Measurements of relative chemical shift tensor orientations in solid-state NMR: new slow magic angle spinning dipolar recoupling experiments.

PubMed

Jurd, Andrew P S; Titman, Jeremy J

2009-08-28

Solid-state NMR experiments can be used to determine conformational parameters, such as interatomic distances and torsion angles. The latter can be obtained from measurements of the relative orientation of two chemical shift tensors, if the orientation of these with respect to the surrounding bonds is known. In this paper, a new rotor-synchronized magic angle spinning (MAS) dipolar correlation experiment is described which can be used in this way. Because the experiment requires slow MAS rates, a novel recoupling sequence, designed using symmetry principles, is incorporated into the mixing period. This recoupling sequence is based in turn on a new composite cyclic pulse referred to as COAST (for combined offset and anisotropy stabilization). The new COAST-C7(2)(1) sequence is shown to give good theoretical and experimental recoupling efficiency, even when the CSA far exceeds the MAS rate. In this regime, previous recoupling sequences, such as POST-C7(2)(1), exhibit poor recoupling performance. The effectiveness of the new method has been explored by a study of the dipeptide L-phenylalanyl-L-phenylalanine.

Competition of the connectivity with the local and the global order in polymer melts and crystals

NASA Astrophysics Data System (ADS)

Bernini, S.; Puosi, F.; Barucco, M.; Leporini, D.

2013-11-01

The competition between the connectivity and the local or global order in model fully flexible chain molecules is investigated by molecular-dynamics simulations. States with both missing (melts) and high (crystal) global order are considered. Local order is characterized within the first coordination shell (FCS) of a tagged monomer and found to be lower than in atomic systems in both melt and crystal. The role played by the bonds linking the tagged monomer to FCS monomers (radial bonds), and the bonds linking two FCS monomers (shell bonds) is investigated. The detailed analysis in terms of Steinhardt's orientation order parameters Ql (l = 2 - 10) reveals that increasing the number of shell bonds decreases the FCS order in both melt and crystal. Differently, the FCS arrangements organize the radial bonds. Even if the molecular chains are fully flexible, the distribution of the angle formed by adjacent radial bonds exhibits sharp contributions at the characteristic angles θ ≈ 70°, 122°, 180°. The fractions of adjacent radial bonds with θ ≈ 122°, 180° are enhanced by the global order of the crystal, whereas the fraction with 70° ≲ θ ≲ 110° is nearly unaffected by the crystallization. Kink defects, i.e., large lateral displacements of the chains, are evidenced in the crystalline state.

One-step formation of straight nanostripes from a mammal lipid-oleamide directly on highly oriented pyrolytic graphite.

PubMed

Zhang, Renjie; Möhwald, Helmuth; Kurth, Dirk G

2009-02-17

Hierarchical nanostructures are obtained directly on highly oriented pyrolytic graphite (HOPG) by spin coating of dilute chloroform solution of 9-Z-octadecenamide (oleamide), a natural lipid with cis-CdC- conformation, existing in the cerebrospinal fluid of mammal animals and being an additive for medical use and food packaging. Straight separated nanostripes with a length of 70-300 nm exist in the topmost layer and compact nanostripes in the bottom layer contacting HOPG. Compact nanostripes have a periodicity spacing of 3.8 nm, indicating H-bonding between two rows of oleamide molecules. The orientation of the hierarchical nanostructures differs by n60 degrees+/-8 degrees (n=1 or 2), reflecting the epitaxial ordering along theHOPGsubstrate. The nanostripes are stable against annealing.Amolecular packing scheme for the nanostructures is proposed, where the -C=C bond angle in oleamide is 120 degrees and the plane of the carbon skeleton lies parallel to the HOPG substrate. Nanostripes in the topmost layer are formed from separated rows of oleamide molecules, due to the short-range surface potential of the substrate. The scheme involves direct influence ofHOPGon the orientation of oleamide molecules to form nanostripes without any purposely added saturated alkanes and H-bonds between amide groups in adjacent two rows of oleamide molecules.

In situ ultra-small-angle X-ray scattering study under uniaxial stretching of colloidal crystals prepared by silica nanoparticles bearing hydrogen-bonding polymer grafts

DOE PAGES

Ishige, Ryohei; Williams, Gregory A.; Higaki, Yuji; ...

2016-04-19

A molded film of single-component polymer-grafted nanoparticles (SPNP), consisting of a spherical silica core and densely grafted polymer chains bearing hydrogen-bonding side groups capable of physical crosslinking, was investigated byin situultra-small-angle X-ray scattering (USAXS) measurement during a uniaxial stretching process. Static USAXS revealed that the molded SPNP formed a highly oriented twinned face-centered cubic (f.c.c.) lattice structure with the [11-1] plane aligned nearly parallel to the film surface in the initial state. Structural analysis ofin situUSAXS using a model of uniaxial deformation induced by rearrangement of the nanoparticles revealed that the f.c.c. lattice was distorted in the stretching direction inmore » proportion to the macroscopic strain until the strain reached 35%, and subsequently changed into other f.c.c. lattices with different orientations. The lattice distortion and structural transition behavior corresponded well to the elastic and plastic deformation regimes, respectively, observed in the stress–strain curve. The attractive interaction of the hydrogen bond is considered to form only at the top surface of the shell and then plays an effective role in cross-linking between nanoparticles. The rearrangement mechanism of the nanoparticles is well accounted for by a strong repulsive interaction between the densely grafted polymer shells of neighboring particles.« less

Membrane Perturbation Induced by Interfacially Adsorbed Peptides

PubMed Central

Zemel, Assaf; Ben-Shaul, Avinoam; May, Sylvio

2004-01-01

The structural and energetic characteristics of the interaction between interfacially adsorbed (partially inserted) α-helical, amphipathic peptides and the lipid bilayer substrate are studied using a molecular level theory of lipid chain packing in membranes. The peptides are modeled as “amphipathic cylinders” characterized by a well-defined polar angle. Assuming two-dimensional nematic order of the adsorbed peptides, the membrane perturbation free energy is evaluated using a cell-like model; the peptide axes are parallel to the membrane plane. The elastic and interfacial contributions to the perturbation free energy of the “peptide-dressed” membrane are evaluated as a function of: the peptide penetration depth into the bilayer's hydrophobic core, the membrane thickness, the polar angle, and the lipid/peptide ratio. The structural properties calculated include the shape and extent of the distorted (stretched and bent) lipid chains surrounding the adsorbed peptide, and their orientational (C-H) bond order parameter profiles. The changes in bond order parameters attendant upon peptide adsorption are in good agreement with magnetic resonance measurements. Also consistent with experiment, our model predicts that peptide adsorption results in membrane thinning. Our calculations reveal pronounced, membrane-mediated, attractive interactions between the adsorbed peptides, suggesting a possible mechanism for lateral aggregation of membrane-bound peptides. As a special case of interest, we have also investigated completely hydrophobic peptides, for which we find a strong energetic preference for the transmembrane (inserted) orientation over the horizontal (adsorbed) orientation. PMID:15189858

Application of database methods to the prediction of B3LYP-optimized polyhedral water cluster geometries and electronic energies

NASA Astrophysics Data System (ADS)

Anick, David J.

2003-12-01

A method is described for a rapid prediction of B3LYP-optimized geometries for polyhedral water clusters (PWCs). Starting with a database of 121 B3LYP-optimized PWCs containing 2277 H-bonds, linear regressions yield formulas correlating O-O distances, O-O-O angles, and H-O-H orientation parameters, with local and global cluster descriptors. The formulas predict O-O distances with a rms error of 0.85 pm to 1.29 pm and predict O-O-O angles with a rms error of 0.6° to 2.2°. An algorithm is given which uses the O-O and O-O-O formulas to determine coordinates for the oxygen nuclei of a PWC. The H-O-H formulas then determine positions for two H's at each O. For 15 test clusters, the gap between the electronic energy of the predicted geometry and the true B3LYP optimum ranges from 0.11 to 0.54 kcal/mol or 4 to 18 cal/mol per H-bond. Linear regression also identifies 14 parameters that strongly correlate with PWC electronic energy. These descriptors include the number of H-bonds in which both oxygens carry a non-H-bonding H, the number of quadrilateral faces, the number of symmetric angles in 5- and in 6-sided faces, and the square of the cluster's estimated dipole moment.

Crystal structure of 2-oxopyrrolidin-3-yl 4-(2-phenyl-diazen-1-yl)benzoate.

PubMed

Elkin, Igor; Maris, Thierry; Melkoumov, Alexandre; Hildgen, Patrice; Banquy, Xavier; Leclair, Grégoire; Barrett, Christopher

2018-04-01

In the title compound, C 17 H 15 N 3 O 3 , the plane of the pyrrolidone ring is inclined at an angle of 59.791 (2)° to that of the azo-benzene segment, which adopts a configuration close to planar. In the crystal, mol-ecules are oriented pairwise by (2-oxopyrrolidin-3-yl)-oxy moieties at an angle of 76.257 (3)°, linked by hydrogen bonds and π-stacking inter-actions, forming zigzag supra-molecular chains parallel to [010] further linked via additional C-H⋯π inter-actions.

7-Chloro-5-(2-ethoxy­phen­yl)-1-methyl-3-propyl-2,6-dihydro-1H-pyrazolo[4,3-d]pyrimidine

PubMed Central

Zhou, Ming-Qiu; Zhu, Kai; Lv, Xiao-Ping; Han, Ping-Fang; Wei, Ping

2009-01-01

In the title compound, C17H21ClN4O, the benzene ring is oriented at dihedral angles of 1.59 (3) and 1.27 (3)° with respect to the pyrimidine and pyrazole rings, while the dihedral angle between the pyrimidine and pyrazole rings is 0.83 (3)°. An intra­molecular N—H⋯O hydrogen bond results in the formation of a planar (r.m.s. deviation 0.004 Å) six-membered ring. PMID:21577789

2-(Naphthalen-1-yl)-4-(naphthalen-1-yl­methyl­idene)-1,3-oxazol-5(4H)-one

PubMed Central

Gündoğdu, Cevher; Alp, Serap; Ergün, Yavuz; Tercan, Barış; Hökelek, Tuncer

2011-01-01

In the title compound, C24H15NO2, the oxazole ring is oriented at dihedral angles of 10.09 (4) and 6.04 (4)° with respect to the mean planes of the naphthalene ring systems, while the two naphthalene ring systems make a dihedral angle of 4.32 (3)°. Intra­molecular C—H⋯N hydrogen bonds link the oxazole N atom to the naphthalene ring systems. In the crystal, inter­molecular weak C—H⋯O hydrogen bonds link the mol­ecules into centrosymmetric dimers. π–π contacts between the oxazole and naphthalene rings and between the naphthalene ring systems [centroid–centroid distances = 3.5947 (9) and 3.7981 (9) Å] may further stabilize the crystal structure. Three weak C—H⋯π inter­actions also occur. PMID:21754548

Photoelectron diffraction from single oriented molecules: Towards ultrafast structure determination of molecules using x-ray free-electron lasers

NASA Astrophysics Data System (ADS)

Kazama, Misato; Fujikawa, Takashi; Kishimoto, Naoki; Mizuno, Tomoya; Adachi, Jun-ichi; Yagishita, Akira

2013-06-01

We provide a molecular structure determination method, based on multiple-scattering x-ray photoelectron diffraction (XPD) calculations. This method is applied to our XPD data on several molecules having different equilibrium geometries. Then it is confirmed that, by our method, bond lengths and bond angles can be determined with a resolution of less than 0.1 Å and 10∘, respectively. Differently from any other scenario of ultrafast structure determination, we measure the two- or three-dimensional XPD of aligned or oriented molecules in the energy range from 100 to 200 eV with a 4π detection velocity map imaging spectrometer. Thanks to the intense and ultrashort pulse properties of x-ray free-electron lasers, our approach exhibits the most probable method for obtaining ultrafast real-time structural information on small to medium-sized molecules consisting of light elements, i.e., a “molecular movie.”

Correlation between protein secondary structure, backbone bond angles, and side-chain orientations.

PubMed

Lundgren, Martin; Niemi, Antti J

2012-08-01

We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central C(α) carbon of a protein backbone, and for this we develop new visualization techniques to analyze high-resolution x-ray structures in the Protein Data Bank. We observe that there is a correlation between the deformations of the ideal tetrahedral symmetry and the local secondary structure of the protein. We propose a universal coarse-grained energy function to describe the ensuing side-chain geometry in terms of the C(β) carbon orientations. The energy function can model the side-chain geometry with a subatomic precision. As an example we construct the C(α)-C(β) structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 Å in root-mean-square distance from the experimental x-ray structure.

Angle-adjustable density field formulation for the modeling of crystalline microstructure

NASA Astrophysics Data System (ADS)

Wang, Zi-Le; Liu, Zhirong; Huang, Zhi-Feng

2018-05-01

A continuum density field formulation with particle-scale resolution is constructed to simultaneously incorporate the orientation dependence of interparticle interactions and the rotational invariance of the system, a fundamental but challenging issue in modeling the structure and dynamics of a broad range of material systems across variable scales. This generalized phase field crystal-type approach is based upon the complete expansion of particle direct correlation functions and the concept of isotropic tensors. Through applications to the modeling of various two- and three-dimensional crystalline structures, our study demonstrates the capability of bond-angle control in this continuum field theory and its effects on the emergence of ordered phases, and provides a systematic way of performing tunable angle analyses for crystalline microstructures.

Theoretical and experimental examination of SFG polarization analysis at acetonitrile-water solution surfaces.

PubMed

Saito, Kengo; Peng, Qiling; Qiao, Lin; Wang, Lin; Joutsuka, Tatsuya; Ishiyama, Tatsuya; Ye, Shen; Morita, Akihiro

2017-03-29

Sum frequency generation (SFG) spectroscopy is widely used to observe molecular orientation at interfaces through a combination of various types of polarization. The present work thoroughly examines the relation between the polarization dependence of SFG signals and the molecular orientation, by comparing SFG measurements and molecular dynamics (MD) simulations of acetonitrile/water solutions. The present SFG experiment and MD simulations yield quite consistent results on the ratios of χ (2) elements, supporting the reliability of both means. However, the subsequent polarization analysis tends to derive more upright tilt angles of acetonitrile than the direct MD calculations. The reasons for discrepancy are examined in terms of three issues; (i) anisotropy of the Raman tensor, (ii) cross-correlation, and (iii) orientational distribution. The analysis revealed that the issues (i) and (iii) are the main causes of errors in the conventional polarization analysis of SFG spectra. In methyl CH stretching, the anisotropy of Raman tensor cannot be estimated from the simple bond polarizability model. The neglect of the orientational distribution is shown to systematically underestimate the tilt angle of acetonitrile. Further refined use of polarization analysis in collaboration with MD simulations should be proposed.

Method of making porous conductive supports for electrodes. [by electroforming and stacking nickel foils

NASA Technical Reports Server (NTRS)

Schaer, G. R. (Inventor)

1973-01-01

Porous conductive supports for electrochemical cell electrodes are made by electroforming thin corrugated nickel foil, and by stacking pieces of the corrugated foil alternatively with pieces of thin flat nickel foil. Corrugations in successive corrugated pieces are oriented at different angles. Adjacent pieces of foil are bonded by heating in a hydrogen atmosphere and then cutting the stack in planes perpendicular to the foils.

Carbon Nanotube Bonding Strength Enhancement Using Metal "Wicking" Process

NASA Technical Reports Server (NTRS)

Lamb, James L.; Dickie, Matthew R.; Kowalczyk, Robert S.; Liao, Anna; Bronikowski, Michael J.

2012-01-01

Carbon nanotubes grown from a surface typically have poor bonding strength at the interface. A process has been developed for adding a metal coat to the surface of carbon nano tubes (CNTs) through a wicking process, which could lead to an enhanced bonding strength at the interface. This process involves merging CNTs with indium as a bump-bonding enhancement. Classical capillary theory would not normally allow materials that do not wet carbon or graphite to be drawn into the spacings by capillary action because the contact angle is greater than 90 degrees. However, capillary action can be induced through JPL's ability to fabricate oriented CNT bundles to desired spacings, and through the use of deposition techniques and temperature to control the size and mobility of the liquid metal streams and associated reservoirs. A reflow and plasma cleaning process has also been developed and demonstrated to remove indium oxide, and to obtain smooth coatings on the CNT bundles.

Viscosity of dilute suspensions of rodlike particles: A numerical simulation method

NASA Astrophysics Data System (ADS)

Yamamoto, Satoru; Matsuoka, Takaaki

1994-02-01

The recently developed simulation method, named as the particle simulation method (PSM), is extended to predict the viscosity of dilute suspensions of rodlike particles. In this method a rodlike particle is modeled by bonded spheres. Each bond has three types of springs for stretching, bending, and twisting deformation. The rod model can therefore deform by changing the bond distance, bond angle, and torsion angle between paired spheres. The rod model can represent a variety of rigidity by modifying the bond parameters related to Young's modulus and the shear modulus of the real particle. The time evolution of each constituent sphere of the rod model is followed by molecular-dynamics-type approach. The intrinsic viscosity of a suspension of rodlike particles is derived from calculating an increased energy dissipation for each sphere of the rod model in a viscous fluid. With and without deformation of the particle, the motion of the rodlike particle was numerically simulated in a three-dimensional simple shear flow at a low particle Reynolds number and without Brownian motion of particles. The intrinsic viscosity of the suspension of rodlike particles was investigated on orientation angle, rotation orbit, deformation, and aspect ratio of the particle. For the rigid rodlike particle, the simulated rotation orbit compared extremely well with theoretical one which was obtained for a rigid ellipsoidal particle by use of Jeffery's equation. The simulated dependence of the intrinsic viscosity on various factors was also identical with that of theories for suspensions of rigid rodlike particles. For the flexible rodlike particle, the rotation orbit could be obtained by the particle simulation method and it was also cleared that the intrinsic viscosity decreased as occurring of recoverable deformation of the rodlike particle induced by flow.

Investigation on the structure of liquid N-methylformamide-dimethylsulfoxide mixtures

NASA Astrophysics Data System (ADS)

Cordeiro, João M. M.; Soper, Alan K.

2011-03-01

The structures of liquid mixtures of N-methylformamide (NMF) and dimethyl sulfoxide (DMSO) at two concentrations (80% and 50% NMF) are investigated using a combination of neutron diffraction augmented with isotopic substitution and empirical potential structure refinement simulations. The results indicate that the NMF and DMSO molecules are hydrogen-bonded to one another with a preference for NMF-DMSO hydrogen bonding, compared to the NMF-NMF ones. The liquid is orientationally structured as a consequence of these hydrogen bonds between molecules. NMF-DMSO dimers are very stable species in the bulk of the mixture. The structure of the dimers is such that the angle between the molecular dipole moments is around 60°. The NMF molecules are well solvated in DMSO with potential implications for peptides solvation in this solvent.

Crystal structure of 2-((1E)-{2-[bis-(2-methyl-benzyl-sulfan-yl)methyl-idene]hydrazin-1-yl-idene}meth-yl)-6-meth-oxy-phenol.

PubMed

Yusof, Enis Nadia Md; Ravoof, Thahira Begum S A; Tahir, Mohamed Ibrahim Mohamed; Tiekink, Edward R T

2015-04-01

In the title compound, C25H26N2O2S2, the central CN2S2 atoms are almost coplanar (r.m.s. deviation = 0.0058 Å). One phenyl ring clearly lies to one side of the central plane, while the other is oriented in the plane but splayed. Despite the different relative orientations, the phenyl rings form similar dihedral angles of 64.90 (3) and 70.06 (3)° with the central plane, and 63.28 (4)° with each other. The benzene ring is twisted with respect to the central plane, forming a dihedral angle of 13.17 (7)°. The S2C=N, N-N and N-N=C bond lengths of 1.2919 (19), 1.4037 (17) and 1.2892 (19) Å, respectively, suggest limited conjugation over these atoms; the configuration about the N-N=C bond is E. An intra-molecular O-H⋯N hydrogen bond is noted. In the crystal, phen-yl-meth-oxy C-H⋯O and phen-yl-phenyl C-H⋯π inter-actions lead to supra-molecular double chains parallel to the b axis. These are connected into a layer via meth-yl-phenyl C-H⋯π inter-actions, and layers stack along the a axis, being connected by weak π-π inter-actions between phenyl rings [inter-centroid distance = 3.9915 (9) Å] so that a three-dimensional architecture ensues.

Rotation elastogram: a novel method to visualize local rigid body rotation under quasi-static compression

NASA Astrophysics Data System (ADS)

Sowmiya, C.; Kothawala, Ali Arshad; Thittai, Arun K.

2016-04-01

During manual palpation of breast masses, the perception of its stiffness and slipperiness are the two commonly used information by the physician. In order to reliably and quantitatively obtain this information several non-invasive elastography techniques have been developed that seek to provide an image of the underlying mechanical properties, mostly stiffness-related. Very few approaches have visualized the "slip" at the lesion-background boundary that only occurs for a loosely-bonded benign lesion. It has been shown that axial-shear strain distribution provides information about underlying slip. One such feature, referred to as "fill-in" was interpreted as a surrogate of the rotation undergone by an asymmetrically-oriented-loosely bonded-benign-lesion under quasi-static compression. However, imaging and direct visualization of the rotation itself has not been addressed yet. In order to accomplish this, the quality of lateral displacement estimation needs to be improved. In this simulation study, we utilize spatial compounding approach and assess the feasibility to obtain good quality rotation elastogram. The angular axial and lateral displacement estimates were obtained at different insonification angles from a phantom containing an elliptical inclusion oriented at 45°, subjected to 1% compression from the top. A multilevel 2D-block matching algorithm was used for displacement tracking and 2D-least square compounding of angular axial and lateral displacement estimates was employed. By varying the maximum steering angle and incremental angle, the improvement in the lateral motion tracking accuracy and its effects on the quality of rotational elastogram were evaluated. Results demonstrate significantly-improved rotation elastogram using this technique.

An Ultrasonic Guided Wave Method to Estimate Applied Biaxial Loads (Preprint)

DTIC Science & Technology

2011-11-01

VALIDATION A fatigue test was performed with an array of six surface-bonded PZT transducers on a 6061 aluminum plate as shown in Figure 4. The specimen...direct paths of propagation are oriented at different angles. This method is applied to experimental sparse array data recorded during a fatigue test...and the additional complication of the resulting fatigue cracks interfering with some of the direct arrivals is addressed via proper selection of

Anisotropic toughness and strength in graphene and its atomistic origin

NASA Astrophysics Data System (ADS)

Hossain, M. Zubaer; Ahmed, Tousif; Silverman, Benjamin; Khawaja, M. Shehroz; Calderon, Justice; Rutten, Andrew; Tse, Stanley

2018-01-01

This paper presents the implication of crystallographic orientation on toughness and ideal strength in graphene under lattice symmetry-preserving and symmetry-breaking deformations. In symmetry-preserving deformation, both toughness and strength are isotropic, regardless of the chirality of the lattice; whereas, in symmetry-breaking deformation they are strongly anisotropic, even in the presence of vacancy defects. The maximum and minimum of toughness or strength occur for loading along the zigzag direction and the armchair direction, respectively. The anisotropic behavior is governed by a complex interplay among bond-stretching deformation, bond-bending deformation, and the chirality of the lattice. Nevertheless, the condition for crack-nucleation is dictated by the maximum bond-force required for bond rupture, and it is independent of the chiral angle of the lattice or loading direction. At the onset of crack-nucleation a localized nucleation zone is formed, wherein the bonds rupture locally satisfying the maximum bond-force criterion. The nucleation zone acts as the physical origin in triggering the fracture nucleation process, but its presence is undetectable from the macroscopic stress-strain data.

Ethyl 2-{N-[N-(4-chloro-6-methoxy­pyrimidin-2-yl)carbamo­yl]sulfamo­yl}benzoate

PubMed Central

Lu, Chui; Li, Fang-Shi; Yu, Da-Sheng; Yao, Wei; Liu, Yin-Hong

2008-01-01

The asymmetric unit of the title compound, C15H15ClN4O6S, contains two independent mol­ecules, in which the pyrimidine and benzene rings are oriented at dihedral angles of 75.21 (3) and 86.00 (3)°. Intra­molecular N—H⋯N and C—H⋯O hydrogen bonds result in the formation of two five- and two six-membered rings. The six-membered rings have flattened-boat conformations, while the five-membered rings adopt envelope conformations. In the crystal structure, inter­molecular N—H⋯O hydrogen bonds link the mol­ecules. PMID:21202882

The microscopic protein structure of the lens with a theory for cataract formation as determined by Raman spectroscopy of intact bovine lenses.

PubMed

Schachar, R A; Solin, S A

1975-05-01

Intact bovine lenses have been studied using the polarized Raman spectroscopic technique. A brief theoretical and experimental review of Raman spectroscopy is presented. From the dependence of the Raman depolarization ratio on the propagation direction of the incident radiation we have determined that the uniaxial qualities of the lens result from microscopic anisotropy and have established the quantitative positional correlation of specific chemical bonds with respect to the lens optic axis. In particular, the hydrogen bonded linear CONH groups of the antiparallel beta-pleated sheet are preferentially oriented in directions orthogonal to the lens optic axis. The Raman spectra of intact lenses do not exhibit bands at positions characteristic of either the alpha-helix or the random coil protein structure. The antiparallel beta-pleated sheet protein microstructure and the lens fiber cross-sectional macrostructure exhibit a remarkable similarity. This similarity may be causal and is consistent with the protein concentration of the lens, the birefringent properties observed by both Lenhard and Brewster, the CONH bond angle distribution with respect to the optic axis, and the lens anatomy. It is suggested that cortical cataracts are caused by fluctuations in protein orientational order.

Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.

PubMed

Fenn, Timothy D; Schnieders, Michael J; Mustyakimov, Marat; Wu, Chuanjie; Langan, Paul; Pande, Vijay S; Brunger, Axel T

2011-04-13

Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints, and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here, we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen-bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms. Copyright © 2011 Elsevier Ltd. All rights reserved.

Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Application to Neutron Crystallography and DNA Hydration

PubMed Central

Fenn, Timothy D.; Schnieders, Michael J.; Mustyakimov, Marat; Wu, Chuanjie; Langan, Paul; Pande, Vijay S.; Brunger, Axel T.

2011-01-01

Summary Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms. PMID:21481775

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

Weiss, Paul

Spectroscopic imaging tools and methods, based on scanning tunneling microscopes (STMs), are being developed and applied to examine buried layers and interfaces with ultrahigh resolution. These new methods measure buried contacts, molecule-substrate bonds, buried dipoles in molecular layers, and key structural aspects of adsorbed molecules, such as tilt angles. We are developing the ability to locate lateral projections of molecular parts as a means of determining the structures of molecular layers. We are developing the ability to measure the orientation of buried functionality.

Symmetric Tilt Grain Boundaries of Synthetic Forsterite Bicrystals

NASA Astrophysics Data System (ADS)

Heinemann, S.; Wirth, R.; Dresen, G.

2002-12-01

{ indent1.5em skip0ex Structure and transport properties of grain boundaries in rocks are still poorly understood. For example, grain boundary diffusivity and mobility depend on orientation, and they are different for low and high angle grain boundaries. The transition from low to high angle grain boundaries in rock-forming minerals is not studied in detail, but a high angle grain boundary is commonly defined by a lattice misorientation of >10°-15°. To investigate the physical properties of olivine grain boundaries we produced a series of synthetic forsterite bicrystals with symmetric tilt grain boundaries by direct bonding [1,2]. For each bicrystal two oriented synthetic forsterite single crystals were joined at room temperature and annealed at 400°C for one week. All bicrystals were cut in two parts and one part was annealed further at 1650°C for 48h. The tilt axis of the boundary in the synthesized bicrystals is parallel to the a direction, and the tilt angles of the series range from 9° to 21°. Specimens were prepared for investigations in the transmission electron microscope (TEM) using focused ion beam (FIB) technique. High-resolution TEM investigations of symmetric tilt grain boundaries reveal dislocation arrays between undisturbed crystal regions in samples annealed at 400°C and 1650°C. This suggests that bonding of bicrystals occurred already below or at 400°C. The burgers vectors of the dislocations are parallel to c. Dislocation cores do not overlap up to a tilt angle of 21°. This indicates that for forsterite small angle grain boundaries exist up to tilt angles of 21°. The dislocation model of small angle grain boundaries can be applied and the observed dislocation spacings d are related to tilt angle θ and burgers vector length b by Franks formula [3]: d = b/(2sin(2/θ )) ~ b/θ . With tilt angles increasing from 9° to 21° the dislocation spacing decreased. Using Frank's equation and the observation that dislocations do not overlap at a misorientation of 21° allows to estimate the maximum radius of the dislocation cores, r0<1.4b.} {skip0ex \\small [1] Heinemann S et al. (2001) Phys Chem Minerals 28, 685 [2] Heinemann S et al. (2002) Beih Eur Mineral 14(1), 66 [3] Frank FC (1951) Pittsburgh Symposium on the Plastic Deformation of Solids. 150}

Formation of highly preferred orientation of β-Sn grains in solidified Cu/SnAgCu/Cu micro interconnects under temperature gradient effect

NASA Astrophysics Data System (ADS)

Zhao, N.; Zhong, Y.; Dong, W.; Huang, M. L.; Ma, H. T.; Wong, C. P.

2017-02-01

β-Sn grain orientation and configuration are becoming crucial factors to dominate the lifetime of solder interconnects in three-dimensional integrated circuit packaging. In this paper, we found that a temperature gradient during solidification significantly dominated the orientation and configuration of the final β-Sn grains in Cu/SnAgCu/Cu micro interconnects. Being different from the random orientations and growth fronts meeting or cyclic twin boundary forming near the center after homogeneous temperature bonding, the β-Sn grains solidified under a certain temperature gradient were observed to follow a highly preferred orientation with their c-axis departing from the direction of temperature gradient by about 45°-88°. Meanwhile, these preferred oriented β-Sn grains consisted of low angle grain boundary structures with misorientation in the range of 0°-15°. The mechanism was explained in terms of the anisotropy and directional growth of β-Sn grains. The results pave the way for grain orientation control in 3D packaging technology.

Crystal structure of 2-((1E)-{2-[bis­(2-methyl­benzyl­sulfan­yl)methyl­idene]hydrazin-1-yl­idene}meth­yl)-6-meth­oxy­phenol

PubMed Central

Yusof, Enis Nadia Md; Ravoof, Thahira Begum S. A.; Tahir, Mohamed Ibrahim Mohamed; Tiekink, Edward R. T.

2015-01-01

In the title compound, C25H26N2O2S2, the central CN2S2 atoms are almost coplanar (r.m.s. deviation = 0.0058 Å). One phenyl ring clearly lies to one side of the central plane, while the other is oriented in the plane but splayed. Despite the different relative orientations, the phenyl rings form similar dihedral angles of 64.90 (3) and 70.06 (3)° with the central plane, and 63.28 (4)° with each other. The benzene ring is twisted with respect to the central plane, forming a dihedral angle of 13.17 (7)°. The S2C=N, N—N and N—N=C bond lengths of 1.2919 (19), 1.4037 (17) and 1.2892 (19) Å, respectively, suggest limited conjugation over these atoms; the configuration about the N—N=C bond is E. An intra­molecular O—H⋯N hydrogen bond is noted. In the crystal, phen­yl–meth­oxy C—H⋯O and phen­yl–phenyl C—H⋯π inter­actions lead to supra­molecular double chains parallel to the b axis. These are connected into a layer via meth­yl–phenyl C—H⋯π inter­actions, and layers stack along the a axis, being connected by weak π–π inter­actions between phenyl rings [inter-centroid distance = 3.9915 (9) Å] so that a three-dimensional architecture ensues. PMID:26029435

2,4-Bis(3-methoxy-phen-yl)-3-aza-bicyclo-[3.3.1]nonan-9-one.

PubMed

Parthiban, P; Ramkumar, V; Jeong, Yeon Tae

2009-12-04

In the crystal structure, the title compound, C(22)H(25)NO(3), exists in a twin-chair conformation with equatorial orientations of the meta-methoxy-phenyl groups on both sides of the secondary amino group. The title compound is a positional isomer of 2,4-bis-(2-methoxy-phen-yl)-3-aza-bicyclo-[3.3.1]nonan-9-one and 2,4-bis-(4-methoxy-phen-yl)-3-aza-bicyclo-[3.3.1]nonan-9-one, which both also exhibit twin-chair conformations with equatorial dispositions of the anisyl rings on both sides of the secondary amino group. In the title compound, the meta-methoxy-phenyl rings are orientated at an angle of 25.02 (3)° with respect to each other, whereas in the ortho and para isomers, the anisyl rings are orientated at dihedral angles of 33.86 (3) and 37.43 (4)°, respectively. The crystal packing is dominated by van der Waals inter-actions and by an inter-molecular N-H⋯O hydrogen bond, whereas in the ortho isomer, an inter-molecular N-H⋯π inter-action (H⋯Cg = 2.75 Å) is found.

Photoisomerization in bacteriorhodopsin studied by FTIR, linear dichroism and photoselection experiments combined with quantum chemical theoretical analysis

NASA Astrophysics Data System (ADS)

Fahmy, K.; Siebert, F.; Großjean, M. F.; Tavan, P.

1989-12-01

Orientations of IR transition moments of the retinal chromophore of bacteriorhodopsin (BR) and of the apo-protein are investigated by FTIR linear dichroism and photoselection measurements. Low temperature difference spectra for the photoinduced transitions of BR to its photocycle intermediates K and L are evaluated using improved methods. Quantum chemical calculations of directions of IR and electronic transition moments of model chromophores are employed to analyze corresponding observations. The chromophore of light-adapted BR 568 is shown to exhibit small (15-30°) twists around the CC single bonds of retinals polyene chain but no large overall helicity (⩽15°). The average retinal plane is demonstrated to form an angle of 90±20° with the plane of the purple membrane. The C 9C 10 double bond of retinal is found approximately parallel to the plane of the membrane. Upon photoisomerization the orientation of the chromophore moiety from C 1 to C 13 is estimated to be largely conserved. The single bond twists of the chromophore in L are shown to be larger than those in BR 568. This result is in agreement with the previous prediction of increased single bond twists in L, which can cause a p K decrease of the chromophore and, thereby, enforce its deprotonation in the L→M transition [Schulten and Tavan, Nature, 272 (1978) 85].

Synthesis, spectroscopic characterization and theoretical calculations of ClF2CC(O)NPCl3 ([chloro(difluor)acetyl]phosphorimidic trichloride).

PubMed

Iriarte, Ana G; Cutin, Edgardo H; Argüello, Gustavo A

2014-01-01

The synthesis of [chloro(difluor)acetyl]phosphorimidic trichloride (ClF2CC(O)NPCl3), together with a tentative assignment of the vibrational, NMR and mass spectra, are reported. Quantum chemical calculations (MP2 and B3LYP methods with 6-311+G(d) and 6-311+G(2df,p) basis sets) predict three stable conformers in the gas phase (syn, gauche and anti, defined according to the rotation around both the ClCCN and the CCNP dihedral angles). However, only a single C1 symmetry conformer is observed in the liquid phase, possessing the CO double bond in synperiplanar orientation with respect to the PN double bond, and the ClC bond distorted from the plane defined by the CC(O)NP entity. A Natural Bond Orbital (NBO) analysis was carried out for the title compound and related molecules in order to provide an explanation about the electronic properties. Copyright © 2013 Elsevier B.V. All rights reserved.

2-Propyl-4H-thia­zolo[3,2-a][1,3,5]triazine-4-thione

PubMed Central

Yunus, Uzma; Tahir, Muhammad Kalim; Bhatti, Moazzam Hussain; Wong, Wai-Yeung

2008-01-01

In the title compound, C8H9N3S2, the n-propyl chain is disordered over two orientations (site-occupancy ratio = 0.522:0.478) and is roughly perpendicular to the fused thia­zolotriazine system. The angle between the fused ring and the propyl chain is 83.6 (1)° [ 82.2 (1)° for the disordered chain]. The structure is stabilized by C—H⋯N hydrogen bonds. PMID:21202112

3-(2,4-Dichloro­anilino)iso­benzo­furan-1(3H)-one1

PubMed Central

Odabaşoğlu, Mustafa; Büyükgüngör, Orhan

2008-01-01

In the mol­ecule of the title compound, C14H9Cl2NO2, the essentially planar phthalide group is oriented at a dihedral angle of 63.23 (5)° with respect to the substituted aromatic ring. In the crystal structure, inter­molecular C—H⋯O and N—H⋯O hydrogen bonds link the mol­ecules, generating R 4 4(21) ring motifs to form a three-dimensional network. PMID:21202144

Angles between orthogonal spd bond orbitals with maximum strength.

PubMed

Pauling, L

1976-05-01

An equation is derived for values of bond angles for two equivalent best spd hybrid bond orbitals with given amounts of s, p, and d character, and is applied in the discussion of structures of transargononic compounds, including the xenon and halogen fluorides. Bond orbitals with a rather small amount of d character tend to lie at angles 90 degrees and 180 degrees , and those with a larger amount, at somewhat smaller angles.

