroying the dormant tubercle bacilli which are not destroyed by other common TB drugs. Temperature dependent Raman spectra suggest polymorphic phase change from α → γ form of pyrazinamide between 145 and 146 °C. In situ Raman spectra of pyrazinamide between 145 and 146 °C show the conversion of α → γ form by the shift in Cdbnd O stretching vibration accompanied by several other changes. The phase change is characterized by the breaking of two linear Nsbnd H ⋯ O type hydrogen bonds associated with Cdbnd O stretching vibration in α dimer and formation of one linear Nsbnd H ⋯ N type hydrogen bond along with a weak intramolecular Csbnd H ⋯ O type hydrogen bond in the γ dimer.

Diffuse scattering measurements of static atomic displacements in crystalline binary solid solutions

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

Ice, G.E.; Sparks, C.J.; Jiang, X.

1997-09-01

Diffuse x-ray scattering from crystalline solid solutions is sensitive to both local chemical order and local bond distances. In short-range ordered alloys, fluctuations of chemistry and bond distances break the long-range symmetry of the crystal within a local region and contribute to the total energy of the alloy. Recent use of tunable synchrotron radiation to change the x-ray scattering contrast between elements has greatly advanced the measurement of bond distances between the three kinds of atom pairs found in crystalline binary alloys. The estimated standard deviation on these recovered static displacements approaches {+-}0.001 {angstrom} (0.0001 nm) which is an ordermore » of magnitude more precise than obtained with EXAFS. In addition, both the radial and tangential displacements can be recovered to five near neighbors and beyond. These static displacement measurements provide new information which challenges the most advanced theoretical models of binary crystalline alloys. 29 refs., 8 figs., 2 tabs.« less

Electrochemistry-Assisted Top-Down Characterization of Disulfide-Containing Proteins

PubMed Central

Zhang, Yun; Cui, Weidong; Zhang, Hao; Dewald, Howard D.; Chen, Hao

2013-01-01

Covalent disulfide bond linkage in a protein represents an important challenge for mass spectrometry (MS)-based top-down protein structure analysis as it reduces the backbone cleavage efficiency for MS/MS dissociation. This study presents a strategy for solving this critical issue via integrating electrochemistry (EC) online with top-down MS approach. In this approach, proteins undergo electrolytic reduction in an electrochemical cell to break disulfide bonds and then online ionized into gaseous ions for analysis by electron-capture dissociation (ECD) and collision-induced dissociation (CID). The electrochemical reduction of proteins allows to remove disulfide bond constraints and also leads to increased charge numbers of the resulting protein ions. As a result, sequence coverage was significantly enhanced, as exemplified by β-lactoglobulin A (24 vs. 73 backbone cleavages before and after electrolytic reduction, respectively) and lysozyme (5 vs. 66 backbone cleavages before and after electrolytic reduction, respectively). This methodology is fast and does not need chemical reductants, which would have an important impact in high-throughput proteomics research. PMID:22448817

Electrochemistry-assisted top-down characterization of disulfide-containing proteins.

PubMed

Zhang, Yun; Cui, Weidong; Zhang, Hao; Dewald, Howard D; Chen, Hao

2012-04-17

Covalent disulfide bond linkage in a protein represents an important challenge for mass spectrometry (MS)-based top-down protein structure analysis as it reduces the backbone cleavage efficiency for MS/MS dissociation. This study presents a strategy for solving this critical issue via integrating electrochemistry (EC) online with a top-down MS approach. In this approach, proteins undergo electrolytic reduction in an electrochemical cell to break disulfide bonds and then undergo online ionization into gaseous ions for analysis by electron-capture dissociation (ECD) and collision-induced dissociation (CID). The electrochemical reduction of proteins allows one to remove disulfide bond constraints and also leads to increased charge numbers of the resulting protein ions. As a result, sequence coverage was significantly enhanced, as exemplified by β-lactoglobulin A (24 vs 75 backbone cleavages before and after electrolytic reduction, respectively) and lysozyme (5 vs 66 backbone cleavages before and after electrolytic reduction, respectively). This methodology is fast and does not need chemical reductants, which would have an important impact in high-throughput proteomics research.

A non-JKL density matrix functional for intergeminal correlation between closed-shell geminals from analysis of natural orbital configuration interaction expansions

NASA Astrophysics Data System (ADS)

van Meer, R.; Gritsenko, O. V.; Baerends, E. J.

2018-03-01

Almost all functionals that are currently used in density matrix functional theory have been created by some a priori ansatz that generates approximations to the second-order reduced density matrix (2RDM). In this paper, a more consistent approach is used: we analyze the 2RDMs (in the natural orbital basis) of rather accurate multi-reference configuration interaction expansions for several small molecules (CH4, NH3, H2O, FH, and N2) and use the knowledge gained to generate new functionals. The analysis shows that a geminal-like structure is present in the 2RDMs, even though no geminal theory has been applied from the onset. It is also shown that the leading non-geminal dynamical correlation contributions are generated by a specific set of double excitations. The corresponding determinants give rise to non-JKL (non Coulomb/Exchange like) multipole-multipole dispersive attractive terms between geminals. Due to the proximity of the geminals, these dispersion terms are large and cannot be omitted, proving pure JKL functionals to be essentially deficient. A second correction emerges from the observation that the "normal" geminal-like exchange between geminals breaks down when one breaks multiple bonds. This problem can be fixed by doubling the exchange between bond broken geminals, effectively restoring the often physically correct high-spin configurations on the bond broken fragments. Both of these corrections have been added to the commonly used antisymmetrized product of strongly orthogonal geminals functional. The resulting non-JKL functional Extended Löwdin-Shull Dynamical-Multibond is capable of reproducing complete active space self-consistent field curves, in which one active orbital is used for each valence electron.

HIGH-ENERGY ELECTRON IRRADIATION OF INTERSTELLAR CARBONACEOUS DUST ANALOGS: COSMIC-RAY EFFECTS ON THE CARRIERS OF THE 3.4 μ m ABSORPTION BAND

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

Maté, Belén; Molpeceres, Germán; Jiménez-Redondo, Miguel

2016-11-01

The effects of cosmic rays on the carriers of the interstellar 3.4 μ m absorption band have been investigated in the laboratory. This band is attributed to stretching vibrations of CH{sub 3} and CH{sub 2} in carbonaceous dust. It is widely observed in the diffuse interstellar medium, but disappears in dense clouds. Destruction of CH{sub 3} and CH{sub 2} by cosmic rays could become relevant in dense clouds, shielded from the external ultraviolet field. For the simulations, samples of hydrogenated amorphous carbon (a-C:H) have been irradiated with 5 keV electrons. The decay of the band intensity versus electron fluence reflectsmore » a-C:H dehydrogenation, which is well described by a model assuming that H{sub 2} molecules, formed by the recombination of H atoms liberated through CH bond breaking, diffuse out of the sample. The CH bond destruction rates derived from the present experiments are in good accordance with those from previous ion irradiation experiments of HAC. The experimental simplicity of electron bombardment has allowed the use of higher-energy doses than in the ion experiments. The effects of cosmic rays on the aliphatic components of cosmic dust are found to be small. The estimated cosmic-ray destruction times for the 3.4 μ m band carriers lie in the 10{sup 8} yr range and cannot account for the disappearance of this band in dense clouds, which have characteristic lifetimes of 3 × 10{sup 7} yr. The results invite a more detailed investigation of the mechanisms of CH bond formation and breaking in the intermediate region between diffuse and dense clouds.« less

Fragmentation and bond strength of airborne diesel soot agglomerates

PubMed Central

Rothenbacher, Sonja; Messerer, Armin; Kasper, Gerhard

2008-01-01

Background The potential of diesel soot aerosol particles to break up into smaller units under mechanical stress was investigated by a direct impaction technique which measures the degree of fragmentation of individual agglomerates vs. impact energy. Diesel aerosol was generated by an idling diesel engine used for passenger vehicles. Both the aerosol emitted directly and aerosol that had undergone additional growth by Brownian coagulation ("aging") was investigated. Optionally a thermo-desoption technique at 280°C was used to remove all high-volatility and the majority of low-volatility HC adsorbates from the aerosol before aging. Results It was found that the primary soot agglomerates emitted directly from the engine could not be fragmented at all. Soot agglomerates permitted to grow additionally by Brownian coagulation of the primary emitted particles could be fragmented to a maximum of 75% and 60% respectively, depending on whether adsorbates were removed from their surface prior to aging or not. At most, these aged agglomerates could be broken down to roughly the size of the agglomerates from the primary emission. The energy required for a 50% fragmentation probability of all bonds within an agglomerate was reduced by roughly a factor of 2 when aging "dry" agglomerates. Average bond energies derived from the data were 0.52*10-16 and 1.2*10-16 J, respectively. This is about 2 orders of magnitude higher than estimates for pure van-der-Waals agglomerates, but agrees quite well with other observations. Conclusion Although direct conclusions regarding the behavior of inhaled diesel aerosol in contact with body fluids cannot be drawn from such measurements, the results imply that highly agglomerated soot aerosol particles are unlikely to break up into units smaller than roughly the size distribution emitted as tail pipe soot. PMID:18533015

Computational Insight into the Mechanism of Alkane Hydroxylation by Non-heme Fe(PyTACN) Iron Complexes. Effects of the Substrate and Solvent.

PubMed

Postils, Verònica; Company, Anna; Solà, Miquel; Costas, Miquel; Luis, Josep M

2015-09-08

The reaction mechanisms for alkane hydroxylation catalyzed by non-heme Fe(V)O complexes presented in the literature vary from rebound stepwise to concerted highly asynchronous processes. The origin of these important differences is still not completely understood. Herein, in order to clarify this apparent inconsistency, the hydroxylation of a series of alkanes (methane and substrates bearing primary, secondary, and tertiary C-H bonds) through a Fe(V)O species, [Fe(V)(O)(OH)(PyTACN)](2+) (PyTACN = 1-(2'-pyridylmethyl)-4,7-dimethyl-1,4,7-triazacyclononane), has been computationally examined at the gas phase and in acetonitrile solution. The initial breaking of the C-H bond can occur via hydrogen atom transfer (HAT), leading to an intermediate where there is an interaction between the radical substrate and [Fe(IV)(OH)2(PyTACN)](2+), or through hydride transfer to form a cationic substrate interacting with the [Fe(III)(OH)2(PyTACN)](+) species. Our calculations show the following: (i) except for methane in the rest of the alkanes studied, the intermediate formed by R(+) and [Fe(III)(OH)2(PyTACN)](+) is more stable than that involving the alkyl radical and the [Fe(IV)(OH)2(PyTACN)](2+) complex; (ii) in spite of (i), the first step of the reaction mechanism for all substrates is a HAT instead of hydride abstraction; (iii) the HAT is the rate-determining step for all analyzed cases; and (iv) the barrier for the HAT decreases along methane → primary → secondary → tertiary carbon. The second part of the reaction mechanism corresponds to the rebound process. Therefore, the stereospecific hydroxylation of alkane C-H bonds by non-heme Fe(V)(O) species occurs through a rebound stepwise mechanism that resembles that taking place at heme analogues. Finally, our study also shows that, to properly describe alkane hydroxylation processes mediated by Fe(V)O species, it is essential to consider the solvent effects during geometry optimizations. The use of gas-phase geometries explains the variety of mechanisms for the hydroxylation of alkanes reported in the literature.

Reactive Molecular Dynamics Simulations to Understand Mechanical Response of Thaumasite under Temperature and Strain Rate Effects.

PubMed

Hajilar, Shahin; Shafei, Behrouz; Cheng, Tao; Jaramillo-Botero, Andres

2017-06-22

Understanding the structural, thermal, and mechanical properties of thaumasite is of great interest to the cement industry, mainly because it is the phase responsible for the aging and deterioration of civil infrastructures made of cementitious materials attacked by external sources of sulfate. Despite the importance, effects of temperature and strain rate on the mechanical response of thaumasite had remained unexplored prior to the current study, in which the mechanical properties of thaumasite are fully characterized using the reactive molecular dynamics (RMD) method. With employing a first-principles based reactive force field, the RMD simulations enable the description of bond dissociation and formation under realistic conditions. From the stress-strain curves of thaumasite generated in the x, y, and z directions, the tensile strength, Young's modulus, and fracture strain are determined for the three orthogonal directions. During the course of each simulation, the chemical bonds undergoing tensile deformations are monitored to reveal the bonds responsible for the mechanical strength of thaumasite. The temperature increase is found to accelerate the bond breaking rate and consequently the degradation of mechanical properties of thaumasite, while the strain rate only leads to a slight enhancement of them for the ranges considered in this study.

Methanol clusters (CH3OH)n, n = 3-6 in external electric fields: density functional theory approach.

PubMed

Rai, Dhurba; Kulkarni, Anant D; Gejji, Shridhar P; Pathak, Rajeev K

2011-07-14

Structural evolution of cyclic and branched-cyclic methanol clusters containing three to six molecules, under the influence of externally applied uniform static electric field is studied within the density functional theory. Akin to the situation for water clusters, the electric field is seen to stretch the intermolecular hydrogen bonds, and eventually break the H-bonded network at certain characteristic threshold field values of field strength in the range 0.009-0.016 a.u., yielding linear or branched structures with a lower energy. These structural transitions are characterized by an abrupt increase in the electric dipole moment riding over its otherwise steady nonlinear increase with the applied field. The field tends to rupture the H-bonded structure; consequently, the number of hydrogen bonds decreases with increasing field strength. Vibrational spectra analyzed for fields applied perpendicular to the cyclic ring structures bring out the shifts in the OH ring vibrations (blueshift) and the CO stretch vibrations (redshift). For a given field strength, the blueshifts increase with the number of molecules in the ring and are found to be generally larger than those in the corresponding water cluster counterparts.

Stability Limits and Dynamics of Nonaxisymmetric Liquid Bridges

NASA Technical Reports Server (NTRS)

Alexander, J. Iwan D.

1996-01-01

Theoretical and experimental investigation of the stability of nonaxisymmetric and axisymmetric bridges contained between equal and unequal radii disks as a function of Bond and Weber number with emphasis on the transition from unstable axisymmetric to stable nonaxisymmetric shapes. Numerical analysis of the stability of nonaxisymmetric bridges between unequal disks for various orientations of the gravity vector Experimental and numerical investigation of bridge stability (nonaxisymmetric and axisymmetric), large amplitude (nonaxisymmetric) oscillations and breaking.

Analysis of the market for a new frozen coal release device

NASA Technical Reports Server (NTRS)

Taglio, S.

1981-01-01

Conditions that contribute to coal freezing and the costs of frozen coal handling are discussed. The various methods currently used to handle frozen coal are examined and assessed relative to costs, effectiveness, and advantages and disadvantages. A NASA designed gas detonation lance for breaking the ice bonds between frozen coal nuggets is described and illustrated. Market demand for the controlled gas detonation lance is estimated to be at least 10 units.

Preignition and Autoignition Behavior of the Xylene Isomers

DTIC Science & Technology

2010-03-01

3 β-scission is the breaking of the carbon-carbon bond at the carbon atom one removed from the radical site (Law, 2006). 10...jet fuel (TS-1); this sample matches the average paraffin, naphthene , and aromatic content of jet fuel samples fairly well (Holley et al., 2007). A...Moreover, Lenhert et al. (2009) identified phenol as an intermediate from toluene oxidation in the PFR facility. This also removes concern that phenol may

Atomic Oxygen Effects

NASA Technical Reports Server (NTRS)

Miller, Sharon K. R.

2014-01-01

Atomic oxygen, which is the most predominant species in low Earth orbit, is highly reactive and can break chemical bonds on the surface of a wide variety of materials leading to volatilization or surface oxidation which can result in failure of spacecraft materials and components. This presentation will give an overview of how atomic oxygen reacts with spacecraft materials, results of space exposure testing of a variety of materials, and examples of failures caused by atomic oxygen.

31 CFR 224.3 - When may a surety corporation provide a bond without appointing a process agent?

Code of Federal Regulations, 2011 CFR

2011-07-01

... MANAGEMENT SERVICE FEDERAL PROCESS AGENTS OF SURETY CORPORATIONS § 224.3 When may a surety corporation provide a bond without appointing a process agent? A surety corporation may provide a bond without... a bond without appointing a process agent? 224.3 Section 224.3 Money and Finance: Treasury...

Mechanical response of transient telechelic networks with many-part stickers

NASA Astrophysics Data System (ADS)

Sing, Michelle K.; Ramírez, Jorge; Olsen, Bradley D.

2017-11-01

A central question in soft matter is understanding how several individual, weak bonds act together to produce collective interactions. Here, gel-forming telechelic polymers with multiple stickers at each chain end are studied through Brownian dynamics simulations to understand how collective interaction of the bonds affects mechanical response of the gels. These polymers are modeled as finitely extensible dumbbells using an explicit tau-leap algorithm and the binding energy of these associations was kept constant regardless of the number of stickers. The addition of multiple bonds to the associating ends of telechelic polymers increases or decreases the network relaxation time depending on the relative kinetics of association but increases both shear stress and extensional viscosity. The relationship between the rate of association and the Rouse time of dangling chains results in two different regimes for the equilibrium stress relaxation of associating physical networks. In case I, a dissociated dangling chain is able to fully relax before re-associating to the network, resulting in two characteristic relaxation times and a non-monotonic terminal relaxation time with increasing number of bonds per polymer endgroup. In case II, the dissociated dangling chain is only able to relax a fraction of the way before it re-attaches to the network, and increasing the number of bonds per endgroup monotonically increases the terminal relaxation time. In flow, increasing the number of stickers increases the steady-state shear and extensional viscosities even though the overall bond kinetics and equilibrium constant remain unchanged. Increased dissipation in the simulations is primarily due to higher average chain extension with increasing bond number. These results indicate that toughness and dissipation in physically associating networks can both be increased by breaking single, strong bonds into smaller components.

Analysis of factors influencing the bond strength in roll bonding processes

NASA Astrophysics Data System (ADS)

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.

A coarse-grained model for synergistic action of multiple enzymes on cellulose

DOE PAGES

Asztalos, Andrea; Daniels, Marcus; Sethi, Anurag; ...

2012-08-01

In this study, degradation of cellulose to glucose requires the cooperative action of three classes of enzymes, collectively known as cellulases. Endoglucanases randomly bind to cellulose surfaces and generate new chain ends by hydrolyzing -1,4-D-glycosidic bonds. Exoglucanases bind to free chain ends and hydrolyze glycosidic bonds in a processive manner releasing cellobiose units. Then, -glucosidases hydrolyze soluble cellobiose to glucose. Optimal synergistic action of these enzymes is essential for efficient digestion of cellulose. Experiments show that as hydrolysis proceeds and the cellulose substrate becomes more heterogeneous, the overall degradation slows down. As catalysis occurs on the surface of crystalline cellulose,more » several factors affect the overall hydrolysis. Therefore, spatial models of cellulose degradation must capture effects such as enzyme crowding and surface heterogeneity, which have been shown to lead to a reduction in hydrolysis rates. As a result, we present a coarse-grained stochastic model for capturing the key events associated with the enzymatic degradation of cellulose at the mesoscopic level. This functional model accounts for the mobility and action of a single cellulase enzyme as well as the synergy of multiple endo- and exo-cellulases on a cellulose surface. The quantitative description of cellulose degradation is calculated on a spatial model by including free and bound states of both endo- and exo-cellulases with explicit reactive surface terms (e.g., hydrogen bond breaking, covalent bond cleavages) and corresponding reaction rates. The dynamical evolution of the system is simulated by including physical interactions between cellulases and cellulose. In conclusion, our coarse-grained model reproduces the qualitative behavior of endoglucanases and exoglucanases by accounting for the spatial heterogeneity of the cellulose surface as well as other spatial factors such as enzyme crowding. Importantly, it captures the endo-exo synergism of cellulase enzyme cocktails. This model constitutes a critical step towards testing hypotheses and understanding approaches for maximizing synergy and substrate properties with a goal of cost effective enzymatic hydrolysis.« less

Laccase catalysed grafting of phenolic onto xylan to improve its applicability in films

NASA Astrophysics Data System (ADS)

Pei, Jicheng; Wang, Bing; Zhang, Fangdong; Li, Zhongyang; Yin, Yunbei; Zhang, Dongxu

2015-07-01

Xylan can be tailored for various value-added applications. However, its use in aqueous systems is hampered by its complex structure, and small molecular weight. This research aimed at improving the xylan molecular weight and changing its structure. Laccase-catalysed oxidation of 4-coumaric acid (PCA), ferulic acid (FA), syringaldehyde (SD), and vanillin (VA) onto xylan was grafted to study the changes in its structure, tensile properties, and antibacterial activities. A Fourier transform infrared (FTIR) spectrum analyser was used to observe the changes in functional groups of xylan. The results showed a band at 1635 cm-1 corresponding to the stretching vibration of conjugated carbonyl carboxy hemoglobin and a benzene ring structure were strengthened; the appearance of a new band between 1200 cm-1 and 1270 cm-1 corresponding to alkyl ethers on the aryl C-O stretching vibration was due to the fact that during the grafting process, the number of benzene ring structures increased and covalent connections occurred between phenols and xylan. The reaction mechanism for the laccase-catalysed oxidation of phenol compounds onto xylan was preliminary explored by 13C-NMR. The results showed that PCA-xylan, FA-xylan graft poly onto xylan by Cγ ester bond, SD-xylan graft poly onto xylan by ether bond and an ester bond, and VD-xylan graft poly onto xylan by ether bond. The film strength of xylan derivatives has been significantly increased, especially for the PCA-xylan derivative. The increases in tensile stress at break, tensile strength, tensile yield stress, and Young's modulus were: 24.04%, 31.30%, 55.56%, and 28.21%, respectively. After laccase/phenolics were modified, xylan had a good antibacterial effect to E. coli, Corynebacterium glutamicum, and Bacillus subtilis. The SD-xylan, FA-xylan, and PCA-xylan showed a greater efficacy against E. coli, Corynebacterium glutamicum, and Bacillus subtilis, respectively.

Processing Load Imposed by Line Breaks in English Temporal Wh-Questions

PubMed Central

Hirotani, Masako; Terry, J. Michael; Sadato, Norihiro

2016-01-01

Prosody plays an important role in online sentence processing both explicitly and implicitly. It has been shown that prosodically packaging together parts of a sentence that are interpreted together facilitates processing of the sentence. This applies not only to explicit prosody but also implicit prosody. The present work hypothesizes that a line break in a written text induces an implicit prosodic break, which, in turn, should result in a processing bias for interpreting English wh-questions. Two experiments—one self-paced reading study and one questionnaire study—are reported. Both supported the “line break” hypothesis mentioned above. The results of the self-paced reading experiment showed that unambiguous wh-questions were read faster when the location of line breaks (or frame breaks) matched the scope of a wh-phrase (main or embedded clause) than when they did not. The questionnaire tested sentences with an ambiguous wh-phrase, one that could attach either to the main or the embedded clause. These sentences were interpreted as attaching to the main clause more often than to the embedded clause when a line break appeared after the main verb, but not when it appeared after the embedded verb. PMID:27774072

Bio-Electron-Fenton (BEF) process driven by microbial fuel cells for triphenyltin chloride (TPTC) degradation.

PubMed

Yong, Xiao-Yu; Gu, Dong-Yan; Wu, Yuan-Dong; Yan, Zhi-Ying; Zhou, Jun; Wu, Xia-Yuan; Wei, Ping; Jia, Hong-Hua; Zheng, Tao; Yong, Yang-Chun

2017-02-15

The intensive use of triphenyltin chloride (TPTC) has caused serious environmental pollution. In this study, an effective method for TPTC degradation was proposed based on the Bio-Electron-Fenton process in microbial fuel cells (MFCs). The maximum voltage of the MFC with graphite felt as electrode was 278.47% higher than that of carbon cloth. The electricity generated by MFC can be used for in situ generation of H 2 O 2 to a maximum of 135.96μmolL -1 at the Fe@Fe 2 O 3(*) /graphite felt composite cathode, which further reacted with leached Fe 2+ to produce hydroxyl radicals. While 100μmolL -1 TPTC was added to the cathodic chamber, the degradation efficiency of TPTC reached 78.32±2.07%, with a rate of 0.775±0.021μmolL -1 h -1 . This Bio-Electron-Fenton driving TPTC degradation might involve in SnC bonds breaking and the main process is probably a stepwise dephenylation until the formation of inorganic tin and CO 2 . This study provides an energy saving and efficient approach for TPTC degradation. Copyright © 2016 Elsevier B.V. All rights reserved.

Intermediate states and structure evolution in the free-falling process of the dislocation in graphene

NASA Astrophysics Data System (ADS)

Wang, Shaofeng; Yao, Yin; Bai, Jianhui; Wang, Rui

2017-04-01

This paper investigated the intermediate states and the structure evolution of the dislocation in graphene when it falls freely from the saddle point of the energy landscape. The O-type dislocation, an unstable equilibrium structure located at the saddle point, is obtained from the lattice theory of the dislocation structure and improved by the ab initio calculation to take the buckling into account. Intermediate states along the kinetics path in the falling process are obtained from the ab initio simulation. Once the dislocation falls from the saddle point to the energy valley, this O-type dislocation transforms into the stable structure that is referred to as the B-type dislocation, and in the meantime, it moves a distance that equals half a Burgers vector. The structure evolution and the energy variation in the free-falling process are revealed explicitly. It is observed that rather than smooth change, a platform manifests itself in the energy curve. The unusual behaviour in the energy curve is mainly originated from symmetry breaking and bond formation in the dislocation core. The results can provide deep insight in the mechanism of the brittle feature of covalent materials.

Advanced water remediation from ofloxacin by ionizing radiation

NASA Astrophysics Data System (ADS)

Esposito, Biagio R.; Capobianco, Massimo L.; Martelli, Alessandro; Navacchia, Maria Luisa; Pretali, Luca; Saracino, Michela; Zanelli, Alberto; Emmi, Salvatore S.

2017-12-01

The performances of remediation processes initiated by ionizing radiation on ofloxacin are investigated in ambient conditions. The effectiveness of the decomposition of ofloxacin has been assessed both by γ-rays and electron beam in various aqueous solutions differentiated by the dissolved gases (Air or oxygen saturated) and H2O2. By HPLC it is shown that ofloxacin is removed according to a first order process vs. dose in any system. O2 accelerates the decomposition rate, while H2O2 does not seem to enhance any oxidation effect. The simultaneous oxidative-reductive treatment (no additive) demonstrated to have better mineralizing performances than the fully oxidative one (H2O2 present). Mineralization by γ results to be more efficient than by EB. The Total Organic Carbon decrease was investigated in dependence of dose and of the •OH production rate. The latter parameter was changed over 7 orders of magnitude by controlling dose rate and/or by adding H2O2. A steep increase of acidity remarks the phases of fluorine-carbon bond break.

Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance

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

Pluta, Radoslaw; Boer, D. Roeland; Lorenzo-Diaz, Fabian

Relaxases are metal-dependent nucleases that break and join DNA for the initiation and completion of conjugative bacterial gene transfer. Conjugation is the main process through which antibiotic resistance spreads among bacteria, with multidrug-resistant staphylococci and streptococci infections posing major threats to human health. The MOB V family of relaxases accounts for approximately 85% of all relaxases found in Staphylococcus aureus isolates. Here, we present six structures of the MOB V relaxase MobM from the promiscuous plasmid pMV158 in complex with several origin of transfer DNA fragments. A combined structural, biochemical, and computational approach reveals that MobM follows a previously uncharacterizedmore » histidine/metal-dependent DNA processing mechanism, which involves the formation of a covalent phosphoramidate histidine-DNA adduct for cell-to-cell transfer. In conclusion, we discuss how the chemical features of the high-energy phosphorus-nitrogen bond shape the dominant position of MOB V histidine relaxases among small promiscuous plasmids and their preference toward Gram-positive bacteria.« less

Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance

DOE PAGES

Pluta, Radoslaw; Boer, D. Roeland; Lorenzo-Diaz, Fabian; ...

2017-07-24

Relaxases are metal-dependent nucleases that break and join DNA for the initiation and completion of conjugative bacterial gene transfer. Conjugation is the main process through which antibiotic resistance spreads among bacteria, with multidrug-resistant staphylococci and streptococci infections posing major threats to human health. The MOB V family of relaxases accounts for approximately 85% of all relaxases found in Staphylococcus aureus isolates. Here, we present six structures of the MOB V relaxase MobM from the promiscuous plasmid pMV158 in complex with several origin of transfer DNA fragments. A combined structural, biochemical, and computational approach reveals that MobM follows a previously uncharacterizedmore » histidine/metal-dependent DNA processing mechanism, which involves the formation of a covalent phosphoramidate histidine-DNA adduct for cell-to-cell transfer. In conclusion, we discuss how the chemical features of the high-energy phosphorus-nitrogen bond shape the dominant position of MOB V histidine relaxases among small promiscuous plasmids and their preference toward Gram-positive bacteria.« less

Short Term Preservation of Hide Using Vacuum: Influence on Properties of Hide and of Processed Leather

PubMed Central

Gudro, Ilze; Valeika, Virgilijus; Sirvaitytė, Justa

2014-01-01

The objective of this work was to investigate vacuum influence on hide preservation time and how it affects hide structure. It was established that vacuum prolongs the storage time without hide tissue putrefaction up to 21 days when the storage temperature is 4°C. The microorganisms act for all storage times, but the action is weak and has no observable influence on the quality of hide during the time period mentioned. The hide shrinkage temperature decrease is negligible, which shows that breaking of intermolecular bonds does not occur. Optical microscopy, infrared spectroscopy and differential scanning calorimetry also did not show any structural changes which can influence the quality of leather produced from such hide. The qualitative indexes of wet blue processed under laboratory conditions and of leather produced during industrial trials are presented. Indexes such as chromium compounds exhaustion, content of chromium in leather, content of soluble matter in dichloromethane, strength properties, and shrinkage temperature were determined. Properties of the leather produced from vacuumed hide under industrial conditions conformed to the requirements of shoe upper leather. PMID:25393637

Fabrication of Wood-Rubber Composites Using Rubber Compound as a Bonding Agent Instead of Adhesives

PubMed Central

Shao, Dongwei; Xu, Min; Cai, Liping; Shi, Sheldon Q.