Angles between orthogonal spd bond orbitals with maximum strength*

PubMed Central

Pauling, Linus

1976-01-01

An equation is derived for values of bond angles for two equivalent best spd hybrid bond orbitals with given amounts of s, p, and d character, and is applied in the discussion of structures of transargononic compounds, including the xenon and halogen fluorides. Bond orbitals with a rather small amount of d character tend to lie at angles 90° and 180°, and those with a larger amount, at somewhat smaller angles. PMID:16592315

High resolution crystal structure of the methylcobalamin analogues ethylcobalamin and butylcobalamin by X-ray synchrotron diffraction.

PubMed

Hannibal, Luciana; Smith, Clyde A; Smith, Jessica A; Axhemi, Armend; Miller, Abby; Wang, Sihe; Brasch, Nicola E; Jacobsen, Donald W

2009-07-20

The X-ray crystal structures of the methylcobalamin (MeCbl) analogues ethylcobalamin (EtCbl) and butylcobalamin (BuCbl) are reported. The X-ray crystal structures of EtCbl and BuCbl were obtained with some of the lowest crystallographic residuals ever achieved for cobalamins (R = 0.0468 and 0.0438, respectively). The Co-C bond distances for EtCbl and BuCbl are 2.023(2) and 2.028(4) A, whereas the Co-alpha-5,6-dimethylbenzimidazole (Co-N3B) bond distances were 2.232(1) and 2.244(1) A, respectively. Although EtCbl and BuCbl displayed a longer Co-N3B bond than that observed in the naturally occurring methylcobalamin, the orientation of the alpha-5,6-dimethylbenzimidazole moiety with respect to the corrin ring did not vary substantially among the structures. The lengthening of both Co-C and Co-N3B bonds in EtCbl and BuCbl can be attributed to the "inverse" trans influence exerted by the sigma-donating alkyl groups, typically observed in alkylcobalamins. Analysis of the molecular surface maps showed that the alkyl ligands in EtCbl and BuCbl are directed toward the hydrophobic side of the corrin ring. The corrin fold angles in EtCbl and BuCbl were determined to be 14.7 degrees and 13.1 degrees, respectively. A rough correlation exists between the corrin fold angle and the length of the Co-N3B bond, and both alkylcobalamins follow the same trend.

High Resolution Crystal Structure of the Methylcobalamin Analogs Ethylcobalamin and Butylcobalamin by X-ray Synchrotron Diffraction

PubMed Central

Hannibal, Luciana; Smith, Clyde A; Smith, Jessica A.; Axhemi, Armend; Miller, Abby; Wang, Sihe; Brasch, Nicola E.; Jacobsen, Donald W.

2009-01-01

The X-ray crystal structures of the methylcobalamin (MeCbl) analogs ethylcobalamin (EtCbl) and butylcobalamin (BuCbl) are reported. The X-ray crystal structures of EtCbl and BuCbl were obtained with some of the lowest crystallographic residuals ever achieved for cobalamins (R = 0.0468 and 0.0438, respectively). The Co-C bond distances for EtCbl and BuCbl are 2.023(2) and 2.028(4) Å, whereas the Co-α-5,6-dimethylbenzimidazole (Co-N3B) bond distances were 2.232(1) and 2.244(1) Å, respectively. Although EtCbl and BuCbl displayed a longer Co-N3B bond than that observed in the naturally occurring methylcobalamin, the orientation of the α-5,6-dimethylbenzimidazole moiety with respect to the corrin ring did not vary substantially amongst the structures. The lengthening of both Co-C and Co-N3B bonds in EtCbl and BuCbl can be attributed to the “inverse” trans influence exerted by the σ-donating alkyl groups, typically observed in alkylcobalamins. Analysis of the molecular surface maps showed that the alkyl ligands in EtCbl and BuCbl are directed towards the hydrophobic side of the corrin ring. The corrin fold angles in EtCbl and BuCbl were determined to be 14.7° and 13.1°, respectively. A rough correlation exists between the corrin fold angle and the length of the Co-N3B bond, and both alkylcobalamins follow the same trend. PMID:19545130

Development of impact resistant boron/aluminum composites for turbojet engine fan blades

NASA Technical Reports Server (NTRS)

Melnyk, P.; Toth, I. J.

1975-01-01

Composite fabrication was performed by vacuum press diffusion bonding by both the foil-filament array and preconsolidated monotape methods. The effect of matrix material, fiber diameter, matrix enhancement, fiber volume reinforcement, test temperature, angle-plying, notch, impact orientation, processing variables and fabrication methods on tensile strength and Charpy impact resistance are evaluated. Root attachment concepts, were evaluated by room and elevated temperature tensile testing, as well as by pendulum-Izod and ballistic impact testing. Composite resistance to foreign object damage was also evaluated by ballistic impacting of panels using projectiles of gelatin, RTV rubber and steel at various velocities, and impingement angles. A significant improvement in the pendulum impact resistance of B-Al composites was achieved.

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

N, Rekha T.; Rajkumar, Beulah J. M., E-mail: beulah-rajkumar@yahoo.co.in

Charge transfer properties of pentacene adsorbed on silver is investigated using DFT methods. Optimized geometry of pentacene after adsorption on silver indicates distortion in hexagonal structure of the ring close to the silver cluster and deviations in co-planarity of carbon atoms due to the variations in bond angles and dihedral angles. Theoretically simulated absorption spectrum has a symmetric surface plasmon resonance peak around 486nm corresponding to the transfer of charge from HOMO-2 to LUMO. Theoretical SERS confirms the process of adsorption, tilted orientation of pentacene on silver surface and the charge transfers reported. Localization of electron density arising from redistributionmore » of electrostatic potential together with a reduced bandgap of pentacene after adsorption on silver suggests its utility in the design of electro active organic semiconducting devices.« less

Smoothed particle hydrodynamics study of the roughness effect on contact angle and droplet flow

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

Shigorina, Elena; Kordilla, Jannes; Tartakovsky, Alexandre M.

We employ a pairwise force Smoothed Particle Hydrodynamics (PF-SPH) model to simulate sessile and transient droplets on rough hydrophobic and hydrophilic surfaces. PF-SPH allows for modeling of free surface flow without discretizing the air phase, which is achieved by imposing the surface tension and dynamic contact angles with pairwise interaction forces. We use the PF-SPH model to study the effect of surface roughness and microscopic contact angle on the effective contact angle and droplet dynamics. In the first part of this work, we investigate static contact angles of sessile droplets on rough surfaces in a shape of a sinusoidal functionmore » and made of rectangular bars placed on top of a flat surface. We find that the effective static contact angles of Cassie and Wenzel droplets on a rough surface are greater than the corresponding microscale static contact angles. As a result, microscale hydrophobic rough surfaces also show effective hydrophobic behavior. On the other hand, microscale hydrophilic surfaces may be macroscopically hydrophilic or hydrophobic, depending on the type of roughness. Next, we study the impact of the roughness orientation (i.e., an anisotropic roughness) and surface inclination on droplet flow velocities. Simulations show that droplet flow velocities are lower if the surface roughness is oriented perpendicular to the flow direction. If the predominant elements of surface roughness are in alignment with the flow direction, the flow velocities increase compared to smooth surfaces, which can be attributed to the decrease in fluid-solid contact area similar to the classical lotus effect. We demonstrate that linear scaling relationships between Bond and capillary number for droplet flow on flat surfaces also hold for flow on rough surfaces.« less

An X-ray study of the effect of the bite angle of chelating ligands on the geometry of palladium(allyl) complexes: implications for the regioselectivity in the allylic alkylation.

PubMed

van Haaren, R J; Goubitz, K; Fraanje, J; van Strijdonck, G P; Oevering, H; Coussens, B; Reek, J N; Kamer, P C; van Leeuwen, P W

2001-07-02

X-ray crystal structures of a series of cationic (P-P)palladium(1,1-(CH(3))(2)C(3)H(3)) complexes (P-P = dppe (1,2-bis(diphenylphosphino)ethane), dppf (1,1'-bis(diphenylphosphino)ferrocene), and DPEphos (2,2'-bis(diphenylphosphino)diphenyl ether)) and the (Xantphos)Pd(C(3)H(5))BF(4) (Xantphos = 4,5-bis(diphenylphosphino)-9,9-dimethylxanthene) complex have been determined. In the solid state structure, the phenyl rings of the ligand are oriented in the direction of the nonsymmetrically bound [1,1-(CH(3))(2)C(3)H(3)] moiety. An increase of the bite angle of the chelating ligand results in an increase of the cone angle. In complexes containing ligands having a large cone angle, the distances between the phenyl rings and the allyl moiety become small, resulting in a distortion of the symmetry of the palladium-allyl bond. In solution, two types of dynamic exchange have been observed, the pi-sigma rearrangement and the apparent rotation of the allyl moiety. At the same time, the folded structure of the ligand changes from an endo to an exo orientation or vice versa. The regioselectivity in the palladium-catalyzed allylic alkylation of 3-methyl-but-2-enyl acetate is determined by the cone angle of the bidentate phosphine ligand. Nucleophilic attack by a malonate anion takes place preferentially at the allylic carbon atom having the largest distance to palladium. Ligands with a larger cone angle direct the regioselectivity to the formation of the branched product, from 8% for dppe (1) to 61% found for Xantphos (6). The influence of the cone angle on the regioselectivity has been assigned to a sterically induced electronic effect.

Quantum chemical calculations in the structural analysis of phloretin

NASA Astrophysics Data System (ADS)

Gómez-Zavaglia, Andrea

2009-07-01

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

High-Resolution Coarse-Grained Modeling Using Oriented Coarse-Grained Sites.

PubMed

Haxton, Thomas K

2015-03-10

We introduce a method to bring nearly atomistic resolution to coarse-grained models, and we apply the method to proteins. Using a small number of coarse-grained sites (about one per eight atoms) but assigning an independent three-dimensional orientation to each site, we preferentially integrate out stiff degrees of freedom (bond lengths and angles, as well as dihedral angles in rings) that are accurately approximated by their average values, while retaining soft degrees of freedom (unconstrained dihedral angles) mostly responsible for conformational variability. We demonstrate that our scheme retains nearly atomistic resolution by mapping all experimental protein configurations in the Protein Data Bank onto coarse-grained configurations and then analytically backmapping those configurations back to all-atom configurations. This roundtrip mapping throws away all information associated with the eliminated (stiff) degrees of freedom except for their average values, which we use to construct optimal backmapping functions. Despite the 4:1 reduction in the number of degrees of freedom, we find that heavy atoms move only 0.051 Å on average during the roundtrip mapping, while hydrogens move 0.179 Å on average, an unprecedented combination of efficiency and accuracy among coarse-grained protein models. We discuss the advantages of such a high-resolution model for parametrizing effective interactions and accurately calculating observables through direct or multiscale simulations.

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. II. Backbone-local potentials of coarse-grained O 1 →4 -bonded polyglucose chains

NASA Astrophysics Data System (ADS)

Lubecka, Emilia A.; Liwo, Adam

2017-09-01

Based on the theory of the construction of coarse-grained force fields for polymer chains described in our recent work [A. K. Sieradzan et al., J. Chem. Phys. 146, 124106 (2017)], in this work effective coarse-grained potentials, to be used in the SUGRES-1P model of polysaccharides that is being developed in our laboratory, have been determined for the O ⋯O ⋯O virtual-bond angles (θ ) and for the dihedral angles for rotation about the O ⋯O virtual bonds (γ ) of 1 → 4 -linked glucosyl polysaccharides, for all possible combinations of [α ,β ]-[d,l]-glucose. The potentials of mean force corresponding to the virtual-bond angles and the virtual-bond dihedral angles were calculated from the free-energy surfaces of [α ,β ]-[d,l]-glucose pairs, determined by umbrella-sampling molecular-dynamics simulations with the AMBER12 force field, or combinations of the surfaces of two pairs sharing the overlapping residue, respectively, by integrating the respective Boltzmann factor over the dihedral angles λ for the rotation of the sugar units about the O ⋯O virtual bonds. Analytical expressions were subsequently fitted to the potentials of mean force. The virtual-bond-torsional potentials depend on both virtual-bond-dihedral angles and virtual-bond angles. The virtual-bond-angle potentials contain a single minimum at about θ =14 0° for all pairs except β -d-[α ,β ] -l-glucose, where the global minimum is shifted to θ =150° and a secondary minimum appears at θ =90°. The torsional potentials favor small negative γ angles for the α -d-glucose and extended negative angles γ for the β -d-glucose chains, as observed in the experimental structures of starch and cellulose, respectively. It was also demonstrated that the approximate expression derived based on Kubo's cluster-cumulant theory, whose coefficients depend on the identity of the disugar units comprising a trisugar unit that defines a torsional potential, fits simultaneously all torsional potentials very well, thus reducing the number of parameters significantly.

(2SR,3RS)-Benz­yl[4-chloro-1-(4-chloro­phen­yl)-1-methoxy­carbon­yl-2-but­yl]­ammonium chloride

PubMed Central

Kaupang, Åsmund; Bolsønes, Marianne; Gamadeku, Thywill; Hansen, Tore; Hennum, Martin Johanson; Görbitz, Carl Henrik

2008-01-01

In the racemic hydro­chloride salt of the title ester, C19H22Cl2NO2 +·Cl−, the penta­noic acid chain shows a mixture of trans and gauche orientations to give an overall helical conformation. The dihedral angle between the two aromatic rings is 26.11 (10)°. The charged secondary amine function participates in two N—H⋯Cl hydrogen bonds. PMID:21201230

Charge transfer properties of pentacene adsorbed on silver: DFT study

NASA Astrophysics Data System (ADS)

N, Rekha T.; Rajkumar, Beulah J. M.

2015-06-01

Charge transfer properties of pentacene adsorbed on silver is investigated using DFT methods. Optimized geometry of pentacene after adsorption on silver indicates distortion in hexagonal structure of the ring close to the silver cluster and deviations in co-planarity of carbon atoms due to the variations in bond angles and dihedral angles. Theoretically simulated absorption spectrum has a symmetric surface plasmon resonance peak around 486nm corresponding to the transfer of charge from HOMO-2 to LUMO. Theoretical SERS confirms the process of adsorption, tilted orientation of pentacene on silver surface and the charge transfers reported. Localization of electron density arising from redistribution of electrostatic potential together with a reduced bandgap of pentacene after adsorption on silver suggests its utility in the design of electro active organic semiconducting devices.

Effect of phase symmetry on the NMR spectrum of acetonitrile oriented in a uniaxial-biaxial-uniaxial phase

NASA Astrophysics Data System (ADS)

Deepak, H. S. Vinay; Yelamaggad, C. V.; Khetrapal, C. L.; Ramanathan, K. V.

2016-09-01

We report here the measurement of the Csbnd H and the Hsbnd H dipolar couplings of the methyl group of acetonitrile oriented in the biaxial liquid crystal potassium laurate/1-decanol/water system. These parameters show large variations when measured as a function of temperature. The variations follow the symmetry of the phase as the liquid crystal goes through the sequence of uniaxial - biaxial - uniaxial phases and show a close correspondence to the phase changes that occur in the liquid crystalline solvent coinciding with the onset of biaxiality. The Hsbnd Csbnd H bond angle calculated after incorporating vibrational corrections to the dipolar couplings is discussed in terms of contributions in the case of the biaxial liquid crystal arising from vibration-rotation interaction effects.

Bond angles in transition metal tetracarbonyl compounds: A further test of the theory of hybrid bond orbitals*

PubMed Central

Pauling, Linus

1978-01-01

An equation for the bond angles OC—M—CO for tetracarbonyl groups in which the transition metal atom M is enneacovalent, derived from the simple theory of hybrid sp3d5 bond orbitals, is tested by comparison of the calculated values of the angles with the experimental values reported for many compounds containing M(CO)4 groups, especially those with M = Fe, Mn, Re, Cr, or Mo. The importance of the energy of resonance of single bonds and double bonds in stabilizing octahedral complexes of chromium and manganese with carbonyl, phosphine, arsine, and thio groups is also discussed. PMID:16592490

Anisotropic crystal structure distortion of the monoclinic polymorph of acetaminophen at high hydrostatic pressures.

PubMed

Boldyreva, E V; Shakhtshneider, T P; Vasilchenko, M A; Ahsbahs, H; Uchtmann, H

2000-04-01

The anisotropy of structural distortion of the monoclinic polymorph of acetaminophen induced by hydrostatic pressure up to 4.0 GPa was studied by single-crystal X-ray diffraction in a Merrill-Bassett diamond anvil cell (DAC). The space group (P2(1)/n) and the general structural pattern remained unchanged with pressure. Despite the overall decrease in the molar volume with pressure, the structure expanded in particular crystallographic directions. One of the linear cell parameters (c) passed through a minimum as the pressure increased. The intramolecular bond lengths changed only slightly with pressure, but the changes in the dihedral and torsion angles were very large. The compressibility of the intermolecular hydrogen bonds NH...O and OH...O was measured. NH...O bonds were shown to be slightly more compressible than OH...O bonds. The anisotropy of structural distortion was analysed in detail in relation to the pressure-induced changes in the molecular conformations, to the compression of the hydrogen-bond network, and to the changes in the orientation of molecules with respect to each other in the pleated sheets in the structure. Dirichlet domains were calculated in order to analyse the relative shifts of the centroids of the hydrogen-bonded cycles and of the centroids of the benzene rings with pressure.

Crystal structure of (E)-4-hy-droxy-N'-(3-meth-oxy-benzyl-idene)benzohydrazide.

PubMed

Chantrapromma, Suchada; Prachumrat, Patcharawadee; Ruanwas, Pumsak; Boonnak, Nawong; Kassim, Mohammad B

2016-09-01

The title compound, C 15 H 14 N 2 O 3 , crystallizes with two independent mol-ecules ( A and B ) in the asymmetric unit that differ in the orientation of the 3-meth-oxy-phenyl group with respect to the methyl-idenebenzohydrazide unit. The dihedral angles between the two benzene rings are 24.02 (10) and 29.30 (9)° in mol-ecules A and B , respectively. In mol-ecule A , the meth-oxy group is twisted slightly relative to its bound benzene ring, with a C meth-yl -O-C-C torsion angle of 14.2 (3)°, whereas it is almost co-planar in mol-ecule B , where the corresponding angle is -2.4 (3)°. In the crystal, the mol-ecules are linked by N-H⋯O, O-H⋯N and O-H⋯O hydrogen bonds, as well as by weak C-H⋯O inter-actions, forming sheets parallel to the bc plane. The N-H⋯O hydrogen bond and weak C-H⋯O inter-action link different mol-ecules ( A ⋯ B ) whereas both O-H⋯N and O-H⋯O hydrogen bonds link like mol-ecules ( A ⋯ A ) and ( B ⋯ B ). Pairs of inversion-related B mol-ecules are stacked approximately along the a axis by π-π inter-actions in which the distance between the centroids of the 3-meth-oxy-phenyl rings is 3.5388 (12) Å. The B mol-ecules also participate in weak C-H⋯π inter-actions between the 4-hy-droxy-phenyl and the 3-meth-oxy-phenyl rings.

Reorientation of the ‘free OH’ group in the top-most layer of air/water interface of sodium fluoride aqueous solution probed with sum-frequency generation vibrational spectroscopy

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

Feng, Ran-Ran; Guo, Yuan; Wang, Hongfei

2014-09-17

Many experimental and theoretical studies have established the specific anion, as well as cation effects on the hydrogen-bond structures at the air/water interface of electrolyte solutions. However, the ion effects on the top-most layer of the air/water interface, which is signified by the non-hydrogen-bonded so-called ‘free O-H’ group, has not been discussed or studied. In this report, we present the measurement of changes of the orientational angle of the ‘free O-H’ group at the air/water interface of the sodium fluoride (NaF) solutions at different concentrations using the interface selective sum-frequency generation vibrational spectroscopy (SFG-VS) in the ssp and ppp polarizations.more » The polarization dependent SFG-VS results show that the average tilt angle of the ‘free O-H’ changes from about 35.3 degrees ± 0.5 degrees to 43.4 degrees ± 2.1degrees as the NaF concentration increase from 0 to 0.94M (nearly saturated). Such tilt angle change is around the axis of the other O-H group of the same water molecule at the top-most layer at the air/water interface that is hydrogen-bonded to the water molecules below the top-most layer. These results provide quantitative molecular details of the ion effects of the NaF salt on the structure of the water molecules at the top-most layer of the air/water interfacial, even though both the Na+ cation and the F- anion are believed to be among the most excluded ions from the air/water interface.« less

Molecular structural property and potential energy dependence on nonequilibrium-thermodynamic state point of liquid n-hexadecane under shear.

PubMed

Tseng, Huan-Chang; Chang, Rong-Yeu; Wu, Jiann-Shing

2011-01-28

Extensive computer experiments have been conducted in order to shed light on the macroscopic shear flow behavior of liquid n-hexadecane fluid under isobaric-isothermal conditions through the nonequilibrium molecular dynamic methodology. With respect to shear rates, the accompanying variations in structural properties of the fluid span the microscopic range of understanding from the intrinsic to extrinsic characteristics. As drawn from the average value of bond length and bond angle, the distribution of dihedral angle, and the radius distribution function of intramolecular and intermolecular van der Waals distances, these intrinsic structures change with hardness, except in the situation of extreme shear rates. The shear-induced variation of thermodynamic state curve along with the shear rate studied is shown to consist of both the quasiequilibrium state plateau and the nonequilibrium-thermodynamic state slope. Significantly, the occurrence of nonequilibrium-thermodynamic state behavior is attributed to variations in molecular potential energies, which include bond stretching, bond bending, bond torsion, and intra- and intermolecular van der Waals interactions. To unfold the physical representation of extrinsic structural deformation, under the aggressive influence of a shear flow field, the molecular dimension and appearance can be directly described via the squared radius of gyration and the sphericity angle, R(g)(2) and ϕ, respectively. In addition, a specific orientational order S(x) defines the alignment of the molecules with the flow direction of the x-axis. As a result, at low shear rates, the overall molecules are slightly stretched and shaped in a manner that is increasingly ellipsoidal. Simultaneously, there is an obvious enhancement in the order. In contrast to high shear rates, the molecules spontaneously shrink themselves with a decreased value of R(g)(2), while their shape and order barely vary with an infinite value of ϕ and S(x). It is important to note that under different temperatures and pressures, these three parameters are integrated within a molecular description in response to thermodynamic state variable of density and rheological material function of shear viscosity.

Piperidinium bis­(2-oxidobenzoato-κ2 O 1,O 2)borate

PubMed Central

Tang, Zhi-Hua; Huang, Chaojun

2009-01-01

The asymmetric unit of the title compound, C5H12N+·C14H8BO6 − or [C5H12N][BO4(C7H4O)2], contains two piperidinium cations and two bis­(salicylato)borate anions. The coordination geometries around the B atoms are distorted tetra­hedral. In the two mol­ecules, the aromatic rings are oriented at dihedral angles of 76.27 (3) and 83.86 (3)°. The rings containing B atoms have twist-boat conformations, while the two cations adopt chair conformations. In the crystal, the component species are linked by N—H⋯O hydrogen bonds. In the crystal structure, intra- and inter­molecular N—H⋯O hydrogen bonds link the mol­ecules. PMID:21581628

Quantitative spectral and orientational analysis in surface sum frequency generation vibrational spectroscopy (SFG-VS)

NASA Astrophysics Data System (ADS)

Wang, Hong-Fei; Gan, Wei; Lu, Rong; Rao, Yi; Wu, Bao-Hua

Sum frequency generation vibrational spectroscopy (SFG-VS) has been proven to be a uniquely effective spectroscopic technique in the investigation of molecular structure and conformations, as well as the dynamics of molecular interfaces. However, the ability to apply SFG-VS to complex molecular interfaces has been limited by the ability to abstract quantitative information from SFG-VS experiments. In this review, we try to make assessments of the limitations, issues and techniques as well as methodologies in quantitative orientational and spectral analysis with SFG-VS. Based on these assessments, we also try to summarize recent developments in methodologies on quantitative orientational and spectral analysis in SFG-VS, and their applications to detailed analysis of SFG-VS data of various vapour/neat liquid interfaces. A rigorous formulation of the polarization null angle (PNA) method is given for accurate determination of the orientational parameter D = /, and comparison between the PNA method with the commonly used polarization intensity ratio (PIR) method is discussed. The polarization and incident angle dependencies of the SFG-VS intensity are also reviewed, in the light of how experimental arrangements can be optimized to effectively abstract crucial information from the SFG-VS experiments. The values and models of the local field factors in the molecular layers are discussed. In order to examine the validity and limitations of the bond polarizability derivative model, the general expressions for molecular hyperpolarizability tensors and their expression with the bond polarizability derivative model for C3v, C2v and C∞v molecular groups are given in the two appendixes. We show that the bond polarizability derivative model can quantitatively describe many aspects of the intensities observed in the SFG-VS spectrum of the vapour/neat liquid interfaces in different polarizations. Using the polarization analysis in SFG-VS, polarization selection rules or guidelines are developed for assignment of the SFG-VS spectrum. Using the selection rules, SFG-VS spectra of vapour/diol, and vapour/n-normal alcohol (n˜ 1-8) interfaces are assigned, and some of the ambiguity and confusion, as well as their implications in previous IR and Raman assignment, are duly discussed. The ability to assign a SFG-VS spectrum using the polarization selection rules makes SFG-VS not only an effective and useful vibrational spectroscopy technique for interface studies, but also a complementary vibrational spectroscopy method in general condensed phase studies. These developments will put quantitative orientational and spectral analysis in SFG-VS on a more solid foundation. The formulations, concepts and issues discussed in this review are expected to find broad applications for investigations on molecular interfaces in the future.

Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function.

PubMed

Prill, Dragica; Juhás, Pavol; Billinge, Simon J L; Schmidt, Martin U

2016-01-01

A method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may be used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.

Effect of Watson-Crick and Hoogsteen base pairing on the conformational stability of C8-phenoxyl-2'-deoxyguanosine adducts.

PubMed

Millen, Andrea L; Churchill, Cassandra D M; Manderville, Richard A; Wetmore, Stacey D

2010-10-14

Bulky DNA addition products (adducts) formed through attack at the C8 site of guanine can adopt the syn orientation about the glycosidic bond due to changes in conformational stability or hydrogen-bonding preferences directly arising from the bulky group. Indeed, the bulky substituent may improve the stability of (non-native) Hoogsteen pairs. Therefore, such adducts often result in mutations upon DNA replication. This work examines the hydrogen-bonded pairs between the Watson-Crick and Hoogsteen faces of the ortho or para C8-phenoxyl-2'-deoxyguanosine adduct and each natural (undamaged) nucleobase with the goal to clarify the conformational preference of this type of damage, as well as provide insight into the likelihood of subsequent mutation events. B3LYP/6-311+G(2df,p)//B3LYP/6-31G(d) hydrogen-bond strengths were determined using both nucleobase and nucleoside models for adduct pairs, as well as the corresponding complexes involving natural 2'-deoxyguanosine. In addition to the magnitude of the binding strengths, the R(C1'···C1') distances and ∠(N9C1'C1') angles, as well as the degree of propeller-twist and buckle distortions, were carefully compared to the values observed in natural DNA strands. Due to structural changes in the adduct monomer upon inclusion of the sugar moiety, the monomer deformation energy significantly affects the relative hydrogen-bond strengths calculated with the nucleobase and nucleoside models. Therefore, we recommend the use of at least a nucleoside model to accurately evaluate hydrogen-bond strengths of base pairs involving flexible, bulky nucleobase adducts. Our results also emphasize the importance of considering both the magnitude of the hydrogen-bond strength and the structure of the base pair when predicting the preferential binding patterns of nucleobases. Using our best models, we conclude that the Watson-Crick face of the ortho phenoxyl adduct forms significantly more stable complexes than the Hoogsteen face, which implies that the anti orientation of the damaged base will be favored by hydrogen bonding in DNA helices. Additionally, regardless of the hydrogen-bonding face involved, cytosine forms the most stable base pair with the ortho adduct, which implies that misincorporation due to this type of damage is unlikely. Similarly, cytosine is the preferred binding partner for the Watson-Crick face of the para adduct. However, Hoogsteen interactions with the para adduct are stronger than those with natural 2'-deoxyguanosine or the ortho adduct, and this form of damage binds with nearly equal stability to both cytosine and guanine in the Hoogsteen orientation. Therefore, the para adduct may adopt multiple orientations in DNA helices and potentially cause mutations by forming pairs with different natural bases. Models of oligonucleotide duplexes must be used in future work to further evaluate other factors (stacking, major groove contacts) that may influence the conformation and binding preference of these adducts in DNA helices.

Relationships between clubshaft motions and clubface orientation during the golf swing.

PubMed

Takagi, Tokio; Yokozawa, Toshiharu; Inaba, Yuki; Matsuda, Yuji; Shiraki, Hitoshi

2017-09-01

Since clubface orientation at impact affects ball direction and ball spin, the ability to control clubface orientation is one of the most important skills for golfers. This study presents a new method to describe clubface orientation as a function of the clubshaft motions (i.e., swing plane orientation, clubshaft angle in the swing plane, and clubshaft rolling angle) during a golf swing and investigates the relationships between the clubshaft motions and clubface orientation at impact. The club motion data of driver shots were collected from eight skilled golfers using a three-dimensional motion capture system. The degrees of influence of the clubshaft motions on the clubface orientation were investigated using sensitivity analysis. The sensitivity analysis revealed that the swing plane horizontal angle affected the clubface horizontal angle to an extent of 100%, that the clubshaft angle in the swing plane affected both the clubface vertical and horizontal angles to extents of 74 and 68%, respectively, and that the clubshaft rolling angle affected both the clubface vertical and horizontal angles to extents of -67 and 75%, respectively. Since the method presented here relates clubface orientation to clubshaft motions, it is useful for understanding the clubface control of a golfer.

Sterically allowed configuration space for amino acid dipeptides

NASA Astrophysics Data System (ADS)

Caballero, Diego; Maatta, Jukka; Sammalkorpi, Maria; O'Hern, Corey; Regan, Lynne

2014-03-01

Despite recent improvements in computational methods for protein design, we still lack a quantitative, predictive understanding of the intrinsic propensities for amino acids to be in particular backbone or side-chain conformations. This question has remained unsettled for years because of the discrepancies between different experimental approaches. To address it, I performed all-atom hard-sphere simulations of hydrophobic residues with stereo-chemical constraints and non-attractive steric interactions between non-bonded atoms for ALA, ILE, LEU and VAL dipeptide mimetics. For these hard-sphere MD simulations, I show that transitions between α-helix and β-sheet structures only occur when the bond angle τ(N -Cα - C) >110° , and the probability distribution of bond angles for structures in the `bridge' region of ϕ- ψ space is shifted to larger angles compared to that in other regions. In contrast, the relevant bond-angle distributions obtained from most molecular dynamics packages are broader and shifter to larger values. I encounter similar correlations between bond angles and side-chain dihedral angles. The success of these studies is an argument for re-incorporating local stereochemical constraints into computational protein design methodology.

Crystal Chemical Controls on Equation of State

NASA Astrophysics Data System (ADS)

Thompson, R. M.; McCarthy, A. C.; Downs, R. T.

2007-12-01

Minerals are known to compress through a number of mechanisms, ranging from polyhedral distortion to electronic transitions. Two mechanisms which can produce significant volume decreases are angle-bending and bond compression. The crystal chemical effects of these two mechanisms have been studied and documented for years. With more recent advances in theory and software enabling the accurate determination of bonding topologies, M-O bonding to bridging oxygens has been shown to modify compressibility by changing angle-bending force constants. Minerals that compress mainly through angle-bending tend be soft. Good examples are quartz and cristobalite, minerals composed solely of corner-sharing silicate tetrahedra with bulk moduli of 37 and 12 GPa, respectively. Rock salt structured oxides must compress strictly by bond compression, and are much stiffer - lime and periclase have bulk moduli of 111 and 156 GPa, respectively. Feldspars have bulk moduli intermediate to the above examples. Based solely on the presence of Al-O-Si angles, theoretically softer than Si-O-Si angles, feldspars should be softer than quartz or cristobalite, but the T-O-T angles are stiffened by bonds to interstitial cations. The number and nature of these bonds affects compressibility sufficiently to create exceptions to Bridgman's law, which correlates bulk modulus with ambient unit cell volume in isostructural materials. In this paper, we present new high-pressure refinements of the crystal structures of jadeite, aegirine, and NaGa- clinopyroxene. Bulk moduli of these pyroxenes and all other end-member clinopyroxenes we could find in the literature (19 total) are plotted vs. unit cell volumes to test Bridgman's law. The data fall along two trends, each of which is separately consistent with Bridgman's law. Pyroxenes in one trend are dramatically stiffer than those in the other trend, with bulk moduli that differ by approximately 40 GPa. The only difference between the topologies of the structures in the two trends is in the bonding around M2. Structures in the less compressible trend have M2-O3 bonds that oppose Si-O-Si angle-bending in the tetrahedral chains. This angle-bending is an important compression mechanism in pyroxenes. McCarthy et al. (in press) term these bonds "antipathetic". Pyroxenes in the more compressible trend lack these bonds. There are other M2-O3 bonds that visual inspection suggests might tend to encourage angle-bending, but do not appear to have an effect. McCarthy et al. term these bonds "apathetic," and suggest the term "sympathetic" for M-O bonds that actually soften angles. Other examples from the literature will be presented including one from the feldspars that may be a truly sympathetic bond. McCarthy, A.C., Downs, R.T., and Thompson, R.M. (in press) Compressibility trends of the clinopyroxenes, and in- situ high-pressure single-crystal X-ray diffraction study of jadeite. American Mineralogist.

1-(2,4-Dinitro­phen­yl)-2-(1,2,3,4-tetra­hydro­naphthalen-1-yl­idene)hydrazine

PubMed Central

Danish, M.; Hamid, Masood; Tahir, M. Nawaz; Ahmad, Nazir; Ghafoor, Sabiha

2010-01-01

In the title compound, C14H14N4O4, the dihedral angle between the benzene rings is 10.42 (8)°. The nitro groups make dihedral angles of 5.3 (2) and 6.47 (15)° with their parent ring and are oriented at 11.2 (3)° with respect to each other. An intra­molecular N—H⋯O hydrogen bond completes an S(6) ring motif. In the crystal, mol­ecules are linked by C—H⋯O inter­actions, thus forming (010) chains in which R 2 2(13) ring motifs are present. There also exist aromatic π–π stacking inter­actions [centroid–centroid separation = 3.7046 (9) Å]. PMID:21588393

3-(6-Methyl-2-pyrid­yl)-2-phenyl-3,4-dihydro-1,3,2-benzoxaza­phosphinine 2-oxide

PubMed Central

Surendra Babu, V. H. H.; Krishnaiah, M.; Anil Kumar, M.; Suresh Reddy, C.; Kant, Rajni

2009-01-01

In the title compound, C19H17N2O2P, the six-membered 1,3,2-oxaza­phosphinine ring adopts a boat conformation with the phosphoryl O atom in an equatorial position. The dihedral angle between the 6-methyl-2-pyridyl and phenyl groups is 75.5 (1)°. These substituents are trans to each other, and are oriented at angles of 57.2 (1) and 74.8 (1)°, respectively, to the benzene ring. The crystal structure is stabilized by intra- and inter­molecular hydrogen bonds. The phosphoryl O atom participates in inter­molecular C—H⋯O inter­actions with the neighbouring mol­ecules, forming centrosymmetric R 2 2(14) dimers. PMID:21578300

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. I. Backbone potentials of coarse-grained polypeptide chains

NASA Astrophysics Data System (ADS)

Sieradzan, Adam K.; Makowski, Mariusz; Augustynowicz, Antoni; Liwo, Adam

2017-03-01

A general and systematic method for the derivation of the functional expressions for the effective energy terms in coarse-grained force fields of polymer chains is proposed. The method is based on the expansion of the potential of mean force of the system studied in the cluster-cumulant series and expanding the all-atom energy in the Taylor series in the squares of interatomic distances about the squares of the distances between coarse-grained centers, to obtain approximate analytical expressions for the cluster cumulants. The primary degrees of freedom to average about are the angles for collective rotation of the atoms contained in the coarse-grained interaction sites about the respective virtual-bond axes. The approach has been applied to the revision of the virtual-bond-angle, virtual-bond-torsional, and backbone-local-and-electrostatic correlation potentials for the UNited RESidue (UNRES) model of polypeptide chains, demonstrating the strong dependence of the torsional and correlation potentials on virtual-bond angles, not considered in the current UNRES. The theoretical considerations are illustrated with the potentials calculated from the ab initio potential-energy surface of terminally blocked alanine by numerical integration and with the statistical potentials derived from known protein structures. The revised torsional potentials correctly indicate that virtual-bond angles close to 90° result in the preference for the turn and helical structures, while large virtual-bond angles result in the preference for polyproline II and extended backbone geometry. The revised correlation potentials correctly reproduce the preference for the formation of β-sheet structures for large values of virtual-bond angles and for the formation of α-helical structures for virtual-bond angles close to 90°.

Ordering in bio-inorganic hybrid nanomaterials probed by in situ scanning transmission X-ray microscopy

DOE PAGES

Lee, Jonathan R. I.; Bagge-Hansen, Michael; Tunuguntla, Ramya; ...