2016-01-01

Differing from the hot-pressing method in the manufacturing of traditional wood-rubber composites (WRCs), this study was aimed at fabricating WRCs using rubber processing to improve water resistance and mechanical properties. Three steps were used to make WRCs, namely, fiber-rubber mixing, tabletting, and the vulcanization molding process. Ninety-six WRC panels were made with wood fiber contents of 0%–50% at rotor rotational speeds of 15–45 rpm and filled coefficients of 0.55–0.75. Four regression equations, i.e., the tensile strength (Ts), elongation at break (Eb), hardness (Ha) and rebound resilience (Rr) as functions of fiber contents, rotational speed and filled coefficient, were derived and a nonlinear programming model were developed to obtain the optimum composite properties. Although the Ts, Eb and Rr of the panels were reduced, Ha was considerably increased by 17%–58% because of the wood fiber addition. Scanning electron microscope images indicated that fibers were well embedded in rubber matrix. The 24 h water absorption was only 1%–3%, which was much lower than commercial wood-based composites. PMID:28773591

Quantitative analysis of the thermal requirements for stepwise physical dormancy-break in seeds of the winter annual Geranium carolinianum (Geraniaceae)

PubMed Central

Gama-Arachchige, N. S.; Baskin, J. M.; Geneve, R. L.; Baskin, C. C.

2013-01-01

Background and Aims Physical dormancy (PY)-break in some annual plant species is a two-step process controlled by two different temperature and/or moisture regimes. The thermal time model has been used to quantify PY-break in several species of Fabaceae, but not to describe stepwise PY-break. The primary aims of this study were to quantify the thermal requirement for sensitivity induction by developing a thermal time model and to propose a mechanism for stepwise PY-breaking in the winter annual Geranium carolinianum. Methods Seeds of G. carolinianum were stored under dry conditions at different constant and alternating temperatures to induce sensitivity (step I). Sensitivity induction was analysed based on the thermal time approach using the Gompertz function. The effect of temperature on step II was studied by incubating sensitive seeds at low temperatures. Scanning electron microscopy, penetrometer techniques, and different humidity levels and temperatures were used to explain the mechanism of stepwise PY-break. Key Results The base temperature (Tb) for sensitivity induction was 17·2 °C and constant for all seed fractions of the population. Thermal time for sensitivity induction during step I in the PY-breaking process agreed with the three-parameter Gompertz model. Step II (PY-break) did not agree with the thermal time concept. Q10 values for the rate of sensitivity induction and PY-break were between 2·0 and 3·5 and between 0·02 and 0·1, respectively. The force required to separate the water gap palisade layer from the sub-palisade layer was significantly reduced after sensitivity induction. Conclusions Step I and step II in PY-breaking of G. carolinianum are controlled by chemical and physical processes, respectively. This study indicates the feasibility of applying the developed thermal time model to predict or manipulate sensitivity induction in seeds with two-step PY-breaking processes. The model is the first and most detailed one yet developed for sensitivity induction in PY-break. PMID:23456728

9 CFR 590.520 - Breaking room facilities.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 9 Animals and Animal Products 2 2014-01-01 2014-01-01 false Breaking room facilities. 590.520..., Processing, and Facility Requirements § 590.520 Breaking room facilities. (a) The breaking room shall have at.... (d) Ventilation shall provide for: (1) A positive flow of outside filtered air through the room; (2...

9 CFR 590.520 - Breaking room facilities.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 9 Animals and Animal Products 2 2012-01-01 2012-01-01 false Breaking room facilities. 590.520..., Processing, and Facility Requirements § 590.520 Breaking room facilities. (a) The breaking room shall have at.... (d) Ventilation shall provide for: (1) A positive flow of outside filtered air through the room; (2...

9 CFR 590.520 - Breaking room facilities.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 9 Animals and Animal Products 2 2013-01-01 2013-01-01 false Breaking room facilities. 590.520..., Processing, and Facility Requirements § 590.520 Breaking room facilities. (a) The breaking room shall have at.... (d) Ventilation shall provide for: (1) A positive flow of outside filtered air through the room; (2...

An active-site phenylalanine directs substrate binding and C-H cleavage in the alpha-ketoglutarate-dependent dioxygenase TauD.

PubMed

McCusker, Kevin P; Klinman, Judith P

2010-04-14

Enzymes that cleave C-H bonds are often found to depend on well-packed hydrophobic cores that influence the distance between the hydrogen donor and acceptor. Residue F159 in taurine alpha-ketoglutarate dioxygenase (TauD) is demonstrated to play an important role in the binding and orientation of its substrate, which undergoes a hydrogen atom transfer to the active site Fe(IV)=O. Mutation of F159 to smaller hydrophobic side chains (L, V, A) leads to substantially reduced rates for substrate binding and for C-H bond cleavage, as well as increased contribution of the chemical step to k(cat) under steady-state turnover conditions. The greater sensitivity of these substrate-dependent processes to mutation at position 159 than observed for the oxygen activation process supports a previous conclusion of modularity of function within the active site of TauD (McCusker, K. P.; Klinman, J. P. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 19791-19795). Extraction of intrinsic deuterium kinetic isotope effects (KIEs) using single turnover transients shows 2- to 4-fold increase in the size of the KIE for F159V in relation to wild-type and F159L. It appears that there is a break in behavior following removal of a single methylene from the side chain of F159L to generate F159V, whereby the protein active site loses its ability to restore the internuclear distance between substrate and Fe(IV)=O that supports optimal hydrogenic wave function overlap.

The molecular structure and absorption spectrum of hydroxy substituted dibenzoylmethanatoboron difluoride in solution: A theoretical and experimental study

NASA Astrophysics Data System (ADS)

Gelfand, Natalia; Freidzon, Alexandra; Fedorenko, Elena

2018-01-01

Electronic spectroscopy and quantum chemistry are used to study the structure and absorption spectra of the hydroxy substituted dibenzoylmethanatoboron difluoride (OHDBMBF2) in solutions. Introducing a hydroxy group in the diketonate moiety allows the dye to form intermolecular complexes with proton acceptors, such as solvents or analytes, thus making it a promising chemical sensor. Our calculations show that donor oxygen-containing solvents break the intramolecular hydrogen bond Osbnd H···Odik and form an intermolecular Osbnd H···Osolv bond thus disrupting the coplanarity of the dye and affecting the position and shape of its absorption bands. The spectra calculated with explicit solvent combined with polarizable continuum model (PCM) better agree with the experiment than those calculated only within PCM.

Subangstrom resolution X-ray structure details aquaporin-water interactions.

PubMed

Eriksson, Urszula Kosinska; Fischer, Gerhard; Friemann, Rosmarie; Enkavi, Giray; Tajkhorshid, Emad; Neutze, Richard

2013-06-14

Aquaporins are membrane channels that facilitate the flow of water across biological membranes. Two conserved regions are central for selective function: the dual asparagine-proline-alanine (NPA) aquaporin signature motif and the aromatic and arginine selectivity filter (SF). Here, we present the crystal structure of a yeast aquaporin at 0.88 angstrom resolution. We visualize the H-bond donor interactions of the NPA motif's asparagine residues to passing water molecules; observe a polarized water-water H-bond configuration within the channel; assign the tautomeric states of the SF histidine and arginine residues; and observe four SF water positions too closely spaced to be simultaneously occupied. Strongly correlated movements break the connectivity of SF waters to other water molecules within the channel and prevent proton transport via a Grotthuss mechanism.

DNA Nucleotide Sequence Restricted by the RI Endonuclease

PubMed Central

Hedgpeth, Joe; Goodman, Howard M.; Boyer, Herbert W.

1972-01-01

The sequence of DNA base pairs adjacent to the phosphodiester bonds cleaved by the RI restriction endonuclease in unmodified DNA from coliphage λ has been determined. The 5′-terminal nucleotide labeled with 32P and oligonucleotides up to the heptamer were analyzed from a pancreatic DNase digest. The following sequence of nucleotides adjacent to the RI break made in λ DNA was deduced from these data and from the 3′-dinucleotide sequence and nearest-neighbor analysis obtained from repair synthesis with the DNA polymerase of Rous sarcoma virus [Formula: see text] The RI endonuclease cleavage of the phosphodiester bonds (indicated by arrows) generates 5′-phosphoryls and short cohesive termini of four nucleotides, pApApTpT. The most striking feature of the sequence is its symmetry. PMID:4343974

Efficient dehydrogenation of formic acid using Al12N12 nanocage: A DFT study

NASA Astrophysics Data System (ADS)

Esrafili, Mehdi D.; Nurazar, Roghaye

2014-11-01

We have studied the adsorption and decomposition of formic acid (HCOOH) on the surface of Al12N12 fullerene-like nanocage using density functional theory. Different adsorption modes were found for HCOOH on the Al12N12, i.e. molecular and dissociative monodentate or bidentate adsorption. Three reaction pathways were proposed to understand gas-phase HCOOH decomposition on the Al12N12 nanocage. Our results reveal that for the decomposition of HCOOH into CO2 and H2, the most favorable pathway should be the Csbnd H bond activation reaction. The reaction energies and the activation barriers obtained here suggest that for the dissociative adsorption configuration on the Al12N12 surface, the rate-determining step is the Csbnd H bond breaking.

Electrostatic Manipulation of Graphene On Graphite

NASA Astrophysics Data System (ADS)

Untiedt, Carlos; Rubio-Verdu, Carmen; Saenz-Arce, Giovanni; Martinez-Asencio, Jesús; Milan, David C.; Moaied, Mohamed; Palacios, Juan J.; Caturla, Maria Jose

2015-03-01

Here we report the use of a Scanning Tunneling Microscope (STM) under ambient and vacuum conditions to study the controlled exfoliation of the last layer of a graphite surface when an electrostatic force is applied from a STM tip. In this work we have focused on the study of two parameters: the applied voltage needed to compensate the graphite interlayer attractive force and the one needed to break atomic bonds to produce folded structures. Additionally, we have studied the influence of edge structure in the breaking geometry. Independently of the edge orientation the graphite layer is found to tear through the zig-zag direction and the lifled layer shows a zig-zag folding direction. Molecular Dinamics simulations and DFT calculations have been performed to understand our results, showing a strong correlation with the experiments. Comunidad Valenciana through Prometeo project.

Dissociative electron attachment studies on acetone

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

Prabhudesai, Vaibhav S., E-mail: vaibhav@tifr.res.in; Tadsare, Vishvesh; Ghosh, Sanat

Dissociative electron attachment (DEA) to acetone is studied in terms of the absolute cross section for various fragment channels in the electron energy range of 0–20 eV. H{sup −} is found to be the most dominant fragment followed by O{sup −} and OH{sup −} with only one resonance peak between 8 and 9 eV. The DEA dynamics is studied by measuring the angular distribution and kinetic energy distribution of fragment anions using Velocity Slice Imaging technique. The kinetic energy and angular distribution of H{sup −} and O{sup −} fragments suggest a many body break-up for the lone resonance observed. Themore » ab initio calculations show that electron is captured in the multi-centered anti-bonding molecular orbital which would lead to a many body break-up of the resonance.« less

Amphiphilic nanoparticles suppress droplet break-up in a concentrated emulsion flowing through a narrow constriction

PubMed Central

Gai, Ya; Kim, Minkyu; Pan, Ming; Tang, Sindy K. Y.

2017-01-01

This paper describes the break-up behavior of a concentrated emulsion comprising drops stabilized by amphiphilic silica nanoparticles flowing in a tapered microchannel. Such geometry is often used in serial droplet interrogation and sorting processes in droplet microfluidics applications. When exposed to high viscous stresses, drops can undergo break-up and compromise their physical integrity. As these drops are used as micro-reactors, such compromise leads to a loss in the accuracy of droplet-based assays. Here, we show droplet break-up is suppressed by replacing the fluoro-surfactant similar to the one commonly used in current droplet microfluidics applications with amphiphilic nanoparticles as droplet stabilizer. We identify parameters that influence the break-up of these drops and demonstrate that break-up probability increases with increasing capillary number and confinement, decreasing nanoparticle size, and is insensitive to viscosity ratio within the range tested. Practically, our results reveal two key advantages of nanoparticles with direct applications to droplet microfluidics. First, replacing surfactants with nanoparticles suppresses break-up and increases the throughput of the serial interrogation process to 3 times higher than that in surfactant system under similar flow conditions. Second, the insensitivity of break-up to droplet viscosity makes it possible to process samples having different composition and viscosities without having to change the channel and droplet geometry in order to maintain the same degree of break-up and corresponding assay accuracy. PMID:28652887

The difficulties experienced by nurses and healthcare staff involved in the process of breaking bad news.

PubMed

Warnock, Clare; Buchanan, Jean; Tod, Angela Mary

2017-07-01

The aim of this study was to explore the difficulties experienced by nurses and healthcare professionals when engaging in the process of breaking bad news. The challenges faced by staff when breaking bad news have previously been researched in relation to particular settings or participants. This study involved staff from diverse settings and roles to develop broader insights into the range of difficulties experienced in clinical practice. The study used a descriptive survey design involving self-reported written accounts and framework analysis. Data were collected using a structured questionnaire containing a free text section that asked participants to describe a difficult experience they had encountered when involved in the process of breaking bad news. Data were collected from healthcare staff from hospital, community, hospice and care home settings attending training days on breaking bad news between April 2011 and April 2014. Multiple inter-related factors presented challenges to staff engaging in activities associated with breaking bad news. Traditional subjects such as diagnostic and treatment information were described but additional topics were identified such as the impact of illness and care at the end of life. A descriptive framework was developed that summarizes the factors that contribute to creating difficult experiences for staff when breaking bad news. The framework provides insights into the scope of the challenges faced by staff when they engage in the process of breaking bad news. This provides the foundation for developing interventions to support staff that more closely matches their experiences in clinical practice. © 2017 John Wiley & Sons Ltd.