2015-04-15

Here, phospholipid bilayer coated Si nanowires are one-dimensional (1D) composites that provide versatile bio-nanoelectronic functionality via incorporation of a wide variety of biomolecules into the phospholipid matrix. The physiochemical behaviour of the phospholipid bilayer is strongly dependent on its structure and, as a consequence, substantial modelling and experimental efforts have been directed at the structural characterization of supported bilayers and unsupported phospholipid vesicles; nonetheless, the experimental studies conducted to date have exclusively involved volume-averaged techniques, which do not allow for the assignment of spatially resolved structural variations that could critically impact the performance of the 1D phospholipid-Si NW composites. Inmore » this manuscript, we use scanning transmission X-ray microscopy (STXM) to probe bond orientation and bilayer thickness as a function of position with a spatial resolution of ~30 nm for Δ9-cis 1,2-dioleoyl-sn-glycero-3-phosphocholine layers prepared Si NWs. When coupled with small angle X-ray scattering measurements, the STXM data reveal structural motifs of the Si NWs that give rise to multi-bilayer formation and enable assignment of the orientation of specific bonds known to affect the order and rigidity of phospholipid bilayers.« less

Smoothed particle hydrodynamics study of the roughness effect on contact angle and droplet flow.

PubMed

Shigorina, Elena; Kordilla, Jannes; Tartakovsky, Alexandre M

2017-09-01

We employ a pairwise force smoothed particle hydrodynamics (PF-SPH) model to simulate sessile and transient droplets on rough hydrophobic and hydrophilic surfaces. PF-SPH allows modeling of free-surface flows without discretizing the air phase, which is achieved by imposing the surface tension and dynamic contact angles with pairwise interaction forces. We use the PF-SPH model to study the effect of surface roughness and microscopic contact angle on the effective contact angle and droplet dynamics. In the first part of this work, we investigate static contact angles of sessile droplets on different types of rough surfaces. We find that the effective static contact angles of Cassie and Wenzel droplets on a rough surface are greater than the corresponding microscale static contact angles. As a result, microscale hydrophobic rough surfaces also show effective hydrophobic behavior. On the other hand, microscale hydrophilic surfaces may be macroscopically hydrophilic or hydrophobic, depending on the type of roughness. We study the dependence of the transition between Cassie and Wenzel states on roughness and droplet size, which can be linked to the critical pressure for the given fluid-substrate combination. We observe good agreement between simulations and theoretical predictions. Finally, we study the impact of the roughness orientation (i.e., an anisotropic roughness) and surface inclination on droplet flow velocities. Simulations show that droplet flow velocities are lower if the surface roughness is oriented perpendicular to the flow direction. If the predominant elements of surface roughness are in alignment with the flow direction, the flow velocities increase compared to smooth surfaces, which can be attributed to the decrease in fluid-solid contact area similar to the lotus effect. We demonstrate that classical linear scaling relationships between Bond and capillary numbers for droplet flow on flat surfaces also hold for flow on rough surfaces.

Curved cap corrugated sheet

NASA Technical Reports Server (NTRS)

Davis, R. C.; Bales, T. T.; Royster, D. M.; Jackson, L. R. (Inventor)

1984-01-01

The report describes a structure for a strong, lightweight corrugated sheet. The sheet is planar or curved and includes a plurality of corrugation segments, each segment being comprised of a generally U-shaped corrugation with a part-cylindrical crown and cap strip, and straight side walls and with secondary corrugations oriented at right angles to said side walls. The cap strip is bonded to the crown and the longitudinal edge of said cap strip extends beyond edge at the intersection between said crown and said side walls. The high strength relative to weight of the structure makes it desirable for use in aircraft or spacecraft.

Benzil bis-(ketazine).

PubMed

Patra, Goutam Kumar; Mukherjee, Anindita; Ng, Seik Weng

2009-07-04

1,1',2,2'-tetra-phenyl-2,2'-azinodiethanone), C(28)H(20)N(2)O(2), was obtained by the reaction of benzil monohydrazone with chromium(III) nitrate. The dibenzyl-idene hydrazine unit is nearly planar (r.m.s. deviation = 0.073 Å) and the two benzoyl units are oriented almost perpendicular to it [dihedral angle = 87.81 (2), 87.81 (2)°]. The mol-ecules are linked into chains along the c axis by C-H⋯O hydrogen bonds and the chains are cross-linked via C-H⋯π inter-actions involving the benzoyl phenyl rings.

Backbone amide 15N chemical shift tensors report on hydrogen bonding interactions in proteins: A magic angle spinning NMR study.

PubMed

Paramasivam, Sivakumar; Gronenborn, Angela M; Polenova, Tatyana

2018-08-01

Chemical shift tensors (CSTs) are an exquisite probe of local geometric and electronic structure. 15 N CST are very sensitive to hydrogen bonding, yet they have been reported for very few proteins to date. Here we present experimental results and statistical analysis of backbone amide 15 N CSTs for 100 residues of four proteins, two E. coli thioredoxin reassemblies (1-73-(U- 13 C, 15 N)/74-108-(U- 15 N) and 1-73-(U- 15 N)/74-108-(U- 13 C, 15 N)), dynein light chain 8 LC8, and CAP-Gly domain of the mammalian dynactin. The 15 N CSTs were measured by a symmetry-based CSA recoupling method, ROCSA. Our results show that the principal component δ 11 is very sensitive to the presence of hydrogen bonding interactions due to its unique orientation in the molecular frame. The downfield chemical shift change of backbone amide nitrogen nuclei with increasing hydrogen bond strength is manifested in the negative correlation of the principal components with hydrogen bond distance for both α-helical and β-sheet secondary structure elements. Our findings highlight the potential for the use of 15 N CSTs in protein structure refinement. Copyright © 2018 Elsevier Inc. All rights reserved.

Bond-orientational order in liquid Si

NASA Technical Reports Server (NTRS)

Wang, Z. Q.; Stroud, D.

1991-01-01

Bond-orientational order in liquid Si via Monte Carlo simulation in conjuncation with empirical two- and three-body potentials of the form proposed by Stillinger and Weber are studied. Bond-orientational order (BOO) is described in terms of combinations of spherical harmonic functions. Liquid Si is found to have pronounced short-range BOO corresponding to l = 3, as expected for a structure with local tetrahedral order. No long-range BOO is found either in the equilibrium or the supercooled liquid. When the three-body potential is artificially removed, the tetrahedral bond-orientation order disappears and the liquid assumes a close-packed structure.

High-resolution orientation and depth of insertion of the voltage-sensing S4 helix of a potassium channel in lipid bilayers.

PubMed

Doherty, Tim; Su, Yongchao; Hong, Mei

2010-08-27

The opening and closing of voltage-gated potassium (Kv) channels are controlled by several conserved Arg residues in the S4 helix of the voltage-sensing domain. The interaction of these positively charged Arg residues with the lipid membrane has been of intense interest for understanding how membrane proteins fold to allow charged residues to insert into lipid bilayers against free-energy barriers. Using solid-state NMR, we have now determined the orientation and insertion depth of the S4 peptide of the KvAP channel in lipid bilayers. Two-dimensional (15)N correlation experiments of macroscopically oriented S4 peptide in phospholipid bilayers revealed a tilt angle of 40 degrees and two possible rotation angles differing by 180 degrees around the helix axis. Remarkably, the tilt angle and one of the two rotation angles are identical to those of the S4 helix in the intact voltage-sensing domain, suggesting that interactions between the S4 segment and other helices of the voltage-sensing domain are not essential for the membrane topology of the S4 helix. (13)C-(31)P distances between the S4 backbone and the lipid (31)P indicate a approximately 9 A local thinning and 2 A average thinning of the DMPC (1,2-dimyristoyl-sn-glycero-3-phosphochloline)/DMPG (1,2-dimyristoyl-sn-glycero-3-phosphatidylglycerol) bilayer, consistent with neutron diffraction data. Moreover, a short distance of 4.6 A from the guanidinium C(zeta) of the second Arg to (31)P indicates the existence of guanidinium phosphate hydrogen bonding and salt bridges. These data suggest that the structure of the Kv gating helix is mainly determined by protein-lipid interactions instead of interhelical protein-protein interactions, and the S4 amino acid sequence encodes sufficient information for the membrane topology of this crucial gating helix. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Two Comments on Bond Angles

NASA Astrophysics Data System (ADS)

Glaister, P.

1997-09-01

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

Methyl 4-(4-fluoro­phen­yl)-6-isopropyl-2-[N-methyl-N-(methylsulfonyl)amino]­pyrimidine-5-carboxyl­ate

PubMed Central

He, Wei; Yang, Dong-Ling; Cui, Yong-Tao; Xu, Ye-Ming; Guo, Cheng

2008-01-01

In the mol­ecule of the title compound, C17H20FN3O4S, the pyrimidine and benzene rings are oriented at a dihedral angle of 35.59 (3)°. Intra­molecular C—H⋯N and C—H⋯O hydrogen bonds result in the formation of one five- and two six-membered non-planar rings. One of the six-membered rings adopts a chair conformation, while the other six-membered ring and the five-membered ring exhibit envelope conformations with O and N atoms displaced by 0.837 (3) and 0.152 (3) Å, respectively from the planes of the other ring atoms. In the crystal structure, inter­molecular C—H⋯F hydrogen bonds link the mol­ecules into infinite chains. PMID:21202637

3D variations in human crown dentin tubule orientation: a phase-contrast microtomography study.

PubMed

Zaslansky, Paul; Zabler, Simon; Fratzl, Peter

2010-01-01

Tubules dominate the microstructure of dentin, and in crowns of human teeth they are surrounded by thick mineralized peritubular cuffs of high stiffness. Here we examine the three-dimensional (3D) arrangement of tubules in relation to enamel on the buccal and lingual aspects of intact premolars and molars. Specifically we investigate the angular orientation of tubules relative to the plane of the junction of dentin with enamel (DEJ) by means of wet, non-destructive and high-resolution phase-contrast (coherent) tomography. Enamel capped dentin samples (n=16), cut from the buccal and lingual surfaces of upper and lower premolar and molar teeth, were imaged in water by high-resolution synchrotron-based phase-contrast X-ray radiography. Reconstructed 3D virtual images were co-aligned with respect to the DEJ plane. The average tubule orientation was determined at increasing distances from the DEJ, based on integrated projections onto orthogonal virtual planes. The angle and curl of the tubules were determined every 100 microm to a depth of 1.4mm beneath the DEJ. Most tubules do not extend at right angles from the DEJ. Even when they do, tubules always change their orientations substantially within the first half-millimeter zone beneath the DEJ, both on the buccal and lingual aspects of premolar and molar teeth. Tubules also tend to curl and twist within this zone. Student t-tests indicate that lower teeth seem to have greater tilts in the tubule orientations relative to the DEJ normal with an average angle of 42 degrees (+/-2.0 degrees), whereas upper teeth exhibit a smaller change of orientation, with an average of 32 degrees (+/-2.1 degrees). Tubules are a central characteristic of dentin, with important implications on how it is arranged and what the properties are. Knowing about the path that tubules follow is important for various reasons, ranging form improving control over restorative procedures to understanding or simulating the mechanical properties of teeth. At increasing depths of dentin beneath enamel, tubules are significantly tilted relative to the DEJ norm, which may be important to understand clinical challenges such as sensitivity, effectiveness of bonding techniques or prediction of possible paths for bacterial invasion. Our data show dissimilar average tubule angles of upper versus lower teeth with respect to the DEJ which presumably contributes to different shear responses of the tissue under function. The degree to which this may warrant improved restoratives or new adhesive techniques to enhance adhesive restorations merits further investigation.

A statistical mechanical theory for a two-dimensional model of water

PubMed Central

Urbic, Tomaz; Dill, Ken A.

2010-01-01

We develop a statistical mechanical model for the thermal and volumetric properties of waterlike fluids. Each water molecule is a two-dimensional disk with three hydrogen-bonding arms. Each water interacts with neighboring waters through a van der Waals interaction and an orientation-dependent hydrogen-bonding interaction. This model, which is largely analytical, is a variant of the Truskett and Dill (TD) treatment of the “Mercedes-Benz” (MB) model. The present model gives better predictions than TD for hydrogen-bond populations in liquid water by distinguishing strong cooperative hydrogen bonds from weaker ones. We explore properties versus temperature T and pressure p. We find that the volumetric and thermal properties follow the same trends with T as real water and are in good general agreement with Monte Carlo simulations of MB water, including the density anomaly, the minimum in the isothermal compressibility, and the decreased number of hydrogen bonds for increasing temperature. The model reproduces that pressure squeezes out water’s heat capacity and leads to a negative thermal expansion coefficient at low temperatures. In terms of water structuring, the variance in hydrogen-bonding angles increases with both T and p, while the variance in water density increases with T but decreases with p. Hydrogen bonding is an energy storage mechanism that leads to water’s large heat capacity (for its size) and to the fragility in its cagelike structures, which are easily melted by temperature and pressure to a more van der Waals-like liquid state. PMID:20550408

A statistical mechanical theory for a two-dimensional model of water

NASA Astrophysics Data System (ADS)

Urbic, Tomaz; Dill, Ken A.

2010-06-01

We develop a statistical mechanical model for the thermal and volumetric properties of waterlike fluids. Each water molecule is a two-dimensional disk with three hydrogen-bonding arms. Each water interacts with neighboring waters through a van der Waals interaction and an orientation-dependent hydrogen-bonding interaction. This model, which is largely analytical, is a variant of the Truskett and Dill (TD) treatment of the "Mercedes-Benz" (MB) model. The present model gives better predictions than TD for hydrogen-bond populations in liquid water by distinguishing strong cooperative hydrogen bonds from weaker ones. We explore properties versus temperature T and pressure p. We find that the volumetric and thermal properties follow the same trends with T as real water and are in good general agreement with Monte Carlo simulations of MB water, including the density anomaly, the minimum in the isothermal compressibility, and the decreased number of hydrogen bonds for increasing temperature. The model reproduces that pressure squeezes out water's heat capacity and leads to a negative thermal expansion coefficient at low temperatures. In terms of water structuring, the variance in hydrogen-bonding angles increases with both T and p, while the variance in water density increases with T but decreases with p. Hydrogen bonding is an energy storage mechanism that leads to water's large heat capacity (for its size) and to the fragility in its cagelike structures, which are easily melted by temperature and pressure to a more van der Waals-like liquid state.

A statistical mechanical theory for a two-dimensional model of water.

PubMed

Urbic, Tomaz; Dill, Ken A

2010-06-14

We develop a statistical mechanical model for the thermal and volumetric properties of waterlike fluids. Each water molecule is a two-dimensional disk with three hydrogen-bonding arms. Each water interacts with neighboring waters through a van der Waals interaction and an orientation-dependent hydrogen-bonding interaction. This model, which is largely analytical, is a variant of the Truskett and Dill (TD) treatment of the "Mercedes-Benz" (MB) model. The present model gives better predictions than TD for hydrogen-bond populations in liquid water by distinguishing strong cooperative hydrogen bonds from weaker ones. We explore properties versus temperature T and pressure p. We find that the volumetric and thermal properties follow the same trends with T as real water and are in good general agreement with Monte Carlo simulations of MB water, including the density anomaly, the minimum in the isothermal compressibility, and the decreased number of hydrogen bonds for increasing temperature. The model reproduces that pressure squeezes out water's heat capacity and leads to a negative thermal expansion coefficient at low temperatures. In terms of water structuring, the variance in hydrogen-bonding angles increases with both T and p, while the variance in water density increases with T but decreases with p. Hydrogen bonding is an energy storage mechanism that leads to water's large heat capacity (for its size) and to the fragility in its cagelike structures, which are easily melted by temperature and pressure to a more van der Waals-like liquid state.

XRD- and infrared-probed anisotropic thermal expansion properties of an organic semiconducting single crystal.

PubMed

Mohanraj, J; Capria, E; Benevoli, L; Perucchi, A; Demitri, N; Fraleoni-Morgera, A

2018-01-17

The anisotropic thermal expansion properties of an organic semiconducting single crystal constituted by 4-hydroxycyanobenzene (4HCB) have been probed by XRD in the range 120-300 K. The anisotropic thermal expansion coefficients for the three crystallographic axes and for the crystal volume have been determined. A careful analysis of the crystal structure revealed that the two different H-bonds stemming from the two independent, differently oriented 4HCB molecules composing the unit cell have different rearrangement patterns upon temperature variations, in terms of both bond length and bond angle. Linearly Polarized Mid InfraRed (LP-MIR) measurements carried out in the same temperature range, focused on the O-H bond spectral region, confirm this finding. The same LP-MIR measurements, on the basis of a semi-empirical relation and of geometrical considerations and assumptions, allowed calculation of the -CNH-O- hydrogen bond length along the a and b axes of the crystal. In turn, the so-calculated -CNH-O- bond lengths were used to derive the thermal expansion coefficients along the corresponding crystal axes, as well as the volumetric one, using just the LP-MIR data. Reasonable to good agreement with the same values obtained from XRD measurements was obtained. This proof-of-principle opens interesting perspectives about the possible development of a rapid, low cost and industry-friendly assessment of the thermal expansion properties of organic semiconducting single crystals (OSSCs) involving hydrogen bonds.

Reliability of the pair-defect-sum approximation for the strength of valence-bond orbitals

PubMed Central

Pauling, Linus; Herman, Zelek S.; Kamb, Barclay J.

1982-01-01

The pair-defect-sum approximation to the bond strength of a hybrid orbital (angular wave functions only) is compared to the rigorous value as a function of bond angle for seven types of bonding situations, with between three and eight bond directions equivalent by geometrical symmetry operations and with only one independent bond angle. The approximation is seen to be an excellent one in all cases, and the results provide a rationale for the application of this approximation to a variety of problems. PMID:16593167

Equilibrium composition of interphase boundaries

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

Wynblatt, P.

1990-01-01

Two modeling approaches have been used to investigate segregation effects at interphase boundaries. The first approach is based on the nearest neighbor bond model, used in conjunction with the regular solution approximation, and is an extension of an earlier framework developed to address segregation phenomena at free surfaces. In order to model a semicoherent interphase boundary, we have employed a second modeling approach, based on Monte Carol simulation, in conjunction with the embedded atom method (EAM). The EAM is a powerful new method for describing interatomic interactions in metallic systems. It includes certain many-body interactions that depend on the localmore » environment of an atom. The Monte Carol approach has been applied to semicoherent interphase boundaries in Cu-Ag-Au alloys dilute in Au. These alloys consist of coexisting Cu-rich and Ag-rich phases, which differ in lattice constant by about 12%, such that good matching across in interface occurs when nine structural units of the Cu-rich phase are opposed to eight structural units of the Ag-rich phase. Thus far, interfaces with two different orientations have been studied: {l brace}001{r brace}-Cu//{l brace}001{r brace}-Ag, {l angle}110{r angle}-Cu//{l angle}110{r angle}-Ag; and {l brace}111{r brace}-Cu//{l brace}111{r brace}-Ag, {l angle}110{r angle}-Cu//{l angle}110{r angle}-Ag. These two interfaces will be referred to as the (001) and (111) interphase boundaries, for short. 18 refs.« less

Quadratic elongation: A quantitative measure of distortion in coordination polyhedra

USGS Publications Warehouse

Robinson, Kelly F.; Gibbs, G.V.; Ribbe, P.H.

1971-01-01

Quadratic elongation and the variance of bond angles are linearly correlated for distorted octahedral and tetrahedral coordination complexes, both of which show variations in bond length and bond angle. The quadratic elonga tion is dimensionless, giving a quantitative measure of polyhedral distortion which is independent of the effective size of the polyhedron.

Acoustic Monitoring of Adhesive Bond Curing in Wood Laminates.

NASA Astrophysics Data System (ADS)

Biernacki, Jacek Marek

Challenges in manufacturing of wood products, such as glulam, include difficulty in controlling bonding variables and assessing bond quality. This dissertation investigates an ultrasonic method as a means of monitoring of curing and assessing bond quality in wood laminates. The effect of curing on ultrasonic transmission was studied using specimens of clear Douglas-fir, 100 x 200 x 600 mm, with the adhesive bond in the center of the specimen. Monitoring was performed simultaneously at normal and angular (5 ^circ nominal) incidence to the bond plane. Acoustic measurements were supplemented with destructive cure monitoring, standard bond strength measurement, monitoring of bulk viscosity curing, gel time measurement, and microscopic (SEM) examination. Angular incidence gave greater sensitivity to bond quality and curing status than did normal incidence. Analysis of wave propagation showed that displacement for transmission at a small angle (on the order of 5^circ ) was nearly parallel to the bond, which seems to explain greater sensitivity of angular incidence. Experimental results showed that this method was effective in detection of curing phases, such as spread, penetration, and hardening, defective bonds, and the effect of clamping pressure. An "unloading effect", measured as a relative transmission reduction after the clamping load was released, was sensitive to defective bonds, including uncured (kissing), underspread, and uneven spread bonds. Thick bonds (0.5 and 1.0 mm) caused the greatest increase in transmission, since waves at start of curing were highly attenuated. In angular transmission, thick-bond curing curves showed a characteristic inflection, which may be used to identify thick bonds and measure the curing rate. The results of this dissertation could be utilized to develop commercial systems in glulam manufacturing, which could evaluate: (a) phase of and completion of curing (b) bond quality (c) optimum clamping pressure. Similar systems could also be developed to monitor lumber and panel products curing at high temperature, such as LVL (laminated veneer lumber), OSB (oriented strandboard) and particleboard.

Friction pull plug welding: chamfered heat sink pull plug design

NASA Technical Reports Server (NTRS)

Coletta, Edmond R. (Inventor); Cantrell, Mark A. (Inventor)

2005-01-01

The average strength of a pull plug weld is increased and weak bonding eliminated by providing a dual included angle at the top one third of the pull plug. Plugs using the included angle of the present invention had consistent high strength, no weak bonds and were substantially defect free. The dual angle of the pull plug body increases the heat and pressure of the weld in the region of the top one third of the plug. This allows the plug to form a tight high quality solid state bond. The dual angle was found to be successful in elimination of defects on both small and large plugs.

Effects of interfacial alignments on the stability of graphene on Ru(0001) substrate

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

Gao, Lei; Liu, Yanmin; Ma, Tianbao, E-mail: mtb@mail.tsinghua.edu.cn

2016-06-27

Structure and electronic properties of two-dimensional materials could be tuned by interfacial misfit or orientation angles. However, graphene grown on Ru(0001) substrate usually shows stable moiré superlattice with a periodicity of 3.0 nm indicating an aligned geometry. The reason for the absence of misaligned structure is still unknown. We have performed first-principles calculation to investigate the microstructure and morphology of graphene on Ru(0001) substrate in both aligned and misaligned geometries with rotation angles of 0°, 7.6°, and 23.4°, respectively. Our results indicate that both the graphene corrugation and moiré superlattice periodicity decrease as the rotation angle increases. Meanwhile the interaction energymore » between graphene and Ru(0001) substrate also becomes weakened with the rotation angle, as the decrease and discretization of intense charge transfer sites at the graphene/Ru interface, which is closely related to the interface stacking structure. Counterintuitively, the strain energy in graphene also increases anomalously with the rotation angle, which is attributed to the highly distorted local deformation of graphene due to the strong but discrete covalent bonding with Ru substrate. The simultaneous increase in both the interaction energy and strain energy in graphene/Ru(0001) heterostructure with rotation angle contributes to the preferred configuration in the aligned state.« less

A High-Resolution 3D Separated-Local-Field Experiment by Means of Magic-Angle Turning

PubMed

Hu; Alderman; Pugmire; Grant

1997-05-01

A 3D separated-local-field (SLF) experiment based on the 2D PHORMAT technique is described. In the 3D experiment, the conventional 2D SLF powder pattern for each chemically inequivalent carbon is separated according to their different isotropic chemical shifts. The dipolar coupling constant of a C-H pair, hence the bond distance, and the relative orientation of the chemical-shift tensor to the C-H vector can all be determined for the protonated carbons with a single measurement. As the sample turns at only about 30 Hz in a MAT experiment, the SLF patterns obtained approach those of a stationary sample, and an accuracy in the measurement similar to that obtained on a stationary sample is expected. The technique is demonstrated on 2,6-dimethoxynaphthalene, where the 13 C-1 H separated-local-field powder patterns for the six chemically inequivalent carbons are clearly identified and measured. The observed dipolar coupling for the methoxy carbon is effectively reduced by the fast rotation of the group about its C3 symmetry axis. The average angle between the C-H bond direction and the C3 rotation axis in the OCH3 group is found to be about 66°.

Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function

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

Prill, Dragica; Juhas, Pavol; Billinge, Simon J. L.

2016-01-01

In this study, a method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may bemore » used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.« less

Probing the Importance of Charge Flux in Force Field Modeling.

PubMed

Sedghamiz, Elaheh; Nagy, Balazs; Jensen, Frank

2017-08-08

We analyze the conformational dependence of atomic charges and molecular dipole moments for a selection of ∼900 conformations of peptide models of the 20 neutral amino acids. Based on a set of reference density functional theory calculations, we partition the changes into effects due to changes in bond distances, bond angles, and torsional angles and into geometry and charge flux contributions. This allows an assessment of the limitations of fixed charge force fields and indications for how to design improved force fields. The torsional degrees of freedom are the main contribution to conformational changes of atomic charges and molecular dipole moments, but indirect effects due to change in bond distances and angles account for ∼25% of the variation. Charge flux effects dominate for changes in bond distances and are also the main component of the variation in bond angles, while they are ∼25% compared to the geometry variations for torsional degrees of freedom. The geometry and charge flux contributions to some extent produce compensating effects.

Molecular structures of carotenoids as predicted by MNDO-AM1 molecular orbital calculations

NASA Astrophysics Data System (ADS)

Hashimoto, Hideki; Yoda, Takeshi; Kobayashi, Takayoshi; Young, Andrew J.

2002-02-01

Semi-empirical molecular orbital calculations using AM1 Hamiltonian (MNDO-AM1 method) were performed for a number of biologically important carotenoid molecules, namely all- trans-β-carotene, all- trans-zeaxanthin, and all- trans-violaxanthin (found in higher plants and algae) together with all- trans-canthaxanthin, all- trans-astaxanthin, and all- trans-tunaxanthin in order to predict their stable structures. The molecular structures of all- trans-β-carotene, all- trans-canthaxanthin, and all- trans-astaxanthin predicted based on molecular orbital calculations were compared with those determined by X-ray crystallography. Predicted bond lengths, bond angles, and dihedral angles showed an excellent agreement with those determined experimentally, a fact that validated the present theoretical calculations. Comparison of the bond lengths, bond angles and dihedral angles of the most stable conformer among all the carotenoid molecules showed that the displacements are localized around the substituent groups and hence around the cyclohexene rings. The most stable conformers of all- trans-zeaxanthin and all- trans-violaxanthin gave rise to a torsion angle around the C6-C7 bond to be ±48.7 and -84.8°, respectively. This difference is a key factor in relation to the biological function of these two carotenoids in plants and algae (the xanthophyll cycle). Further analyses by calculating the atomic charges and using enpartment calculations (division of bond energies between component atoms) were performed to ascribe the cause of the different observed torsion angles.

Bis[2-(2-pyridylmethyl­eneamino)benzene­sulfonato-κ3 N,N′,O]cobalt(II) dihydrate

PubMed Central

Huang, Xue-Ren; Ou-Yang, Miao; Yang, Ge-Ge; Meng, Xiu-Jin; Jiang, Yi-Min

2009-01-01

The title complex, [Co(C12H9N2O3S)2]·2H2O, has site symmetry 2 with the CoII cation located on a twofold rotation axis. Two tridentate 2-(2-pyridylmethyl­eneamino)benzene­sulfonate (paba) ligands chelate to the CoII cation in a distorted octa­hedral geometry. The pyridine and benzene rings in the paba ligand are oriented at a dihedral angle of 42.86 (13)°. Inter­molecular O—H⋯O and C—H⋯O hydrogen bonding is present in the crystal structure. PMID:21578190

Benzil bis­(ketazine)

PubMed Central

Patra, Goutam Kumar; Mukherjee, Anindita; Ng, Seik Weng

2009-01-01

The title compound (systematic name: 1,1′,2,2′-tetra­phenyl-2,2′-azinodiethanone), C28H20N2O2, was obtained by the reaction of benzil monohydrazone with chromium(III) nitrate. The dibenzyl­idene hydrazine unit is nearly planar (r.m.s. deviation = 0.073 Å) and the two benzoyl units are oriented almost perpendicular to it [dihedral angle = 87.81 (2), 87.81 (2)°]. The mol­ecules are linked into chains along the c axis by C—H⋯O hydrogen bonds and the chains are cross-linked via C—H⋯π inter­actions involving the benzoyl phenyl rings. PMID:21583456

High-pressure effect on the dynamics of solvated peptides.

PubMed

Nellas, Ricky B; Glover, Mary M; Hamelberg, Donald; Shen, Tongye

2012-04-14

The dynamics of peptides has a direct connection to how quickly proteins can alter their conformations. The speed of exploring the free energy landscape depend on many factors, including the physical parameters of the environment, such as pressure and temperature. We performed a series of molecular dynamics simulations to investigate the pressure-temperature effects on peptide dynamics, especially on the torsional angle and peptide-water hydrogen bonding (H-bonding) dynamics. Here, we show that the dynamics of the omega angle and the H-bonding dynamics between water and the peptide are affected by pressure. At high temperature (500 K), both the dynamics of the torsional angle ω and H-bonding slow down significantly with increasing pressure, interestingly, at approximately the same rate. However, at a lower temperature of 300 K, the observed trend on H-bonding dynamics as a function of pressure reverses, i.e., higher pressure speeds up H-bonding dynamics.

Orientational order in smectic liquid-crystalline phases of amphiphilic diols

NASA Astrophysics Data System (ADS)

Giesselmann, Frank; Germer, Roland; Saipa, Alexander

2005-07-01

The thermotropic smectic phases of amphiphilic 2-(trans-4-n-alkylcyclohexyl)-propane-1,3-diols were investigated by means of small- and wide-angle x-ray scattering and values of the smectic (bi-)layer spacing, the orientational order parameters ⟨P2⟩ and ⟨P4⟩, the orientational distribution function as well as the intralayer correlation length were extracted from the scattering profiles. The results for the octyl homolog indicate that these smectic phases combine a very high degree of smectic one-dimensional-translational order with remarkably low orientational order, the order parameter of which (⟨P2⟩≈0.56) is far below those values typically found in nonamphiphilic smectics. This combination, quite exceptional in thermotropic smectics, most likely originates from the intermolecular hydrogen bonding between the terminal diol groups which seems to be the specific driving force in the formation of the thermotropic smectic structure in these amphiphiles and leads to a type of microphase segregation. Even in the absence of a solvent, the liquid-crystalline ordering of the amphiphilic mesogens comes close to the structure of the so-called neat soaps, found in lyotropic liquid crystals.

Roles of bond orientational ordering in glass transition and crystallization.

PubMed

Tanaka, Hajime

2011-07-20

It is widely believed that crystallization in three dimensions is primarily controlled by positional ordering, and not by bond orientational ordering. In other words, bond orientational ordering is usually considered to be merely a consequence of positional ordering and thus has often been ignored. This one-order-parameter (density) description may be reasonable when we consider an equilibrium liquid-solid transition, but may not be enough to describe a metastable state and the kinetics of the transition. Here we propose that bond orientational ordering can play a key role in (i) crystallization, (ii) the ordering to quasi-crystal and (iii) vitrification, which occurs under rather weak frustration against crystallization. In a metastable supercooled state before crystallization, a system generally tends to have bond orientational order at least locally as a result of a constraint of dense packing. For a system interacting with hard-core repulsions, the constraint is intrinsically of geometrical origin and thus the basic physics is the same as nematic ordering of rod-like particles upon densification. Furthermore, positional ordering is easily destroyed even by weak frustration such as polydispersity and anisotropic interactions which favour a symmetry not consistent with that of the equilibrium crystal. Thus we may say that vitrification can be achieved by disturbing and prohibiting long-range positional ordering. Even in such a situation, bond orientational ordering still survives, accompanying its critical-like fluctuations, which are the origin of dynamic heterogeneity for this case. This scenario naturally explains both the absence of positional order and the development of bond orientational order upon cooling in a supercooled state. Although our argument is speculative in nature, we emphasize that this physical picture can coherently explain crystallization, vitrification, quasi-crystallization and their relationship in a natural manner. For a strongly frustrated system, even bond orientational order can be destroyed. Even in such a case there may still appear a structural signature of dense packing, which is linked to slow dynamics.

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

Ishige, Ryohei; Williams, Gregory A.; Higaki, Yuji

A molded film of single-component polymer-grafted nanoparticles (SPNP), consisting of a spherical silica core and densely grafted polymer chains bearing hydrogen-bonding side groups capable of physical crosslinking, was investigated byin situultra-small-angle X-ray scattering (USAXS) measurement during a uniaxial stretching process. Static USAXS revealed that the molded SPNP formed a highly oriented twinned face-centered cubic (f.c.c.) lattice structure with the [11-1] plane aligned nearly parallel to the film surface in the initial state. Structural analysis ofin situUSAXS using a model of uniaxial deformation induced by rearrangement of the nanoparticles revealed that the f.c.c. lattice was distorted in the stretching direction inmore » proportion to the macroscopic strain until the strain reached 35%, and subsequently changed into other f.c.c. lattices with different orientations. The lattice distortion and structural transition behavior corresponded well to the elastic and plastic deformation regimes, respectively, observed in the stress–strain curve. The attractive interaction of the hydrogen bond is considered to form only at the top surface of the shell and then plays an effective role in cross-linking between nanoparticles. The rearrangement mechanism of the nanoparticles is well accounted for by a strong repulsive interaction between the densely grafted polymer shells of neighboring particles.« less

2-(3-Cyano-4-{3-[1-(2-hy-droxy-eth-yl)-3,3-dimethyl-1,3-di-hydro-indol-2-yl-idene]prop-2-en-yl}-5,5-dimethyl-5H-furan-2-yl-idene)malono-nitrile.

PubMed

Gainsford, Graeme J; Bhuiyan, M Delower H; Kay, Andrew J

2014-01-01

The title compound, C25H24N4O2, adopts a cisoid configuration and has twofold orientational disorder of the 2-hy-droxy-ethyl group. The mol-ecule is twisted from planarity so that the dihedral angle between the terminating indol-2-yl-idene and the furan-2-yl-idene moiety mean planes is 12.75 (7)°. Conformational disorder occurs at the indol-2-yl-idene N atom, which results in two orientations for the hy-droxy-ethyl group [occupancy ratio = 0.896 (2):0.104 (2)], and the hy-droxy O atom of the 2-hy-droxy-ethyl group is located over three sites [occupancy ratio = 0.548 (2):0.348 (2):0.104 (2)]. An intra-molecular C-H⋯O hydrogen bond involving the lowest occupancy hy-droxy O atom is observed. In the crystal, the mol-ecules pack in parallel dimeric sheets about centres of symmetry, utilizing O-H⋯N(cyano), C-H⋯N(cyano) and O-H⋯O hydrogen bonds, in two sets parallel to (02-1) and (021) planes.

Antifreeze Proteins at the Ice/Water Interface: Three Calculated Discriminating Properties for Orientation of Type I Proteins

PubMed Central

Wierzbicki, Andrzej; Dalal, Pranav; Cheatham, Thomas E.; Knickelbein, Jared E.; Haymet, A. D. J.; Madura, Jeffry D.

2007-01-01

Antifreeze proteins (AFPs) protect many plants and organisms from freezing in low temperatures. Of the different AFPs, the most studied AFP Type I from winter flounder is used in the current computational studies to gain molecular insight into its adsorption at the ice/water interface. Employing molecular dynamics simulations, we calculate the free energy difference between the hydrophilic and hydrophobic faces of the protein interacting with ice. Furthermore, we identify three properties of Type I “antifreeze” proteins that discriminate among these two orientations of the protein at the ice/water interface. The three properties are: the “surface area” of the protein; a measure of the interaction of the protein with neighboring water molecules as determined by the number of hydrogen bond count, for example; and the side-chain orientation angles of the threonine residues. All three discriminants are consistent with our free energy results, which clearly show that the hydrophilic protein face orientations toward the ice/water interface, as hypothesized from experimental and ice/vacuum simulations, are incorrect and support the hypothesis that the hydrophobic face is oriented toward the ice/water interface. The adsorption free energy is calculated to be 2–3 kJ/mol. PMID:17526572

Diffraction evidence for the structure of cellulose microfibrils in bamboo, a model for grass and cereal celluloses.

PubMed

Thomas, Lynne H; Forsyth, V Trevor; Martel, Anne; Grillo, Isabelle; Altaner, Clemens M; Jarvis, Michael C

2015-06-23

Cellulose from grasses and cereals makes up much of the potential raw material for biofuel production. It is not clear if cellulose microfibrils from grasses and cereals differ in structure from those of other plants. The structures of the highly oriented cellulose microfibrils in the cell walls of the internodes of the bamboo Pseudosasa amabilis are reported. Strong orientation facilitated the use of a range of scattering techniques. Small-angle neutron scattering provided evidence of extensive aggregation by hydrogen bonding through the hydrophilic edges of the sheets of chains. The microfibrils had a mean centre-to-centre distance of 3.0 nm in the dry state, expanding on hydration. The expansion on hydration suggests that this distance between centres was through the hydrophilic faces of adjacent microfibrils. However in the other direction, perpendicular to the sheets of chains, the mean, disorder-corrected Scherrer dimension from wide-angle X-ray scattering was 3.8 nm. It is possible that this dimension is increased by twinning (crystallographic coalescence) of thinner microfibrils over part of their length, through the hydrophobic faces. The wide-angle scattering data also showed that the microfibrils had a relatively large intersheet d-spacing and small monoclinic angle, features normally considered characteristic of primary-wall cellulose. Bamboo microfibrils have features found in both primary-wall and secondary-wall cellulose, but are crystallographically coalescent to a greater extent than is common in celluloses from other plants. The extensive aggregation and local coalescence of the microfibrils are likely to have parallels in other grass and cereal species and to influence the accessibility of cellulose to degradative enzymes during conversion to liquid biofuels.

Crystal structure of catena-poly[[aquadi-n-propyl­tin(IV)]-μ-oxalato

PubMed Central

Reichelt, Martin; Reuter, Hans

2014-01-01

The title compound, [Sn(C3H7)2(H2O)(C2O4)]n, represents the first diorganotin(IV) oxalate hydrate to be structurally characterized. The tin(IV) atom of the one-dimensional coordination polymer is located on a twofold rotation axis and is coordinated by two chelating oxalate ligands with two slightly different Sn—O bond lengths of 2.290 (2) and 2.365 (2) Å, two symmetry-related n-propyl groups with a Sn—C bond lengths of 2.127 (3) Å, and a water mol­ecule with a Sn—O bond length of 2.262 (2) Å. The coordination polyhedron around the SnIV atom is a slightly distorted penta­gonal bipyramid with a nearly linear axis between the trans-oriented n-propyl groups [C—Sn—C = 176.8 (1)°]. The bond angles between the oxygen atoms of the equatorial plane range from 70.48 (6)° to 76.12 (8)°. A one-dimensional coordination polymer results from the less asymmetric bilateral coordination of the centrosymmetric oxalate anion, inter­nally reflected by two slightly different C—O bond lengths of 1.248 (3) and 1.254 (3) Å. The chains of the polymer propagate parallel to [001] and are held together by hydrogen bonds between water mol­ecules and oxalate anions of neighboring chains, leading to a two-dimensional network parallel to (100). PMID:25249862

Surface fluorination of zirconia: adhesive bond strength comparison to commercial primers.

PubMed

Piascik, Jeffrey R; Swift, Edward J; Braswell, Krista; Stoner, Brian R

2012-06-01

This study evaluated contact angle and shear bond strength of three commercial zirconia primers and compared them to a recently developed fluorination pre-treatment. Earlier investigations reported that plasma fluorinated zirconia modifies the chemical bonding structure creating a more reactive surface. Yttria-stabilized zirconia (LAVA, 3M ESPE) plates were highly polished using 3μm diamond paste (R(a) ∼200nm) prior to pretreatments. After primer and fluorination treatment, contact angles were measured to quantify surface hydrophobicity before and after ethanol clean. Additionally, simple shear bond tests were performed to measure the adhesion strength to a composite resin. Plasma fluorination produced the lowest contact angle (7.8°) and the highest shear bond strength (37.3MPa) suggesting this pretreatment facilitates a more "chemically" active surface for adhesive bonding. It is hypothesized that plasma fluorination increase hydroxylation at the surface, making it more reactive, thus allowing for covalent bonding between zirconia surface and resin cement. A strong correlation was observed between contact angle and adhesion strength for all specimens; a relationship which may help understand the frequency and modes of failures, clinically. It is also believed that this surface treatment can increase long-term viability of zirconia restorations over other adhesive techniques. Copyright © 2012 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

X-ray Birefringence: A New Strategy for Determining Molecular Orientation in Materials.

PubMed

Palmer, Benjamin A; Edwards-Gau, Gregory R; Morte-Ródenas, Anabel; Kariuki, Benson M; Lim, Gin Keat; Harris, Kenneth D M; Dolbnya, Igor P; Collins, Stephen P

2012-11-01

While the phenomenon of birefringence is well-established in the case of visible radiation and is exploited in many fields (e.g., through the use of the polarizing optical microscope), the analogous phenomenon for X-rays has been a virtually neglected topic. Here, we demonstrate the scope and potential for exploiting X-ray birefringence to determine the orientational properties of specific types of bonds in solids. Specifically, orientational characteristics of C-Br bonds in the bromocyclohexane/thiourea inclusion compound are elucidated from X-ray birefringence measurements at energies close to the bromine K-edge, revealing inter alia the changes in the orientational distribution of the C-Br bonds associated with a low-temperature order-disorder phase transition. From fitting a theoretical model to the experimental data, reliable quantitative information on the orientational properties of the C-Br bonds is determined. The experimental strategy reported here represents the basis of a new approach for gaining insights into the orientational properties of molecules in anisotropic materials.

Spontaneous adsorption on a hydrophobic surface governed by hydrogen bonding.

PubMed

Dang, Fuquan; Hasegawa, Takeshi; Biju, Vasudevanpillai; Ishikawa, Mitsuru; Kaji, Noritada; Yasui, Takao; Baba, Yoshinobu

2009-08-18

Spontaneous adsorption from solution onto solid surface is a common phenomenon in nature, but the force that governs adsorption is still a matter of considerable debate. (1, 2) We found that surfactants and cellulose adsorb from solution onto a poly(methyl methacrylate) (PMMA) surface in an ordered and cooperative way governed by hydrogen bonding. The glucose rings of n-dodecyl-beta-D-maltoside (DDM) and hydroxyethylcellulose (HEC) stand perpendicular to the surface, H-bond to the surface COOMe groups with their C=O and Me-O bonds parallel to the surface, and form a tight monolayer. The non-H-bonded COOMe groups orient their C=O bonds perpendicular to the surface. In contrast, the glucose rings of hydrophobically modified hydroxyethylcellulose (HMHEC) lie flat with the side chains perpendicular to the surface and H-bond to the perpendicular-oriented C=O groups. The non-H-bonded COOMe groups orient their C=O bonds parallel but Me-O bonds near-perpendicular to the surface for stabilizing HMHEC. The current work provides a detailed picture of how surface-active molecules interact with a solid surface and self-assemble into greatly different architectures.

Bonding Strength Properties of Adhesively-Timber Joint with Thixotropic and Room Temperature Cured Epoxy Based Adhesive Reinforced with Nano- and Micro-particles

NASA Astrophysics Data System (ADS)

Ahmad, Z.; Ansell, M. P.; Smedley, D.

2011-02-01

This research work is concerned with in situ bonded-in timber connection using pultruded rod; where the manufacturing of such joint requires adhesive which can produce thick glue-lines and does not allow any use of pressure and heat. Four types of thixotropic (for ease application) and room temperature cured epoxy based were used namely CB10TSS (regarded as standards adhesive), Nanopox (modification of CB10TSS with addition of nanosilica), Albipox (modification of CB10TSS with addition of liquid rubber) and Timberset (an epoxy-based adhesive with addition of micro-size ceramic particles). The quality of the adhesive bonds was accessed using block shear test in accordance with ASTM D905. The bond strength depends on how good the adhesive wet the timber surface. Therefore the viscosity and contact angle was also measured. The nano- and microfiller additions increased the bond strength significantly. The viscosity correlates well with contact angle measurements where lower viscosities are associated with lower contact angles. However contact angle contradicts with measured strength and wettability.

Probing the Orientation of Surface-Immobilized Protein G B1 Using ToF-SIMS Sum Frequency Generation and NEXAFS Spectroscopy

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

L Baugh; T Weidner; J Baio

2011-12-31

The ability to orient active proteins on surfaces is a critical aspect of many medical technologies. An important related challenge is characterizing protein orientation in these surface films. This study uses a combination of time-of-flight secondary ion mass spectrometry (ToF-SIMS), sum frequency generation (SFG) vibrational spectroscopy, and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy to characterize the orientation of surface-immobilized Protein G B1, a rigid 6 kDa domain that binds the Fc fragment of IgG. Two Protein G B1 variants with a single cysteine introduced at either end were immobilized via the cysteine thiol onto maleimide-oligo(ethylene glycol)-functionalized gold and baremore » gold substrates. X-ray photoelectron spectroscopy was used to measure the amount of immobilized protein, and ToF-SIMS was used to measure the amino acid composition of the exposed surface of the protein films and to confirm covalent attachment of protein thiol to the substrate maleimide groups. SFG and NEXAFS were used to characterize the ordering and orientation of peptide or side chain bonds. On both substrates and for both cysteine positions, ToF-SIMS data showed enrichment of mass peaks from amino acids located at the end of the protein opposite to the cysteine surface position as compared with nonspecifically immobilized protein, indicating end-on protein orientations. Orientation on the maleimide substrate was enhanced by increasing pH (7.0-9.5) and salt concentration (0-1.5 M NaCl). SFG spectral peaks characteristic of ordered {alpha}-helix and {beta}-sheet elements were observed for both variants but not for cysteine-free wild type protein on the maleimide surface. The phase of the {alpha}-helix and {beta}-sheet peaks indicated a predominantly upright orientation for both variants, consistent with an end-on protein binding configuration. Polarization dependence of the NEXAFS signal from the N 1s to {pi}* transition of {beta}-sheet peptide bonds also indicated protein ordering, with an estimated tilt angle of inner {beta}-strands of 40-50{sup o} for both variants (one variant more tilted than the other), consistent with SFG results. The combined results demonstrate the power of using complementary techniques to probe protein orientation on surfaces.« less

The Polarization Orientation Shift Estimation and Compensation of PolSAR Data in Forest Area

NASA Astrophysics Data System (ADS)

Zhao, Lei; Chen, Erxue; Li, Zengyuan; Li, Lan; Gu, Xinzhi

2016-08-01

Polarization orientation angle (POA) is a major parameter of electromagnetic wave. This angle will be shift due to azimuth slopes, which will affect the radiometric quality of PolSAR data. Under the assumption of reflection symmetrical medium, the shift value of polarization orientation angle (POAs) can be estimated by Circular Polarization Method (CPM). Then, the shift angle can be used to compensate PolSAR data or extract DEM information. However, it is less effective when using high-frequency SAR (L-, C-band) in the forest area. The main reason is that the polarization orientation angle shift of forest area not only influenced by topography, but also affected by the forest canopy. Among them, the influence of the former belongs to the interference information should be removed, but the impact of the latter belongs to the polarization feature information needs to be retained. The ALOS2 PALSAR2 L-band full polarimetric SAR data was used in this study. Base on the Circular Polarization and DEM-based method, we analyzed the variation of shift value of polarization orientation angle and developed the polarization orientation shift estimation and compensation of PolSAR data in forest.

Crystal structure of benzyl (E)-2-(3,4-di-meth-oxy-benzyl-idene)hydrazine-1-carbodi-thio-ate.

PubMed

Tan, Yew-Fung; Break, Mohammed Khaled Bin; Tahir, M Ibrahim M; Khoo, Teng-Jin

2015-02-01

The title compound, C17H18N2O2S2, synthesized via a condensation reaction between S-benzyl di-thio-carbazate and 3,4-di-meth-oxy-benzaldehyde, crystallized with two independent mol-ecules (A and B) in the asymmetric unit. Both mol-ecules have an L-shape but differ in the orientation of the benzyl ring with respect to the 3,4-di-meth-oxy-benzyl-idine ring, this dihedral angle is 65.59 (8)° in mol-ecule A and 73.10 (8)° in mol-ecule B. In the crystal, the A and B mol-ecules are linked via pairs of N-H⋯S hydrogen bonds, forming dimers with an R 2 (2)(8) ring motif. The dimers are linked via pairs of C-H⋯O hydrogen bonds, giving inversion dimers of dimers. These units are linked by C-H⋯π inter-actions, forming ribbons propagating in the [100] direction.

How shared preferences in music create bonds between people: values as the missing link.

PubMed

Boer, Diana; Fischer, Ronald; Strack, Micha; Bond, Michael H; Lo, Eva; Lam, Jason

2011-09-01

How can shared music preferences create social bonds between people? A process model is developed in which music preferences as value-expressive attitudes create social bonds via conveyed value similarity. The musical bonding model links two research streams: (a) music preferences as indicators of similarity in value orientations and (b) similarity in value orientations leading to social attraction. Two laboratory experiments and one dyadic field study demonstrated that music can create interpersonal bonds between young people because music preferences can be cues for similar or dissimilar value orientations, with similarity in values then contributing to social attraction. One study tested and ruled out an alternative explanation (via personality similarity), illuminating the differential impact of perceived value similarity versus personality similarity on social attraction. Value similarity is the missing link in explaining the musical bonding phenomenon, which seems to hold for Western and non-Western samples and in experimental and natural settings.

Beyond parenting practices: extended kinship support and the academic adjustment of African-American and European-American teens.

PubMed

Pallock, Linda L; Lamborn, Susie D

2006-10-01

This study examined adolescents' perceptions of parenting practices and extended kinship support in relation to academic adjustment for 104 African American and 60 European American 9th and 10th graders (14 and 15 year olds). For African-American teens, parental acceptance was associated with school values, teacher bonding, and work orientation. Higher levels of behavioral control and lower levels of psychological control were associated with a stronger work orientation. After accounting for the demographic variables and the three parenting practices, higher levels of extended kinship support related to stronger school values, higher teacher bonding, and a stronger work orientation. For European-American teens, parental acceptance related to academic adjustment, including stronger school values, higher teacher bonding, and a stronger work orientation. European-American adolescents with stronger extended kinship networks reported higher teacher bonding and a stronger work orientation. Results indicate the importance of extended kinship support for both African-American and European-American adolescents.

Crystal structure of 4-fluoro-N-[2-(4-fluoro-benzo-yl)hydra-zine-1-carbono-thio-yl]benzamide.

PubMed

Firdausiah, Syadza; Salleh Huddin, Ameera Aqeela; Hasbullah, Siti Aishah; Yamin, Bohari M; Yusoff, Siti Fairus M

2014-09-01

In the title compound, C15H11F2N3O2S, the dihedral angle between the fluoro-benzene rings is 88.43 (10)° and that between the central semithiocarbazide grouping is 47.00 (11)°. The dihedral angle between the amide group and attached fluoro-benzene ring is 50.52 (11)°; the equivalent angle between the carbonyl-thio-amide group and its attached ring is 12.98 (10)°. The major twists in the mol-ecule occur about the C-N-N-C bonds [torsion angle = -138.7 (2)°] and the Car-Car-C-N (ar = aromatic) bonds [-132.0 (2)°]. An intra-molecular N-H⋯O hydrogen bond occurs, which generates an S(6) ring. In the crystal, the mol-ecules are linked by N-H⋯O and N-H⋯S hydrogen bonds, generating (001) sheets. Weak C-H⋯O and C-H⋯F inter-actions are also observed.

Diaqua­bis­(4-meth­oxy­benzoato-κO 1)bis­(nicotinamide-κN 1)cobalt(II) dihydrate

PubMed Central

Hökelek, Tuncer; Dal, Hakan; Tercan, Barış; Tenlik, Erdinç; Necefoğlu, Hacali

2010-01-01

In the mononuclear title compound, [Co(C8H7O3)2(C6H6N2O)2(H2O)2]·2H2O, the CoII ion is located on a crystallographic inversion center. The asymmetric unit is completed by one 4-meth­oxy­benzoate anion, one nicotinamide (NA) ligand and one coordinated and one uncoordinated water mol­ecule. All ligands act in a monodentate mode. The four O atoms in the equatorial plane around the CoII ion form a slightly distorted square-planar arrangement, while the slightly distorted octa­hedral coordination is completed by the two pyridine N atoms of the NA ligands in the axial positions. The dihedral angle between the carboxyl­ate group and the attached benzene ring is 6.47 (7)°, while the pyridine and benzene rings are oriented at a dihedral angle of 72.80 (4)°. An O—H⋯O hydrogen bond links the uncoordinated water mol­ecule to one of the carboxyl­ate groups. In the crystal structure, inter­molecular O—H⋯O, N—H⋯O and C—H⋯O hydrogen bonds link the mol­ecules into a three-dimensional network. PMID:21588149

Crystal structures of 4-meth-oxy-N-(4-methyl-phenyl)benzene-sulfonamide and N-(4-fluoro-phenyl)-4-meth-oxy-benzene-sulfonamide.

PubMed

Rodrigues, Vinola Z; Preema, C P; Naveen, S; Lokanath, N K; Suchetan, P A

2015-11-01

Crystal structures of two N-(ar-yl)aryl-sulfonamides, namely, 4-meth-oxy-N-(4-methyl-phen-yl)benzene-sulfonamide, C14H15NO3S, (I), and N-(4-fluoro-phen-yl)-4-meth-oxy-benzene-sulfonamide, C13H12FNO3S, (II), were determined and analyzed. In (I), the benzene-sulfonamide ring is disordered over two orientations, in a 0.516 (7):0.484 (7) ratio, which are inclined to each other at 28.0 (1)°. In (I), the major component of the sulfonyl benzene ring and the aniline ring form a dihedral angle of 63.36 (19)°, while in (II), the planes of the two benzene rings form a dihedral angle of 44.26 (13)°. In the crystal structure of (I), N-H⋯O hydrogen bonds form infinite C(4) chains extended in [010], and inter-molecular C-H⋯πar-yl inter-actions link these chains into layers parallel to the ab plane. The crystal structure of (II) features N-H⋯O hydrogen bonds forming infinite one dimensional C(4) chains along [001]. Further, a pair of C-H⋯O inter-molecular inter-actions consolidate the crystal packing of (II) into a three-dimensional supra-molecular architecture.

Influence of Fiber Orientation on Single-Point Cutting Fracture Behavior of Carbon-Fiber/Epoxy Prepreg Sheets.

PubMed

Wei, Yingying; An, Qinglong; Cai, Xiaojiang; Chen, Ming; Ming, Weiwei

2015-10-02

The purpose of this article is to investigate the influences of carbon fibers on the fracture mechanism of carbon fibers both in macroscopic view and microscopic view by using single-point flying cutting method. Cutting tools with three different materials were used in this research, namely, PCD (polycrystalline diamond) tool, CVD (chemical vapor deposition) diamond thin film coated carbide tool and uncoated carbide tool. The influence of fiber orientation on the cutting force and fracture topography were analyzed and conclusions were drawn that cutting forces are not affected by cutting speeds but significantly influenced by the fiber orientation. Cutting forces presented smaller values in the fiber orientation of 0/180° and 15/165° but the highest one in 30/150°. The fracture mechanism of carbon fibers was studied in different cutting conditions such as 0° orientation angle, 90° orientation angle, orientation angles along fiber direction, and orientation angles inverse to the fiber direction. In addition, a prediction model on the cutting defects of carbon fiber reinforced plastic was established based on acoustic emission (AE) signals.

Influence of Fiber Orientation on Single-Point Cutting Fracture Behavior of Carbon-Fiber/Epoxy Prepreg Sheets

PubMed Central

Wei, Yingying; An, Qinglong; Cai, Xiaojiang; Chen, Ming; Ming, Weiwei

2015-01-01

The purpose of this article is to investigate the influences of carbon fibers on the fracture mechanism of carbon fibers both in macroscopic view and microscopic view by using single-point flying cutting method. Cutting tools with three different materials were used in this research, namely, PCD (polycrystalline diamond) tool, CVD (chemical vapor deposition) diamond thin film coated carbide tool and uncoated carbide tool. The influence of fiber orientation on the cutting force and fracture topography were analyzed and conclusions were drawn that cutting forces are not affected by cutting speeds but significantly influenced by the fiber orientation. Cutting forces presented smaller values in the fiber orientation of 0/180° and 15/165° but the highest one in 30/150°. The fracture mechanism of carbon fibers was studied in different cutting conditions such as 0° orientation angle, 90° orientation angle, orientation angles along fiber direction, and orientation angles inverse to the fiber direction. In addition, a prediction model on the cutting defects of carbon fiber reinforced plastic was established based on acoustic emission (AE) signals. PMID:28793597

Fourier transform infrared spectra and normal mode analysis of drug molecules: Zidovudine

NASA Astrophysics Data System (ADS)

Jain, Nivedita; Prabhakar, Santosh; Singh, R. A.

2013-03-01

The FTIR spectra of zidovudine molecule have been recorded in the range 4000-400 cm-1. The title compound is used as a drug against AIDS or HIV. The molecular structure, fundamental vibrational frequencies and intensities of vibrational bands are evaluated using density functional theory (DFT) using BLYP, B3LYP, B3PW91 and MPW1PW91 methods with 6-31+G(d,p) standard basis set. Comparison of simulated spectra with the experimental spectrum provides important informations and the ability of the computational method to describe the vibrational modes. These calculations have allowed finding most stable conformational structure of AZT. Calculated results of the title compound indicate that the drug molecule has syn orientation. The glycosidic bond in AZT and a minimum-energy structure in which the glycosy torsion angle χ and torsion angle γ values are consistent with those in the conformation of AZT in the AZT5-triphosphate bound to HIV RT is determined.

Do Halogen–Hydrogen Bond Donor Interactions Dominate the Favorable Contribution of Halogens to Ligand–Protein Binding?

PubMed Central

2017-01-01

Halogens are present in a significant number of drugs, contributing favorably to ligand–protein binding. Currently, the contribution of halogens, most notably chlorine and bromine, is largely attributed to halogen bonds involving favorable interactions with hydrogen bond acceptors. However, we show that halogens acting as hydrogen bond acceptors potentially make a more favorable contribution to ligand binding than halogen bonds based on quantum mechanical calculations. In addition, bioinformatics analysis of ligand–protein crystal structures shows the presence of significant numbers of such interactions. It is shown that interactions between halogens and hydrogen bond donors (HBDs) are dominated by perpendicular C–X···HBD orientations. Notably, the orientation dependence of the halogen–HBD (X–HBD) interactions is minimal over greater than 100° with favorable interaction energies ranging from −2 to −14 kcal/mol. This contrasts halogen bonds in that X–HBD interactions are substantially more favorable, being comparable to canonical hydrogen bonds, with a smaller orientation dependence, such that they make significant, favorable contributions to ligand–protein binding and, therefore, should be actively considered during rational ligand design. PMID:28657759

Characterization of beta-turn and Asx-turns mimicry in a model peptide: stabilization via C--H . . . O interaction.

PubMed

Thakur, A K; Kishore, R

2006-04-15

The chemical synthesis and single-crystal X-ray diffraction analysis of a model peptide, Boc-Thr-Thr-NH2 (1) comprised of proteinogenic residues bearing an amphiphilic Cbeta -stereogenic center, has been described. Interestingly, the analysis of its molecular structure revealed the existence of a distinct conformation that mimics a typical beta-turn and Asx-turns, i.e., the two Thr residues occupy the left- and right-corner positions. The main-chain torsion angles of the N- and C-terminal residues i.e., semiextended: phi = -68.9 degrees , psi = 128.6 degrees ; semifolded: phi = -138.1 degrees , psi = 2.5 degrees conformations, respectively, in conjunction with a gauche- disposition of the obligatory C-terminus Thr CgammaH3 group, characterize the occurrence of the newly described beta-turn- and Asx-turns-like topology. The preferred molecular structure is suggested to be stabilized by an effective nonconventional main-chain to side-chain Ci=O . . . H--Cgamma(i+2)-type intraturn hydrogen bond. Noteworthy, the observed topology of the resulting 10-membered hydrogen-bonded ring is essentially similar to the one perceived for a classical beta-turn and the Asx-turns, stabilized by a conventional intraturn hydrogen bond. Considering the signs as well as magnitudes of the backbone torsion angles and the orientation of the central peptide bond, the overall mimicked topology resembles the type II beta-turn or type II Asx-turns. An analysis of Xaa-Thr sequences in high-resolution X-ray elucidated protein structures revealed the novel topology prevalence in functional proteins (unpublished). In view of indubitable structural as well as functional importance of nonconventional interactions in bioorganic and biomacromolecules, we intend to highlight the participation of Thr CgammaH in the creation of a short-range C=O . . . H--Cgamma -type interaction in peptides and proteins. Copyright 2006 Wiley Periodicals, Inc.

Effects of silver nanoparticles on the bonding of three adhesive systems to fluorotic enamel.

PubMed

Torres-Méndez, Fernando; Martinez-Castañon, Gabriel-Alejandro; Torres-Gallegos, Iranzihuatl; Zavala-Alonso, Norma-Verónica; Patiño-Marin, Nuria; Niño-Martínez, Nereyda; Ruiz, Facundo

2017-05-31

The objective was to evaluate the effect of adding silver nanoparticles into three commercial adhesive systems (Excite™, Adper Prompt L-Pop™ and AdheSE™). Nanoparticles were prepared by a chemical method then mixed with the commercial adhesive systems. This was later applied to the fluorotic enamel, and then micro-tensile bond strength, contact angle measurements and scanning electron microscopy observations were conducted. The commercial adhesive systems achieved the lowest micro-tensile bond strength (Excite™: 11.0±2.1, Adper Prompt L-Pop™: 14.0±5.4 and AdheSE™: 16.0±3.0 MPa) with the highest adhesive failure mode related with the highest contact angle (46.0±0.6º, 30.0±0.5º and 28.0±0.4º respectively). The bond strength achieved in all the experimental adhesive systems (19.0±5.4, 20.0±4.0 and 19.0±3.5 MPa respectively) was statistically higher (p<0.05) than the control and showed the highest cohesive failures related to the lowest contact angle. Adding silver nanoparticles in order to decrease the contact angle improve the adhesive system wetting and its bond strength.

Hexatic smectic phase with algebraically decaying bond-orientational order

NASA Astrophysics Data System (ADS)

Agosta, Lorenzo; Metere, Alfredo; Dzugutov, Mikhail

2018-05-01

The hexatic phase predicted by the theories of two-dimensional melting is characterized by the power-law decay of the orientational correlations, whereas the in-layer bond orientational order in all the hexatic smectic phases observed so far was found to be long range. We report a hexatic smectic phase where the in-layer bond orientational correlations decay algebraically, in quantitative agreement with the hexatic ordering predicted by the theory for two dimensions. The phase was formed in a molecular dynamics simulation of a one-component system of particles interacting via a spherically symmetric potential. The present results thus demonstrate that the theoretically predicted two-dimensional hexatic order can exist in a three-dimensional system.

Correlation between micrometer-scale ripple alignment and atomic-scale crystallographic orientation of monolayer graphene

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

Choi, Jin Sik; Chang, Young Jun; Woo, Sungjong

Deformation normal to the surface is intrinsic in two-dimensional materials due to phononic thermal fluctuations at finite temperatures. Graphene's negative thermal expansion coefficient is generally explained by such an intrinsic property. Recently, friction measurements on graphene exfoliated on a silicon oxide surface revealed an anomalous anisotropy whose origin was believed to be the formation of ripple domains. Here, we uncover the atomistic origin of the observed friction domains using a cantilever torsion microscopy in conjunction with angle-resolved photoemission spectroscopy. We experimentally demonstrate that ripples on graphene are formed along the zigzag direction of the hexagonal lattice. The formation of zigzagmore » directional ripple is consistent with our theoretical model that takes account of the atomic-scale bending stiffness of carbon-carbon bonds and the interaction of graphene with the substrate. Lastly, the correlation between micrometer-scale ripple alignment and atomic-scale arrangement of exfoliated monolayer graphene is first discovered and suggests a practical tool for measuring lattice orientation of graphene.« less

Correlation between micrometer-scale ripple alignment and atomic-scale crystallographic orientation of monolayer graphene

DOE PAGES

Choi, Jin Sik; Chang, Young Jun; Woo, Sungjong; ...

2014-12-01

Deformation normal to the surface is intrinsic in two-dimensional materials due to phononic thermal fluctuations at finite temperatures. Graphene's negative thermal expansion coefficient is generally explained by such an intrinsic property. Recently, friction measurements on graphene exfoliated on a silicon oxide surface revealed an anomalous anisotropy whose origin was believed to be the formation of ripple domains. Here, we uncover the atomistic origin of the observed friction domains using a cantilever torsion microscopy in conjunction with angle-resolved photoemission spectroscopy. We experimentally demonstrate that ripples on graphene are formed along the zigzag direction of the hexagonal lattice. The formation of zigzagmore » directional ripple is consistent with our theoretical model that takes account of the atomic-scale bending stiffness of carbon-carbon bonds and the interaction of graphene with the substrate. Lastly, the correlation between micrometer-scale ripple alignment and atomic-scale arrangement of exfoliated monolayer graphene is first discovered and suggests a practical tool for measuring lattice orientation of graphene.« less

Correlation between micrometer-scale ripple alignment and atomic-scale crystallographic orientation of monolayer graphene.

PubMed

Choi, Jin Sik; Chang, Young Jun; Woo, Sungjong; Son, Young-Woo; Park, Yeonggu; Lee, Mi Jung; Byun, Ik-Su; Kim, Jin-Soo; Choi, Choon-Gi; Bostwick, Aaron; Rotenberg, Eli; Park, Bae Ho

2014-12-01

Deformation normal to the surface is intrinsic in two-dimensional materials due to phononic thermal fluctuations at finite temperatures. Graphene's negative thermal expansion coefficient is generally explained by such an intrinsic property. Recently, friction measurements on graphene exfoliated on a silicon oxide surface revealed an anomalous anisotropy whose origin was believed to be the formation of ripple domains. Here, we uncover the atomistic origin of the observed friction domains using a cantilever torsion microscopy in conjunction with angle-resolved photoemission spectroscopy. We experimentally demonstrate that ripples on graphene are formed along the zigzag direction of the hexagonal lattice. The formation of zigzag directional ripple is consistent with our theoretical model that takes account of the atomic-scale bending stiffness of carbon-carbon bonds and the interaction of graphene with the substrate. The correlation between micrometer-scale ripple alignment and atomic-scale arrangement of exfoliated monolayer graphene is first discovered and suggests a practical tool for measuring lattice orientation of graphene.

Does hemipelvis structure and position influence acetabulum orientation?

PubMed

Musielak, Bartosz; Jóźwiak, Marek; Rychlik, Michał; Chen, Brian Po-Jung; Idzior, Maciej; Grzegorzewski, Andrzej

2016-03-16

Although acetabulum orientation is well established anatomically and radiographically, its relation to the innominate bone has rarely been addressed. If explored, it could open the discussion on patomechanisms of such complex disorders as femoroacetabular impingement (FAI). We therefore evaluated the influence of pelvic bone position and structure on acetabular spatial orientation. We describe this relation and its clinical implications. This retrospective study was based on computed tomography scanning of three-dimensional models of 31 consecutive male pelvises (62 acetabulums). All measurements were based on CT spatial reconstruction with the use of highly specialized software (Rhinoceros). Relations between acetabular orientation (inclination, tilt, anteversion angles) and pelvic structure were evaluated. The following parameters were evaluated to assess the pelvic structure: iliac opening angle, iliac tilt angle, interspinous distance (ISD), intertuberous distance (ITD), height of the pelvis (HP), and the ISD/ITD/HP ratio. The linear and nonlinear dependence of the acetabular angles and hemipelvic measurements were examined with Pearson's product - moment correlation and Spearman's rank correlation coefficient. Correlations different from 0 with p < 0.05 were considered statistically significant. Comparison of the axis position with pelvis structure with orientation in the horizontal plane revealed a significant positive correlation between the acetabular anteversion angle and the iliac opening angle (p = 0.041 and 0.008, respectively). In the frontal plane, there was a positive correlation between the acetabular inclination angle and the iliac tilt angle (p = 0.025 and 0.014, respectively) and the acetabular inclination angle and the ISD/ITD/HP ratio (both p = 0.048). There is a significant correlation of the hemipelvic structure and acetabular orientation under anatomic conditions, especially in the frontal and horizontal planes. In the anteroposterior view, the more tilted-down innominate bone causes a more caudally oriented acetabulum axis, whereas in the horizontal view this relation is reversed. This study may serve as a basis for the discussion on the role of the pelvis in common disorders of the hip.

Statistical thermodynamics of protein folding: Comparison of a mean-field theory with Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Hao, Ming-Hong; Scheraga, Harold A.

1995-01-01

A comparative study of protein folding with an analytical theory and computer simulations, respectively, is reported. The theory is based on an improved mean-field formalism which, in addition to the usual mean-field approximations, takes into account the distributions of energies in the subsets of conformational states. Sequence-specific properties of proteins are parametrized in the theory by two sets of variables, one for the energetics of mean-field interactions and one for the distribution of energies. Simulations are carried out on model polypeptides with different sequences, with different chain lengths, and with different interaction potentials, ranging from strong biases towards certain local chain states (bond angles and torsional angles) to complete absence of local conformational preferences. Theoretical analysis of the simulation results for the model polypeptides reveals three different types of behavior in the folding transition from the statistical coiled state to the compact globular state; these include a cooperative two-state transition, a continuous folding, and a glasslike transition. It is found that, with the fitted theoretical parameters which are specific for each polypeptide under a different potential, the mean-field theory can describe the thermodynamic properties and folding behavior of the different polypeptides accurately. By comparing the theoretical descriptions with simulation results, we verify the basic assumptions of the theory and, thereby, obtain new insights about the folding transitions of proteins. It is found that the cooperativity of the first-order folding transition of the model polypeptides is determined mainly by long-range interactions, in particular the dipolar orientation; the local interactions (e.g., bond-angle and torsion-angle potentials) have only marginal effect on the cooperative characteristic of the folding, but have a large impact on the difference in energy between the folded lowest-energy structure and the unfolded conformations of a protein.

The effect of gravity on liquid plug propagation in a two-dimensional channel

NASA Astrophysics Data System (ADS)

Suresh, V.; Grotberg, J. B.

2005-03-01

The effect of plug propagation speed and gravity on the quasisteady motion of a liquid plug in a two-dimensional liquid-lined channel oriented at an angle α with respect to gravity is studied. The problem is motivated by the transport of liquid plugs instilled into pulmonary airways in medical treatments such as surfactant replacement therapy, drug delivery, and liquid ventilation. The capillary number Ca is assumed to be small, while the Bond number Bo is arbitrary. Using matched asymptotic expansions and lubrication theory, expressions are obtained for the thickness of the trailing films left behind by the plug and the pressure drop across it as functions of Ca, Bo, α and the thickness of the precursor films. When the Bond number is small it is found that the trailing film thickness and the flow contribution to the pressure drop scale as Ca2/3 at leading order with coefficients that depend on Bo and α. The first correction to the film thickness is found to occur at O(Ca) compared to O(Ca4/3) in the Bo=0 case. Asymmetry in the liquid distribution is quantified by calculating the ratio of liquid volumes above and below the centerline of the channel, VR ˙. VR=1 at Bo=0, indicating a symmetric distribution, and decreases with Bo and Ca, but increases with the plug length Lp. The decrease of VR with Ca suggests that higher propagation speeds in small airways may result in less homogenous liquid distribution, which is in contrast to the expected effect in large airways. For given values of the other parameters, a maximum capillary number Cac is identified above which the plug will eventually rupture. When the Bond number becomes equal to an orientation-dependent critical value Boc, it is found that the scaling of the film thickness and pressure drop change to Ca1/2 and Ca1/6, respectively. It is shown that this scaling is valid for small increments of the Bond number over its critical value, Bo=Boc+BCa1/6, but for higher Bond numbers the asymptotic approach breaks down.

The Role of Grain Orientation and Grain Boundary Characteristics in the Mechanical Twinning Formation in a High Manganese Twinning-Induced Plasticity Steel

NASA Astrophysics Data System (ADS)

Shterner, Vadim; Timokhina, Ilana B.; Rollett, Anthony D.; Beladi, Hossein

2018-04-01

In the current study, the dependence of mechanical twinning on grain orientation and grain boundary characteristics was investigated using quasi in-situ tensile testing. The grains of three main orientations (i.e., <111>, <110>, and <100> parallel to the tensile axis (TA)) and certain characteristics of grain boundaries (i.e., the misorientation angle and the inclination angle between the grain boundary plane normal and the TA) were examined. Among the different orientations, <111> and <100> were the most and the least favored orientations for the formation of mechanical twins, respectively. The <110> orientation was intermediate for twinning. The annealing twin boundaries appeared to be the most favorable grain boundaries for the nucleation of mechanical twinning. No dependence was found for the inclination angle of annealing twin boundaries, but the orientation of grains on either side of the annealing twin boundary exhibited a pronounced effect on the propensity for mechanical twinning. Annealing twin boundaries adjacent to high Taylor factor grains exhibited a pronounced tendency for twinning regardless of their inclination angle. In general, grain orientation has a significant influence on twinning on a specific grain boundary.

Evidence from bond lengths and bond angles for enneacovalence of cobalt, rhodium, iridium, iron, ruthenium, and osmium in compounds with elements of medium electronegativity.