Understanding Lithium Solvation and Diffusion through Topological Analysis of First-Principles Molecular Dynamics

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

Bhatia, Harsh; Gyulassy, Attila; Ong, Mitchell

2016-09-27

The performance of lithium-ion batteries is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact, both, the solvation and diffusivity of Li ions. In this work, we present our application of the topological techniques to extract and predict such behavior in the data generated by the first-principles molecular dynamics simulation of Li ions in an important organic solvent -ethylene carbonate. More specifically, we use the scalar topology of the electron charge density field tomore » analyze the evolution of the solvation structures. This allows us to derive a parameter-free bond definition for lithium-oxygen bonds, to provide a quantitative measure for bond strength, and to understand the regions of influence of each atom in the simulation. This has provided new insights into how and under what conditions certain bonds may form and break. As a result, we can identify and, more importantly, predict, unstable configurations in solvation structures. This can be very useful in understanding when small changes to the atoms' movements can cause significantly different bond structures to evolve. Ultimately, this promises to allow scientists to explore lithium ion solvation and diffusion more systematically, with the aim of new insights and potentially accelerating the calculations themselves.« less

Explosive bonding of metal-matrix composites

NASA Technical Reports Server (NTRS)

Reece, O. Y.

1969-01-01

Explosive bonding process produces sheet composites of aluminum alloy reinforced by high-strength stainless steel wires. The bonds are excellent metallurgically, no external heat is required, various metals can be bonded, and the process is inexpensive.

Experimental research on the dam-break mechanisms of the Jiadanwan landslide dam triggered by the Wenchuan earthquake in China.

PubMed

Xu, Fu-gang; Yang, Xing-guo; Zhou, Jia-wen; Hao, Ming-hui

2013-01-01

Dam breaks of landslide dams are always accompanied by large numbers of casualties, a large loss of property, and negative influences on the downstream ecology and environment. This study uses the Jiadanwan landslide dam, created by the Wenchuan earthquake, as a case study example. Several laboratory experiments are carried out to analyse the dam-break mechanism of the landslide dam. The different factors that impact the dam-break process include upstream flow, the boulder effect, dam size, and channel discharge. The development of the discharge channel and the failure of the landslide dam are monitored by digital video and still cameras. Experimental results show that the upstream inflow and the dam size are the main factors that impact the dam-break process. An excavated discharge channel, especially a trapezoidal discharge channel, has a positive effect on reducing peak flow. The depth of the discharge channel also has a significant impact on the dam-break process. The experimental results are significant for landslide dam management and flood disaster prevention and mitigation.

Experimental Research on the Dam-Break Mechanisms of the Jiadanwan Landslide Dam Triggered by the Wenchuan Earthquake in China

PubMed Central

Xu, Fu-gang; Yang, Xing-guo; Hao, Ming-hui

2013-01-01

Dam breaks of landslide dams are always accompanied by large numbers of casualties, a large loss of property, and negative influences on the downstream ecology and environment. This study uses the Jiadanwan landslide dam, created by the Wenchuan earthquake, as a case study example. Several laboratory experiments are carried out to analyse the dam-break mechanism of the landslide dam. The different factors that impact the dam-break process include upstream flow, the boulder effect, dam size, and channel discharge. The development of the discharge channel and the failure of the landslide dam are monitored by digital video and still cameras. Experimental results show that the upstream inflow and the dam size are the main factors that impact the dam-break process. An excavated discharge channel, especially a trapezoidal discharge channel, has a positive effect on reducing peak flow. The depth of the discharge channel also has a significant impact on the dam-break process. The experimental results are significant for landslide dam management and flood disaster prevention and mitigation. PMID:23844387

Nuclear ARP2/3 drives DNA break clustering for homology-directed repair.

PubMed

Schrank, Benjamin R; Aparicio, Tomas; Li, Yinyin; Chang, Wakam; Chait, Brian T; Gundersen, Gregg G; Gottesman, Max E; Gautier, Jean

2018-06-20

DNA double-strand breaks repaired by non-homologous end joining display limited DNA end-processing and chromosomal mobility. By contrast, double-strand breaks undergoing homology-directed repair exhibit extensive processing and enhanced motion. The molecular basis of this movement is unknown. Here, using Xenopus laevis cell-free extracts and mammalian cells, we establish that nuclear actin, WASP, and the actin-nucleating ARP2/3 complex are recruited to damaged chromatin undergoing homology-directed repair. We demonstrate that nuclear actin polymerization is required for the migration of a subset of double-strand breaks into discrete sub-nuclear clusters. Actin-driven movements specifically affect double-strand breaks repaired by homology-directed repair in G2 cell cycle phase; inhibition of actin nucleation impairs DNA end-processing and homology-directed repair. By contrast, ARP2/3 is not enriched at double-strand breaks repaired by non-homologous end joining and does not regulate non-homologous end joining. Our findings establish that nuclear actin-based mobility shapes chromatin organization by generating repair domains that are essential for homology-directed repair in eukaryotic cells.

Weld bonding of titanium with polyimide adhesives

NASA Technical Reports Server (NTRS)

Vaughan, R. W.; Sheppard, C. H.; Orell, M. K.

1975-01-01

A conductive adhesive primer and a capillary flow adhesive were developed for weld bonding titanium alloy joints. Both formulations contained ingredients considered to be non-carcinogenic. Lap-shear joint test specimens and stringer-stiffened panels were weld bonded using a capillary flow process to apply the adhesive. Static property information was generated for weld bonded joints over the temperature range of 219K (-65 F) to 561K (550 F). The capillary flow process was demonstrated to produce weld bonded joints of equal strength to the weld through weld bonding process developed previously.

A Novel Process for Joining Ti Alloy and Al Alloy using Two-Stage Sintering Powder Metallurgy

NASA Astrophysics Data System (ADS)

Long, Luping; Liu, Wensheng; Ma, Yunzhu; Wu, Lei; Liu, Chao

2018-04-01

The major challenges for conventional diffusion bonding of joining Ti alloy and Al alloy are the undesirable interfacial reaction, low matrixes and joint strength. To avoid the problem in diffusion bonding, a novel two-stage sintering powder metallurgy process is developed. In the present work, the interface characterization and joint performance of the bonds obtained by powder metallurgy bonding are investigated and are compared with the diffusion bonded Ti/Al joints obtained with the same and the optimized process parameters. The results show that no intermetallic compound is visible in the Ti/Al joint obtained by powder metallurgy bonding, while a new layer formed at the joint diffusion bonded with the same parameters. The maximum tensile strength of joint obtained by diffusion bonding is 58 MPa, while a higher tensile strength reaching 111 MPa for a bond made by powder metallurgy bonding. Brittle fractures occur at all the bonds. It is shown that the powder metallurgy bonding of Ti/Al is better than diffusion bonding. The results of this study should benefit the bonding quality.

Vacuum pull down method for an enhanced bonding process

DOEpatents

Davidson, James C.; Balch, Joseph W.

1999-01-01

A process for effectively bonding arbitrary size or shape substrates. The process incorporates vacuum pull down techniques to ensure uniform surface contact during the bonding process. The essence of the process for bonding substrates, such as glass, plastic, or alloys, etc., which have a moderate melting point with a gradual softening point curve, involves the application of an active vacuum source to evacuate interstices between the substrates while at the same time providing a positive force to hold the parts to be bonded in contact. This enables increasing the temperature of the bonding process to ensure that the softening point has been reached and small void areas are filled and come in contact with the opposing substrate. The process is most effective where at least one of the two plates or substrates contain channels or grooves that can be used to apply vacuum between the plates or substrates during the thermal bonding cycle. Also, it is beneficial to provide a vacuum groove or channel near the perimeter of the plates or substrates to ensure bonding of the perimeter of the plates or substrates and reduce the unbonded regions inside the interior region of the plates or substrates.

Investigation of the local structure variance of water molecules in laser-induced thermal desorption process

NASA Astrophysics Data System (ADS)

Ju, Shin-Pon; Weng, Cheng-I.

2004-05-01

This paper presents the use of molecular dynamics simulation in the study of laser-induced thermal desorption (LITD) of water molecules adjacent to a laser-heated Au substrate. The local structure of the water molecules is investigated by considering the densities of the oxygen and hydrogen atoms, the average number of neighbors, nNN, and the average number of H-bonds, nHB. At an equilibrium temperature of 300 K, the simulation results show that three adsorption water layers are formed in the immediate vicinity of the Au surface, and that each four-fold hollow site on the uppermost Au(0 0 1) surface is occupied by a single water molecule. Following laser-induced heating of the Au substrate with a sub-picosecond laser pulse of 350 fs, the substrate temperature increases to 1000 K. This causes a gradual heating of the adjacent water film, which is accompanied by a decrease in the values of nNN and nHB. Hence, it can be concluded that an increase in the water film temperature destroys the hydrogen-bonding network throughout the water film. Although the maximum local temperature of the water film occurs in the region immediately adjacent to the Au substrate, it is determined that the attractive energy between the Au atoms and the water molecules in this region causes the water molecules to aggregate together to form three-dimensional water clusters. Furthermore, this energy prevents the hydrogen bonds in this region from breaking apart as violently as those within the phase explosion region. Finally, it is observed that the phase explosion phenomenon occurs in the region of the water film where the values of nNN and nHB are at a minimum.

The nature of the [TTF]˙+···[TTF]˙+ interactions in the [TTF]2(2+) dimers embedded in charged [3]catenanes: room-temperature multicenter long bonds.

PubMed

Capdevila-Cortada, Marçal; Novoa, Juan J

2012-04-23

The properties of tetrathiafulvalene dimers ([TTF](2)(2+)) and the functionalized ring-shaped bispropargyl (BPP)-functionalized TTF dimers, [BPP-TTF](2)(2+), found at room temperature in charged [3]catenanes, were evaluated by M06L calculations. The results showed that their isolated [TTF](2)(2+) and [BPP-TTF](2)(2+) dimers are energetically unstable towards dissociation. When enclosed in the 4(+)-charged central cyclophane ring of charged [3]catenanes (CBPQT(4+)), [TTF](2)(2+) and [BPP-TTF](2)(2+) dimers are also energetically unstable with respect to leaving the CBPQT(4+) ring; since the barrier for the exiting process is only about 3 kcal mol(-1), that is, within the reach of thermal energies at room temperature (neutral [TTF](2)(0) dimers are stable within the CBPQT(4+) ring). However, the [BPP-TTF](2)(2+) dimers in charged [3]catenanes cannot exit, because this would imply breaking the covalent bonds of the BPP-TTF(+) macrocycle. Finally, it was shown that the [TTF](2)(2+), [BPP-TTF](2)(2+) dimers, and charged [3]catenanes are energetically stable in solution and in crystals of their salts, in the first case due to the interactions with the solvent, and in the second case mostly due to cation-anion interactions. In these environmental conditions at room temperature the TTF units of the [BPP-TTF](2)(2+) dimers make short contacts, thus allowing their SOMO orbitals to overlap: a room-temperature multicenter long bond is formed, similar to those previously found in other [TTF](2)(2+) salts and their solutions. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High activity of cubic PtRh alloys supported on graphene towards ethanol electrooxidation.

PubMed

Rao, Lu; Jiang, Yan-Xia; Zhang, Bin-Wei; Cai, Yuan-Rong; Sun, Shi-Gang

2014-07-21

Cubic PtRh alloys supported on graphene (PtxRhy/GN) with different atomic ratio of Pt and Rh were directly synthesized for the first time using the modified polyol method with Br(-) for the shape-directing agents. The process didn't use surface-capping agents such as PVP that easily occupy the active sites of electrocatalysts and are difficult to remove. Graphene is the key factor for cubic shape besides Br(-) and keeping catalysts high-dispersed. The X-ray diffraction (XRD), scanning electron microscope (SEM) and transmission electron microscope (TEM) were used to characterize the structure and morphology of these electrocatalysts. The results showed that they were composed of homogeneous cubic PtRh alloys. Traditional electrochemical methods, such as cyclic voltammetry and chronoamperometry, were used to investigate the electrocatalytic properties of PtxRhy/GN towards ethanol electrooxidation. It can be seen that PtxRhy/GN with all atomic ratios exhibited high catalytic activity, and the most active one has a composition with Pt : Rh = 9 : 1 atomic ratio. Electrochemical in situ FTIR spectroscopy was used to evaluate the cleavage of C-C bond in ethanol at room temperature in acidic solutions, the results illustrated that Rh in an alloy can promote the split of C-C bond in ethanol, and the alloy catalyst with atomic ratio Pt : Rh = 1 : 1 showed obviously better performance for the C-C bond breaking in ethanol and higher selectivity for the enhanced activity of ethanol complete oxidation to CO2 than alloys with other ratios of Pt and Rh. The investigation indicates that high activity of PtxRhy/GN electrocatalyst towards ethanol oxidation is due to the specific shape of alloys and the synergistic effect of two metal elements as well as graphene support.

Skylab

NASA Image and Video Library

1973-01-01

Breaking the grip of the closed magnetic loops that constrain other gases around it, a spray of chromospheric material surges upward, free of the Sun. Views 1 through 5 were recorded about 5 minutes apart by Skylab and comprise a composite of separate images made in chromospheric (red), transition region (green), and coronal (blue) temperatures of an ultraviolet sequence that depicts a solar eruption. Eruption begins (view 2) as material in or near a small, compact loop develops enough energy to overcome the Sun's magnetic bonds.

Effects of Aging and Environmental Conditions on Ammunition/Explosives Storage Magazines - Paper 1

DTIC Science & Technology

2010-07-01

dropped below 9.5.  Corrosion of the Reinforcing Steel: Steel reinforcement is normally placed within a 2 inches of a concrete surface. Under most...alkalinity of the concrete . The steel is also protected by the relatively high electrical resistance of the concrete . Still, corrosion of the...pressures to force the concrete /reinforcement steel bond to break. Corrosion of the steel will cause spalling, section loss of the steel, and eventually

Dynamics and Statics of Nonaxisymmetric Liquid Bridges

NASA Technical Reports Server (NTRS)

Alexander, J. Iwan D.; Resnick, Andrew H.; Slobozhanin, L. A.

1996-01-01

Theoretical and experimental investigation of the stability of nonaxisymmetric and nonaxisymmetric bridges contained between equal and unequal radii disks as a function of Bond and Weber number with emphasis on the transition from unstable axisymmetric to stable nonaxisymmetric shapes, are conducted. Numerical analysis of the stability of nonaxisymmetric bridges between unequal disks for various orientations of the gravity vector is performed. Experimental and theoretical investigation of large (nonaxisymmetric) oscillations and breaking of liquid bridges are also conducted.

Chain-breaking antioxidant activity of hydroxylated and methoxylated magnolol derivatives: the role of H-bonds.

PubMed

Baschieri, Andrea; Pulvirenti, Luana; Muccilli, Vera; Amorati, Riccardo; Tringali, Corrado

2017-07-26

Chemical modification of magnolol, an uncommon dimeric neolignan contained in Magnolia genus trees, provides a unique array of polyphenols having interesting biological activity potentially related to radical scavenging. The chain-breaking antioxidant activity of four new hydroxylated and methoxylated magnolol derivatives was explored by experimental and computational methods. The measurement of the rate constant of the reaction with ROO˙ radicals (k inh ) in an apolar solvent showed that the introduction of hydroxyl groups ortho to the phenolic OH in magnolol increased the k inh value, being 2.4 × 10 5 M -1 s -1 and 3.3 × 10 5 M -1 s -1 for the mono and the dihydroxy derivatives respectively (k inh of magnolol is 6.1 × 10 4 M -1 s -1 ). The di-methoxylated derivative is less reactive than magnolol (k inh = 1.1 × 10 4 M -1 s -1 ), while the insertion of both hydroxyl and methoxyl groups showed no effect (6.0 × 10 4 M -1 s -1 ). Infrared spectroscopy and theoretical calculations allowed a rationalization of these results and pointed out the crucial role of intramolecular H-bonds. We also show that a correct estimation of the rate constant of the reaction with ROO˙ radicals, by using BDE(OH) calculations, requires that the geometry of the radical is as close as possible to that of the parent phenol.

Modeling dynamics of large tabular icebergs submerged in the ocean

NASA Astrophysics Data System (ADS)

Adcroft, A.; Stern, A. A.; Sergienko, O. V.

2017-12-01

Large tabular icebergs account for a major fraction of the ice calved from the Antarctic ice shelves, and have long lifetimes due to their size. They drift for long distances, interacting with the local ocean circulation, impacting bottom-water formation, sea-ice formation, and biological productivity in the vicinity of the icebergs. However, due to their large horizontal extent and mass, it is challenging to consistently represent large tabular icebergs in global ocean circulation models and so large tabular icebergs are not currently represented in climate models. In this study we develop a novel framework to model large tabular icebergs submerged in the ocean. In this framework, a tabular iceberg is represented by a collection of Lagrangian elements that are linked through rigid bonds. The Lagrangian elements are finite-area modifications of the point-particles used in previous studies to represent small icebergs. These elements interact with the ocean by exerting pressure on the ocean surface, and through melt water and momentum exchange. A breaking of the rigid bonds allows the model to emulate calving events (i.e. detachment of a tabular iceberg from an ice shelf), and to emulate the breaking up of tabular icebergs into smaller pieces. Idealized simulations of the calving of a tabular iceberg, subsequent drift and breakup, demonstrate the capabilities of the new framework with a promise that climate models may soon be able to represent large tabular icebergs.

Adhesive restorations: comparative evaluation between the adhesion of the glass-ceramics to the composite cement and the adhesion of the ceromer to the composite cement.

PubMed

Ceruti, P; Erovigni, F; Casella, F; Lombardo, S

2005-10-01

The aim of this work is to compare the adhesion of the glass-ceramic (empress II) to the composite cement and the adhesion of the ceromer to the composite cement. From each of the above materials, 10 little blocks, of 8 x 6 x 2 mm size, have been prepared. All the surface treatments suggested by the manufacturing industry have been performed: sandblasting and acid-etching of the ceramic, ceromer surface roughening with diamond bur and silanization and bonding application on both materials. A homogeneous layer of cement has been placed between couples of blocks of the same material and photopolymerised. Every sample, consisting of 2 bonded blocks, has been submitted to a traction force on a universal test machine connected with a computerized measure system (SINTEC D/10). Samples have been anchored to the machine binding devices by a bicomponent epoxy glue. Data on the breaking charge have been recorded and an analysis of the broken surfaces has been performed in order to classify the breaking modalities. The results ontained showed that the composite-glass-ceramic adhesion force (mean value 64 Mpa) was remarkably higher than the composite-ceromer adhesion (mean value 37.21 Mpa). The analysis of the broken surfaces by SEM showed that a mixed fracture occurred in all samples (both partly adhesive and cohesive).

Wave-induced stress and breaking of sea ice in a coupled hydrodynamic discrete-element wave-ice model

NASA Astrophysics Data System (ADS)

Herman, Agnieszka

2017-11-01

In this paper, a coupled sea ice-wave model is developed and used to analyze wave-induced stress and breaking in sea ice for a range of wave and ice conditions. The sea ice module is a discrete-element bonded-particle model, in which ice is represented as cuboid grains floating on the water surface that can be connected to their neighbors by elastic joints. The joints may break if instantaneous stresses acting on them exceed their strength. The wave module is based on an open-source version of the Non-Hydrostatic WAVE model (NHWAVE). The two modules are coupled with proper boundary conditions for pressure and velocity, exchanged at every wave model time step. In the present version, the model operates in two dimensions (one vertical and one horizontal) and is suitable for simulating compact ice in which heave and pitch motion dominates over surge. In a series of simulations with varying sea ice properties and incoming wavelength it is shown that wave-induced stress reaches maximum values at a certain distance from the ice edge. The value of maximum stress depends on both ice properties and characteristics of incoming waves, but, crucially for ice breaking, the location at which the maximum occurs does not change with the incoming wavelength. Consequently, both regular and random (Jonswap spectrum) waves break the ice into floes with almost identical sizes. The width of the zone of broken ice depends on ice strength and wave attenuation rates in the ice.

Role, perspective and knowledge of Iranian critical care nurses about breaking bad news.

PubMed

Imanipour, Masoomeh; Karim, Zahra; Bahrani, Naser

2016-05-01

Given the issue of caring critically ill patients, nurses are involved in the process of breaking bad news in critical care units, while little research has been conducted on this challenging issue. The purpose of this study was to determine the role, perspective and knowledge of Iranian critical care nurses regarding breaking bad news. This descriptive study was conducted on a sample of 160 nurses working in critical care units of hospitals affiliated to Tehran University of Medical Sciences. Stratified and quota sampling methods were used. The data collection tool was a four-part questionnaire with validity and reliability confirmed via content validity and test-retest, respectively. The study showed that most critical care nurses were involved in breaking bad news, with different roles. The majority of participants (91.2%) had a positive attitude towards involvement of nurses in breaking bad news. In this study, 78.8% of nurses had moderate knowledge about how to break bad news, and only a few had good level of knowledge (16.2%). According to the findings, while critical care nurses took different roles in the process of breaking bad news and they had positive attitude towards participation in this process, yet their knowledge about this process was inadequate. Thus, designing educational programmes to enhance critical care nurses' knowledge and skills in this area seems necessary. Copyright © 2015 Australian College of Critical Care Nurses Ltd. Published by Elsevier Ltd. All rights reserved.

Un formalisme de systemes a sauts pour la recirculation optimale des casses dans une machine a papier

NASA Astrophysics Data System (ADS)

Khanbaghi, Maryam

Increasing closure of white water circuits is making mill productivity and quality of paper produced increasingly affected by the occurrence of paper breaks. In this thesis the main objective is the development of white water and broke recirculation policies. The thesis consists of three main parts, respectively corresponding to the synthesis of a statistical model of paper breaks in a paper mill, the basic mathematical setup for the formulation of white water and broke recirculation policies in the mill as a jump linear quadratic regulation problem, and finally the tuning of the control law based on first passage-time theory, and its extension to the case of control sensitive paper break rates. More specifically, in the first part a statistical model of paper machine breaks is developed. We start from the hypothesis that the breaks process is a Markov chain with three states: the first state is the operational one, while the two others are associated with the general types of paper-breaks that can take place in the mill (wet breaks and dry breaks). The Markovian hypothesis is empirically validated. We also establish how paper-break rates are correlated with machine speed and broke recirculation ratio. Subsequently, we show how the obtained Markov chain model of paper-breaks can be used to formulate a machine operating speed parameter optimization problem. In the second part, upon recognizing that paper breaks can be modelled as a Markov chain type of process which, when interacting with the continuous mill dynamics, yields a jump Markov model, jump linear theory is proposed as a means of constructing white water and broke recirculation strategies which minimize process variability. Reduced process variability comes at the expense of relatively large swings in white water and broke tanks level. Since the linear design does not specifically account for constraints on the state-space, under the resulting law, damaging events of tank overflow or emptiness can occur. A heuristic simulation-based approach is proposed to choose the performance measure design parameters to keep the mean time between incidents of fluid in broke and white water tanks either overflowing, or reaching dangerously low levels, sufficiently long. In the third part, a methodology, mainly founded on the first passage-time theory of stochastic processes, is proposed to choose the performance measure design parameters to limit process variability while accounting for the possibility of undesirable tank overflows or tank emptiness. The heart of the approach is an approximation technique for evaluating mean first passage-times of the controlled tanks levels. This technique appears to have an applicability which largely exceeds the problem area it was designed for. Furthermore, the introduction of control sensitive break rates and the analysis of the ensuing control problem are presented. This is to account for the experimentally observed increase in breaks concomitant with flow rate variability.

Atomic Covalent Functionalization of Graphene

PubMed Central

Johns, James E.; Hersam, Mark C.

2012-01-01

Conspectus Although graphene’s physical structure is a single atom thick, two-dimensional, hexagonal crystal of sp2 bonded carbon, this simple description belies the myriad interesting and complex physical properties attributed to this fascinating material. Because of its unusual electronic structure and superlative properties, graphene serves as a leading candidate for many next generation technologies including high frequency electronics, broadband photodetectors, biological and gas sensors, and transparent conductive coatings. Despite this promise, researchers could apply graphene more routinely in real-world technologies if they could chemically adjust graphene’s electronic properties. For example, the covalent modification of graphene to create a band gap comparable to silicon (~1 eV) would enable its use in digital electronics, and larger band gaps would provide new opportunities for graphene-based photonics. Towards this end, researchers have focused considerable effort on the chemical functionalization of graphene. Due to its high thermodynamic stability and chemical inertness, new methods and techniques are required to create covalent bonds without promoting undesirable side reactions or irreversible damage to the underlying carbon lattice. In this Account, we review and discuss recent theoretical and experimental work studying covalent modifications to graphene using gas phase atomic radicals. Atomic radicals have sufficient energy to overcome the kinetic and thermodynamic barriers associated with covalent reactions on the basal plane of graphene but lack the energy required to break the C-C sigma bonds that would destroy the carbon lattice. Furthermore, because they are atomic species, radicals substantially reduce the likelihood of unwanted side reactions that confound other covalent chemistries. Overall, these methods based on atomic radicals show promise for the homogeneous functionalization of graphene and the production of new classes of two-dimensional materials with fundamentally different electronic and physical properties. Specifically, we focus on recent studies of the addition of atomic hydrogen, fluorine, and oxygen to the basal plane of graphene. In each of these reactions a high energy, activating step initiates the process, breaking the local π structure and distorting the surrounding lattice. Scanning tunneling microscopy experiments reveal that substrate mediated interactions often dominate when the initial binding event occurs. We then compare these substrate effects with the results of theoretical studies that typically assume a vacuum environment. As the surface coverage increases, clusters often form around the initial distortion, and the stoichiometric composition of the saturated end product depends strongly on both the substrate and reactant species. In addition to these chemical and structural observations, we review how covalent modification can extend the range of physical properties that are achievable in two-dimensional materials. PMID:23030800

Reducing shingle waste at a manufacturing facility: 1990 MNTAP summer intern report

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

Menke, D.

1990-12-31

CertainTeed manufactures roofing shingles at it`s Shakopee, MN facility. Two process coating lines, and one assembly line, produce fifteen shingle types in fifteen different colors. The wastes generated by this process were the result of planned and unplanned variations in the continuous production process. Planned variations included changes in color, while felt breaks were common unplanned variations. Five options were identified that could reduce the amount of waste generated: Using a standard procedure for recovering from felt breaks, Creating a process cushion to maintain continuous production in the event of temporary shutdowns, An automated color change process, Manufacture of amore » new product from waste material, Minor process changes to reduce the frequency of breaks.« less

Distinct Patterns of Cognitive Conflict Dynamics in Promise Keepers and Promise Breakers.

PubMed

Calluso, Cinzia; Saulin, Anne; Baumgartner, Thomas; Knoch, Daria

2018-01-01

On a daily basis, we see how different people can be in keeping or breaking a given promise. However, we know very little about the cognitive conflict dynamics that underlie the decision to keep or break a promise and whether this is shaped by inter-individual variability. In order to fill this gap, we applied an ecologically valid promise decision task with real monetary consequences for all involved interaction partners and used mouse tracking to identify the dynamic, on-line cognitive processes that underlie the decision to keep or break a promise. Our findings revealed that on average, the process of breaking a promise is associated with largely curved mouse trajectories, while the process of keeping a promise was not, indicating that breaking a promise is associated with a larger conflict. Interestingly, however, this conflict pattern was strongly shaped by individual differences. Individuals who always kept their promises did not show any signs of conflict (i.e., straight mouse trajectories), indicating that they were not tempted by the monetary benefits associated with breaking the promise. In contrast, individuals who did not always keep their promise exhibited a large conflict (i.e., curved mouse trajectories), irrespective of whether they broke or kept their promise. A possible interpretation of these findings is that these individuals were always tempted by the unchosen decision option - the desire to act in a fair manner when breaking the promise and the monetary benefits when keeping the promise. This study provides the first piece of evidence that there are substantial inter-individual differences in cognitive conflict dynamics that underlie the decision to keep or break promises and that mouse tracking is able to illuminate important insights into individual differences in complex human's decision processes.

Cleanliness inspection tool for RSRM bond surfaces

NASA Technical Reports Server (NTRS)

Mattes, Robert A.

1995-01-01

Using optically stimulated electron emission (OSEE), Thiokol has monitored bond surfaces in process for contamination on the Redesigned Solid Rocket Motor (RSRM). This technique provides process control information to help assure bond surface quality and repeatability prior to bonding. This paper will describe OSEE theory of operation and the instrumentation implemented at Thiokol Corporation since 1987. Data from process hardware will be presented.

Direct microscopic image and measurement of the atomization process of a port fuel injector

NASA Astrophysics Data System (ADS)

Esmail, Mohamed; Kawahara, Nobuyuki; Tomita, Eiji; Sumida, Mamoru

2010-07-01

The main objective of this study is to observe and investigate the phenomena of atomization, i.e. the fuel break-up process very close to the nozzle exit of a practical port fuel injector (PFI). In order to achieve this objective, direct microscopic images of the atomization process were obtained using an ultra-high-speed video camera that could record 102 frames at rates of up to 1 Mfps, coupled with a long-distance microscope and Barlow lens. The experiments were carried out using a PFI in a closed chamber at atmospheric pressure. Time-series images of the spray behaviour were obtained with a high temporal resolution using backlighting. The direct microscopic images of a liquid column break-up were compared with experimental results from laser-induced exciplex fluorescence (LIEF), and the wavelength obtained from the experimental results compared with that predicated from the Kelvin-Helmholtz break-up model. The droplet size diameters from a ligament break-up were compared with results predicated from Weber's analysis. Furthermore, experimental results of the mean droplet diameter from a direct microscopic image were compared with the results obtained from phase Doppler anemometry (PDA) experimental results. Three conclusions were obtained from this study. The atomization processes and detailed characterizations of the break-up of a liquid column were identified; the direct microscopic image results were in good agreement with the results obtained from LIEF, experimental results of the wavelength were in good agreement with those from the Kelvin-Helmholtz break-up model. The break-up process of liquid ligaments into droplets was investigated, and Weber's analysis of the predicated droplet diameter from ligament break-up was found to be applicable only at larger wavelengths. Finally, the direct microscopic image method and PDA method give qualitatively similar trends for droplet size distribution and quantitatively similar values of Sauter mean diameter.