PubMed

Pauling, L

1984-03-01

Enneacovalence of neutral atoms can be achieved for Co, Rh, and Ir by promoting some electrons from the nd orbital to the (n + 1)s and (n + 1)p orbitals and for Fe, Ru, and Os by a similar promotion together with the addition of an electron, which may be provided by an electron pair from a singly bonded carbonyl group or other group. The bond lengths and bond angles are predicted by the theory of enneacovalence to be significantly different for the different transition metals. Recently reported experimental values are shown to be in good agreement with the predicted values, providing support for the theory of enneacovalence and the theory of hybrid sp(3)d(5) bond orbitals.

Crystal structure of 4-fluoro-N-[2-(4-fluoro­benzo­yl)hydra­zine-1-carbono­thio­yl]benzamide

PubMed Central

Firdausiah, Syadza; Salleh Huddin, Ameera Aqeela; Hasbullah, Siti Aishah; Yamin, Bohari M.; Yusoff, Siti Fairus M.

2014-01-01

In the title compound, C15H11F2N3O2S, the dihedral angle between the fluoro­benzene rings is 88.43 (10)° and that between the central semithiocarbazide grouping is 47.00 (11)°. The dihedral angle between the amide group and attached fluoro­benzene ring is 50.52 (11)°; the equivalent angle between the carbonyl­thio­amide group and its attached ring is 12.98 (10)°. The major twists in the mol­ecule occur about the C—N—N—C bonds [torsion angle = −138.7 (2)°] and the Car—Car—C—N (ar = aromatic) bonds [−132.0 (2)°]. An intra­molecular N—H⋯O hydrogen bond occurs, which generates an S(6) ring. In the crystal, the mol­ecules are linked by N—H⋯O and N—H⋯S hydrogen bonds, generating (001) sheets. Weak C—H⋯O and C—H⋯F inter­actions are also observed. PMID:25309250

A cascaded two-step Kalman filter for estimation of human body segment orientation using MEMS-IMU.

PubMed

Zihajehzadeh, S; Loh, D; Lee, M; Hoskinson, R; Park, E J

2014-01-01

Orientation of human body segments is an important quantity in many biomechanical analyses. To get robust and drift-free 3-D orientation, raw data from miniature body worn MEMS-based inertial measurement units (IMU) should be blended in a Kalman filter. Aiming at less computational cost, this work presents a novel cascaded two-step Kalman filter orientation estimation algorithm. Tilt angles are estimated in the first step of the proposed cascaded Kalman filter. The estimated tilt angles are passed to the second step of the filter for yaw angle calculation. The orientation results are benchmarked against the ones from a highly accurate tactical grade IMU. Experimental results reveal that the proposed algorithm provides robust orientation estimation in both kinematically and magnetically disturbed conditions.

AceDRG: a stereochemical description generator for ligands

PubMed Central

Emsley, Paul; Gražulis, Saulius; Merkys, Andrius; Vaitkus, Antanas

2017-01-01

The program AceDRG is designed for the derivation of stereochemical information about small molecules. It uses local chemical and topological environment-based atom typing to derive and organize bond lengths and angles from a small-molecule database: the Crystallography Open Database (COD). Information about the hybridization states of atoms, whether they belong to small rings (up to seven-membered rings), ring aromaticity and nearest-neighbour information is encoded in the atom types. All atoms from the COD have been classified according to the generated atom types. All bonds and angles have also been classified according to the atom types and, in a certain sense, bond types. Derived data are tabulated in a machine-readable form that is freely available from CCP4. AceDRG can also generate stereochemical information, provided that the basic bonding pattern of a ligand is known. The basic bonding pattern is perceived from one of the computational chemistry file formats, including SMILES, mmCIF, SDF MOL and SYBYL MOL2 files. Using the bonding chemistry, atom types, and bond and angle tables generated from the COD, AceDRG derives the ‘ideal’ bond lengths, angles, plane groups, aromatic rings and chirality information, and writes them to an mmCIF file that can be used by the refinement program REFMAC5 and the model-building program Coot. Other refinement and model-building programs such as PHENIX and BUSTER can also use these files. AceDRG also generates one or more coordinate sets corresponding to the most favourable conformation(s) of a given ligand. AceDRG employs RDKit for chemistry perception and for initial conformation generation, as well as for the interpretation of SMILES strings, SDF MOL and SYBYL MOL2 files. PMID:28177307

Toggling Bistable Atoms via Mechanical Switching of Bond Angle

NASA Astrophysics Data System (ADS)

Sweetman, Adam; Jarvis, Sam; Danza, Rosanna; Bamidele, Joseph; Gangopadhyay, Subhashis; Shaw, Gordon A.; Kantorovich, Lev; Moriarty, Philip

2011-04-01

We reversibly switch the state of a bistable atom by direct mechanical manipulation of bond angle using a dynamic force microscope. Individual buckled dimers at the Si(100) surface are flipped via the formation of a single covalent bond, actuating the smallest conceivable in-plane toggle switch (two atoms) via chemical force alone. The response of a given dimer to a flip event depends critically on both the local and nonlocal environment of the target atom—an important consideration for future atomic scale fabrication strategies.

Synthesis and Small-Angle X-Ray Scattering Investigations of Ureido-Pyrimidone Hydrogen Bonding Star and Linear Poly(ethylene-co-propylene)s

DTIC Science & Technology

2006-02-01

Synthesis and Small-Angle X-ray Scattering Investigations of Ureido- Pyrimidone Hydrogen Bonding Star and Linear Poly(ethylene-co-propylene)s...Scattering Investigations of Ureido- Pyrimidone Hydrogen Bonding Star and Linear Poly(ethylene-co-propylene)s Frederick L. Beyer Weapons and...control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS. 1. REPORT DATE (DD-MM-YYYY) February 2006 2 . REPORT TYPE Interim 3. DATES

Evidence of monotropic hexatic tilted smectic phase in the phase sequence of ferroelectric liquid crystal

NASA Astrophysics Data System (ADS)

Różycka, Anna; Deptuch, Aleksandra; Jaworska-Gołąb, Teresa; Węgłowska, Dorota; Marzec, Monika

2018-02-01

Physical properties of a new ferroelectric liquid crystal have been studied by complementary methods: differential scanning calorimetry, polarizing optical microscopy, dielectric and X-ray diffraction. It was found that next to enantiotropic ferroelectric smectic C* phase, the monotropic smectic phase appears at cooling. X-ray diffraction measurements allowed to identify this phase as hexatic tilted smectic. Temperature dependence of spontaneous polarization, tilt angle of molecules and switching time were found in both liquid crystalline phases at cooling. Based on the dielectric results, the dielectric processes were identified as Goldstone mode in the smectic C* phase, whereas as the bond-orientation-like phason and the bulk domain mode in the monotropic hexatic tilted smectic phase.

Refusing to Twist: Demonstration of a Line Hexatic Phase in DNA Liquid Crystals

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

Strey, H. H.; NICHD/LPSB, National Institutes of Health, Building 12A/2041, Bethesda, Maryland 20892-5626; Wang, J.

2000-04-03

We report conclusive high resolution small angle x-ray scattering evidence that long DNA fragments form an untwisted line hexatic phase between the cholesteric and the crystalline phases. The line hexatic phase is a liquid-crystalline phase with long-range hexagonal bond-orientational order, long-range nematic order, but liquidlike, i.e., short-range, positional order. So far, it has not been seen in any other three dimensional system. By line-shape analysis of x-ray scattering data we found that positional order decreases when the line hexatic phase is compressed. We suggest that such anomalous behavior is a result of the chiral nature of DNA molecules. (c) 2000more » The American Physical Society.« less

The role of interplanetary shock orientation on SC/SI rise time and geoeffectiveness

NASA Astrophysics Data System (ADS)

Selvakumaran, R.; Veenadhari, B.; Ebihara, Y.; Kumar, Sandeep; Prasad, D. S. V. V. D.

2017-03-01

Interplanetary (IP) shocks interact with the Earth's magnetosphere, resulting in compression of the magnetosphere which in turn increases the Earth's magnetic field termed as Sudden commencement/Sudden impulse (SC/SI). Apart from IP shock speed and solar wind dynamic pressure, IP shock orientation angle also plays a major role in deciding the SC rise time. In the present study, the IP shock orientation angle and SC/SI rise time for 179 IP shocks are estimated which occurred during solar cycle 23. More than 50% of the Shock orientations are in the range of 140°-160°. The SC/SI rise time decreases with the increase in the orientation angle and IP shock speed. In this work, the type of IP shocks i.e., Radio loud (RL) and Radio quiet (RQ) are examined in connection with SC/SI rise time. The RL associated IP shock speeds show a better correlation than RQ shocks with SC/SI rise time irrespective of the orientation angle. Magnetic Cloud (MC) associated shocks dominate in producing less rise time when compared to Ejecta (EJ) shocks. Magneto hydrodynamic (MHD) simulations are used for three different IP shock orientation categories to see the importance of orientation angle in determining the geoeffectiveness. Simulations results reveal that shocks hitting parallel to the magnetosphere are more geoeffective as compared to oblique shocks by means of change in magnetic field, pressure and Field Aligned Current (FAC).

Introducing Quantum Mechanics into General Chemistry

NASA Astrophysics Data System (ADS)

Popkowski, Iwona; Bascal, Hafed

2008-10-01

Periodicity has long been recognized as the tool that chemists can use to bring some order to investigating the chemistry of more than one hundred elements. Such studies provide useful tools for understanding a wide array of chemical principles. The advances in computational chemistry make it possible to study and teach such trends with hands on approach. In this study we utilize recently acquired software Spartan Pro to illustrate theoretical measurements of bond length, bond angle and dipole as compared to experimental data. We constructed a matrix of values obtained from the theoretical calculations and obtained trends in bond length, bond angle and dipoles for the several periodic groups.

A new potential for radiation studies of borosilicate glass

NASA Astrophysics Data System (ADS)

Alharbi, Amal F.; Jolley, Kenny; Smith, Roger; Archer, Andrew J.; Christie, Jamieson K.

2017-02-01

Borosilicate glass containing 70 mol% SiO2 and 30 mol% B2O3 is investigated theoretically using fixed charge potentials. An existing potential parameterisation for borosilicate glass is found to give good agreement for the bond angle and bond length distributions compared to experimental values but the optimal density is 30% higher than experiment. Therefore the potential parameters are refitted to give an optimal density of 2.1 g/cm3, in line with experiment. To determine the optimal density, a series of random initial structures are quenched at a rate of 5 × 1012 K/s using constant volume molecular dynamics. An average of 10 such quenches is carried out for each fixed volume. For each quenched structure, the bond angles, bond lengths, mechanical properties and melting points are determined. The new parameterisation is found to give the density, bond angles, bond lengths and Young's modulus comparable with experimental data, however, the melting points and Poisson's ratio are higher than the reported experimental values. The displacement energy thresholds are computed to be similar to those determined with the earlier parameterisation, which is lower than those for ionic crystalline materials.

Orientation hydrogen-bonding effect on vibronic spectra of isoquinoline in water solvent: Franck-Condon simulation and interpretation

NASA Astrophysics Data System (ADS)

Liu, Yu-Hui; Wang, Shi-Ming; Wang, Chen-Wen; Zhu, Chaoyuan; Han, Ke-Li; Lin, Sheng-Hsien

2016-10-01

The excited-state orientation hydrogen-bonding dynamics, and vibronic spectra of isoquinoline (IQ) and its cationic form IQc in water have been investigated at the time-dependent density functional theory quantum chemistry level plus Franck-Condon simulation and interpretation. The excited-state orientation hydrogen bond strengthening has been found in IQ:H2O complex due to the charge redistribution upon excitation; this is interpreted by simulated 1:1 mixed absorption spectra of free IQ and IQ:H2O complex having best agreement with experimental results. Conversely, the orientation hydrogen bond in IQc:H2O complex would be strongly weakening in the S1 state and this is interpreted by simulated absorption spectra of free IQc having best agreement with experimental results. By performing Franck-Condon simulation, it reveals that several important vibrational normal modes with frequencies about 1250 cm-1 involving the wagging motion of the hydrogen atoms are very sensitive to the formation of the orientation hydrogen bond for the IQ/IQc:H2O complex and this is confirmed by damped Franck-Condon simulation with free IQ/IQc in water. However, the emission spectra of the IQ and IQc in water have been found differently. Upon the excitation, the simulated fluorescence of IQ in water is dominated by the IQ:H2O complex; thus hydrogen bond between IQ and H2O is much easier to form in the S1 state. While the weakened hydrogen bond in IQc:H2O complex is probably cleaved upon the laser pulse because the simulated emission spectrum of the free IQc is in better agreement with the experimental results.

Development of non-bonded interaction parameters between graphene and water using particle swarm optimization.

PubMed

Bejagam, Karteek K; Singh, Samrendra; Deshmukh, Sanket A

2018-05-05

New Lennard-Jones parameters have been developed to describe the interactions between atomistic model of graphene, represented by REBO potential, and five commonly used all-atom water models, namely SPC, SPC/E, SPC/Fw, SPC/Fd, and TIP3P/Fs by employing particle swarm optimization (PSO) method. These new parameters were optimized to reproduce the macroscopic contact angle of water on a graphene sheet. The calculated line tension was in the order of 10 -11 J/m for the droplets of all water models. Our molecular dynamics simulations indicate the preferential orientation of water molecules near graphene-water interface with one OH bond pointing toward the graphene surface. Detailed analysis of simulation trajectories reveals the presence of water molecules with ≤∼1, ∼2, and ∼4 hydrogen bonds at the surface of air-water interface, graphene-water interface, and bulk region of the water droplet, respectively. Presence of water molecules with ≤∼1 and ∼2 hydrogen bonds suggest the existence of water clusters of different sizes at these interfaces. The trends observed in the libration, bending, and stretching bands of the vibrational spectra are closely associated with these structural features of water. The inhomogeneity in hydrogen bond network of water at the air-water and graphene-water interface is manifested by broadening of the peaks in the libration band for water present at these interfaces. The stretching band for the molecules in water droplet shows a blue shift as compared to the pure bulk water, which conjecture the presence of weaker hydrogen bond network in a droplet. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Amber Plug-In for Protein Shop

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

Oliva, Ricardo

2004-05-10

The Amber Plug-in for ProteinShop has two main components: an AmberEngine library to compute the protein energy models, and a module to solve the energy minimization problem using an optimization algorithm in the OPTI-+ library. Together, these components allow the visualization of the protein folding process in ProteinShop. AmberEngine is a object-oriented library to compute molecular energies based on the Amber model. The main class is called ProteinEnergy. Its main interface methods are (1) "init" to initialize internal variables needed to compute the energy. (2) "eval" to evaluate the total energy given a vector of coordinates. Additional methods allow themore » user to evaluate the individual components of the energy model (bond, angle, dihedral, non-bonded-1-4, and non-bonded energies) and to obtain the energy of each individual atom. The Amber Engine library source code includes examples and test routines that illustrate the use of the library in stand alone programs. The energy minimization module uses the AmberEngine library and the nonlinear optimization library OPT++. OPT++ is open source software available under the GNU Lesser General Public License. The minimization module currently makes use of the LBFGS optimization algorithm in OPT++ to perform the energy minimization. Future releases may give the user a choice of other algorithms available in OPT++.« less

Bond angles in transition-metal tricarbonyl compounds: A test of the theory of hybrid bond orbitals*

PubMed Central

Pauling, Linus

1978-01-01

The theory of hybrid bond orbitals is used to calculate equations giving the value of the bond angle OC—M—CO in relation to the bond number of the metal—carbonyl bond for tricarbonyl groups in which the transition-metal atom is enneacovalent or octacovalent and the group has approximate trigonal symmetry. For cobalt and iron and their congeners the average experimental values lie within about 1° of the theoretical values for enneacovalence, which are 101.9° for Co(CO)3 and 94.5° for Fe(CO)3. This agreement provides strong support for the theory. For Mn(CO)3 and Cr(CO)3 the experimental values indicate the average covalence to be about 8.4 and 7.7, respectively, in agreement with considerations based on the electroneutrality principle. PMID:16592477

Evidence from bond lengths and bond angles for enneacovalence of cobalt, rhodium, iridium, iron, ruthenium, and osmium in compounds with elements of medium electronegativity

PubMed Central

Pauling, Linus

1984-01-01

Enneacovalence of neutral atoms can be achieved for Co, Rh, and Ir by promoting some electrons from the nd orbital to the (n + 1)s and (n + 1)p orbitals and for Fe, Ru, and Os by a similar promotion together with the addition of an electron, which may be provided by an electron pair from a singly bonded carbonyl group or other group. The bond lengths and bond angles are predicted by the theory of enneacovalence to be significantly different for the different transition metals. Recently reported experimental values are shown to be in good agreement with the predicted values, providing support for the theory of enneacovalence and the theory of hybrid sp3d5 bond orbitals. PMID:16593439

Urban-area extraction from polarimetric SAR image using combination of target decomposition and orientation angle

NASA Astrophysics Data System (ADS)

Zou, Bin; Lu, Da; Wu, Zhilu; Qiao, Zhijun G.

2016-05-01

The results of model-based target decomposition are the main features used to discriminate urban and non-urban area in polarimetric synthetic aperture radar (PolSAR) application. Traditional urban-area extraction methods based on modelbased target decomposition usually misclassified ground-trunk structure as urban-area or misclassified rotated urbanarea as forest. This paper introduces another feature named orientation angle to improve urban-area extraction scheme for the accurate mapping in urban by PolSAR image. The proposed method takes randomness of orientation angle into account for restriction of urban area first and, subsequently, implements rotation angle to improve results that oriented urban areas are recognized as double-bounce objects from volume scattering. ESAR L-band PolSAR data of the Oberpfaffenhofen Test Site Area was used to validate the proposed algorithm.

Some general aspects of torsional sensitivity and the GG-effect

NASA Astrophysics Data System (ADS)

Yu, C.-H.; Schäfer, L.; Ramek, M.; Miller, D. M.; Teppen, B. J.

1999-08-01

The geometries of 28 compounds of type X-C1-C2-C3-Y, with X,Y=CH 3, F, Cl, OH, NH 2, COH, and COOH, were fully optimized by ab initio HF/4-21G calculations at 30° grid points in their respective φ(X-C1-C2-C3), ψ(C1-C2-C3-Y)-torsional spaces. The results make it possible to construct parameter surfaces and their gradients in φ, ψ-space. The magnitude of the gradient, |∇ P|=[( ∂P/ ∂φ) 2+( ∂P/ ∂ψ) 2] 1/2, of a structural parameter P (a bond length, bond angle, or non-bonded distance) in φ, ψ-torsional space is a measure of torsional sensitivity (TS); i.e. a measure of the extent to which bond lengths, bond angles, and non-bonded distances change at a point in φ, ψ-space with backbone torsional angles. It is found that TS is not constant throughout the conformational space of a molecule, but varies in a characteristic way. It seems that, regardless of the nature of X or Y, extended forms are typically in regions of low TS; puckered conformations, of high TS. Conformations with two sequential gauche torsional angles (GG sequences) are characterized by high TS of 1,5-non-bonded distances concomitant with relatively low TS of other internal coordinates. This property of GG sequences is the source of a stabilizing and cooperative energy increment that is not afforded by other torsional sequences, such as trans- trans or trans- gauche. A structural data base, consisting of thousands of HF/4-21G structures of X-C-C-Y and X-C-C-C-Y systems has been assembled and is available on a CD.

Thermal and Structural Analysis of a Hollow Core Space Shuttle Main Engine (SSME) Turbine Blade

NASA Technical Reports Server (NTRS)

Abdul-Aziz, Ali; Kalluri, Sreeramesh; McGaw, Michael A.

1995-01-01

The influence of primary and secondary orientations on the elastic response of a hollow core, (001)-oriented nickel base single-crystal superalloy turbine blade, was investigated under combined thermal and mechanical conditions. Finite element techniques is employed through MARC finite element code to conduct the analyses on a hollow core SSME turbine blade made out of PWA 1480 single crystal material. Primary orientation of the single crystal superalloy was varied in increments of 2 deg, from 0 to 10 deg, from the (001) direction. Two secondary orientations (0 and 45 deg) were considered with respect to the global coordinate system, as the primary orientation angle was varied. The stresses developed within the single crystal blade were determined for different orientations of the blade. The influence of angular offsets such as the single crystal's primary and secondary orientations and the loading conditions on the elastic stress response of the PWA 1480 hollow blade are summarized. The influence of he primary orientation angle, when constrained between the bounds considered, was not found to be as significant as the influence of the secondary orientation angle.

The influence of primary and secondary orientations on the elastic response of a nickel-base single-crystal superalloy

NASA Technical Reports Server (NTRS)

Abdul-Aziz, Ali; Kalluri, Sreeramesh; Mcgaw, Michael A.

1993-01-01

The influence of primary orientation on the elastic response of a (001)-oriented nickel-base single-crystal superalloy, PWA 1480, was investigated under mechanical, thermal, and combined thermal and mechanical loading conditions using finite element techniques. Elastic stress analyses were performed using the MARC finite element code on a square plate of PWA 1480 material. Primary orientation of the single crystal superalloy was varied in increments of 2 deg, from 0 to 10 deg, from the (001) direction. Two secondary orientations (0 and 45 deg) were considered, with respect to the global coordinate system, as the primary orientation angle was varied. The stresses developed within the single crystal plate were determined for each loading condition. In this paper, the influence of the angular offset between the primary crystal orientation and the loading direction on the elastic stress response of the PWA 1480 plate is presented for different loading conditions. The influence of primary orientation angle, when constrained between the bounds considered, was not found to be as significant as the influence of the secondary orientation angle, which is not typically controlled.

Structure, bonding nature, and binding energy of alkanethiolate on As-rich GaAs (001) surface: a density functional theory study.

PubMed

Voznyy, Oleksandr; Dubowski, Jan J

2006-11-30

Chemisorption of alkanethiols on As-rich GaAs (001) surface under a low coverage condition was studied using first principles density functional calculations in a periodic supercell approach. The thiolate adsorption site, tilt angle and its direction are dictated by the high directionality of As dangling bond and sulfur 3p orbital participating in bonding and steric repulsion of the first three CH2 units from the surface. Small charge transfer between thiolate and surface, strong dependence of total energy on tilt angle, and a relatively short length of 2.28 A of the S-As bond indicate the highly covalent nature of the bonding. Calculated binding energy of 2.1 eV is consistent with the available experimental data.

Modeling of layered anisotropic composite material based on effective medium theory

NASA Astrophysics Data System (ADS)

Bao, Yang; Song, Jiming

2018-04-01

In this paper, we present an efficient method to simulate multilayered anisotropic composite material with effective medium theory. Effective permittivity, permeability and orientation angle for a layered anisotropic composite medium are extracted with this equivalent model. We also derive analytical expressions for effective parameters and orientation angle with low frequency (LF) limit, which will be shown in detail. Numerical results are shown in comparing extracted effective parameters and orientation angle with analytical results from low frequency limit. Good agreements are achieved to demonstrate the accuracy of our efficient model.

Reduction of Line Edge Roughness of Polystyrene-block-Poly(methyl methacrylate) Copolymer Nanopatterns By Introducing Hydrogen Bonding at the Junction Point of Two Block Chains.

PubMed

Lee, Kyu Seong; Lee, Jaeyong; Kwak, Jongheon; Moon, Hong Chul; Kim, Jin Kon

2017-09-20

To apply well-defined block copolymer nanopatterns to next-generation lithography or high-density storage devices, small line edge roughness (LER) of nanopatterns should be realized. Although polystyrene-block-poly(methyl methacrylate) copolymer (PS-b-PMMA) has been widely used to fabricate nanopatterns because of easy perpendicular orientation of the block copolymer nanodomains and effective removal of PMMA block by dry etching, the fabricated nanopatterns show poorer line edge roughness (LER) due to relatively small Flory-Huggins interaction parameter (χ) between PS and PMMA chains. Here, we synthesized PS-b-PMMA with urea (U) and N-(4-aminomethyl-benzyl)-4-hydroxymethyl-benzamide (BA) moieties at junction of PS and PMMA chains (PS-U-BA-PMMA) to improve the LER. The U-BA moieties serves as favorable interaction (hydrogen bonding) sites. The LER of PS line patterns obtained from PS-U-BA-PMMA was reduced ∼25% compared with that obtained from neat PS-b-PMMA without BA and U moieties. This is attributed to narrower interfacial width induced by hydrogen bonding between two blocks, which is confirmed by small-angle X-ray scattering. This result implies that the introduction of hydrogen bonding into block copolymer interfaces offers an opportunity to fabricate well-defined nanopatterns with improved LER by block copolymer self-assembly, which could be a promising alternative to next-generation extreme ultraviolet lithography.

Laser Surface Preparation and Bonding of Aerospace Structural Composites

NASA Technical Reports Server (NTRS)

Belcher, Marcus A.; Wohl, Christopher J.; Connell, John W.

2009-01-01

A Nd:YAG laser was used to etch patterns conducive to adhesive bonding onto CFRP surfaces. These were compared to typical pre-bonding surface treatments including grit blasting, manual abrasion, and peel ply. Laser treated composites were then subjected to optical microscopy, contact angle measurements, and post-bonding mechanical testing.

Mapping local orientation of aligned fibrous scatterers for cancerous tissues using backscattering Mueller matrix imaging

NASA Astrophysics Data System (ADS)

He, Honghui; Sun, Minghao; Zeng, Nan; Du, E.; Liu, Shaoxiong; Guo, Yihong; Wu, Jian; He, Yonghong; Ma, Hui

2014-10-01

Polarization measurements are sensitive to the microstructure of tissues and can be used to detect pathological changes. Many tissues contain anisotropic fibrous structures. We obtain the local orientation of aligned fibrous scatterers using different groups of the backscattering Mueller matrix elements. Experiments on concentrically well-aligned silk fibers and unstained human papillary thyroid carcinoma tissues show that the m22, m33, m23, and m32 elements have better contrast but higher degeneracy for the extraction of orientation angles. The m12 and m13 elements show lower contrast, but allow us to determine the orientation angle for the fibrous scatterers along all directions. Moreover, Monte Carlo simulations based on the sphere-cylinder scattering model indicate that the oblique incidence of the illumination beam introduces some errors in the orientation angles obtained by both methods. Mapping the local orientation of anisotropic tissues may not only provide information on pathological changes, but can also give new leads to reduce the orientation dependence of polarization measurements.

Measurement of local structural configurations associated with reversible photostructural changes in arsenic trisulfide films

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

Yang, C.Y.; Paesler, M.A.; Sayers, D.E.

1987-12-15

Extended x-ray-absorption fine-structure measurements have been made on three reversible and reproducible cycles of thermally annealed and light-soaked amorphous As/sub 2/S/sub 3/ films. Associated with the light-soaked material are (1) a very small increase in the population of wrong bonds in the first shell, (2) an enlarged As: S: As bond angle with an expansion of As: As distance in the second shell, (3) a larger spread in the distribution of As: S: As bond angles, and (4) an absence of any change in the third As: S shell. From these data, we present the first quantitative correlation between observedmore » local atomic structural changes and measured macroscopic properties that are associated with photodarkening. Our data demonstrate that the photoinduced structural changes mainly involve bonding alterations at S atoms as well as a change in the dihedral angle relationship between adjacent AsS/sub 3/ pyramids joined at S atoms.« less

Crystal structure of cis-tetra-aqua-dichlorido-cobalt(II) sulfolane disolvate.

PubMed

Boudraa, Mhamed; Bouacida, Sofiane; Bouchareb, Hasna; Merazig, Hocine; Chtoun, El Hossain

2015-02-01

In the title compound, [CoCl2(H2O)4]·2C4H8SO2, the Co(II) cation is located on the twofold rotation axis and is coordinated by four water mol-ecules and two adjacent chloride ligands in a slightly distorted octa-hedral coordination environment. The cisoid angles are in the range 83.27 (5)-99.66 (2)°. The three transoid angles deviate significantly from the ideal linear angle. The crystal packing can be described as a linear arrangement of complex units along c formed by bifurcated O-H⋯Cl hydrogen bonds between two water mol-ecules from one complex unit towards one chloride ligand of the neighbouring complex. Two solvent mol-ecules per complex are attached to this infinite chain via O-H⋯O hydrogen bonds in which water mol-ecules act as the hydrogen-bond donor and sulfolane O atoms as the hydrogen-bond acceptor sites.

Spectroscopic and theoretical investigations of alkali metal linoleates and oleinates

NASA Astrophysics Data System (ADS)

Świsłocka, Renata; Regulska, Ewa; Jarońko, Paweł; Lewandowski, Włodzimierz

2017-11-01

The influence of lithium, sodium, potassium, rubidium and cesium on the electronic system of the linoleic (cis-9,cis-12-octadecadienoic) and oleic (cis-9-octadecenoic) acids was investigated. The complementary analytical methods: vibrational (IR, Raman) and electronic (UV) molecular absorption spectroscopy as well as DFT quantum mechanical calculations (charge distribution, angles between bonds, bond lengths, theoretical IR and NMR spectra) were carried out. The regular shifts of bands connected with carboxylate anion in the spectra of studied salts were observed. Some bonds and angles reduced or elongated in the series: acid→Li→Na→K linoleates/oleinates. The highest changes were noted for bond lengths and angles concerning COO- ion. The electronic charge distribution in studied molecules was also discussed. Total atomic charges of carboxylate anion decrease as a result of the replacement of hydrogen atom with alkali metal cation. The increasing values of dipole moment and decreasing values of total energy in the order: linoleic/oleic acid→lithium→sodium→potassium linoleates/oleinates indicate an increase in stability of the compounds.

Structure and dynamics of water in nonionic reverse micelles: a combined time-resolved infrared and small angle x-ray scattering study.

PubMed

van der Loop, Tibert H; Panman, Matthijs R; Lotze, Stephan; Zhang, Jing; Vad, Thomas; Bakker, Huib J; Sager, Wiebke F C; Woutersen, Sander

2012-07-28

We study the structure and reorientation dynamics of nanometer-sized water droplets inside nonionic reverse micelles (water/Igepal-CO-520/cyclohexane) with time-resolved mid-infrared pump-probe spectroscopy and small angle x-ray scattering. In the time-resolved experiments, we probe the vibrational and orientational dynamics of the O-D bonds of dilute HDO:H(2)O mixtures in Igepal reverse micelles as a function of temperature and micelle size. We find that even small micelles contain a large fraction of water that reorients at the same rate as water in the bulk, which indicates that the polyethylene oxide chains of the surfactant do not penetrate into the water volume. We also observe that the confinement affects the reorientation dynamics of only the first hydration layer. From the temperature dependent surface-water dynamics, we estimate an activation enthalpy for reorientation of 45 ± 9 kJ mol(-1) (11 ± 2 kcal mol(-1)), which is close to the activation energy of the reorientation of water molecules in ice.

Origin of anisotropic negative Poisson's ratio in graphene.

PubMed

Qin, Zhenzhen; Qin, Guangzhao; Hu, Ming

2018-06-07

Negative Poisson's ratio (NPR) in auxetic materials is of great interest due to the typically enhanced toughness, shear resistance, and sound and vibration absorption, which enables plenty of novel applications such as aerospace and defense. Insight into the mechanism underlying NPR is significant to the design of auxetic nanomaterials and nanostructures. However, the analysis of NPR in previous studies mainly remains on the level of the evolution of geometry parameters, such as bond length and bond angle, while a thorough and fundamental understanding is lacking. In this paper, we report anisotropic differential NPR in graphene for uniaxial strains applied along both zigzag and armchair directions based on first-principles calculations. The mechanism underlying the emergence of NPR in graphene (evolution of bond length and bond angle) is found to be different from the conclusions from previous classical molecular dynamics simulations with empirical potential. We propose that the decentralized electron localization function (ELF) driven by strain leads to ELF coupling between different types of bonds, which results in the counter-intuitive anomalous increase of the bond angle and thus the emergence of NPR in graphene. Moreover, the NPR phenomenon can be anticipated to emerge in other nanomaterials or nanostructures with a similar honeycomb structure as that of graphene, where the ELF coupling would also be possible.

Gauche effect in 1,2-difluoroethane. Hyperconjugation, bent bonds, steric repulsion.

PubMed

Goodman, Lionel; Gu, Hongbing; Pophristic, Vojislava

2005-02-17

Natural bond orbital deletion calculations show that whereas the gauche preference arises from vicinal hyperconjugative interaction between anti C-H bonds and C-F* antibonds, the cis C-H/C-F* interactions are substantial (approximately 25% of the anti interaction). The established significantly >60 degrees FCCF dihedral angle for the equilibrium conformer can then be rationalized in terms of the hyperconjugation model alone by taking into account both anti interactions that maximize near 60 degrees and the smaller cis interactions that maximize at a much larger dihedral angle. This explanation does not invoke repulsive forces to rationalize the 72 degrees equilibrium conformer angle. The relative minimum energy for the trans conformer is the consequence of a balance between decreasing hyperconjugative stabilization and decreasing steric destabilization as the FCCF torsional angle approaches 180 degrees . The torsional coordinate is predicted to be strongly contaminated by CCF bending, with the result that approximately half of the trans --> gauche stabilization energy stems from mode coupling.

Using Excel To Study The Relation Between Protein Dihedral Angle Omega And Backbone Length

NASA Astrophysics Data System (ADS)

Shew, Christopher; Evans, Samari; Tao, Xiuping

How to involve the uninitiated undergraduate students in computational biophysics research? We made use of Microsoft Excel to carry out calculations of bond lengths, bond angles and dihedral angles of proteins. Specifically, we studied protein backbone dihedral angle omega by examining how its distribution varies with the length of the backbone length. It turns out Excel is a respectable tool for this task. An ordinary current-day desktop or laptop can handle the calculations for midsized proteins in just seconds. Care has to be taken to enter the formulas for the spreadsheet column after column to minimize the computing load. Supported in part by NSF Grant #1238795.

Combined Use of Residual Dipolar Couplings and Solution X-ray Scattering To Rapidly Probe Rigid-Body Conformational Transitions in a Non-phosphorylatable Active-Site Mutant of the 128 kDa Enzyme I Dimer

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

Takayama, Yuki; Schwieters, Charles D.; Grishaev, Alexander

2012-10-23

The first component of the bacterial phosphotransferase system, enzyme I (EI), is a multidomain 128 kDa dimer that undergoes large rigid-body conformational transitions during the course of its catalytic cycle. Here we investigate the solution structure of a non-phosphorylatable active-site mutant in which the active-site histidine is substituted by glutamine. We show that perturbations in the relative orientations and positions of the domains and subdomains can be rapidly and reliably determined by conjoined rigid-body/torsion angle/Cartesian simulated annealing calculations driven by orientational restraints from residual dipolar couplings and shape and translation information afforded by small- and wide-angle X-ray scattering. Although histidinemore » and glutamine are isosteric, the conformational space available to a Gln side chain is larger than that for the imidazole ring of His. An additional hydrogen bond between the side chain of Gln189 located on the EIN{sup {alpha}/{beta}} subdomain and an aspartate (Asp129) on the EIN{sup {alpha}} subdomain results in a small ({approx}9{sup o}) reorientation of the EIN{sup {alpha}} and EIN{sup {alpha}/{beta}} subdomains that is in turn propagated to a larger reorientation ({approx}26{sup o}) of the EIN domain relative to the EIC dimerization domain, illustrating the positional sensitivity of the EIN domain and its constituent subdomains to small structural perturbations.« less

TANGLE: Two-Level Support Vector Regression Approach for Protein Backbone Torsion Angle Prediction from Primary Sequences

PubMed Central

Song, Jiangning; Tan, Hao; Wang, Mingjun; Webb, Geoffrey I.; Akutsu, Tatsuya

2012-01-01

Protein backbone torsion angles (Phi) and (Psi) involve two rotation angles rotating around the Cα-N bond (Phi) and the Cα-C bond (Psi). Due to the planarity of the linked rigid peptide bonds, these two angles can essentially determine the backbone geometry of proteins. Accordingly, the accurate prediction of protein backbone torsion angle from sequence information can assist the prediction of protein structures. In this study, we develop a new approach called TANGLE (Torsion ANGLE predictor) to predict the protein backbone torsion angles from amino acid sequences. TANGLE uses a two-level support vector regression approach to perform real-value torsion angle prediction using a variety of features derived from amino acid sequences, including the evolutionary profiles in the form of position-specific scoring matrices, predicted secondary structure, solvent accessibility and natively disordered region as well as other global sequence features. When evaluated based on a large benchmark dataset of 1,526 non-homologous proteins, the mean absolute errors (MAEs) of the Phi and Psi angle prediction are 27.8° and 44.6°, respectively, which are 1% and 3% respectively lower than that using one of the state-of-the-art prediction tools ANGLOR. Moreover, the prediction of TANGLE is significantly better than a random predictor that was built on the amino acid-specific basis, with the p-value<1.46e-147 and 7.97e-150, respectively by the Wilcoxon signed rank test. As a complementary approach to the current torsion angle prediction algorithms, TANGLE should prove useful in predicting protein structural properties and assisting protein fold recognition by applying the predicted torsion angles as useful restraints. TANGLE is freely accessible at http://sunflower.kuicr.kyoto-u.ac.jp/~sjn/TANGLE/. PMID:22319565

Truncated Long-Range Percolation on Oriented Graphs

NASA Astrophysics Data System (ADS)

van Enter, A. C. D.; de Lima, B. N. B.; Valesin, D.