Breaking bad news: issues relating to nursing practice.

PubMed

Warnock, Clare

2014-07-15

The breaking of bad news was traditionally regarded to be the time when a doctor and nurse sat down with a patient and family members to provide information about, for example, a life-limiting diagnosis or a poor prognosis. However, breaking bad news is now generally accepted as a process, not a one-off event, and is considered to refer to any bad, sad or difficult information that alters patients' perceptions of their present and future. Nurses have an important role in the process of providing information and helping patients prepare for, receive, understand and cope with the bad news they have been given. This article aims to help nurses understand the process of breaking bad news and discuss the challenges and difficulties that nurses can face when they are involved with patients who have been given bad news. It also provides guidance with regard to preparing for breaking bad news, giving difficult information, responding to possible reactions, and supporting patients and their relatives after they have received bad news.

Modeling single molecule junction mechanics as a probe of interface bonding

NASA Astrophysics Data System (ADS)

Hybertsen, Mark S.

2017-03-01

Using the atomic force microscope based break junction approach, applicable to metal point contacts and single molecule junctions, measurements can be repeated thousands of times resulting in rich data sets characterizing the properties of an ensemble of nanoscale junction structures. This paper focuses on the relationship between the measured force extension characteristics including bond rupture and the properties of the interface bonds in the junction. A set of exemplary model junction structures has been analyzed using density functional theory based calculations to simulate the adiabatic potential surface that governs the junction elongation. The junction structures include representative molecules that bond to the electrodes through amine, methylsulfide, and pyridine links. The force extension characteristics are shown to be most effectively analyzed in a scaled form with maximum sustainable force and the distance between the force zero and force maximum as scale factors. Widely used, two parameter models for chemical bond potential energy versus bond length are found to be nearly identical in scaled form. Furthermore, they fit well to the present calculations of N-Au and S-Au donor-acceptor bonds, provided no other degrees of freedom are allowed to relax. Examination of the reduced problem of a single interface, but including relaxation of atoms proximal to the interface bond, shows that a single-bond potential form renormalized by an effective harmonic potential in series fits well to the calculated results. This allows relatively accurate extraction of the interface bond energy. Analysis of full junction models shows cooperative effects that go beyond the mechanical series inclusion of the second bond in the junction, the spectator bond that does not rupture. Calculations for a series of diaminoalkanes as a function of molecule length indicate that the most important cooperative effect is due to the interactions between the dipoles induced by the donor-acceptor bond formation at the junction interfaces. The force extension characteristic of longer molecules such as diaminooctane, where the dipole interaction effects drop to a negligible level, accurately fit to the renormalized single-bond potential form. The results suggest that measured force extension characteristics for single molecule junctions could be analyzed with a modified potential form that accounts for the energy stored in deformable mechanical components in series.

Modeling single molecule junction mechanics as a probe of interface bonding

DOE PAGES

Hybertsen, Mark S.

2017-03-07

Using the atomic force microscope based break junction approach, applicable to metal point contacts and single molecule junctions, measurements can be repeated thousands of times resulting in rich data sets characterizing the properties of an ensemble of nanoscale junction structures. This paper focuses on the relationship between the measured force extension characteristics including bond rupture and the properties of the interface bonds in the junction. We analyzed a set of exemplary model junction structures using density functional theory based calculations to simulate the adiabatic potential surface that governs the junction elongation. The junction structures include representative molecules that bond tomore » the electrodes through amine, methylsulfide, and pyridine links. The force extension characteristics are shown to be most effectively analyzed in a scaled form with maximum sustainable force and the distance between the force zero and force maximum as scale factors. Widely used, two parameter models for chemical bond potential energy versus bond length are found to be nearly identical in scaled form. Furthermore, they fit well to the present calculations of N–Au and S–Au donor-acceptor bonds, provided no other degrees of freedom are allowed to relax. Examination of the reduced problem of a single interface, but including relaxation of atoms proximal to the interface bond, shows that a single-bond potential form renormalized by an effective harmonic potential in series fits well to the calculated results. This, then, allows relatively accurate extraction of the interface bond energy. Analysis of full junction models shows cooperative effects that go beyond the mechanical series inclusion of the second bond in the junction, the spectator bond that does not rupture. Calculations for a series of diaminoalkanes as a function of molecule length indicate that the most important cooperative effect is due to the interactions between the dipoles induced by the donor-acceptor bond formation at the junction interfaces. The force extension characteristic of longer molecules such as diaminooctane, where the dipole interaction effects drop to a negligible level, accurately fit to the renormalized single-bond potential form. Our results suggest that measured force extension characteristics for single molecule junctions could be analyzed with a modified potential form that accounts for the energy stored in deformable mechanical components in series.« less

Modeling single molecule junction mechanics as a probe of interface bonding

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

Hybertsen, Mark S.

Using the atomic force microscope based break junction approach, applicable to metal point contacts and single molecule junctions, measurements can be repeated thousands of times resulting in rich data sets characterizing the properties of an ensemble of nanoscale junction structures. This paper focuses on the relationship between the measured force extension characteristics including bond rupture and the properties of the interface bonds in the junction. We analyzed a set of exemplary model junction structures using density functional theory based calculations to simulate the adiabatic potential surface that governs the junction elongation. The junction structures include representative molecules that bond tomore » the electrodes through amine, methylsulfide, and pyridine links. The force extension characteristics are shown to be most effectively analyzed in a scaled form with maximum sustainable force and the distance between the force zero and force maximum as scale factors. Widely used, two parameter models for chemical bond potential energy versus bond length are found to be nearly identical in scaled form. Furthermore, they fit well to the present calculations of N–Au and S–Au donor-acceptor bonds, provided no other degrees of freedom are allowed to relax. Examination of the reduced problem of a single interface, but including relaxation of atoms proximal to the interface bond, shows that a single-bond potential form renormalized by an effective harmonic potential in series fits well to the calculated results. This, then, allows relatively accurate extraction of the interface bond energy. Analysis of full junction models shows cooperative effects that go beyond the mechanical series inclusion of the second bond in the junction, the spectator bond that does not rupture. Calculations for a series of diaminoalkanes as a function of molecule length indicate that the most important cooperative effect is due to the interactions between the dipoles induced by the donor-acceptor bond formation at the junction interfaces. The force extension characteristic of longer molecules such as diaminooctane, where the dipole interaction effects drop to a negligible level, accurately fit to the renormalized single-bond potential form. Our results suggest that measured force extension characteristics for single molecule junctions could be analyzed with a modified potential form that accounts for the energy stored in deformable mechanical components in series.« less

Time Crystal Behavior of Excited Eigenstates

NASA Astrophysics Data System (ADS)

Syrwid, Andrzej; Zakrzewski, Jakub; Sacha, Krzysztof

2017-12-01

In analogy to spontaneous breaking of continuous space translation symmetry in the process of space crystal formation, it was proposed that spontaneous breaking of continuous time translation symmetry could lead to time crystal formation. In other words, a time-independent system prepared in the energy ground state is expected to reveal periodic motion under infinitely weak perturbation. In the case of the system proposed originally by Wilczek, spontaneous breaking of time translation symmetry cannot be observed if one starts with the ground state. We point out that the symmetry breaking can take place if the system is prepared in an excited eigenstate. The latter can be realized experimentally in ultracold atomic gases. We simulate the process of the spontaneous symmetry breaking due to measurements of particle positions and analyze the lifetime of the resulting symmetry broken state.

Time Crystal Behavior of Excited Eigenstates.

PubMed

Syrwid, Andrzej; Zakrzewski, Jakub; Sacha, Krzysztof

2017-12-22

In analogy to spontaneous breaking of continuous space translation symmetry in the process of space crystal formation, it was proposed that spontaneous breaking of continuous time translation symmetry could lead to time crystal formation. In other words, a time-independent system prepared in the energy ground state is expected to reveal periodic motion under infinitely weak perturbation. In the case of the system proposed originally by Wilczek, spontaneous breaking of time translation symmetry cannot be observed if one starts with the ground state. We point out that the symmetry breaking can take place if the system is prepared in an excited eigenstate. The latter can be realized experimentally in ultracold atomic gases. We simulate the process of the spontaneous symmetry breaking due to measurements of particle positions and analyze the lifetime of the resulting symmetry broken state.

Simple model for lambda-doublet propensities in bimolecular reactions

NASA Technical Reports Server (NTRS)

Bronikowski, Michael J.; Zare, Richard N.

1990-01-01

A simple geometric model is presented to account for lambda-doublet propensities in bimolecular reactions A + BC - AB + C. It applies to reactions in which AB is formed in a pi state, and in which the unpaired molecular orbital responsible for lambda-doubling arises from breaking the B-C bond. The lambda-doublet population ratio is predicted to be 2:1 provided that: (1) the motion of A in the transition state determines the plane of rotation of AB; (2) the unpaired pi orbital lying initially along the B-C bond may be resolved into a projection onto the AB plane of rotation and a projection perpendicular to this plane; (3) there is no preferred geometry for dissociation of ABC. The 2:1 lambda-doublet ratio is the 'unconstrained dynamics prior' lambda-doublet distribution for such reactions.

Characterization of Covalent-Reversible EGFR Inhibitors

PubMed Central

2017-01-01

Within the spectrum of kinase inhibitors, covalent-reversible inhibitors (CRIs) provide a valuable alternative approach to classical covalent inhibitors. This special class of inhibitors can be optimized for an extended drug-target residence time. For CRIs, it was shown that the fast addition of thiols to electron-deficient olefins leads to a covalent bond that can break reversibly under proteolytic conditions. Research groups are just beginning to include CRIs in their arsenal of compound classes, and, with that, the understanding of this interesting set of chemical warheads is growing. However, systems to assess both characteristics of the covalent-reversible bond in a simple experimental setting are sparse. Here, we have developed an efficient methodology to characterize the covalent and reversible properties of CRIs and to investigate their potential in targeting clinically relevant variants of the receptor tyrosine kinase EGFR.

Stepwise evolution of protein native structure with electrospray into the gas phase, 10−12 to 102 s

PubMed Central

Breuker, Kathrin; McLafferty, Fred W.

2008-01-01

Mass spectrometry (MS) has been revolutionized by electrospray ionization (ESI), which is sufficiently “gentle” to introduce nonvolatile biomolecules such as proteins and nucleic acids (RNA or DNA) into the gas phase without breaking covalent bonds. Although in some cases noncovalent bonding can be maintained sufficiently for ESI/MS characterization of the solution structure of large protein complexes and native enzyme/substrate binding, the new gaseous environment can ultimately cause dramatic structural alterations. The temporal (picoseconds to minutes) evolution of native protein structure during and after transfer into the gas phase, as proposed here based on a variety of studies, can involve side-chain collapse, unfolding, and refolding into new, non-native structures. Control of individual experimental factors allows optimization for specific research objectives. PMID:19033474

Hydrogen bond breaking dynamics in the water pentamer: Terahertz VRT spectroscopy of a 20 μm libration

NASA Astrophysics Data System (ADS)

Cole, William T. S.; Fellers, Raymond S.; Viant, Mark R.; Saykally, Richard J.

2017-01-01

Hydrogen bonds in solid and liquid water are formed and broken via librational vibrations, hence characterizing the details of these motions is vital to understanding these important dynamics. Here we report the measurement and assignment of 875 transitions comprising 6 subbands originating from out-of-plane librational transitions of the water pentamer-d10 near 512 cm-1. The precisely measured (ca. 1 ppm) transitions reveal bifurcation splittings of ˜1884 MHz, a ˜4000× enhancement over ground state splittings and 100× greater than predicted by theory. The pentamer is thus the third water cluster to display greatly enhanced bifurcation tunneling upon single quantum excitation of librational vibrations. From the intensity pattern of the observed transitions, the mechanism of bifurcation is established by comparison with theoretical predictions.

Hydrogen bond breaking dynamics in the water pentamer: Terahertz VRT spectroscopy of a 20 μm libration.

PubMed

Cole, William T S; Fellers, Raymond S; Viant, Mark R; Saykally, Richard J

2017-01-07

Hydrogen bonds in solid and liquid water are formed and broken via librational vibrations, hence characterizing the details of these motions is vital to understanding these important dynamics. Here we report the measurement and assignment of 875 transitions comprising 6 subbands originating from out-of-plane librational transitions of the water pentamer-d 10 near 512 cm -1 . The precisely measured (ca. 1 ppm) transitions reveal bifurcation splittings of ∼1884 MHz, a ∼4000× enhancement over ground state splittings and 100× greater than predicted by theory. The pentamer is thus the third water cluster to display greatly enhanced bifurcation tunneling upon single quantum excitation of librational vibrations. From the intensity pattern of the observed transitions, the mechanism of bifurcation is established by comparison with theoretical predictions.

Performance of an integrated approach for prediction of bond dissociation enthalpies of phenols extracted from ginger and tea

NASA Astrophysics Data System (ADS)

Nam, Pham Cam; Chandra, Asit K.; Nguyen, Minh Tho

2013-01-01

Integration of the (RO)B3LYP/6-311++G(2df,2p) with the PM6 method into a two-layer ONIOM is found to produce reasonably accurate BDE(O-H)s of phenolic compounds. The chosen ONIOM model contains only two atoms of the breaking bond as the core zone and is able to provide reliable evaluation for BDE(O-H) for phenols and tocopherol. Deviation of calculated values from experiment is ±(1-2) kcal/mol. BDE(O-H) of several curcuminoids and flavanoids extracted from ginger and tea are computed using the proposed model. The BDE(O-H) values of enol curcumin and epigallocatechin gallate are predicted to be 83.3 ± 2.0 and 76.0 ± 2.0 kcal/mol, respectively.