2016-07-01

We consider different problems within the general theme of long-range percolation on oriented graphs. Our aim is to settle the so-called truncation question, described as follows. We are given probabilities that certain long-range oriented bonds are open; assuming that the sum of these probabilities is infinite, we ask if the probability of percolation is positive when we truncate the graph, disallowing bonds of range above a possibly large but finite threshold. We give some conditions in which the answer is affirmative. We also translate some of our results on oriented percolation to the context of a long-range contact process.

Visual orientation performances of desert ants (Cataglyphis bicolor) toward astromenotactic directions and horizon landmarks

NASA Technical Reports Server (NTRS)

Wehner, R.

1972-01-01

Experimental data, on the visual orientation of desert ants toward astromenotactic courses and horizon landmarks involving the cooperation of different direction finding systems, are given. Attempts were made to: (1) determine if the ants choose a compromise direction between astromenotactic angles and the direction toward horizon landmarks when both angles compete with each other or whether they decide alternatively; (2) analyze adaptations of the visual system to the special demands of direction finding by astromenotactic orientation or pattern recognition; and (3) determine parameters of visual learning behavior. Results show separate orientation mechanisms are responsible for the orientation of the ant toward astromenotactic angles and horizon landmarks. If both systems compete with each other, the ants switch over from one system to the other and do not perform a compromise direction.

Exploration of dielectric relaxations of a room temperature anti-ferroelectric liquid crystal mixture

NASA Astrophysics Data System (ADS)

Dwivedi, Aanchal; Verma, Rohit; Dhar, R.; Dabrowski, R.

2018-05-01

Dielectric characterization of a technologically important room temperature anti-ferroelectric liquid crystal (AFLC) mixture has been carried out as a function of temperature and frequency. The mixture has a phase sequence of I-SmA*-SmC*-SmCA* -SmIA* -Cr. Electrical study for the planar anchoring of the molecules demonstrates seven relaxation mechanisms in various mesophases of the mixture. Dielectric spectrum of paraelectric SmA* phase exhibits a relaxation mechanism due to the tilt fluctuation of the molecules. In ferroelectric SmC* phase, Goldstone mode has been observed due to the fluctuation in azimuthal angle. In antiferroelectric SmCA*and hexatic SmIA* phases two relaxation mechanisms are observed due to bond orientation order & anti-phase fluctuation and rotation around the short axes respectively.

Bending wavefunctions for linear molecules

NASA Astrophysics Data System (ADS)

Hirano, Tsuneo; Nagashima, Umpei; Jensen, Per

2018-01-01

The bending motion of a linear triatomic molecule has two unique characteristics: the bending mode is doubly degenerate and only positive values of the bending angle, expressed by the bond angle supplement ρ bar , can be observed. The double degeneracy requires the wavefunction to be described as a two-dimensional oscillator. In the present work, we first review the conventional expressions based on two, symmetrically equivalent normal coordinates. Then we discuss an alternative expression for the bending wavefunction in terms of two geometrical coordinates, the bond angle supplement ρ bar (= π - τ ⩾ 0 , where τ is the bond angle) and the rotation angle χ (0 ⩽ χ < 2 π) describing rotation of the molecule around the molecular axis. In this formalism, defined for the (ρ bar , χ) polar-coordinate space with volume element ρ bar d ρ bar dχ , the one-dimensional wavefunction resulted through re-normalization for χ has zero amplitude at ρ bar = 0 , and the ro-vibrational average of the bending angle, i.e., the expectation value 〈 ρ bar 〉 , attains a non-zero, positive value for any ro-vibrational state including the vibrational ground state. This conclusion appears to cause some controversy since much conventional spectroscopic wisdom insists on 〈 ρ bar 〉 having the value zero.

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

Lawler, Keith V.; Childs, Bradley C.; Mast, Daniel S.

The molecular and electronic structures for the Group 7b heptoxides were investigated by computational methods as both isolated molecules and in the solid-state. The metal-oxygen-metal bending angle of the single molecule increased with increasing atomic number, with Re 2O 7 preferring a linear structure. Natural bond orbital and localized orbital bonding analyses indicate that there is a three-center covalent bond between the metal atoms and the bridging oxygen, and the increasing ionic character of the bonds favors larger bond angles. The calculations accurately reproduce the experimental crystal structures within a few percent. Analysis of the band structures and density ofmore » states shows similar bonding for all of the solid-state heptoxides, including the presence of the three-center covalent bond. DFT+U simulations show that PBE-D3 underpredicts the band gap by ~0.2 eV due to an under-correlation of the metal d conducting states. As a result, homologue and compression studies show that Re 2O 7 adopts a polymeric structure because the Re-oxide tetrahedra are easily distorted by packing stresses to form additional three-center covalent bonds.« less

Effect of contact angle on the orientation, stability, and assembly of dense floating cubes.

PubMed

Daniello, Robert; Khan, Kashan; Donnell, Michael; Rothstein, Jonathan P

2014-02-01

In this paper, the effect of contact angle, density, and size on the orientation, stability, and assembly of floating cubes was investigated. All the cubes tested were more dense than water. Floatation occurred as a result of capillary stresses induced by deformation of the air-water interface. The advancing contact angle of the bare acrylic cubes was measured to be 85°. The contact angle of the cubes was increased by painting the cubes with a commercially available superhydrophobic paint to reach an advancing contact angle of 150°. Depending on their size, density, and contact angle, the cubes were observed to float in one of three primary orientations: edge up, vertex up, and face up. An experimental apparatus was built such that the sum of the gravitational force, buoyancy force, and capillary forces could be measured using a force transducer as a function of cube position as it was lowered through the air-water interface. Measurements showed that the maximum capillary forces were always experienced for the face up orientation. However, when floatation was possible in the vertex up orientation, it was found to be the most stable cube orientation because it had the lowest center of gravity. A series of theoretical predictions were performed for the cubes floating in each of the three primary orientations to calculate the net force on the cube. The theoretical predictions were found to match the experimental measurements well. A cube stability diagram of cube orientation as a function of cube contact angle and size was prepared from the predictions of theory and found to match the experimental observations quite well. The assembly of cubes floating face up and vertex up were also studied for assemblies of two, three, and many cubes. Cubes floating face up were found to assemble face-to-face and form regular square lattice patterns with no free interface between cubes. Cubes floating vertex up were found to assemble in a variety of different arrangements including edge-to-edge, vertex-to-vertex, face-to-face, and vertex-to-face with the most probably assembly being edge-to-edge. Large numbers of vertex up cubes were found to pack with a distribution of orientations and alignments.

Printability Optimization For Fine Pitch Solder Bonding

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

Kwon, Sang-Hyun; Lee, Chang-Woo; Yoo, Sehoon

2011-01-17

Effect of metal mask and pad design on solder printability was evaluated by DOE in this study. The process parameters were stencil thickness, squeegee angle, squeegee speed, mask separating speed, and pad angle of PCB. The main process parameters for printability were stencil thickness and squeegee angle. The response surface showed that maximum printability of 1005 chip was achieved at the stencil thickness of 0.12 mm while the maximum printability of 0603 and 0402 chip was obtained at the stencil thickness of 0.05 mm. The bonding strength of the MLCC chips was also directly related with the printability.

Chemical Stress Cracking of Acrylic Fibers.

DTIC Science & Technology

1982-05-01

stress, high fiber permeability, moderate fibe orientation, and water- plasticization . The proposed mechanism for bond cleava e involves cyclization of...tensile stress, high fiber permeability, moderate fiber orientation, and water- plasticization . The proposed mechanism for bond cleavage involves...chemical composition, plasticization , and other factors. It will be shown that the etching behavior does not reflect underlying hetero- geneities in the

Relating Bond Angles of Dihalo- and Tetrahydro--Methanes, -Silanes, and -Germanes to Electronegativities

ERIC Educational Resources Information Center

Kirschenbaum, Louis J.; Ruekberg, Ben

2012-01-01

Our previous work correlated bond angles of group V and group VI hydrides (AH[subscript 3]E and AH[subscript 2]E[subscript 2], respectively, where E represents a lone electron pair) to the electronegativities of the atoms using the fraction of s character to relate the two. Here we have extended the correlation to the AH[subscript 2]X[subscript 2]…

Dependence of short and intermediate-range order on preparation in experimental and modeled pure a-Si

DOE PAGES

Holmstrom, Eero; Haberl, Bianca; Pakarinen, Olli H.; ...

2016-02-20

Variability in the short-to-intermediate range order of pure amorphous silicon prepared by different experimental and computational techniques is probed by measuring mass density, atomic coordination, bond-angle deviation, and dihedral angle deviation. It is found that there is significant variability in order parameters at these length scales in this archetypal covalently bonded, monoatomic system. This diversity strongly reflects preparation technique and thermal history in both experimental and simulated systems. Experiment and simulation do not fully quantitatively agree, partly due to differences in the way parameters are accessed. However, qualitative agreement in the trends is identified. Relaxed forms of amorphous silicon closelymore » resemble continuous random networks generated by a hybrid method of bond-switching Monte Carlo and molecular dynamics simulation. As-prepared ion implanted amorphous silicon can be adequately modeled using a structure generated from amorphization via ion bombardement using energetic recoils. Preparation methods which narrowly avoid crystallization such as experimental pressure-induced amorphization or simulated melt-quenching result in inhomogeneous structures that contain regions with significant variations in atomic ordering. Ad hoc simulated structures containing small (1 nm) diamond cubic crystal inclusions were found to possess relatively high bond-angle deviations and low dihedral angle deviations, a trend that could not be reconciled with any experimental material.« less

Bite angle effects of diphosphines in C-C and C-X bond forming cross coupling reactions.

PubMed

Birkholz, Mandy-Nicole; Freixa, Zoraida; van Leeuwen, Piet W N M

2009-04-01

Catalytic reactions of C-C and C-X bond formation are discussed in this critical review with particular emphasis on cross coupling reactions catalyzed by palladium and wide bite angle bidentate diphosphine ligands. Especially those studies have been collected that allow comparison of the ligand bite angles for the selected ligands: dppp, BINAP, dppf, DPEphos and Xantphos. Similarities with hydrocyanation and CO/ethene/MeOH reactions have been highlighted, while rhodium hydroformylation has been mentioned as a contrasting example, in which predictability is high and steric and electronic effects follow smooth trends. In palladium catalysis wide bite angles and bulkiness of the ligands facilitate generally the reductive elimination thus giving more efficient cross coupling catalysis (174 references).

Multi-objective Optimization of Solar Irradiance and Variance at Pertinent Inclination Angles

NASA Astrophysics Data System (ADS)

Jain, Dhanesh; Lalwani, Mahendra

2018-05-01

The performance of photovoltaic panel gets highly affected bychange in atmospheric conditions and angle of inclination. This article evaluates the optimum tilt angle and orientation angle (surface azimuth angle) for solar photovoltaic array in order to get maximum solar irradiance and to reduce variance of radiation at different sets or subsets of time periods. Non-linear regression and adaptive neural fuzzy interference system (ANFIS) methods are used for predicting the solar radiation. The results of ANFIS are more accurate in comparison to non-linear regression. These results are further used for evaluating the correlation and applied for estimating the optimum combination of tilt angle and orientation angle with the help of general algebraic modelling system and multi-objective genetic algorithm. The hourly average solar irradiation is calculated at different combinations of tilt angle and orientation angle with the help of horizontal surface radiation data of Jodhpur (Rajasthan, India). The hourly average solar irradiance is calculated for three cases: zero variance, with actual variance and with double variance at different time scenarios. It is concluded that monthly collected solar radiation produces better result as compared to bimonthly, seasonally, half-yearly and yearly collected solar radiation. The profit obtained for monthly varying angle has 4.6% more with zero variance and 3.8% more with actual variance, than the annually fixed angle.

Production of Chemical Structure Drawings Using an Interactive Graphics System.

DTIC Science & Technology

1981-02-01

E Structure display program flowcharts 32 Appendix F Execution exception conditions 39 Table I Order of search for a match between the bonds of a link...see Fig I). Shapes are connected together by a straight line known as a bond and one shape can have several bonds . Each shape definition contains...for each bond , the coordinates of the end of the bond nearest its parent shape together with the angle between the bond and the horizontal. Bonds are

3-[Bis(dimethyl­amino)­methyl­ene]-1,1-diphenyl­urea

PubMed Central

Tiritiris, Ioannis

2012-01-01

In the title compound, C18H22N4O, the C=N and C—N bond lengths in the CN3 unit are 1.3179 (11), 1.3551 (11) and 1.3737 (11) Å, indicating double- and single-bond character, respectively. The N—C—N angles are 115.91 (8), 118.20 (8) and 125.69 (8), showing a deviation of the CN3 plane from an ideal trigonal–planar geometry. The bonds between the N atoms and the terminal C-methyl groups all have values close to a typical single bond [1.4529 (12)–1.4624 (12) Å]. The dihedral angle between the phenyl rings is 79.63 (4)°. In the crystal, the mol­ecules are connected via weak C—H⋯O hydrogen bonds, generating chains along [100]. PMID:23284417

A method to determine the orientation of the upper arm about its longitudinal axis during dynamic motions.

PubMed

Gordon, Brian J; Dapena, Jesús

2013-01-04

Inaccuracy in determining the orientation of the upper arm about its longitudinal axis (twist orientation) has been a pervasive problem in sport biomechanics research. The purpose of this study was to develop a method to improve the calculation of the upper arm twist orientation in dynamic sports activities. The twist orientation of the upper arm is defined by the orientation of its mediolateral axis. The basis for the new method is that at any angle in the flexion/extension range of an individual's elbow, it is possible to define a true mediolateral axis and also a surrogate mediolateral axis perpendicular to the plane containing the shoulder, elbow and wrist joints. The difference between the twist orientations indicated by these two versions of the mediolateral axis will vary from one elbow angle to another, but if the elbow joint deforms equally in different activities, for any given subject the difference should be constant at any given value of the elbow angle. Application of the new method required individuals to execute sedate elbow extension trials prior to the dynamic trials. Three-dimensional motion analysis of the sedate extension trials allowed quantification of the difference between the true and surrogate mediolateral axes for all angles in the entire flexion/extension range of an individual's elbow. This made it possible to calculate in any dynamic trial the twist orientation defined by the true mediolateral axis from the twist orientation defined by the surrogate mediolateral axis. The method was tested on a wooden model of the arm. Copyright © 2012 Elsevier Ltd. All rights reserved.

HYDROGEN BONDING IN THE METHANOL DIMER

USDA-ARS?s Scientific Manuscript database

In this work, two methanol molecules are placed in different arrangements to study hydrogen bonding in carbohydrate materials such as cellulose. Energy was calculated as a function of both hydrogen bond length and angle over wide ranges, using quantum mechanics (QM). The QM wavefunctions are analyze...

A kryptoracemic salt: 2-{[2,8-bis-(tri-fluoro-meth-yl)quinolin-4-yl](hy-droxy)meth-yl}piperidin-1-ium (+)-3,3,3-tri-fluoro-2-meth-oxy-2-phenyl-propanoate.

PubMed

Wardell, James L; Wardell, Solange M S V; Tiekink, Edward R T

2016-06-01

The asymmetric unit of the title salt, C17H17F6N2O(+)·C10H8F3O3 (-), comprises two piperidin-1-ium cations and two carboxyl-ate anions. The cations, each having an l-shaped conformation owing to the near orthogonal relationship between the quinolinyl and piperidin-1-ium residues, are pseudo-enanti-omeric. The anions have the same absolute configuration but differ in the relative orientations of the carboxyl-ate, meth-oxy and benzene groups. Arguably, the most prominent difference between the anions occurs about the Cq-Om bond as seen in the Cc-Cq-Om-Cm torsion angles of -176.1 (3) and -67.1 (4)°, respectively (q = quaternary, m = meth-oxy and c = carboxyl-ate). The presence of Oh-H⋯Oc and Np-H⋯Oc hydrogen bonds leads to the formation of a supra-molecular chain along the a axis (h = hy-droxy and p = piperidin-1-ium); weak intra-molecular Np-H⋯Oh hydrogen bonds are also noted. Chains are connected into a three-dimensional architecture by C-H⋯F inter-actions. Based on a literature survey, related mol-ecules/cations adopt a uniform conformation in the solid state based on the letter L.

The determinants of bond angle variability in protein/peptide backbones: A comprehensive statistical/quantum mechanics analysis.

PubMed

Improta, Roberto; Vitagliano, Luigi; Esposito, Luciana

2015-11-01

The elucidation of the mutual influence between peptide bond geometry and local conformation has important implications for protein structure refinement, validation, and prediction. To gain insights into the structural determinants and the energetic contributions associated with protein/peptide backbone plasticity, we here report an extensive analysis of the variability of the peptide bond angles by combining statistical analyses of protein structures and quantum mechanics calculations on small model peptide systems. Our analyses demonstrate that all the backbone bond angles strongly depend on the peptide conformation and unveil the existence of regular trends as function of ψ and/or φ. The excellent agreement of the quantum mechanics calculations with the statistical surveys of protein structures validates the computational scheme here employed and demonstrates that the valence geometry of protein/peptide backbone is primarily dictated by local interactions. Notably, for the first time we show that the position of the H(α) hydrogen atom, which is an important parameter in NMR structural studies, is also dependent on the local conformation. Most of the trends observed may be satisfactorily explained by invoking steric repulsive interactions; in some specific cases the valence bond variability is also influenced by hydrogen-bond like interactions. Moreover, we can provide a reliable estimate of the energies involved in the interplay between geometry and conformations. © 2015 Wiley Periodicals, Inc.

Dislocations and charge density distributions of {gamma} phase in Ti47.5Al2.5V deformed at room temperature and 400 {degree}C

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

Zhu, J.; Gao, Y.; Miao, Y.

The observations on quantity and configuration of dislocations by TEM conventional diffraction contrast method as well as the determinations of the electron charge density distributions by the quantitative electron crystallography method in Ti47.5Al2.5V deformed at 400 C and room temperature (R.T.) have been carried out. The metallic bonding between Al-Al or Ti-Ti atom pair along {l_angle}110] and Ti-Ti along {l_angle}112] direction is strengthened; while the metallic bonding between Ti-Al atom pair both along {l_angle}101] and {l_angle}121] direction is weakened at 400 C. The quantities of a/2{l_angle}110], a/2{l_angle}112] and dissociated a{l_angle}101] (a[101]{yields}a/2[1{bar 1}0] + a/3[112] + SISF + a/6[112]) dislocations aremore » increased at 400 C, compared with that at R. T.. The a/2 {l_angle}121] super dislocations have not been seen both at 400 C and R.T.« less

Hydrogen bonded structure, polarity, molecular motion and frequency fluctuations at liquid-vapor interface of a water-methanol mixture: an ab initio molecular dynamics study.

PubMed

Choudhuri, Jyoti Roy; Chandra, Amalendu

2014-10-07

We have performed ab initio molecular dynamics simulations of a liquid-vapor interfacial system consisting of a mixture of water and methanol molecules. Detailed results are obtained for the structural and dynamical properties of the bulk and interfacial regions of the mixture. Among structural properties, we have looked at the inhomogeneous density profiles of water and methanol molecules, hydrogen bond distributions and also the orientational profiles of bulk and interfacial molecules. The methanol molecules are found to have a higher propensity to be at the interface than water molecules. It is found that the interfacial molecules show preference for specific orientations so as to form water-methanol hydrogen bonds at the interface with the hydrophobic methyl group pointing towards the vapor side. It is also found that for both types of molecules, the dipole moment decreases at the interface. It is also found that the local electric field of water influences the dipole moment of methanol molecules. Among the dynamical properties, we have calculated the diffusion, orientational relaxation, hydrogen bond dynamics, and vibrational frequency fluctuations in bulk and interfacial regions. It is found that the diffusion and orientation relaxation of the interfacial molecules are faster than those of the bulk. However, the hydrogen bond lifetimes are longer at the interface which can be correlated with the time scales found from the decay of frequency time correlations. The slower hydrogen bond dynamics for the interfacial molecules with respect to bulk can be attributed to diminished cooperative effects at the interface due to reduced density and number of hydrogen bonds.

A 2:1 co-crystal of p-nitro-benzoic acid and N,N'-bis-(pyridin-3-ylmeth-yl)ethanedi-amide: crystal structure and Hirshfeld surface analysis.

PubMed

Syed, Sabrina; Halim, Siti Nadiah Abdul; Jotani, Mukesh M; Tiekink, Edward R T

2016-01-01

The title 2:1 co-crystal, 2C7H5NO4·C14H14N4O2, in which the complete di-amide mol-ecule is generated by crystallographic inversion symmetry, features a three-mol-ecule aggregate sustained by hydroxyl-O-H⋯N(pyrid-yl) hydrogen bonds. The p-nitro-benzoic acid mol-ecule is non-planar, exhibiting twists of both the carb-oxy-lic acid and nitro groups, which form dihedral angles of 10.16 (9) and 4.24 (4)°, respectively, with the benzene ring. The di-amide mol-ecule has a conformation approximating to a Z shape, with the pyridyl rings lying to either side of the central, almost planar di-amide residue (r.m.s. deviation of the eight atoms being 0.025 Å), and forming dihedral angles of 77.22 (6)° with it. In the crystal, three-mol-ecule aggregates are linked into a linear supra-molecular ladder sustained by amide-N-H⋯O(nitro) hydrogen bonds and orientated along [10-4]. The ladders are connected into a double layer via pyridyl- and benzene-C-H⋯O(amide) inter-actions, which, in turn, are connected into a three-dimensional architecture via π-π stacking inter-actions between pyridyl and benzene rings [inter-centroid distance = 3.6947 (8) Å]. An evaluation of the Hirshfeld surfaces confirm the importance of inter-molecular inter-actions involving oxygen atoms as well as the π-π inter-actions.

4-Mercaptophenylboronic acid SAMs on gold: comparison with SAMs derived from thiophenol, 4-mercaptophenol, and 4-mercaptobenzoic acid.

PubMed

Barriet, David; Yam, Chi Ming; Shmakova, Olga E; Jamison, Andrew C; Lee, T Randall

2007-08-14

We report the formation and characterization of self-assembled monolayers (SAMs) derived from the adsorption of 4-mercaptophenylboronic acid (MPBA) on gold. For comparison, SAMs derived from the adsorption of thiophenol (TP), 4-mercaptophenol (MP), and 4-mercaptobenzoic acid (MBA) were also examined. The structure and properties of the SAMs were evaluated by ellipsometry, contact-angle goniometry, polarization-modulation infrared reflection-absorption spectroscopy (PM-IRRAS), and X-ray photoelectron spectroscopy (XPS). Specifically, ellipsometry was used to assess the formation of monolayer films, and contact angle measurements were used to determine the surface hydrophilicity and homogeneity. Separately, PM-IRRAS was used to evaluate the molecular composition and orientation as well as the intermolecular hydrogen bonding within the SAMs. Finally, XPS was used to evaluate the film composition and surface coverage (i.e., packing density), which was observed to increase in the following order: TP < MP < MPBA < MBA. A rationalization for the observed packing differences is presented. The XPS data indicate further that ultrahigh vacuum conditions induce the partial dehydration of MPBA SAMs with the concomitant formation of surface boronic anhydride species. Overall, the analytical data collectively show that the MPBA moieties in the SAMs exist in the acid form rather than the anhydride form under ambient laboratory conditions. Furthermore, stability studies find that MPBA SAMs are surprisingly labile in basic solution, where the terminal B-C bonds are cleaved by the attack of hydroxide ion and strongly basic amine nucleophiles. The unanticipated lability observed here should be considered by those wishing to use MPBA moieties in carbohydrate-sensing applications.

Substrate dependent structure of adsorbed aryl isocyanides studied by sum frequency generation (SFG) spectroscopy.

PubMed

Ito, Mikio; Noguchi, Hidenori; Ikeda, Katsuyoshi; Uosaki, Kohei

2010-04-07

Effects of metal substrate on the bonding nature of isocyanide group of two aryl isocyanides, 1,4-phenylene diisocyanide (PDI) and 4-methylphenyl isocyanide (MPI), and tilt angle of MPI were examined by measuring sum frequency generation (SFG) spectra of the self-assembled monolayers (SAMs) of these molecules on Au, Pt, Ag, and Pd surfaces. The SFG peaks due to "metal bonded" and "free"-NC groups were resolved by comparing the SFG spectra of PDI with IR spectra obtained by DFT calculations and previous results of vibrational spectroscopy. Based on the peak positions of the "metal bonded"-NC, it is clarified that while PDI and MPI were adsorbed at top sites on Au, Ag, and Pt surfaces, they adsorbed at bridge sites on the Pd surface. The tilt angles of MPI were determined from the intensity ratio between the SFG peaks of C-H symmetric and asymmetric stretching vibrational modes of the CH(3) group. The tilt angles of the MPI SAMs were in the order of Pt < Pd < Ag < Au, reflecting the bonding nature between the -NC group and the substrate atoms.

[How safe are orthoroentgenograms in determining the amount of correction for varus deformities?].

PubMed

Gürsu, Sarper; Yıldırım, Timur; Issın, Ahmet; Sofu, Hakan; Sahin, Vedat

2014-01-01

In this study, we evaluated the effects of the distance of the legs from the midline on alignment and angles of the lower extremities in orthoroentgenograms. Between March 2012 and April 2013, 95 limbs of 56 patients with varus deformity who underwent orthoroentgenogram to identify the amount of joint laxity in two positions were included in this study. The initial X-ray was performed with the feet in contact, while the other was performed as the legs were abducted to be in line with the shoulders. For each orthoroentgenogram, the mean mechanical axis angle, anatomical axis, and joint line orientation angles were measured retrospectively. These measurements were repeated for 43 limbs with varus deformity >10°. In the orthoroentgenograms with the feet in contact, the mean mechanical axis angle was 9.58°±5.7°, (0.20°; 26.0°), the mean anatomical axis angle 3.65°±6.14°, (-9.0°; 21.0°), and the mean joint line orientation angle -3.41°±2.52°, (-12.0°; 1.60°). In the orthoroentgenograms with the legs abducted, the mean mechanical axis angle was 7.73°±5.58°, (-3.0°; 23.0°), the mean anatomical axis angle 2.62°±5.87°, (-11.0°; 18.30°), and mean joint line orientation angle was -2.44°±2.41°, (-13.0°; 3.0°). The differences in the angles between the two positions were statistically significant (p<0.005). Our study results showed that the mean values of mechanical axis angle, anatomical axis and the joint line orientation angle were higher in orthoroentgenograms with the feet in contact than the orthoroentgenograms with the legs abducted in patients with varus gonarthrosis. We suggest that this may lead to mistakes in the preoperative planning. Ideal positions should be standardized to minimize possible problems.

3D printed, bio-inspired prototypes and analytical models for structured suture interfaces with geometrically-tuned deformation and failure behavior

NASA Astrophysics Data System (ADS)

Lin, Erica; Li, Yaning; Ortiz, Christine; Boyce, Mary C.

2014-12-01

Geometrically structured interfaces in nature possess enhanced, and often surprising, mechanical properties, and provide inspiration for materials design. This paper investigates the mechanics of deformation and failure mechanisms of suture interface designs through analytical models and experiments on 3D printed polymer physical prototypes. Suture waveforms with generalized trapezoidal geometries (trapezoidal, rectangular, anti-trapezoidal, and triangular) are studied and characterized by several important geometric parameters: the presence or absence of a bonded tip region, the tip angle, and the geometry. It is shown that a wide range (in some cases as great as an order of magnitude) in stiffness, strength, and toughness is achievable dependent on tip bonding, tip angle, and geometry. Suture interfaces with a bonded tip region exhibit a higher initial stiffness due to the greater load bearing by the skeletal teeth, a double peak in the stress-strain curve corresponding to the failure of the bonded tip and the failure of the slanted interface region or tooth, respectively, and an additional failure and toughening mechanism due to the failure of the bonded tip. Anti-trapezoidal geometries promote the greatest amplification of properties for suture interfaces with a bonded tip due the large tip interface area. The tip angle and geometry govern the stress distributions in the teeth and the ratio of normal to shear stresses in the interfacial layers, which together determine the failure mechanism of the interface and/or the teeth. Rectangular suture interfaces fail by simple shearing of the interfaces. Trapezoidal and triangular suture interfaces fail by a combination of shear and tensile normal stresses in the interface, leading to plastic deformation, cavitation events, and subsequent stretching of interface ligaments with mostly elastic deformation in the teeth. Anti-trapezoidal suture interfaces with small tip angles have high stress concentrations in the teeth and fail catastrophically by tooth failure, whereas larger tip angles exhibit a shear failure of the interfaces. Therefore, larger tip angles and trapezoidal or triangular geometries promote graceful failure, and smaller tip angles and anti-trapezoidal geometries promote more brittle-like failure. This dependence is reminiscent of biological systems, which exhibit a range of failure behaviors with limited materials and varied geometry. Triangular geometries uniquely exhibit uniform stress distributions in its teeth and promote the greatest amplification of mechanical properties. In both the bonded and unbonded cases, the predictions from the presented analytical models and experimental results on 3D printed prototypes show excellent agreement. This validates the analytical models and allows for the models to be used as a tool for the design of new materials and interfaces with tailored mechanical behavior.

Quantum chemical calculations of Cr2O3/SnO2 using density functional theory method

NASA Astrophysics Data System (ADS)

Jawaher, K. Rackesh; Indirajith, R.; Krishnan, S.; Robert, R.; Das, S. Jerome

2018-03-01

Quantum chemical calculations have been employed to study the molecular effects produced by Cr2O3/SnO2 optimised structure. The theoretical parameters of the transparent conducting metal oxides were calculated using DFT / B3LYP / LANL2DZ method. The optimised bond parameters such as bond lengths, bond angles and dihedral angles were calculated using the same theory. The non-linear optical property of the title compound was calculated using first-order hyperpolarisability calculation. The calculated HOMO-LUMO analysis explains the charge transfer interaction between the molecule. In addition, MEP and Mulliken atomic charges were also calculated and analysed.

Resting Orientations of Dinosaur Scapulae and Forelimbs: A Numerical Analysis, with Implications for Reconstructions and Museum Mounts.

PubMed

Senter, Phil; Robins, James H

2015-01-01

The inclination of the scapular blade and the resting pose of the forelimb in dinosaurs differ among reconstructions and among skeletal mounts. For most dinosaurian taxa, no attempt has previously been made to quantify the correct resting positions of these elements. Here, we used data from skeletons preserved in articulation to quantify the resting orientations of the scapula and forelimb in dinosaurs. Specimens were included in the study only if they were preserved lying on their sides; for each specimen the angle between forelimb bones at a given joint was included in the analysis only if the joint was preserved in articulation. Using correlation analyses of the angles between the long axis of the sacrum, the first dorsal centrum, and the scapular blade in theropods and Eoraptor, we found that vertebral hyperextension does not influence scapular orientation in saurischians. Among examined taxa, the long axis of the scapular blade was found to be most horizontal in bipedal saurischians, most vertical in basal ornithopods, and intermediate in hadrosauroids. We found that in bipedal dinosaurs other than theropods with semilunate carpals, the resting orientation of the elbow is close to a right angle and the resting orientation of the wrist is such that the hand exhibits only slight ulnar deviation from the antebrachium. In theropods with semilunate carpals the elbow and wrist are more flexed at rest, with the elbow at a strongly acute angle and with the wrist approximately at a right angle. The results of our study have important implications for correct orientations of bones in reconstructions and skeletal mounts. Here, we provide recommendations on bone orientations based on our results.

Modeling the intermolecular interactions: molecular structure of N-3-hydroxyphenyl-4-methoxybenzamide.

PubMed

Karabulut, Sedat; Namli, Hilmi; Kurtaran, Raif; Yildirim, Leyla Tatar; Leszczynski, Jerzy

2014-03-01

The title compound, N-3-hydroxyphenyl-4-methoxybenzamide (3) was prepared by the acylation reaction of 3-aminophenol (1) and 4-metoxybenzoylchloride (2) in THF and characterized by ¹H NMR, ¹³C NMR and elemental analysis. Molecular structure of the crystal was determined by single crystal X-ray diffraction and DFT calculations. 3 crystallizes in monoclinic P2₁/c space group. The influence of intermolecular interactions (dimerization and crystal packing) on molecular geometry has been evaluated by calculations performed for three different models; monomer (3), dimer (4) and dimer with added unit cell contacts (5). Molecular structure of 3, 4 and 5 was optimized by applying B3LYP method with 6-31G+(d,p) basis set in gas phase and compared with X-ray crystallographic data including bond lengths, bond angles and selected dihedral angles. It has been concluded that although the crystal packing and dimerization have a minor effect on bond lengths and angles, however, these interactions are important for the dihedral angles and the rotational conformation of aromatic rings. Copyright © 2013 Elsevier Inc. All rights reserved.

Characteristics of fractures in crystalline bedrock determined by surface and borehole geophysical surveys, eastern surplus superfund site, Meddybemps, Maine

USGS Publications Warehouse

Hansen, Bruce P.; Stone, Janet Radway; Lane, John W.

1999-01-01

Surface and borehole geophysical methods were used to determine fracture orientation in crystalline bedrock at the Eastern Surplus Superfund Site in Meddybemps, Maine. Fracture-orientation information is needed to address concerns about the fate of contaminants in ground water at the site. Azimuthal square-array resistivity surveys were conducted at 3 locations at the site, borehole-acoustic televiewer and borehole-video logs were collected in 10 wells, and single-hole directional radar surveys were conducted in 9 wells. Borehole-video logs were used to supplement the results of other geophysical techniques and are not described in this report. Analysis of azimuthal square-array resistivity data indicated that high-angle fracturing generally strikes northeast-southwest at the three locations. Borehole-acoustic televiewer logs detected one prominent low-angle and two prominent high-angle fracture sets. The low-angle fractures strike generally north-northeast and dip about 20 degrees west-northwest. One high-angle fracture set strikes north-northeast and dips east-southeast; the other high-angle set strikes east-northeast and dips south-southeast. Single-hole directional radar surveys identified two prominent fracture sets: a low-angle set striking north-northeast, dipping west-northwest; and a high-angle fracture set striking north-northeast, dipping east-southeast. Two additional high-angle fracture sets are defined weakly, one striking east-west, dipping north; and a second striking east-west, dipping south. Integrated results from all of the geophysical surveys indicate the presence of three primary fracture sets. A low-angle set strikes north-northeast and dips west-northwest. Two high-angle sets strike north-northeast and east-northeast and dip east-southeast and south-southeast. Statistical correction of the fracture data for orientation bias indicates that high-angle fractures are more numerous than observed in the data but are still less numerous than the low-angle fractures. The orientation and distribution of water-yielding fractures sets were determined by correlating the fracture data from this study with previously collected borehole-flowmeter data. The water-yielding fractures are generally within the three prominent fracture sets observed for the total fracture population. The low-angle water-yielding fractures primarily strike north-northeast to west-northwest and dip west-northwest to south-southwest. Most of the high-angle water-yielding fractures strike either north-northeast or east-west and dip east-southeast or south. The spacing between water-yielding fractures varies but the probable average spacing is estimated to be 30 feet for low-angle fractures; 27 feet for the east-southeast dipping, high-angle fractures; and 43 feet for the south-southeast dipping, high-angle fractures. The median estimated apparent transmissivity of individual water-yielding fractures or fracture zones was 0.3 feet squared per day and ranged from 0.01 to 382 feet squared per day. Ninety-five percent of the water-yielding fractures or fracture zones had an estimated apparent transmissivity of 19.5 feet squared per day or less. The orientation, spacing, and hydraulic properties of water-yielding fractures identified during this study can be used to help estimate recharge, flow, and discharge of ground water contaminants. High-angle fractures provide vertical pathways for ground water to enter the bedrock, interconnections between low-angle fractures, and, subsequently, pathways for water flow within the bedrock along fracture planes. Low-angle fractures may allow horizontal ground-water flow in all directions. The orientation of fracturing and the hydraulic properties of each fracture set strongly affect changes in ground-water flow under stress (pumping) conditions.

Identification and Modelling of the In-Plane Reinforcement Orientation Variations in a CFRP Laminate Produced by Manual Lay-Up

NASA Astrophysics Data System (ADS)

Davila, Yves; Crouzeix, Laurent; Douchin, Bernard; Collombet, Francis; Grunevald, Yves-Henri

2017-08-01

Reinforcement angle orientation has a significant effect on the mechanical properties of composite materials. This work presents a methodology to introduce variable reinforcement angles into finite element (FE) models of composite structures. The study of reinforcement orientation variations uses meta-models to identify and control a continuous variation across the composite ply. First, the reinforcement angle is measured through image analysis techniques of the composite plies during the lay-up phase. Image analysis results show that variations in the mean ply orientations are between -0.5 and 0.5° with standard deviations ranging between 0.34 and 0.41°. An automatic post-treatment of the images determines the global and local angle variations yielding good agreements visually and numerically between the analysed images and the identified parameters. A composite plate analysed at the end of the cooling phase is presented as a case of study. Here, the variation in residual strains induced by the variability in the reinforcement orientation are up to 28% of the strain field of the homogeneous FE model. The proposed methodology has shown its capabilities to introduce material and geometrical variability into FE analysis of layered composite structures.

Identification and Modelling of the In-Plane Reinforcement Orientation Variations in a CFRP Laminate Produced by Manual Lay-Up

NASA Astrophysics Data System (ADS)

Davila, Yves; Crouzeix, Laurent; Douchin, Bernard; Collombet, Francis; Grunevald, Yves-Henri

2018-06-01

Reinforcement angle orientation has a significant effect on the mechanical properties of composite materials. This work presents a methodology to introduce variable reinforcement angles into finite element (FE) models of composite structures. The study of reinforcement orientation variations uses meta-models to identify and control a continuous variation across the composite ply. First, the reinforcement angle is measured through image analysis techniques of the composite plies during the lay-up phase. Image analysis results show that variations in the mean ply orientations are between -0.5 and 0.5° with standard deviations ranging between 0.34 and 0.41°. An automatic post-treatment of the images determines the global and local angle variations yielding good agreements visually and numerically between the analysed images and the identified parameters. A composite plate analysed at the end of the cooling phase is presented as a case of study. Here, the variation in residual strains induced by the variability in the reinforcement orientation are up to 28% of the strain field of the homogeneous FE model. The proposed methodology has shown its capabilities to introduce material and geometrical variability into FE analysis of layered composite structures.

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

Petrik, Nikolay G.; Henderson, Michael A.; Kimmel, Gregory A.

Angle-resolved photon stimulated desorption (PSD) combined with infrared reflection-adsorption spectroscopy and temperature programmed desorption reveal two distinct channels in the photochemistry of acetone on rutile TiO₂(110) surface. During UV irradiation of co-adsorbed oxygen and acetone molecules, methyl radicals (CH₃) are ejected in two different directions: i) normal to the surface and ii) off-normal at ~±66° to the surface normal in the azimuth (i.e. perpendicular to the rows of bridging oxygen and Ti atoms). Both components are relatively narrow and non-cosine, indicating non-thermal evolution of CH₃ radicals. The direction of the “off-normal” PSD component is consistent with orientation of the C–CH₃more » bonds in the n²-acetone diolate—a photoactive form of acetone chemisorption on the oxidized TiO₂(110) surface proposed earlier from experimental and theoretical studies. The direction of the “normal” PSD component requires an orientation of a C–CH₃ bond which is not consistent with the n²-acetone diolate structure. The angular distribution of the CH₃ PSD depends on the acetone coverage. The “off-normal” PSD component dominates at lower acetone coverage (< 0.2 ML), but does not increase at higher coverages in accord with the acetone diolate peak intensity in the infrared reflection-absorption spectra. The “normal” PSD component grows with the acetone coverage up to 0.6 ML. The newly discovered “normal” PSD channel is tentatively assigned to a photo-produced n²- acetone enolate as a potential precursor based on the H/D exchange experiments« less

Towards chiral distributions of dopants in microporous frameworks: helicoidal supramolecular arrangement of (1R,2S)-ephedrine and transfer of chirality.

PubMed

Gómez-Hortigüela, Luis; Álvaro-Muñoz, Teresa; Bernardo-Maestro, Beatriz; Pérez-Pariente, Joaquín

2015-01-07

A molecular-mechanics computational study is performed in order to analyze the arrangement of (1R,2S)-(-)-ephedrine molecules within the 12-MR channels of the AFI aluminophosphate microporous framework and the influence on the spatial distribution of dopants embedded in the tetrahedral network. Results showed that ephedrine molecules arrange exclusively as dimers by π-π stacking of the aromatic rings within the AFI channels. Interestingly, the asymmetric nature of ephedrine and the presence of H-bond-forming groups (NH2 and OH) involve a preferential orientation where consecutive dimers within the channels are rotated by an angle of +30°; this is driven by the establishment of inter-dimer H-bonds. This preferential orientation leads to the development of a supramolecular enantiomerically-pure helicoidal (chiral) arrangement of ephedrine dimers. In addition, the computational results demonstrate that the particular molecular structure of ephedrine imparts a strong trend to attract negative charges to the vicinity of the NH2(+) positively-charged groups. Hence divalent dopants such as Mg, whose replacement by trivalent Al in the aluminophosphate network involves the generation of a negative charge, will tend to locate close to the NH2(+) molecular groups, suggesting that an imprinting of the organic arrangement to the spatial distribution of dopants would be feasible. Combined with the trend of ephedrine to arrange in a helicoidal fashion, an enantiomerically-pure helicoidal distribution of dopants would be expected, thus inducing a new type of chirality in microporous materials.

Atomistic Simulation Studies of Cholesteryl Oleates: Model for the Core of Lipoprotein Particles

PubMed Central

Heikelä, Mikko; Vattulainen, Ilpo; Hyvönen, Marja T.

2006-01-01

We have conducted molecular dynamics simulations to gain insight into the atomic-scale properties of an isotropic system of cholesteryl oleate (CO) molecules. Cholesteryl esters are major constituents of low density lipoprotein particles, the key players in the formation of atherosclerosis, as well as the storage form of cholesterol. Here the aim is to clarify structural and dynamical properties of CO molecules under conditions, which are suggestive of those in the core of low density lipoprotein particles. The simulations in the fluid phase indicate that the system of CO molecules is characterized by an absence of translational order, as expected, while the orientational order between distinct CO molecules is significant at short distances, persisting over a molecular size. As for intramolecular properties, the bonds along the oleate chain are observed to be weakly ordered with respect to the sterol structure, unlike the bonds along the short hydrocarbon chain of cholesterol where the ordering is significant. The orientational distribution of the oleate chain as a whole with respect to the sterol moiety is of broad nature, having a major amount of extended and a less considerable proportion of bended structures. Distinct transient peaks at specific angles also appear. The diffusion of CO molecules is found to be a slow process and characterized by a diffusion coefficient of the order of 2 × 10−9 cm2/s. This is considerably slower than diffusion, e.g., in ordered domains of lipid membranes rich in sphingomyelin and cholesterol. Analysis of the rotational diffusion rates and trans-to-gauche transition rates yield results consistent with experiments. PMID:16399839

Molecular and electronic structures of M 2O 7 (M = Mn, Tc, Re)

DOE PAGES

Lawler, Keith V.; Childs, Bradley C.; Mast, Daniel S.; ...

2017-02-21

The molecular and electronic structures for the Group 7b heptoxides were investigated by computational methods as both isolated molecules and in the solid-state. The metal-oxygen-metal bending angle of the single molecule increased with increasing atomic number, with Re 2O 7 preferring a linear structure. Natural bond orbital and localized orbital bonding analyses indicate that there is a three-center covalent bond between the metal atoms and the bridging oxygen, and the increasing ionic character of the bonds favors larger bond angles. The calculations accurately reproduce the experimental crystal structures within a few percent. Analysis of the band structures and density ofmore » states shows similar bonding for all of the solid-state heptoxides, including the presence of the three-center covalent bond. DFT+U simulations show that PBE-D3 underpredicts the band gap by ~0.2 eV due to an under-correlation of the metal d conducting states. As a result, homologue and compression studies show that Re 2O 7 adopts a polymeric structure because the Re-oxide tetrahedra are easily distorted by packing stresses to form additional three-center covalent bonds.« less

Bond angle variations in XH3 [X = N, P, As, Sb, Bi]: the critical role of Rydberg orbitals exposed using a diabatic state model.

PubMed

Reimers, Jeffrey R; McKemmish, Laura K; McKenzie, Ross H; Hush, Noel S

2015-10-14

Ammonia adopts sp(3) hybridization (HNH bond angle 108°) whereas the other members of the XH3 series PH3, AsH3, SbH3, and BiH3 instead prefer octahedral bond angles of 90-93°. We use a recently developed general diabatic description for closed-shell chemical reactions, expanded to include Rydberg states, to understand the geometry, spectroscopy and inversion reaction profile of these molecules, fitting its parameters to results from Equation of Motion Coupled-Cluster Singles and Doubles (EOM-CCSD) calculations using large basis sets. Bands observed in the one-photon absorption spectrum of NH3 at 18.3 eV, 30 eV, and 33 eV are reassigned from Rydberg (formally forbidden) double excitations to valence single-excitation resonances. Critical to the analysis is the inclusion of all three electronic states in which two electrons are placed in the lone-pair orbital n and/or the symmetric valence σ* antibonding orbital. An illustrative effective two-state diabatic model is also developed containing just three parameters: the resonance energy driving the high-symmetry planar structure, the reorganization energy opposing it, and HXH bond angle in the absence of resonance. The diabatic orbitals are identified as sp hybrids on X; for the radical cations XH3(+) for which only 2 electronic states and one conical intersection are involved, the principle of orbital following dictates that the bond angle in the absence of resonance is acos(-1/5) = 101.5°. The multiple states and associated multiple conical intersection seams controlling the ground-state structure of XH3 renormalize this to acos[3 sin(2)(2(1/2)atan(1/2))/2 - 1/2] = 86.7°. Depending on the ratio of the resonance energy to the reorganization energy, equilibrium angles can vary from these limiting values up to 120°, and the anomalously large bond angle in NH3 arises because the resonance energy is unexpectedly large. This occurs as the ordering of the lowest Rydberg orbital and the σ* orbital swap, allowing Rydbergization to compresses σ* to significantly increase the resonance energy. Failure of both the traditional and revised versions of the valence-shell electron-pair repulsion (VSEPR) theory to explain the ground-state structures in simple terms is attributed to exclusion of this key physical interaction.

Synthesis of Road Networks by Data Conflation

DTIC Science & Technology

2014-04-01

Transform requires basic trigonometric properties. Suppose we have a line oriented as shown in Figure 9 then by defining the parameters, ρ, and θ we...location. Rather than searching for the remaining three parameters, the major and minor axes and the orientation angle, the axes ratio is utilized to...axes ratio and orientation angle are searched on a coarse quantization level and then the local maxima are obtained and a finer resolution area is

Perceived orientation, spatial layout and the geometry of pictures

NASA Technical Reports Server (NTRS)

Goldstein, E. Bruce

1989-01-01

The purpose is to discuss the role of geometry in determining the perception of spatial layout and perceived orientation in pictures viewed at an angle. This discussion derives from Cutting's (1988) suggestion, based on his analysis of some of the author's data (Goldstein, 1987), that the changes in perceived orientation that occur when pictures are viewed at an angle can be explained in terms of geometrically produced changes in the picture's virtual space.

Semiflexible macromolecules in quasi-one-dimensional confinement: Discrete versus continuous bond angles.

PubMed

Huang, Aiqun; Hsu, Hsiao-Ping; Bhattacharya, Aniket; Binder, Kurt

2015-12-28

The conformations of semiflexible polymers in two dimensions confined in a strip of width D are studied by computer simulations, investigating two different models for the mechanism by which chain stiffness is realized. One model (studied by molecular dynamics) is a bead-spring model in the continuum, where stiffness is controlled by a bond angle potential allowing for arbitrary bond angles. The other model (studied by Monte Carlo) is a self-avoiding walk chain on the square lattice, where only discrete bond angles (0° and ±90°) are possible, and the bond angle potential then controls the density of kinks along the chain contour. The first model is a crude description of DNA-like biopolymers, while the second model (roughly) describes synthetic polymers like alkane chains. It is first demonstrated that in the bulk the crossover from rods to self-avoiding walks for both models is very similar, when one studies average chain linear dimensions, transverse fluctuations, etc., despite their differences in local conformations. However, in quasi-one-dimensional confinement two significant differences between both models occur: (i) The persistence length (extracted from the average cosine of the bond angle) gets renormalized for the lattice model when D gets less than the bulk persistence length, while in the continuum model it stays unchanged. (ii) The monomer density near the repulsive walls for semiflexible polymers is compatible with a power law predicted for the Kratky-Porod model in the case of the bead-spring model, while for the lattice case it tends to a nonzero constant across the strip. However, for the density of chain ends, such a constant behavior seems to occur for both models, unlike the power law observed for flexible polymers. In the regime where the bulk persistence length ℓp is comparable to D, hairpin conformations are detected, and the chain linear dimensions are discussed in terms of a crossover from the Daoud/De Gennes "string of blobs"-picture to the flexible rod picture when D decreases and/or the chain stiffness increases. Introducing a suitable further coarse-graining of the chain contours of the continuum model, direct estimates for the deflection length and its distribution could be obtained.

The structure of the ends of α-helices in globular proteins: effect of additional hydrogen bonds and implications for helix formation.

PubMed

Leader, David P; Milner-White, E James

2011-03-01

We prepared a set of about 2000 α-helices from a relational database of high-resolution three-dimensional structures of globular proteins, and identified additional main chain i ← i+3 hydrogen bonds at the ends of the helices (i.e., where the hydrogen bonding potential is not fulfilled by canonical i ← i+4 hydrogen bonds). About one-third of α-helices have such additional hydrogen bonds at the N-terminus, and more than half do so at the C-terminus. Although many of these additional hydrogen bonds at the C-terminus are associated with Schellman loops, the majority are not. We compared the dihedral angles at the termini of α-helices having or lacking the additional hydrogen bonds. Significant differences were found, especially at the C-terminus, where the dihedral angles at positions C2 and C1 in the absence of additional hydrogen bonds deviate substantially from those occurring within the α-helix. Using a novel approach we show how the structure of the C-terminus of the α-helix can emerge from that of constituent overlapping α-turns and β-turns, which individually show a variation in dihedral angles at different positions. We have also considered the direction of propagation of the α-helix using this approach. If one assumes that helices start as a single α-turn and grow by successive addition of further α-turns, the paths for growth in the N → C and C → N directions differ in a way that suggests that extension in the C → N direction is favored. Copyright © 2010 Wiley-Liss, Inc.

A coordination chemistry study of hydrated and solvated cationic vanadium ions in oxidation states +III, +IV, and +V in solution and solid state

PubMed Central

Krakowiak, Joanna; Lundberg, Daniel

2012-01-01

The coordination chemistry of hydrated and solvated vanadium(III), oxovanadium(IV), and dioxovanadium(V) ions in the oxygen donor solvents water, dimethylsulfoxide (dmso) and N,N′-dimethylpropyleneurea (dmpu) has been studied in solution by EXAFS and large angle X-ray scattering (LAXS) and in solid state by single crystal X-ray diffraction and EXAFS. The hydrated vanadium(III) ion has a regular octahedral configuration with a mean V-O bond distance of 1.99 Å. In the hydrated and dimethylsulfoxide solvated oxovanadium(IV) ions vanadium binds strongly to an oxo group at ca. 1.6 Å. The solvent molecule trans to the oxo group is very weakly bound, at ca. 2.2 Å, while the remaining four solvent molecules, with a mean V-O bond distance of 2.0 Å, form a plane slightly below the vanadium atom; the mean O=V-Operp bond angle is ca. 98°. In the dmpu solvated oxovanadium(IV) ion, the space demanding properties of the dmpu molecule leaving no solvent molecule in the trans position to the oxo group which reduces the coordination number to 5. The O=V-O bond angle is consequently much larger, 106°, and the mean V=O and V-O bond distances decrease to 1.58 and 1.97 Å, respectively. The hydrated and dimethylsulfoxide solvated dioxovanadium(V) ions display a very distorted octahedral configuration with the oxo groups in cis position with mean V=O bond distances of 1.6 Å and a O=V=O bond angle of ca. 105°. The solvent molecules trans to the oxo groups are weakly bound, at ca. 2.2 Å, while the remaining two have bond distances of 2.02 Å. The experimental studies of the coordination chemistry of hydrated and solvated vanadium(III,IV,V) ions are complemented by summarizing previously reported crystal structures to yield a comprehensive description of the coordination chemistry of vanadium with oxygen donor ligands. PMID:22950803

Atomistic simulation of orientation dependence in shock-induced initiation of pentaerythritol tetranitrate.

PubMed

Shan, Tzu-Ray; Wixom, Ryan R; Mattsson, Ann E; Thompson, Aidan P

2013-01-24

The dependence of the reaction initiation mechanism of pentaerythritol tetranitrate (PETN) on shock orientation and shock strength is investigated with molecular dynamics simulations using a reactive force field and the multiscale shock technique. In the simulations, a single crystal of PETN is shocked along the [110], [001], and [100] orientations with shock velocities in the range 3-10 km/s. Reactions occur with shock velocities of 6 km/s or stronger, and reactions initiate through the dissociation of nitro and nitrate groups from the PETN molecules. The most sensitive orientation is [110], while [100] is the most insensitive. For the [001] orientation, PETN decomposition via nitro group dissociation is the dominant reaction initiation mechanism, while for the [110] and [100] orientations the decomposition is via mixed nitro and nitrate group dissociation. For shock along the [001] orientation, we find that CO-NO(2) bonds initially acquire more kinetic energy, facilitating nitro dissociation. For the other two orientations, C-ONO(2) bonds acquire more kinetic energy, facilitating nitrate group dissociation.

Valence-bond theory of compounds of transition metals

PubMed Central

Pauling, Linus

1975-01-01

An equation relating the strength (bondforming power) of an spd hybrid bond orbital to the angles it makes with other bond orbitals is formulated and applied in the discussion of the structures of transition-metal carbonyls and other substances by the valence-bond method. The rather simple theory gives results that agree well with those obtained by the complicated and laborious calculation of sets of orthogonal hybrid bond orbitals with maximum strength. PMID:16592279

Simulaid: a simulation facilitator and analysis program.

PubMed

Mezei, Mihaly

2010-11-15

Simulaid performs a large number of simulation-related tasks: interconversion and modification of structure and trajectory files, optimization of orientation, and a large variety of analysis functions. The program can handle structures in PDB (Berman et al., Nucleic Acids Res 2000, 28, 235), Charmm (Brooks et al., J Comput Chem 4, 187) CRD, Amber (Case et al.), Macromodel (Mohamadi et al., J Comput Chem 1990, 11, 440), Gromos/Gromacs (Hess et al.), InsightII (InsightII. Accelrys Inc.: San Diego, 2005), Grasp (Nicholls et al., Proteins: Struct Funct Genet 1991, 11, 281) .crg, Tripos (Tripos International, S. H. R., St. Louis, MO) .mol2 (input only), and in the MMC (Mezei, M.; MMC: Monte Carlo program for molecular assemblies. Available at: http://inka.mssm.edu/~mezei/mmc) formats; and trajectories in the formats of Charmm, Amber, Macromodel, and MMC. Analysis features include (but are not limited to): (1) simple distance calculations and hydrogen-bond analysis, (2) calculation of 2-D RMSD maps (produced both as text file with the data and as a color-coded matrix) and cross RMSD maps between trajectories, (3) clustering based on RMSD maps, (4) analysis of torsion angles, Ramachandran (Ramachandran and Sasiskharan, Adv Protein Chem 1968, 23, 283) angles, proline kink (Visiers et al., Protein Eng 2000, 13, 603) angles, pseudorotational (Altona and Sundaralingam, J Am Chem Soc 1972, 94, 8205; Cremer and Pople, J Am Chem Soc 1975, 97, 1354) angles, and (5) analysis based on circular variance (Mezei, J Mol Graphics Model 2003, 21, 463). Torsion angle evolutions are presented in dial plots (Ravishanker et al., J Biomol Struct Dyn 1989, 6, 669). Several of these features are unique to Simulaid. 2010 Wiley Periodicals, Inc.

Atomistic Monte Carlo Simulation of Lipid Membranes

PubMed Central

Wüstner, Daniel; Sklenar, Heinz

2014-01-01

Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC) simulation of lipid membranes. We provide an introduction into the various move sets that are implemented in current MC methods for efficient conformational sampling of lipids and other molecules. In the second part, we demonstrate for a concrete example, how an atomistic local-move set can be implemented for MC simulations of phospholipid monomers and bilayer patches. We use our recently devised chain breakage/closure (CBC) local move set in the bond-/torsion angle space with the constant-bond-length approximation (CBLA) for the phospholipid dipalmitoylphosphatidylcholine (DPPC). We demonstrate rapid conformational equilibration for a single DPPC molecule, as assessed by calculation of molecular energies and entropies. We also show transition from a crystalline-like to a fluid DPPC bilayer by the CBC local-move MC method, as indicated by the electron density profile, head group orientation, area per lipid, and whole-lipid displacements. We discuss the potential of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol. PMID:24469314

Axial coordination and conformational heterogeneity of nickel(II) tetraphenylprophyrin complexes with nitrogenous bases

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

Jia, S.L.; Song, X.Z.; Ma, J.G.

1998-08-24

Axial ligation of nickel(II) 5,10,15,20-tetraphenylporphyrin (NiTPP) with pyrrolidine or piperidine has been investigated using X-ray crystallography, UV-visible spectroscopy, resonance Raman spectroscopy, and molecular mechanics (MM) calculations. Distinct v{sub 4} Raman lines are found for the 4-, 5-, and 6-coordinate species of NiTPP. The equilibrium constants for addition of the first and second pyrrolidine axial ligands are 1.1 and 3.8 M{sup {minus}1}, respectively. The differences in the calculated energies of the conformers having different ligand rotational angles are small so they may coexist in solution. Because of the similarity in macrocyclic structural parameters of these conformers and the free rotation ofmore » the axial ligands, narrow and symmetric v{sub 2} and v{sub 8} Raman lines are observed. Nonetheless, the normal-coordinate structural-decomposition analysis of the nonplanar distortions of the calculated structures and the crystal structure of the bis(piperidine) complex reveals a relationship between the orientations of axial ligand(s) and the macrocyclic distortions. For the 5-coordinate complex with the plane of the axial ligand bisecting the Ni-N{sub pyrrole} bonds, a primarily ruffled deformation results. With the ligand plane eclipsing the Ni-N{sub pyrrole} bonds, a mainly saddled deformation occurs. With the addition of the second axial ligand, the small doming of the 5-coordinate complexes disappears, and ruffling or saddling deformations change depending on the relative orientation of the two axial ligands. The crystal structure of the NiTPP bis(piperidine) complex shows a macrocycle distortion composed of wav(x) and wav(y) symmetric deformations, but no ruffling, saddling, or doming. The difference in the calculated and observed distortions results partly from the phenyl group orientation imposed by crystal packing forces. MM calculations predict three stable conformers (ruf, sad, and planar) for 4-coordinate NiTPP, and resonance Raman evidence for these conformers was given previously.« less

Multiple groups of orientation-selective visual mechanisms underlying rapid orientated-line detection.

PubMed Central

Foster, D H; Westland, S

1998-01-01

Visual search for an edge or line element differing in orientation from a background of other edge or line elements can be performed rapidly and effortlessly. In this study, based on psychophysical measurements with ten human observers, threshold values of the angle between a target and background line elements were obtained as functions of background-element orientation, in brief masked displays. A repeated-loess analysis of the threshold functions suggested the existence of several groups of orientation-selective mechanisms contributing to rapid orientated-line detection; specifically, coarse, intermediate and fine mechanisms with preferred orientations spaced at angles of approximately 90 degrees, 35 degrees, and 10 degrees-25 degrees, respectively. The preferred orientations of coarse and some intermediate mechanisms coincided with the vertical or horizontal of the frontoparallel plane, but the preferred orientations of fine mechanisms varied randomly from observer to observer, possibly reflecting individual variations in neuronal sampling characteristics. PMID:9753784

Real-time endoscopic image orientation correction system using an accelerometer and gyrosensor.

PubMed

Lee, Hyung-Chul; Jung, Chul-Woo; Kim, Hee Chan

2017-01-01

The discrepancy between spatial orientations of an endoscopic image and a physician's working environment can make it difficult to interpret endoscopic images. In this study, we developed and evaluated a device that corrects the endoscopic image orientation using an accelerometer and gyrosensor. The acceleration of gravity and angular velocity were retrieved from the accelerometer and gyrosensor attached to the handle of the endoscope. The rotational angle of the endoscope handle was calculated using a Kalman filter with transmission delay compensation. Technical evaluation of the orientation correction system was performed using a camera by comparing the optical rotational angle from the captured image with the rotational angle calculated from the sensor outputs. For the clinical utility test, fifteen anesthesiology residents performed a video endoscopic examination of an airway model with and without using the orientation correction system. The participants reported numbers written on papers placed at the left main, right main, and right upper bronchi of the airway model. The correctness and the total time it took participants to report the numbers were recorded. During the technical evaluation, errors in the calculated rotational angle were less than 5 degrees. In the clinical utility test, there was a significant time reduction when using the orientation correction system compared with not using the system (median, 52 vs. 76 seconds; P = .012). In this study, we developed a real-time endoscopic image orientation correction system, which significantly improved physician performance during a video endoscopic exam.

2,4,6,8-Tetra-kis(2-fluoro-phen-yl)-3,7-diaza-bicyclo-[3.3.1]nonan-9-one.

PubMed

Park, Dong Ho; Ramkumar, V; Parthiban, P

2013-02-01

The title compound, C(31)H(24)F(4)N(2)O, exists in a chair-boat conformation with an equatorial orientation of the 2-fluoro-phenyl groups on both sides of the secondary amino group of the chair form. The benzene rings in the 'chair' part are inclined to each other at 19.4 (1)°, while the equivalent angle between the benzene rings in the 'boat' part is 75.6 (1)°. One F atom was treated as disordered over two positions in a 0.838 (4):0.162 (4) ratio. In the crystal, N-H⋯O hydrogen bonds link the mol-ecules into chains along [001] and these chains are held together via weak N-H⋯F and C-H⋯F inter-actions.

A virtual library of constrained cyclic tetrapeptides that mimics all four side-chain orientations for over half the reverse turns in the protein data bank.

PubMed

Arbor, Sage; Marshall, Garland R

2009-02-01

Reverse turns are often recognition sites for protein/protein interactions and, therefore, valuable potential targets for determining recognition motifs in development of potential therapeutics. A virtual combinatorial library of cyclic tetrapeptides (CTPs) was generated and the bonds in the low-energy structures were overlapped with canonical reverse-turn Calpha-Cbeta bonds (Tran et al., J Comput Aided Mol Des 19(8):551-566, 2005) to determine the utility of CTPs as reverse-turn peptidomimetics. All reverse turns in the Protein Data Bank (PDB) with a crystal structures resolution < or = 3.0 A were classified into the same known canonical reverse-turn Calpha-Cbeta bond clusters (Tran et al., J Comput Aided Mol Des 19(8):551-566, 2005). CTP reverse-turn mimics were compiled that mimicked both the relative orientations of three of the four as well as all four Calpha-Cbeta bonds in the reverse turns of the PDB. 54% of reverse turns represented in the PDB had eight or more CTPs structures that mimicked the orientation of all four of the Calpha-Cbeta bonds in the reverse turn.

Abnormal variation of band gap in Zn doped Bi{sub 0.9}La{sub 0.1}FeO{sub 3} nanoparticles: Role of Fe-O-Fe bond angle and Fe-O bond anisotropy

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

Xu, Xunling; Liu, Weifang, E-mail: wfliu@tju.edu.cn, E-mail: shouyu.wang@yahoo.com; Wu, Ping

2015-07-27

Bi{sub 0.9}La{sub 0.1}FeO{sub 3} (BLFO) and Bi{sub 0.9}La{sub 0.1}Fe{sub 0.99}Zn{sub 0.01}O{sub 3} (BLFZO) nanoparticles were prepared via a sol-gel method. The oxygen vacancies and holes increase with Zn doping analyzed through X-ray photoelectron spectroscopy, which could contribute to the increase of leakage current density. However, with the increase of the defects (oxygen vacancies and holes), the band gap of BLFZO also is increased. To explain the abnormal phenomenon, the bandwidth of occupied and unoccupied bands was analyzed based on the structural symmetry driven by the Fe-O-Fe bond angle and Fe-O bond anisotropy.

AB INITIO Molecular Dynamics Simulations on Local Structure and Electronic Properties in Liquid MgxBi1-x Alloys

NASA Astrophysics Data System (ADS)

Hao, Qing-Hai; You, Yu-Wei; Kong, Xiang-Shan; Liu, C. S.

2013-03-01

The microscopic structure and dynamics of liquid MgxBi1-x(x = 0.5, 0.6, 0.7) alloys together with pure liquid Mg and Bi metals were investigated by means of ab initio molecular dynamics simulations. We present results of structure properties including pair correlation function, structural factor, bond-angle distribution function and bond order parameter, and their composition dependence. The dynamical and electronic properties have also been studied. The structure factor and pair correlation function are in agreement with the available experimental data. The calculated bond-angle distribution function and bond order parameter suggest that the stoichiometric composition Mg3Bi2 exhibits a different local structure order compared with other concentrations, which help us understand the appearance of the minimum electronic conductivity at this composition observed in previous experiments.

Molecular-dynamics simulation of polymethylene chain confined in cylindrical potentials. I. Nature of the conformational defects

NASA Astrophysics Data System (ADS)

Yamamoto, Takashi; Kimikawa, Yuichi

1992-10-01

The conformational motion of a polymethylene molecule constrained by a cylindrical potential is simulated up to 100 ps. The molecule consists of 60 CH2 groups and has variable bond lengths, bond angles, and dihedral angles. Our main concern here is the excitation and the dynamics of the conformational defects: kinks, jogs, etc. Under weaker constraint a number of gauche bonds are excited; they mostly form pairs such as gtḡ kinks or gtttḡ jogs. These conformational defects show no continuous drift in space. Instead they often annihilate and then recreate at different sites showing apparently random positional changes. The conformational defects produce characteristic strain fields around them. It seems that the conformational defects interact attractively through these strain fields. This is evidenced by remarkably correlated spatial distributions of the gauche bonds.

Maximum-valence radii of transition metals

PubMed Central

Pauling, Linus

1975-01-01

In many of their compounds the transition metals have covalence 9, forming nine bonds with use of nine hybrid spd bond orbitals. A set of maximum-valence single-bond radii is formulated for use in these compounds. These radii are in reasonably good agreement with observed bond lengths. Quadruple bonds between two transition metal atoms are about 50 pm (iron-group atoms) or 55 pm (palladium and platinum-group atoms) shorter than single bonds. This amount of shortening corresponds to four bent single bonds with the best set of bond angles, 79.24° and 128.8°. PMID:16578730

Analysis of local bond-orientational order for liquid gallium at ambient pressure: Two types of cluster structures.

PubMed

Chen, Lin-Yuan; Tang, Ping-Han; Wu, Ten-Ming

2016-07-14

In terms of the local bond-orientational order (LBOO) parameters, a cluster approach to analyze local structures of simple liquids was developed. In this approach, a cluster is defined as a combination of neighboring seeds having at least nb local-orientational bonds and their nearest neighbors, and a cluster ensemble is a collection of clusters with a specified nb and number of seeds ns. This cluster analysis was applied to investigate the microscopic structures of liquid Ga at ambient pressure (AP). The liquid structures studied were generated through ab initio molecular dynamics simulations. By scrutinizing the static structure factors (SSFs) of cluster ensembles with different combinations of nb and ns, we found that liquid Ga at AP contained two types of cluster structures, one characterized by sixfold orientational symmetry and the other showing fourfold orientational symmetry. The SSFs of cluster structures with sixfold orientational symmetry were akin to the SSF of a hard-sphere fluid. On the contrary, the SSFs of cluster structures showing fourfold orientational symmetry behaved similarly as the anomalous SSF of liquid Ga at AP, which is well known for exhibiting a high-q shoulder. The local structures of a highly LBOO cluster whose SSF displayed a high-q shoulder were found to be more similar to the structure of β-Ga than those of other solid phases of Ga. More generally, the cluster structures showing fourfold orientational symmetry have an inclination to resemble more to β-Ga.

Effect of Surface Oxidation on Interfacial Water Structure at a Pyrite (100) Surface as Studied by Molecular Dynamics Simulation

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

Jin, Jiaqi; Miller, Jan D.; Dang, Liem X.

2015-06-01

In the first part of this paper, a Scanning Electron Microscopy and contact angle study of a pyrite surface (100) is reported describing the relationship between surface oxidation and the hydrophilic surface state. In addition to these experimental results, the following simulated surface states were examined using Molecular Dynamics Simulation (MDS): fresh unoxidized (100) surface; polysulfide at the (100) surface; elemental sulfur at the (100) surface. Crystal structures for the polysulfide and elemental sulfur at the (100) surface were simulated using Density Functional Theory (DFT) quantum chemical calculations. The well known oxidation mechanism which involves formation of a metal deficientmore » layer was also described with DFT. Our MDS results of the behavior of interfacial water at the fresh and oxidized pyrite (100) surfaces without/with the presence of ferric hydroxide include simulated contact angles, number density distribution for water, water dipole orientation, water residence time, and hydrogen-bonding considerations. The significance of the formation of ferric hydroxide islands in accounting for the corresponding hydrophilic surface state is revealed not only from experimental contact angle measurements but also from simulated contact angle measurements using MDS. The hydrophilic surface state developed at oxidized pyrite surfaces has been described by MDS, on which basis the surface state is explained based on interfacial water structure. The Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences (BES), of the DOE funded work performed by Liem X. Dang. Battelle operates the Pacific Northwest National Laboratory for DOE. The calculations were carried out using computer resources provided by BES.« less

Structural transformations of carbon and boron nitride nanoscrolls at high impact collisions.

PubMed

Woellner, C F; Machado, L D; Autreto, P A S; de Sousa, J M; Galvao, D S

2018-02-14

The behavior of nanostructures under high strain-rate conditions has been the object of theoretical and experimental investigations in recent years. For instance, it has been shown that carbon and boron nitride nanotubes can be unzipped into nanoribbons at high-velocity impacts. However, the response of many nanostructures to high strain-rate conditions is still unknown. In this work, we have investigated the mechanical behavior of carbon (CNS) and boron nitride nanoscrolls (BNS) colliding against solid targets at high velocities, using fully atomistic reactive (ReaxFF) molecular dynamics (MD) simulations. CNS (BNS) are graphene (boron nitride) membranes rolled up into papyrus-like structures. Their open-ended topology leads to unique properties not found in their close-ended analogs, such as nanotubes. Our results show that collision products are mainly determined by impact velocities and by two orientation angles, which define the position of the scroll (i) axis and (ii) open edge relative to the target. Our MD results showed that for appropriate velocities and orientations, large-scale deformations and nanoscroll fractures could occur. We also observed unscrolling (scrolls going back to quasi-planar membranes), scroll unzipping into nanoribbons, and significant reconstruction due to breaking and/or formation of new chemical bonds. For particular edge orientations and velocities, conversion from open to close-ended topology is also possible, due to the fusion of nanoscroll walls.

1H NMR studies of the 5-(hydroxymethyl)-2'-deoxyuridine containing TF1 binding site.

PubMed

Pasternack, L B; Bramham, J; Mayol, L; Galeone, A; Jia, X; Kearns, D R

1996-07-15

The pyrimidine base 5-(hydroxymethyl)-2'-deoxyuridine (HmU) is a common nucleotide in SPO1 phage DNA. Numerous transcriptional proteins bind HmU-containing DNA preferentially implicating a regulatory function of HmU. We have investigated the conformation and dynamics of d-(5'-CHmUCHmUACACGHmUGHmUAGAG-OH-3')2 (HmU-DNA). This oligonucleotide mimics the consensus sequence of Transcription Factor 1 (TF1). The HmU-DNA was compared to the thymine-containing oligonucleotide. NOESY and DQF COSY spectroscopy provided resonance assignments of nonexchangeable and exchangeable protons, intranucleotide, internucleotide and intrastrand proton-proton distances, and dihedral angle constraints. Methylene protons of the hydroxymethyl group are nonequivalent protons and the hydroxymethyl group is not freely rotating. The hydroxymethyl group adopts a specific orientation with the OH group oriented on the 3' side of the plane of the base. Analysis of imino proton resonances and NOEs indicates additional end base pair fraying and a temperature-induced transition to a conformation in which the internal HmU-A base pairs are disrupted or have reduced lifetimes. Orientation of the hydroxymethyl group indicates the presence of internucleotide intrastrand hydrogen bonding between the HmU12C5 hydroxyl group and A13. All sugars in both DNAs show a C2'endo conformation (typical of B-DNA).

Evolution of the characteristics of Parametric X-ray Radiation from textured polycrystals under different observation angles

NASA Astrophysics Data System (ADS)

Alekseev, V. I.; Eliseyev, A. N.; Irribarra, E.; Kishin, I. A.; Klyuev, A. S.; Kubankin, A. S.; Nazhmudinov, R. M.; Zhukova, P. N.

2018-02-01

The Parametric X-Ray radiation (PXR) spectra and yield dependencies on the orientation angle are measured during the interaction of 7 MeV electrons with a tungsten textured polycrystalline foil for different observation angles. The effects of PXR spectral density increase and PXR yield orientation dependence broadening in the backward direction is shown experimentally for the first time. The experimental results are compared with PXR kinematical theories for both mosaic crystals and polycrystals.