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

Marchetti, Barbara; Karsili, Tolga N. V.; Ashfold, Michael N. R., E-mail: mike.ashfold@bristol.ac.uk

Velocity map imaging methods, with a new and improved ion optics design, have been used to explore the near ultraviolet photodissociation dynamics of gas phase 2-bromo- and 2-iodothiophene molecules. In both cases, the ground (X) and spin-orbit excited (X*) (where X = Br, I) atom products formed at the longest excitation wavelengths are found to recoil with fast, anisotropic velocity distributions, consistent with prompt C–X bond fission following excitation via a transition whose dipole moment is aligned parallel to the breaking bond. Upon tuning to shorter wavelengths, this fast component fades and is progressively replaced by a slower, isotropic recoilmore » distribution. Complementary electronic structure calculations provide a plausible explanation for this switch in fragmentation behaviour—namely, the opening of a rival C–S bond extension pathway to a region of conical intersection with the ground state potential energy surface. The resulting ground state molecules are formed with more than sufficient internal energy to sample the configuration space associated with several parent isomers and to dissociate to yield X atom products in tandem with both cyclic and ring-opened partner fragments.« less

Covalent Bonding of Pyrrolobenzodiazepines (PBDs) to Terminal Guanine Residues within Duplex and Hairpin DNA Fragments

PubMed Central

Mantaj, Julia; Jackson, Paul J. M.; Karu, Kersti; Rahman, Khondaker M.; Thurston, David E.

2016-01-01

Pyrrolobenzodiazepines (PBDs) are covalent-binding DNA-interactive agents with growing importance as payloads in Antibody Drug Conjugates (ADCs). Until now, PBDs were thought to covalently bond to C2-NH2 groups of guanines in the DNA-minor groove across a three-base-pair recognition sequence. Using HPLC/MS methodology with designed hairpin and duplex oligonucleotides, we have now demonstrated that the PBD Dimer SJG-136 and the C8-conjugated PBD Monomer GWL-78 can covalently bond to a terminal guanine of DNA, with the PBD skeleton spanning only two base pairs. Control experiments with the non-C8-conjugated anthramycin along with molecular dynamics simulations suggest that the C8-substituent of a PBD Monomer, or one-half of a PBD Dimer, may provide stability for the adduct. This observation highlights the importance of PBD C8-substituents, and also suggests that PBDs may bind to terminal guanines within stretches of DNA in cells, thus representing a potentially novel mechanism of action at the end of DNA strand breaks. PMID:27055050

Two-dimensional limit of crystalline order in perovskite membrane films

PubMed Central

Hong, Seung Sae; Yu, Jung Ho; Lu, Di; Marshall, Ann F.; Hikita, Yasuyuki; Cui, Yi; Hwang, Harold Y.

2017-01-01

Long-range order and phase transitions in two-dimensional (2D) systems—such as magnetism, superconductivity, and crystallinity—have been important research topics for decades. The issue of 2D crystalline order has reemerged recently, with the development of exfoliated atomic crystals. Understanding the dimensional limit of crystalline phases, with different types of bonding and synthetic techniques, is at the foundation of low-dimensional materials design. We study ultrathin membranes of SrTiO3, an archetypal perovskite oxide with isotropic (3D) bonding. Atomically controlled membranes are released after synthesis by dissolving an underlying epitaxial layer. Although all unreleased films are initially single-crystalline, the SrTiO3 membrane lattice collapses below a critical thickness (5 unit cells). This crossover from algebraic to exponential decay of the crystalline coherence length is analogous to the 2D topological Berezinskii-Kosterlitz-Thouless (BKT) transition. The transition is likely driven by chemical bond breaking at the 2D layer-3D bulk interface, defining an effective dimensional phase boundary for coherent crystalline lattices. PMID:29167822

Machine learnt bond order potential to investigate the low thermal conductivity of stanene nanostructures

NASA Astrophysics Data System (ADS)

Cherukara, Mathew; Narayanan, Badri; Kinaci, Alper; Sasikumar, Kiran; Gray, Stephen; Chan, Maria; Sankaranarayanan, Subramanian

The growth of stanene on a Bi2Te3\\ substrate has engendered a great deal of interest, in part due to stanene's predicted exotic properties. In particular, stanene shows promise in topological insulation, large-gap 2D quantum spin hall states, lossless electrical conduction, enhanced thermoelectricity, and topological superconductivity. However, atomistic investigations of growth mechanisms (needed to guide synthesis), phonon transport (crucial for designing thermoelectrics), and thermo-mechanical behavior of stanene are scarce. This paucity is primarily due to the lack of inter-atomic potentials that can accurately capture atomic interactions in stanene. To address this, we have developed a machine learnt bond-order potential (BOP) based on Tersoff's formalism that can accurately capture bond breaking/formation events, structure, energetics, thermodynamics, thermal conductivity, and mechanical properties of single layer tin, using a training set derived from density functional theory calculations. Finally, we employed our newly developed BOP to study anisotropy in thermal conductivity of stanene sheets, temperature induced rippling, as well as dependence of anharmonicity and thermal conductivity on temperature.

Two-dimensional limit of crystalline order in perovskite membrane films

DOE PAGES

Hong, Seung Sae; Yu, Jung Ho; Lu, Di; ...

2017-11-17

Long-range order and phase transitions in two-dimensional (2D) systems—such as magnetism, superconductivity, and crystallinity—have been important research topics for decades. The issue of 2D crystalline order has reemerged recently, with the development of exfoliated atomic crystals. Understanding the dimensional limit of crystalline phases, with different types of bonding and synthetic techniques, is at the foundation of low-dimensional materials design. We study ultrathin membranes of SrTiO 3, an archetypal perovskite oxide with isotropic (3D) bonding. Atomically controlled membranes are released after synthesis by dissolving an underlying epitaxial layer. Although all unreleased films are initially single-crystalline, the SrTiO 3 membrane lattice collapsesmore » below a critical thickness (5 unit cells). This crossover from algebraic to exponential decay of the crystalline coherence length is analogous to the 2D topological Berezinskii-Kosterlitz-Thouless (BKT) transition. Finally, the transition is likely driven by chemical bond breaking at the 2D layer-3D bulk interface, defining an effective dimensional phase boundary for coherent crystalline lattices.« less

Crystal and molecular structure of N-(4-nitrophenyl)-β-alanine—Its vibrational spectra and theoretical calculations

NASA Astrophysics Data System (ADS)

Marchewka, M. K.; Drozd, M.; Janczak, J.

2011-08-01

The N-(4-nitrophenyl)-β-alanine in crystalline form directly by the addition of 4-nitroaniline to the acrylic acid in aqueous solution has been obtained. The title β-alanine derivative crystallizes in the P2 1/ c space group of monoclinic system with four molecules per unit cell. The X-ray geometry of β-alanine derivative molecule has been compared with those obtained by molecular orbital calculations corresponding to the gas phase. In the crystal the molecules related by an inversion center interact via symmetrically equivalent O-H⋯O hydrogen bonds with O⋯O distance of 2.656(2) Å forming a dimeric structure. The dimers of β-alanine derivative weakly interact via N-H⋯O hydrogen bonds between the H atom of β-amine groups and one of O atom of nitro groups. The room temperature powder vibrational (infrared and Raman) measurements are in accordance with the X-ray analysis. In aqueous solution of 4-nitroaniline and acrylic acid, the double C dbnd C bond of vinyl group of acrylic acid breaks as result of 4-nitroaniline addition.

Next-generation hollow retroreflectors for lunar laser ranging.

PubMed

Preston, Alix; Merkowitz, Stephen

2013-12-20

The three retroreflector arrays put on the Moon 40 years ago by the Apollo astronauts and the French-built arrays on the Soviet Lunokhod rovers continue to be useful targets, and have provided the most stringent tests of the Strong Equivalence Principle and the time variation of Newton's gravitational constant, as well as valuable insight into the Moon's interior. However, the precision of the ranging measurements are now being limited by the physical size of the arrays and a new generation of retroreflectors is required to make significant advances over current capabilities. Large single-cube retroreflectors represent the most promising approach to overcoming current limitations, and hollow retroreflectors in particular have the potential to maintain their good optical performance over the nearly 300 K temperature swing that occurs during the lunar cycle. Typically, epoxies are used for aligning and bonding hollow retroreflectors, but their thermal stability will predominantly be limited by the difference of the coefficient of thermal expansion (CTE) between the epoxy and the glass. A relatively new bonding method known as hydroxide catalysis bonding (HCB) has been used to adhere complex optical components for space-based missions. HCB has an extremely thin bond, a low CTE, and a high breaking strength that makes it an ideal candidate for bonding hollow retroreflectors for lunar laser ranging (LLR). In this work, we present results of a feasibility study of bonded Pyrex and fused silica hollow retroreflectors using both epoxy and HCB methods, including the results of thermally cycling the hollow retroreflectors from 295 to 185 K. Finally, we discuss the potential for using these retroreflectors for future LLR.

The Effect of Limited Diffusion and Wet-Dry Cycling on Reversible Polymerization Reactions: Implications for Prebiotic Synthesis of Nucleic Acids.

PubMed

Higgs, Paul G

2016-06-08

A long-standing problem for the origins of life is that polymerization of many biopolymers, including nucleic acids and peptides, is thermodynamically unfavourable in aqueous solution. If bond making and breaking is reversible, monomers and very short oligomers predominate. Recent experiments have shown that wetting and drying cycles can overcome this problem and drive the formation of longer polymers. In the dry phase, bond formation is favourable, but diffusion is restricted, and bonds only form between monomers that are initially close together. In the wet phase, some of the bonds are hydrolyzed. However, repositioning of the molecules allows new bonds to form in the next dry phase, leading to an increase in mean polymer length. Here, we consider a simple theoretical model that explains the effect of cycling. There is an equilibrium length distribution with a high mean length that could be achieved if diffusion occurred freely in the dry phase. This equilibrium is inaccessible without diffusion. A single dry cycle without diffusion leads to mean lengths much shorter than this. Repeated cycling leads to a significant increase in polymerization relative to a single cycle. In the most favourable case, cycling leads to the same equilibrium length distribution as would be achieved if free diffusion were possible in the dry phase. These results support the RNA World scenario by explaining a potential route to synthesis of long RNAs; however, they also imply that cycling would be beneficial to the synthesis of other kinds of polymers, including peptides, where bond formation involves a condensation reaction.

The Effect of Limited Diffusion and Wet–Dry Cycling on Reversible Polymerization Reactions: Implications for Prebiotic Synthesis of Nucleic Acids

PubMed Central

Higgs, Paul G.

2016-01-01

A long-standing problem for the origins of life is that polymerization of many biopolymers, including nucleic acids and peptides, is thermodynamically unfavourable in aqueous solution. If bond making and breaking is reversible, monomers and very short oligomers predominate. Recent experiments have shown that wetting and drying cycles can overcome this problem and drive the formation of longer polymers. In the dry phase, bond formation is favourable, but diffusion is restricted, and bonds only form between monomers that are initially close together. In the wet phase, some of the bonds are hydrolyzed. However, repositioning of the molecules allows new bonds to form in the next dry phase, leading to an increase in mean polymer length. Here, we consider a simple theoretical model that explains the effect of cycling. There is an equilibrium length distribution with a high mean length that could be achieved if diffusion occurred freely in the dry phase. This equilibrium is inaccessible without diffusion. A single dry cycle without diffusion leads to mean lengths much shorter than this. Repeated cycling leads to a significant increase in polymerization relative to a single cycle. In the most favourable case, cycling leads to the same equilibrium length distribution as would be achieved if free diffusion were possible in the dry phase. These results support the RNA World scenario by explaining a potential route to synthesis of long RNAs; however, they also imply that cycling would be beneficial to the synthesis of other kinds of polymers, including peptides, where bond formation involves a condensation reaction. PMID:27338479

β-sheet-like hydrogen bonds interlock the helical turns of a photoswitchable foldamer to enhance the binding and release of chloride.

PubMed

Lee, Semin; Hua, Yuran; Flood, Amar H

2014-09-05

Inspired by halorhodopsin's use of photoisomerization to regulate chloride, aryltriazole-based foldamers have been created to "catch and release" chloride ions upon light irradiation of end-appended azobenzenes. The proposed mode of stabilization exploits a β-sheet-like hydrogen-bonding array to cooperatively interlock the ends of a foldamer together with its helical core. We find that the hydrogen-bonding array has a greater influence on stabilizing the helix than the π-stacked seam under the conditions examined (50:50 MeCN/THF). Thus, we show how it is possible to enhance the difference between Cl(-) binding and release using light-dependent control over the foldamer's degree of helix stabilization. Making and breaking three π-π contacts with light caused an 8-fold change in chloride affinity (40 300 M(-1) ⇄ 5000 M(-1)), five π-π contacts produced a 17-fold change (126 000 M(-1) ⇄ 7400 M(-1)), and strategically located hydrogen-bonding units enabled a greater 84-fold differential (970 000 M(-1) ⇄ 11 600 M(-1)). The improved performances were attributed to stepwise increases in the preorganization of the binding pocket that catches chloride while leaving the cis states with just one π-π contact relatively unchanged.

Osteo-odonto-keratoprosthesis (OOKP) and the testing of three different adhesives for bonding bovine teeth with optical poly-(methyl methacrylate) (PMMA) cylinder.

PubMed

Weisshuhn, K; Berg, I; Tinner, D; Kunz, C; Bornstein, M M; Steineck, M; Hille, K; Goldblum, D

2014-07-01

Preparation of the lamina during osteo-odonto-keratoprosthesis (OOKP) design is complex, and its longevity and watertightness important. To date, only acrylic bone cements have been used for bonding the optical cylinder to the tooth dentine. Our aim was to evaluate different dental adhesives for OOKP preparation. Specimens of bovine teeth were produced by preparing 1.5-mm thick dentine slices with holes having a diameter of 3.5 mm. Each group (n=10 per group) was luted with either classic poly-(methyl methacrylate) (PMMA) bone cement, universal resin cement or glass ionomer cement. All specimens underwent force measurement using a uniaxial traction machine. The highest mean force required to break the bond was measured for PMMA bone cement (128.2 N) followed by universal resin cement (127.9 N), with no statistically significant difference. Glass ionomer cement showed significantly lower force resistance (78.1 N). Excellent bonding strength combined with easy application was found for universal resin cement, and thus, it is a potential alternative to acrylic bone cement in OOKP preparation. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Effect of impurities on the mechanical and electronic properties of Au, Ag, and Cu monatomic chain nanowires

NASA Astrophysics Data System (ADS)

Çakır, D.; Gülseren, O.

2011-08-01

In this study, we have investigated the interaction of various different atomic and molecular species (H, C, O, H2, and O2) with the monatomic chains of Au, Ag, and Cu via total-energy calculations using the plane-wave pseudopotential method based on density functional theory. The stability, energetics, mechanical, and electronic properties of the clean and contaminated Au, Ag, and Cu nanowires have been presented. We have observed that the interaction of H, C, or O atoms with the monatomic chains are much stronger than the one of H2 or O2 molecules. The atomic impurities can easily be incorporated into these nanowires; they form stable and strong bonds with these one-dimensional structures when they are inserted in or placed close to the nanowires. Moreover, the metal-atomic impurity bond is much stronger than the metal-metal bond. Upon elongation, the nanowires contaminated with atomic impurities usually break from the remote metal-metal bond. We have observed both metallic and semiconducting contaminated nanowires depending on the type of impurity, whereas all clean monatomic chains of Au, Cu, and Ag exhibit metallic behavior. Our findings indicate that the stability and the electronic properties of these monatomic chains can be tuned by using appropriate molecular or atomic additives.

Rapid adhesive bonding of advanced composites and titanium

NASA Technical Reports Server (NTRS)

Stein, B. A.; Tyeryart, J. R.; Hodgest, W. T.

1985-01-01

Rapid adhesive bonding (RAB) concepts utilize a toroid induction technique to heat the adhesive bond line directly. This technique was used to bond titanium overlap shear specimens with 3 advanced thermoplastic adhesives and APC-2 (graphite/PEEK) composites with PEEK film. Bond strengths equivalent to standard heated-platen press bonds were produced with large reductions in process time. RAB produced very strong bonds in APC-2 adherend specimens; the APC-2 adherends were highly resistant to delamination. Thermal cycling did not significantly affect the shear strengths of RAB titanium bonds with polyimide adhesives. A simple ultrasonic non-destructive evaluation process was found promising for evaluating bond quality.

Low energy supergravity: R-parity breaking and the top quark mass

NASA Astrophysics Data System (ADS)

Carena, Marcela S.; Wagner, Carlos E. M.

1987-03-01

We study the process of spontaneous R-parity breaking in minimal low energy supergravity models. We show that it is very hard to obtain models with heavy top quarks if one wants to preserve the radiative breaking of SU(2)L⊗U(1)Y without breaking R-parity. Fellow of Consejo National de Investigaciones Cientificas y Tecnicas.

DNA breaks and end resection measured genome-wide by end sequencing | Center for Cancer Research

Cancer.gov

About the Cover The cover depicts a ribbon of DNA portrayed as a city skyline. The central gap in the landscape localizes to the precise site of the DNA break. The features surrounding the break denote the processing of DNA-end structures (end-resection) emanating from the break location. Cover artwork by Ethan Tyler, NIH. Abstract

Ethane and Xenon mixing: density functional theory (DFT) simulations and experiments on Sandia's Z machine

NASA Astrophysics Data System (ADS)

Magyar, Rudolph; Root, Seth; Mattsson, Thomas; Cochrane, Kyle

2012-02-01

The combination of ethane and xenon is one of the simplest binary mixtures in which bond breaking is expected to play a role under shock conditions. At cryogenic conditions, xenon is often understood to mix with alkanes such as Ethane as if it were also an alkane, but this model is expected to break down at higher temperatures and pressures. To investigate the breakdown, we have performed density functional theory (DFT) calculations on several xenon/ethane mixtures. Additionally, we have performed shock compression experiments on Xenon-Ethane using the Sandia Z - accelerator. The DFT and experimental results are compared to hydrodynamic simulations using different mixing models in the equation of state. Sandia National Laboratories is a multi-program laboratory operated by Sandia Corporation, a wholly owned subsidiary of the Lockheed Martin company, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Cross-dehydrogenative coupling and oxidative-amination reactions of ethers and alcohols with aromatics and heteroaromatics

PubMed Central

Vuram, Prasanna K.

2017-01-01

Cross-dehydrogenative coupling (CDC) is a process in which, typically, a C–C bond is formed at the expense of two C–H bonds, either catalyzed by metals or other organic compounds, or via uncatalyzed processes. In this perspective, we present various modes of C–H bond-activation at sp3 centers adjacent to ether oxygen atoms, followed by C–C bond formation with aromatic systems as well as with heteroaromatic systems. C–N bond-formation with NH-containing heteroaromatics, leading to hemiaminal ethers, is also an event that can occur analogously to C–C bond formation, but at the expense of C–H and N–H bonds. A large variety of hemiaminal ether-forming reactions have recently appeared in the literature and this perspective also includes this complementary chemistry. In addition, the participation of C–H bonds in alcohols in such processes is also described. Facile access to a wide range of compounds can be attained through these processes, rendering such reactions useful for synthetic applications via Csp3 bond activations. PMID:28970941

Break-up of droplets in a concentrated emulsion flowing through a narrow constriction

NASA Astrophysics Data System (ADS)

Kim, Minkyu; Rosenfeld, Liat; Tang, Sindy; Tang Lab Team

2014-11-01

Droplet microfluidics has enabled a wide range of high throughput screening applications. Compared with other technologies such as robotic screening technology, droplet microfluidics has 1000 times higher throughput, which makes the technology one of the most promising platforms for the ultrahigh throughput screening applications. Few studies have considered the throughput of the droplet interrogation process, however. In this research, we show that the probability of break-up increases with increasing flow rate, entrance angle to the constriction, and size of the drops. Since single drops do not break at the highest flow rate used in the system, break-ups occur primarily from the interactions between highly packed droplets close to each other. Moreover, the probabilistic nature of the break-up process arises from the stochastic variations in the packing configuration. Our results can be used to calculate the maximum throughput of the serial interrogation process. For 40 pL-drops, the highest throughput with less than 1% droplet break-up was measured to be approximately 7,000 drops per second. In addition, the results are useful for understanding the behavior of concentrated emulsions in applications such as mobility control in enhanced oil recovery.

Policies, Practices, and the Effect of Gender Discrimination on the Integration of Women Officers in the Department of the Navy

DTIC Science & Technology

1994-03-01

controls productivity by regulating lunch and toilet breaks as well as physical movement within the workplace . Researchers have observed that women are more...Weak Link. The Feminization of the American Military, that "the presence of women in the military inhibits male bonding, corrupts allegiance to the...assignment policies that restrict most women to "traditional" clerical and fleet- support occupational fields. I. M&SCULINE HEQGONY Then-Commandant of the

Genotoxic properties of haloacetonitriles: drinking water by-products of chlorine disinfection

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

Daniel, F.B.; Schenck, K.M.; Mattox, J.K.

Chlorinated and brominated haloacetonitriles (HAN), known drinking water contaminants which form during chlorine disinfection, were investigated for genotoxic activity. The HAN produced DNA strand breaks in cultured human lymphoblastic (CCRF-CEM) cells, bound to the nucleophilic trapping agent 4-(p-nitrobenzyl)pyridine and formed a covalent bond to polyadenylic acid in a cell-free reaction system. Thus, we have demonstrated that these chemicals are genotoxic, which would indicate a potential for carcinogenic activity and for human health hazard.

Orbital-free bond breaking via machine learning

NASA Astrophysics Data System (ADS)

Snyder, John C.; Rupp, Matthias; Hansen, Katja; Blooston, Leo; Müller, Klaus-Robert; Burke, Kieron

2013-12-01

Using a one-dimensional model, we explore the ability of machine learning to approximate the non-interacting kinetic energy density functional of diatomics. This nonlinear interpolation between Kohn-Sham reference calculations can (i) accurately dissociate a diatomic, (ii) be systematically improved with increased reference data and (iii) generate accurate self-consistent densities via a projection method that avoids directions with no data. With relatively few densities, the error due to the interpolation is smaller than typical errors in standard exchange-correlation functionals.

Method of radiation degradation of PTFE under vacuum conditions

NASA Astrophysics Data System (ADS)

Korenev, Sergey

2004-09-01

A new method of radiation degradation of Polytetrafluoroethylene (PTFE) under vacuum conditions is considered in this report. The combination of glow gas discharge and electrical surface discharge (on surface and inside PTFE) increases the efficiency of thermal-radiation degradation. The main mechanism of this degradation method consists of the breaking of C-C and C-F bonds. The vacuum conditions allow decreasing of the concentration of toxic compounds, such as a HF. Experimental results for degradation of PTFE are presented.

UV waveguides light fabricated in fluoropolymer CYTOP by femtosecond laser direct writing.

PubMed

Hanada, Yasutaka; Sugioka, Koji; Midorikawa, Katsumi

2010-01-18

We have fabricated optical waveguides inside the UV-transparent polymer, CYTOP, by femtosecond laser direct writing for propagating UV light in biochip applications. Femtosecond laser irradiation is estimated to increase the refractive index of CYTOP by 1.7 x 10(-3) due to partial bond breaking in CYTOP. The waveguide in CYTOP has propagation losses of 0.49, 0.77, and 0.91 dB/cm at wavelengths of 632.8, 355, and 266 nm, respectively.

Foundation of a Heterogeneous Electronics Integration Platform

DTIC Science & Technology

2012-05-01

polymer , which we intended to use to encase the die. Analogous to a narrow tube, an individual trench is the container, whereby the SU-8 rises due to...noteworthy property of SU-8 is its ability to cross-link or create intermolecular polymer bonds, 13 which are difficult to break apart and prevent...11 Aug. 2011. <http://www.cleanroom.byu.edu/ su8 .phtml? SU8 -see-all=true (accessed July 2011). 20. MicroChem. SU-8 3000. <http://www.microchem.com

Raman Scattering at Plasmonic Junctions Shorted by Conductive Molecular Bridges

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

El-Khoury, Patrick Z.; Hu, Dehong; Apkarian, V. Ara

2013-04-10

Intensity spikes in Raman scattering, accompanied by switching between line spectra and band spectra, can be assigned to shorting the junction plasmon through molecular conductive bridges. This is demonstrated through Raman trajectories recorded at a plasmonic junction formed by a gold AFM tip in contact with a silver surface coated either with biphenyl-4,4’-dithiol or biphenyl-4-thiol. The fluctuations are absent in the monothiol. In effect, the making and breaking of chemical bonds is tracked.

Structural changes caused by H 2 adsorption on the Si(111)7 × 7 surface

NASA Astrophysics Data System (ADS)

Wolff, S. H.; Wagner, S.; Gibson, J. M.; Loretto, D.; Robinson, I. K.; Bean, J. C.

1990-12-01

Structural changes caused by the adsorption of molecular hydrogen adsorption onto the Si(111)7 × 7 surface reconstruction are quantified using the first structure parameter refinement on transmission electron diffraction (TED) data. We find that initial adsorption of molecular hydrogen onto the Si(111)7 × 7 surface causes a preferential decrease in the occupancy of the center adatoms. Further adsorption of hydrogen results in the breaking of the dimer bonds and the removal of the corner adatoms.

The Hydrogen Abstraction from A Diamond(111) Surface in A Uniform Electric Field

NASA Technical Reports Server (NTRS)

Ricca, Alessandra; Bauschlicher, Charles W., Jr.; Kang, Jeung Ku.; Musgrave, Charles B.; Arnold, James O. (Technical Monitor)

1998-01-01

Bond breaking in a strong electric field is shown to arise from a crossing of the ionic and covalent asymptotes. The specific example of hydrogen abstraction from a diamond(111) surface is studied using a cluster model. The addition of nearby atoms in both the parallel and perpendicular direction to the electric field are found to have an effect. It is also shown that the barrier is not only related to the position of the ionic and covalent asymptotes.

Cross-Linking Interferes With Assessing Sulfur Mustard-Induced DNA Damage in Human Peripheral Blood Lymphocytes Using the Comet Assay

DTIC Science & Technology

2004-01-01

of SM to impede the migration of H,0 2 -damaged mal ian cell lethality with bifunctional alkylating agents . Chemr. Biol. Iriterui. 38:75-86.DNA is an...3100 Ricketts Point Road, Aberdeen Proving Ground, Maryland 21010-5400 N-3 position of adenine, and alkylation leads to depurination of Sulfur...mustard (SM) is a blistering agent that produces DNA DNA strands. Subsequent breakage of phosphodiester bonds at strand breaks. To detect SM-induced DNA

The Effect of Nylon and Polyester Peel Ply Surface Preparation on the Bond Quality of Composite Laminates

NASA Astrophysics Data System (ADS)

Moench, Molly K.

The preparation of the surfaces to be bonded is critical to the success of composite bonds. Peel ply surface preparation is attractive from a manufacturing and quality assurance standpoint, but is a well known example of the extremely system-specific nature of composite bonds. This study examined the role of the surface energy, morphology, and chemistry left by peel ply removal in resulting bond quality. It also evaluated the use of contact angle surface energy measurement techniques for predicting the resulting bond quality of a prepared surface. The surfaces created by preparing three aerospace fiber-reinforced composite prepregs were compared when prepared with a nylon vs a polyester peel ply. The prepared surfaces were characterized with contact angle measurements with multiple fluids, scanning electron microscopy (SEM), and x-ray electron spectroscopy. The laminates were bonded with aerospace grade film adhesives. Bond quality was assessed via double cantilever beam testing followed by optical and scanning electron microscopy of the fracture surfaces.The division was clear between strong bonds (GIC of 600- 1000J/m2 and failure in cohesion) and weak bonds (GIC of 80-400J/m2 and failure in adhesion). All prepared laminates showed the imprint of the peel ply texture and evidence of peel ply remnants after fabric removal, either through SEM or XPS. Within an adhesive system, large amounts of SEM-visible peel ply material transfer correlated with poor bond quality and cleaner surfaces with higher bond quality. The both sides of failed weak bonds showed evidence of peel ply remnants under XPS, showing that at least some failure is occurring through the remnants. The choice of adhesive was found to be significant. AF 555 adhesive was more tolerant of peel ply contamination than MB 1515-3. Although the bond quality results varied substantially between tested combinations, the total surface energies of all prepared surfaces were very similar. Single fluid contact angle measurements/water break tests were therefore not predictive of bond quality, and are recommended against. The multiple fluids used allowed the construction of wettability envelopes, a more detailed look at the surface energy profile. The envelopes of nylon and polyester prepared systems were noticeably different, but while potentially useful for detecting changes or errors in surface preparation of known systems, they were not valid for predicting bond quality in new systems. Ultimately, it was determined that wetting is a necessary but not sufficient condition for bonding.

The Effects of Fiber Orientation and Adhesives on Tensile Properties of Carbon Fiber Reinforced Polymer Matrix Composite with Embedded Nickel-Titanium Shape Memory Alloys

NASA Technical Reports Server (NTRS)

Quade, Derek J.; Jana, Sadhan C.; Morscher, Gregory N.; Kannan, Manigandan; McCorkle, Linda S.

2017-01-01

Nickel-titanium (NiTi) shape memory alloy (SMA) sections were embedded within carbon fiber reinforced polymer matrix composite (CFRPPMC) laminates and their tensile properties were evaluated with simultaneous monitoring of modal acoustic emissions. The test specimens were fabricated in three different layup configurations and two different thin film adhesives were applied to bond the SMA with the PMC. A trio of acoustic sensors were attached to the specimens during tensile testing to monitor the modal acoustic emission (AE) as the materials experienced mechanical failure. The values of ultimate tensile strengths, strains, and moduli were obtained. Cumulative AE energy of events and specimen failure location were determined. In conjunction, optical and scanning electron microscopy techniques were used to examine the break areas of the specimens. The analysis of AE data revealed failure locations within the specimens which were validated from the microscopic images. The placement of 90 deg plies in the outer ply gave the strongest acoustic signals during break as well as the cleanest break of the samples tested. Overlapping 0 deg ply layers surrounding the SMA was found to be the best scenario to prevent failure of the specimen itself.