Insight into hydrogen bonding of uranyl hydroxide layers and capsules by use of 1H magic-angle spinning NMR spectroscopy [Insight into the hydrogen bonding for uranyl hydroxides using 1H MAS NMR spectroscopy

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

Alam, Todd M.; Liao, Zuolei; Nyman, May

Solid-state 1H magic-angle spinning (MAS) NMR was used to investigate local proton environments in anhydrous [UO 2(OH) 2] (α-UOH) and hydrated uranyl hydroxide [(UO 2) 4O(OH) 6·5H 2O (metaschoepite). For the metaschoepite material, proton resonances of the μ 2-OH hydroxyl and interlayer waters were resolved, with two-dimensional (2D) double-quantum (DQ) 1H– 1H NMR correlation experiments revealing strong dipolar interactions between these different proton species. The experimental NMR results were combined with first-principles CASTEP GIPAW (gauge including projector-augmented wave) chemical shift calculations to develop correlations between hydrogen-bond strength and observed 1H NMR chemical shifts. Furthermore, these NMR correlations allowed characterization ofmore » local hydrogen-bond environments in uranyl U 24 capsules and of changes in hydrogen bonding that occurred during thermal dehydration of metaschoepite.« less

Insight into hydrogen bonding of uranyl hydroxide layers and capsules by use of 1H magic-angle spinning NMR spectroscopy [Insight into the hydrogen bonding for uranyl hydroxides using 1H MAS NMR spectroscopy

DOE PAGES

Alam, Todd M.; Liao, Zuolei; Nyman, May; ...

2016-04-27

Solid-state 1H magic-angle spinning (MAS) NMR was used to investigate local proton environments in anhydrous [UO 2(OH) 2] (α-UOH) and hydrated uranyl hydroxide [(UO 2) 4O(OH) 6·5H 2O (metaschoepite). For the metaschoepite material, proton resonances of the μ 2-OH hydroxyl and interlayer waters were resolved, with two-dimensional (2D) double-quantum (DQ) 1H– 1H NMR correlation experiments revealing strong dipolar interactions between these different proton species. The experimental NMR results were combined with first-principles CASTEP GIPAW (gauge including projector-augmented wave) chemical shift calculations to develop correlations between hydrogen-bond strength and observed 1H NMR chemical shifts. Furthermore, these NMR correlations allowed characterization ofmore » local hydrogen-bond environments in uranyl U 24 capsules and of changes in hydrogen bonding that occurred during thermal dehydration of metaschoepite.« less

Effect of triggering angles on the crushing mechanisms of hybrid woven kenaf/aluminum hollow cylinders

NASA Astrophysics Data System (ADS)

Ismail, Al Emran; Mat Noor, Fazimah; Mohamad, Zaleha; Amran Madlan, Mohd; Zulafif Rahim, M.; Rasidi Ibrahim, M.; Ahmad, Sufizar; Nasrull Abdol Rahman, Mohd; Salleh, Salihatun Md; Sadikin, Azmahani; Mahzan, Shahruddin; Nor, Nik Hisyamudin Muhd

2017-10-01

This paper presents the effect of triggering angles constructed on the top of hybrid woven kenaf/aluminium hollow cylinders on the energy absorption performances. The crushing performances of aluminium tubes can be found widely in open literature. However, lack number of work on the hybridizing the aluminium tubes with woven kenaf fibre is found. Woven kenaf mats are produced and bathed with polymeric resin before they are wrapped around the aluminium tubes twice. Different fibre orientations, ±θ° are used where θ = 0, 15, 30 and 45. Once the hybrid composite hardened, one of their end are chamfered using different angles of 0°, 30°, 45° and 60°. The tubes are quasi-statically compressed in order to obtain their force-displacement responses and crashworthiness parameters are extracted and discussed with the relation of fibre orientations and chamfering angles. It is found that the chamfering angles are only affected the force-displacement curves during the first stage of elastic deformation whereas there is no obvious effect in the second stage. However, varying the fibre orientations are slightly increased the force-displacement curves especially when the fibre is orientated with 30°. Based on the fracture mechanism observations, most of composite experienced large fragmentation indicating that the composites absorbed the crushing energy ineffectively.

Fabrication of hierarchical polymer surfaces with superhydrophobicity by injection molding from nature and function-oriented design

NASA Astrophysics Data System (ADS)

Weng, Can; Wang, Fei; Zhou, Mingyong; Yang, Dongjiao; Jiang, Bingyan

2018-04-01

A comparison of processes and wettability characteristics was presented for injection molded superhydrophobic polypropylene surfaces from two fabricating strategies. One is the biomimetic replication of patterns from indocalamus leaf in nature. The contact angle of water sitting on this PP surface was measured as 152 ± 2°, with comparable wetting behavior to natural indocalamus leaf surface. The other strategy is the fabrication of superhydrophobic structure by combining methods that produce structures at different length scales. Regarding both the machinability of mold inserts and function-oriented design, three micro-quadrangular arrays and one hierarchical micro-nano cylinder array were designed with the goal of superhydrophobicity. Particularly, a simple approach to the fabrication of hierarchical structures was proposed by combining the anodized plate and the punching plate. The function-oriented design targets as superhydrophobicity were all reached for the designed four structures. The measured contact angles of droplet for these structures were almost consistent with the calculated equilibrium contact angles from thermodynamic analysis. Among them, the contact angle of droplet on the surface of designed hierarchical structure reached about 163° with the sliding angle of 5°, resulting in self-cleaning characteristic. The superhydrophobicity of function-oriented designed polymer surfaces could be modified and controlled, which is exactly the limitation of replicating from natural organisms.

[Structural and Dipole Structure Peculiarities of Hoogsteen Base Pairs Formed in Complementary Nucleobases according to ab initio Quantum Mechanics Studies].

PubMed

Petrenko, Y M

2015-01-01

Ab initio quantum mechanics studies for the detection of structure and dipole structure peculiarities of Hoogsteen base pairs relative to Watson-Crick base pairs, were performed during our work. These base pairs are formed as a result of complementary interactions. It was revealed, that adenine-thymine Hoogsteen base pair and adenine-thymine Watson-Crick base pairs can be formed depending on initial configuration. Cytosine-guanine Hoogsteen pairs are formed only when cytosine was originally protonated. Both types of Hoogsteen pairs have noticeable difference in the bond distances and angles. These differences appeared in purine as well as in pyrimidine parts of the pairs. Hoogsteen pairs have mostly shorter hydrogen bond lengths and significantly larger angles of hydrogen bonds and larger angles between the hydrogen bonds than Watson-Crick base pairs. Notable differences are also observed with respect to charge distribution and dipole moment. Quantitative data on these differences are shown in our work. It is also reported that the values of local parameters (according to Cambridge classification of the parameters which determine DNA properties) in Hoogsteen base pairs, are greatly different from Watson-Crick ones.

A DFT-D Study on Structural, Electronic, Thermodynamic, and Mechanical Properties of HMX/MPNO Cocrystal under High Pressure

NASA Astrophysics Data System (ADS)

Lin, He; Chen, Jian-Fu; Cui, Yu-Ming; Zhang, Zhen-Jiang; Yang, Dong-Dong; Zhu, Shun-Guan; Li, Hong-Zhen

2017-04-01

An investigation on the structural, electronic, thermodynamic, and mechanical properties of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX)/2-methylpyridine-N-oxide (MPNO) cocrystal was carried out from 0 to 100 GPa by using a dispersion-corrected density functional theory (DFT-D) method. Our calculated crystal structure is in excellent agreement with experimental results at ambient pressure. Based on the analysis of lattice parameters, lattice angles, bond lengths, bond angles, and dihedral angles under high pressure, we observe that HMX molecules in the cocrystal bulk are seriously distorted but MPNO molecules remain relatively unchanged. Hydrogen bond lengths are greatly shortened under high pressure. In addition, with the increase in pressure, the bandgap decreases gradually. However, it increases suddenly at 70 GPa. Some important hydrogen bonds between HMX and MPNO are also observed in the density of states spectrum. According to the thermodynamic analysis, this cocrystal is more easily prepared under low pressure. Finally, we characterized its mechanical properties and the results show that this cocrystal is malleable in nature. We expect that this research can provide a fundamental basis for further HMX cocrystal design and preparation.

Influence of topographically patterned angled guidelines on directed self-assembly of block copolymers

NASA Astrophysics Data System (ADS)

Rebello, Nathan; Sethuraman, Vaidyanathan; Blachut, Gregory; Ellison, Christopher J.; Willson, C. Grant; Ganesan, Venkat

2017-11-01

Single chain in mean-field Monte Carlo simulations were employed to study the self-assembly of block copolymers (BCP) in thin films that use trapezoidal guidelines to direct the orientation and alignment of lamellar patterns. The present study explored the influence of sidewall interactions and geometry of the trapezoidal guidelines on the self-assembly of perpendicularly oriented lamellar morphologies. When both the sidewall and the top surface exhibit preferential interactions to the same block of the BCP, trapezoidal guidelines with intermediate taper angles were found to result in less defective perpendicularly orientated morphologies. Similarly, when the sidewall and top surface are preferential to distinct blocks of the BCP, intermediate tapering angles were found to be optimal in promoting defect free structures. Such results are rationalized based on the energetics arising in the formation of perpendicularly oriented lamella on patterned substrates.

Molecularly Tuning the Radicaloid N-H···O═C Hydrogen Bond.

PubMed

Lu, Norman; Chung, Wei-Cheng; Ley, Rebecca M; Lin, Kwan-Yu; Francisco, Joseph S; Negishi, Ei-Ichi

2016-03-03

Substituent effects on the open shell N-H···O═C hydrogen-bond has never been reported. This study examines how 12 functional groups composed of electron donating groups (EDG), halogen atoms and electron withdrawing groups (EWG) affect the N-H···O═C hydrogen-bond properties in a six-membered cyclic model system of O═C(Y)-CH═C(X)N-H. It is found that group effects on this open shell H-bonding system are significant and have predictive trends when X = H and Y is varied. When Y is an EDG, the N-H···O═C hydrogen-bond is strengthened; and when Y is an EWG, the bond is weakened; whereas the variation in electronic properties of X group do not exhibit a significant impact upon the hydrogen bond strength. The structural impact of the stronger N-H···O═C hydrogen-bond are (1) shorter H and O distance, r(H···O) and (2) a longer N-H bond length, r(NH). The stronger N-H···O═C hydrogen-bond also acts to pull the H and O in toward one another which has an effect on the bond angles. Our findings show that there is a linear relationship between hydrogen-bond angle and N-H···O═C hydrogen-bond energy in this unusual H-bonding system. In addition, there is a linear correlation of the r(H···O) and the hydrogen bond energy. A short r(H···O) distance corresponds to a large hydrogen bond energy when Y is varied. The observed trends and findings have been validated using three different methods (UB3LYP, M06-2X, and UMP2) with two different basis sets.

Theory of third-order spectroscopic methods to extract detailed molecular orientational dynamics for planar surfaces and other uniaxial systems

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

Nishida, Jun; Fayer, Michael D., E-mail: fayer@stanford.edu

Functionalized organic monolayers deposited on planar two-dimensional surfaces are important systems for studying ultrafast orientational motions and structures of interfacial molecules. Several studies have successfully observed the orientational relaxation of functionalized monolayers by fluorescence depolarization experiments and recently by polarization-resolved heterodyne detected vibrational transient grating (HDTG) experiments. In this article we provide a model-independent theory to extract orientational correlation functions unique to interfacial molecules and other uniaxial systems based on polarization-resolved resonant third-order spectroscopies, such as pump-probe spectroscopy, HDTG spectroscopy, and fluorescence depolarization experiment. It will be shown (in the small beam-crossing angle limit) that five measurements are necessary tomore » completely characterize the monolayer's motions: I{sub ∥}(t) and I{sub ⊥}(t) with the incident beams normal to the surface, I{sub ∥}(t) and I{sub ⊥}(t) with a non-zero incident angle, and a time averaged linear dichroism measurement. Once these measurements are performed, two orientational correlation functions corresponding to in-plane and out-of-plane motions are obtained. The procedure is applicable not only for monolayers on flat surfaces, but any samples with uniaxial symmetry such as uniaxial liquid crystals and aligned planar bilayers. The theory is valid regardless of the nature of the actual molecular motions on interface. We then apply the general results to wobbling-in-a-cone model, in which molecular motions are restricted to a limited range of angles. Within the context of the model, the cone angle, the tilt of the cone relative to the surface normal, and the orientational diffusion constant can be determined. The results are extended to describe analysis of experiments where the beams are not crossing in the small angle limit.« less

Effect of Hydrofluoric Acid Concentration on Resin Adhesion to a Feldspathic Ceramic.

PubMed

Venturini, Andressa Borin; Prochnow, Catina; Rambo, Dagma; Gundel, Andre; Valandro, Luiz Felipe

2015-08-01

To evaluate the effect of different concentrations of hydrofluoric acid (HF) on the contact angle and the resin bond strength durability to feldspathic ceramic. To evaluate the contact angles of distilled water on etched feldspathic ceramic, 25 specimens (12×10×2.4 mm) of VitaBlocks Mark II were used, divided into 5 groups (n=5): one unconditioned control (UC) group with no ceramic surface treatment, and 4 other groups that were etched for 60 s with different concentrations of HF: 1% (HF1), 3% (HF3), 5% (HF5) and 10% (HF10). The bond testing utilized 40 ceramic blocks (12×10×4 mm) that were fabricated and subjected to the same surface treatments as previously mentioned (excluding the control). The etched surfaces were silanized and resin cement was applied. After 24 h, the blocks were sectioned to produce bar specimens that were divided into two groups, non-aged (immediate testing) and aged (storage for 230 days+12,000 thermocycles at 5°C and 55°C), and subjected to microtensile testing (μTBS). Micromorphogical analysis of the treated surfaces was also performed (atomic force and scanning electron microscopy). One-way ANOVA and Tukey's tests were applied for data analysis. UC had the highest contact angle (61.4°), whereas HF10 showed the lowest contact angle (17.5°). In non-aged conditions, different acids promoted statistically similar bond strengths (14.2 to 15.7 MPa) (p>0.05); in terms of bond durability, only the bond strength of the HF1 group presented a statistically significant decrease comparing before and after aging (14.5 to 10.2 MPa). When etched with 3%, 5%, or 10% hydrofluoric acid, the ceramic tested showed stable resin adhesion after long-term aging.

Effect of Oxygen Inhibition Layer of Universal Adhesives on Enamel Bond Fatigue Durability and Interfacial Characteristics With Different Etching Modes.

PubMed

Ouchi, H; Tsujimoto, A; Nojiri, K; Hirai, K; Takamizawa, T; Barkmeier, W W; Latta, M A; Miyazaki, M

The purpose of this study was to evaluate the effect of the oxygen inhibition layer of universal adhesive on enamel bond fatigue durability and interfacial characteristics with different etching modes. The three universal adhesives used were Scotchbond Universal Adhesive (3M ESPE, St Paul, MN, USA), Adhese Universal (Ivoclar Vivadent, Schaan, Lichtenstein), and G-Premio Bond (GC, Tokyo, Japan). The initial shear bond strength and shear fatigue strength to enamel was determined in the presence and absence of the oxygen inhibition layer, with and without phosphoric acid pre-etching. The water contact angle was also measured in all groups using the sessile drop method. The enamel bonding specimens with an oxygen inhibition layer showed significantly higher (p<0.05) initial shear bond strengths and shear fatigue strengths than those without, regardless of the adhesive type and etching mode. Moreover, the water contact angles on the specimens with an oxygen inhibition layer were significantly lower (p<0.05) than on those without, regardless of etching mode. The results of this study suggest that the oxygen inhibition layer of universal adhesives significantly increases the enamel bond fatigue durability and greatly changes interfacial characteristics, suggesting that the bond fatigue durability and interfacial characteristics of these adhesives strongly rely on its presence.

AACSD: An atomistic analyzer for crystal structure and defects

NASA Astrophysics Data System (ADS)

Liu, Z. R.; Zhang, R. F.

2018-01-01

We have developed an efficient command-line program named AACSD (Atomistic Analyzer for Crystal Structure and Defects) for the post-analysis of atomic configurations generated by various atomistic simulation codes. The program has implemented not only the traditional filter methods like the excess potential energy (EPE), the centrosymmetry parameter (CSP), the common neighbor analysis (CNA), the common neighborhood parameter (CNP), the bond angle analysis (BAA), and the neighbor distance analysis (NDA), but also the newly developed ones including the modified centrosymmetry parameter (m-CSP), the orientation imaging map (OIM) and the local crystallographic orientation (LCO). The newly proposed OIM and LCO methods have been extended for all three crystal structures including face centered cubic, body centered cubic and hexagonal close packed. More specially, AACSD can be easily used for the atomistic analysis of metallic nanocomposite with each phase to be analyzed independently, which provides a unique pathway to capture their dynamic evolution of various defects on the fly. In this paper, we provide not only a throughout overview on various theoretical methods and their implementation into AACSD program, but some critical evaluations, specific testing and applications, demonstrating the capability of the program on each functionality.

Geometry at the aliphatic tertiary carbon atom: computational and experimental test of the Walsh rule.

PubMed

Böhm, Stanislav; Exner, Otto

2004-02-01

The geometrical parameters of molecules of 2-substituted 2-methylpropanes and 1-substituted bicyclo[2.2.2]octanes were calculated at the B3LYP/6-311+G(d,p) level. They agreed reasonably well with the mean crystallographic values retrieved from the Cambridge Structural Database for a set of diverse non-cyclic structures with a tertiary C atom. The angle deformations at this C atom produced by the immediately bonded substituent are also closely related to those observed previously in benzene mono derivatives (either as calculated or as derived from crystallographic data). The calculated geometrical parameters were used to test the classical Walsh rule: It is evidently true that an electron-attracting substituent increases the proportion of C-atom p-electrons in the bond to the substituent and leaves more s-electrons to the remaining bonds; as a consequence the C-C-C angles at a tertiary carbon are widened and the C-C bonds shortened. However, this rule describes only part of the reality since the bond angles and lengths are controlled by other factors as well, for instance by steric crowding. Another imperfection of the Walsh rule is that the sequence of substituents does not correspond to their electronegativities, as measured by any known scale; more probably it is connected with the inductive effect, but then only very roughly.

Shear induced weakening of the hydrogen bonding lattice of the energetic material 5,5'-Hydrazinebistetrazole at high-pressure

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

Ciezak-Jenkins, Jennifer A.; Jenkins, Timothy A.

5,5'-Hydrazinebistetrazole (HBTA) has been studied by in-situ x-ray diffraction and vibrational spectroscopy to pressures near 25 GPa at room temperature. Analysis of the x-ray diffraction pattern of HBTA collected at ambient pressure and temperature revealed a monoclinic structure consistent with that previously reported. Under compression, the x-ray diffraction reveals little evidence of a phase transition over the pressure range studied. Slight anisotropy in response to compression was noted and the β angle decreased moderately, suggesting geometry modifications occur in the hydrogen bonding lattice and between neighboring HBTA molecules as a result of compression along the c axis. Blue shifts inmore » the Infrared active N-H stretching modes were observed, implying a weakening of the hydrogen bond with compression. The weakening of the hydrogen bonding lattice with pressure may lead to an increase in the bending angle of the C-N=N-C bridge between the tetrazole rings and an increased overlap between the π-bonding orbitals. The Raman spectra showed a number of modes associated with H-N=N-H motions of the bridge become more prominent in the spectra under compression. Additionally, the possibility that the increased bend in the angle of the C-N=N-C bridge results from a shearing deformation is discussed.« less

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.

XRD, TEM, IR, Raman and NMR Spectroscopy of In Situ Crystallization of Lithium Disilicate Glass

NASA Technical Reports Server (NTRS)

Fuss, T.; Mogus-Milankovic, A.; Ray, C. S.; Lesher, C. E.; Youngman, R.; Day, D. E.

2006-01-01

The structure of a Li2O-2SiO2 (LS2) glass was investigated as a function of pressure and temperature up to 6 GPa and 750 C respectively, using XRD, TEM, IR, Raman and NMR spectroscopy. Glass densified at 6 GPa has an average Si-O-Si bond angle approx.7deg lower than that found in glass processed at 4.5 GPa. At 4.5 GPa, lithium disilicate crystallizes from the glass, while at 6 GPa a new high pressure form of lithium metasilicate crystallizes. The new phase, while having lithium metasilicate crystal symmetry, contains at least 4 different Si sites. NMR results for 6 GPa sample indicate the presence of Q4 species with (Q(sup 4))Si-O-Si(Q(sup 4)) bond angles of approx.157deg. This is the first reported occurrence of Q(sup 4) species with such large bond angles in alumina free alkali silicate glass. No five- or six- coordinated Si are found.

Reflectivity quenching of ESR multilayer polymer film reflector in optically bonded scintillator arrays

NASA Astrophysics Data System (ADS)

Loignon-Houle, Francis; Pepin, Catherine M.; Charlebois, Serge A.; Lecomte, Roger

2017-04-01

The 3M-ESR multilayer polymer film is a widely used reflector in scintillation detector arrays. As specified in the datasheet and confirmed experimentally by measurements in air, it is highly reflective (> 98 %) over the entire visible spectrum (400-1000 nm) for all angles of incidence. Despite these outstanding characteristics, it was previously found that light crosstalk between pixels in a bonded LYSO scintillator array with ESR reflector can be as high as ∼30-35%. This unexplained light crosstalk motivated further investigation of ESR optical performance. Analytical simulation of a multilayer structure emulating the ESR reflector showed that the film becomes highly transparent to incident light at large angles when surrounded on both sides by materials of refractive index higher than air. Monte Carlo simulations indicate that a considerable fraction (∼25-35%) of scintillation photons are incident at these leaking angles in high aspect ratio LYSO scintillation crystals. The film transparency was investigated experimentally by measuring the scintillation light transmission through the ESR film sandwiched between a scintillation crystal and a photodetector with or without layers of silicone grease. Strong light leakage, up to nearly 30%, was measured through the reflector when coated on both sides with silicone, thus elucidating the major cause of light crosstalk in bonded arrays. The reflector transparency was confirmed experimentally for angles of incidence larger than 60 ° using a custom designed setup allowing illumination of the bonded ESR film at selected grazing angles. The unsuspected ESR film transparency can be beneficial for detector arrays exploiting light sharing schemes, but it is highly detrimental for scintillator arrays designed for individual pixel readout.

A Study of Three Intrinsic Problems of the Classic Discrete Element Method Using Flat-Joint Model

NASA Astrophysics Data System (ADS)

Wu, Shunchuan; Xu, Xueliang

2016-05-01

Discrete element methods have been proven to offer a new avenue for obtaining the mechanics of geo-materials. The standard bonded-particle model (BPM), a classic discrete element method, has been applied to a wide range of problems related to rock and soil. However, three intrinsic problems are associated with using the standard BPM: (1) an unrealistically low unconfined compressive strength to tensile strength (UCS/TS) ratio, (2) an excessively low internal friction angle, and (3) a linear strength envelope, i.e., a low Hoek-Brown (HB) strength parameter m i . After summarizing the underlying reasons of these problems through analyzing previous researchers' work, flat-joint model (FJM) is used to calibrate Jinping marble and is found to closely match its macro-properties. A parametric study is carried out to systematically evaluate the micro-parameters' effect on these three macro-properties. The results indicate that (1) the UCS/TS ratio increases with the increasing average coordination number (CN) and bond cohesion to tensile strength ratio, but it first decreases and then increases with the increasing crack density (CD); (2) the HB strength parameter m i has positive relationships to the crack density (CD), bond cohesion to tensile strength ratio, and local friction angle, but a negative relationship to the average coordination number (CN); (3) the internal friction angle increases as the crack density (CD), bond cohesion to tensile strength ratio, and local friction angle increase; (4) the residual friction angle has little effect on these three macro-properties and mainly influences post-peak behavior. Finally, a new calibration procedure is developed, which not only addresses these three problems, but also considers the post-peak behavior.

Determining efficacy of monitoring devices on ceramic bond to resin composite

PubMed Central

Osorio, Estrella; Aguilera, Fátima S.; Osorio, Raquel; García-Godoy, Franklin; Cabrerizo-Vilchez, Miguel A.; Toledano, Manuel

2012-01-01

Objectives: This paper aims to assess the effectiveness of 3D nanoroughness and 2D microroughness evaluations, by their correlation with contact angle measurements and shear bond strength test, in order to evaluate the effect of two different acids conditioning on the bonding efficacy of a leucite-based glass-ceramic to a composite resin. Study Design: Ceramic (IPS Empress) blocks were treated as follows: 1) no treatment, 2) 37% phosphoric acid (H3PO4), 15 s, 3) 9% hydrofluoric acid (HF), 5 min. Micro- and nano-roughness were assessed with a profilometer and by means of an atomic force microscopy (AFM). Water contact angle (CA) measurements were determined to assess wettability of the ceramic surfaces with the asixymetric drop shape analysis contact diameter technique. Shear bond strength (SBS) was tested to a resin composite (Z100) with three different adhesive systems (Scotchbond Multipurpose Plus, Clearfil New Bond, ProBOND). Scanning electron microscopy (SEM) images were performed. Results: Nanoroughness values assessed in 50x50 μm areas were higher for the HF group, these differences were not detected by profilometric analysis. HF treatment created the nano- roughest surfaces and the smallest CA (p<0.05), producing the highest SBS to the composite resin with all tested adhesive systems (p<0.05). No differences existed between the SBS produced by the adhesive systems evaluated with any of the surface treatments tested. Conclusions: Nano-roughness obtained in a 50x50 µm scan size areas was the most reliable data to evaluate the topographical changes produced by the different acid treatments on ceramic surfaces. Key words:Dental ceramic, acid etching, bonding efficacy, resin composite, adhesive systems, contact angle, roughness. PMID:22549693

Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling.

PubMed

Perić-Hassler, Lovorka; Hansen, Halvor S; Baron, Riccardo; Hünenberger, Philippe H

2010-08-16

Explicit-solvent molecular dynamics (MD) simulations of the 11 glucose-based disaccharides in water at 300K and 1bar are reported. The simulations were carried out with the GROMOS 45A4 force-field and the sampling along the glycosidic dihedral angles phi and psi was artificially enhanced using the local elevation umbrella sampling (LEUS) method. The trajectories are analyzed in terms of free-energy maps, stable and metastable conformational states (relative free energies and estimated transition timescales), intramolecular H-bonds, single molecule configurational entropies, and agreement with experimental data. All disaccharides considered are found to be characterized either by a single stable (overwhelmingly populated) state ((1-->n)-linked disaccharides with n=1, 2, 3, or 4) or by two stable (comparably populated and differing in the third glycosidic dihedral angle omega ; gg or gt) states with a low interconversion barrier ((1-->6)-linked disaccharides). Metastable (anti-phi or anti-psi) states are also identified with relative free energies in the range of 8-22 kJ mol(-1). The 11 compounds can be classified into four families: (i) the alpha(1-->1)alpha-linked disaccharide trehalose (axial-axial linkage) presents no metastable state, the lowest configurational entropy, and no intramolecular H-bonds; (ii) the four alpha(1-->n)-linked disaccharides (n=1, 2, 3, or 4; axial-equatorial linkage) present one metastable (anti-psi) state, an intermediate configurational entropy, and two alternative intramolecular H-bonds; (iii) the four beta(1-->n)-linked disaccharides (n=1, 2, 3, or 4; equatorial-equatorial linkage) present two metastable (anti-phi and anti-psi) states, an intermediate configurational entropy, and one intramolecular H-bond; (iv) the two (1-->6)-linked disaccharides (additional glycosidic dihedral angle) present no (isomaltose) or a pair of (gentiobiose) metastable (anti-phi) states, the highest configurational entropy, and no intramolecular H-bonds. The observed conformational preferences appear to be dictated by four main driving forces (ring conformational preferences, exo-anomeric effect, steric constraints, and possible presence of a third glycosidic dihedral angle), leaving a secondary role to intramolecular H-bonding and specific solvation effects. In spite of the weak conformational driving force attributed to solvent-exposed H-bonds in water (highly polar protic solvent), intramolecular H-bonds may still have a significant influence on the physico-chemical properties of the disaccharide by decreasing its hydrophilicity. Along with previous work, the results also complete the suggestion of a spectrum of approximate transition timescales for carbohydrates up to the disaccharide level, namely: approximately 30 ps (hydroxyl groups), approximately 1 ns (free lactol group, free hydroxymethyl groups, glycosidic dihedral angleomega in (1-->6)-linked disaccharides), approximately 10 ns to 2 micros (ring conformation, glycosidic dihedral angles phi and psi). The calculated average values of the glycosidic torsional angles agree well with the available experimental data, providing validation for the force-field and simulation methodology employed. Copyright 2010 Elsevier Ltd. All rights reserved.

Correlation of nonorthogonality of best hybrid bond orbitals with bond strength of orthogonal orbitals

PubMed Central

Pauling, Linus

1976-01-01

An expression is derived for the bond length of two spd orbitals with maximum values in two directions forming a given bond angle by consideration of the nonorthogonality integral of two best orbitals in these directions. This equation is equivalent to the expression derived by formulating the pair of orthogonal orbitals. Similar expressions are derived for spdf orbitals. Applications are made to icosahedral and cuboctahedral bonds and to the packing of nucleons in atomic nuclei. PMID:16578736

Correlation of nonorthogonality of best hybrid bond orbitals with bond strength of orthogonal orbitals.

PubMed

Pauling, L

1976-02-01

An expression is derived for the bond length of two spd orbitals with maximum values in two directions forming a given bond angle by consideration of the nonorthogonality integral of two best orbitals in these directions. This equation is equivalent to the expression derived by formulating the pair of orthogonal orbitals. Similar expressions are derived for spdf orbitals. Applications are made to icosahedral and cuboctahedral bonds and to the packing of nucleons in atomic nuclei.

AE Source Orientation by Plate Wave Analysis

NASA Technical Reports Server (NTRS)

Gorman, Michael R.; Prosser, William H.

1991-01-01

Lead breaks (Hsu-Neilsen source) were used to generate simulated acoustic emission signals in an aluminum plate at angles of 0, 30, 60, and 90 degrees with respect to the plane of the plate. This was accomplished by breaking the lead on slots cut into the plate at the respective angles. The out-of-plane and in-plane displacement components of the resulting signals were detected by broad band transducers and digitized. Analysis of the waveforms showed them to consist of the extensional and flexural plate modes. The amplitude of both components of the two modes was dependent on the source orientation angle. This suggests that plate wave analysis may be used to determine the source orientation of acoustic emission sources.

Charging and geometric effects on conduction through Anthracene molecular junctions

NASA Astrophysics Data System (ADS)

Kaur, Rupan Preet; Sawhney, Ravinder Singh; Engles, Derick

We studied the geometric effects on the charge transfer through the anthracenedithiol (ADT) molecular junction using density functional theory combined with the non-equilibrium Green’s function approach. Two major geometric aspects, bond length and bond angle, were moderated to optimize the electrical conduction. From the results established in this paper, we found that the electrical conduction can be tuned from 0.2 G0 to 0.9 G0 by varying the Au-S bond length, whereas the moderation of bonding angle assayed a minor change from 0.37 G0 to 0.47 G0. We attributed this escalating zero bias conductance to the increasing charge on the terminal sulfur atom of the ADT molecule, which increased the energy of the HOMO orbital towards Fermi level and exhibited a semi-metallic behaviour. Therefore, geometry plays a critical role in deciding the charge transport through the metal/molecule interface.

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

Identification of hydrophilic group formation on polymer surface during Ar{sup +} ion irradiation in O{sub 2} environment

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

Cho, J.S.; Choi, W.K.; Jung, H.J.

1997-12-01

Ar{sup +} ion irradiation on low density polyethylene (LDPE), and polystyrene (PS) was performed in an O{sub 2} environment in order to improve wettability of polymers to water and to identify the formation of hydrophilic groups originated from chemical reactions on the surface of polymers. Doses of a broad Ar{sup +} ion beam of 1 keV energy were changed from 5 {times} 10{sup 15} to 1 {times} 10{sup 17}/cm{sup 2} and the rate of oxygen gas flowing near the sample surface was varied from 0 to 7 ml/min. The contact angle of polymers was not reduced much by Ar{sup +}more » ion irradiation without oxygen gas. However, it dropped largely to a minimum of 35{degree} and 26{degree} for Ar{sup +} ion irradiation in the presence of flowing oxygen gas on LDPE and PS, respectively. From x-ray photoelectron spectroscopy analysis, it was observed that hydrophilic groups were formed on the surface of polymers through an ion-assisted chemical reaction between the ion-induced unstable chains and oxygen. The newly formed hydrophilic group was identified as {single_bond}(C{double_bond}){single_bond} bond and {single_bond}(C{double_bond}O){single_bond}O{single_bond} bond. The contact angle of polymer was greatly dependent on the hydrophilic group formed on the surface.« less

On the complexity of Engh and Huber refinement restraints: the angle τ as example

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

Touw, Wouter G.; Vriend, Gert, E-mail: vriend@cmbi.ru.nl

2010-12-01

The angle τ (backbone N—C{sup α}—C) is the most contested Engh and Huber refinement target parameter. It is shown that this parameter is ‘correct’ as a PDB-wide average, but can be improved by taking into account residue types, secondary structures and many other aspects of our knowledge of the biophysical relations between residue type and protein structure. The Engh and Huber parameters for bond lengths and bond angles have been used uncontested in macromolecular structure refinement from 1991 until very recently, despite critical discussion of their ubiquitous validity by many authors. An extensive analysis of the backbone angle τ (N—C{supmore » α}—C) illustrates that the Engh and Huber parameters can indeed be improved and a recent study [Tronrud et al. (2010 ▶), Acta Cryst. D66, 834–842] confirms these ideas. However, the present study of τ shows that improving the Engh and Huber parameters will be considerably more complex than simply making the parameters a function of the backbone ϕ, ψ angles. Many other aspects, such as the cooperativity of hydrogen bonds, the bending of secondary-structure elements and a series of biophysical aspects of the 20 amino-acid types, will also need to be taken into account. Different sets of Engh and Huber parameters will be needed for conceptually different refinement programs.« less

Crystal structure of 3-[(4-benzyl-piperazin-1-yl)meth-yl]-5-(thio-phen-2-yl)-2,3-di-hydro-1,3,4-oxa-diazole-2-thione.

PubMed

Al-Omary, Fatmah A M; El-Emam, Ali A; Ghabbour, Hazem A; Chidan Kumar, C S; Quah, Ching Kheng; Fun, Hoong-Kun

2015-03-01

The title 1,3,4-oxa-diazole-2-thione derivative, C18H20N4OS2, crystallized with two independent mol-ecules (A and B) in the asymmetric unit. The 2-thienyl rings in both mol-ecules are rotationally disordered over two orientations by approximately 180° about the single C-C bond that connects it to the oxa-diazole thione ring; the ratios of site occupancies for the major and minor components were fixed in the structure refinement at 0.8:0.2 and 0.9:0.1 in mol-ecules A and B, respectively. The 1,3,4-oxa-diazole-2-thione ring forms dihedral angles of 7.71 (16), 10.0 (11) and 77.50 (12)° (mol-ecule A), and 6.5 (3), 6.0 (9) and 55.30 (12)° (mol-ecule B) with the major and minor parts of the disordered thio-phene ring and the mean plane of the adjacent piperazine ring, respectively, resulting in approximately V-shaped conformations for the mol-ecules. The piperazine ring in both mol-ecules adopts a chair conformation. The terminal benzene ring is inclined towards the mean plane of the piperazine ring with N-C-C-C torsion angles of -58.2 (3) and -66.2 (3)° in mol-ecules A and B, respectively. In the crystal, no inter-molecular hydrogen bonds are observed. The crystal packing features short S⋯S contacts [3.4792 (9) Å] and π-π inter-actions [3.661 (3), 3.664 (11) and 3.5727 (10) Å], producing a three-dimensional network.

Conformational dynamics of L-lysine, L-arginine, L-ornithine binding protein reveals ligand-dependent plasticity.

PubMed

Silva, Daniel-Adriano; Domínguez-Ramírez, Lenin; Rojo-Domínguez, Arturo; Sosa-Peinado, Alejandro

2011-07-01

The molecular basis of multiple ligand binding affinity for amino acids in periplasmic binding proteins (PBPs) and in the homologous domain for class C G-protein coupled receptors is an unsolved question. Here, using unrestrained molecular dynamic simulations, we studied the ligand binding mechanism present in the L-lysine, L-arginine, L-ornithine binding protein. We developed an analysis based on dihedral angles for the description of the conformational changes upon ligand binding. This analysis has an excellent correlation with each of the two main movements described by principal component analysis (PCA) and it's more convenient than RMSD measurements to describe the differences in the conformational ensembles observed. Furthermore, an analysis of hydrogen bonds showed specific interactions for each ligand studied as well as the ligand interaction with the aromatic residues Tyr-14 and Phe-52. Using uncharged histidine tautomers, these interactions are not observed. On the basis of these results, we propose a model in which hydrogen bond interactions place the ligand in the correct orientation to induce a cation-π interaction with Tyr-14 and Phe-52 thereby stabilizing the closed state. Our results also show that this protein adopts slightly different closed conformations to make available specific hydrogen bond interactions for each ligand thus, allowing a single mechanism to attain multiple ligand specificity. These results shed light on the experimental evidence for ligand-dependent conformational plasticity not explained by the previous crystallographic data. Copyright © 2011 Wiley-Liss, Inc.

Crystal structure of bis-(μ-3-nitro-benzoato)-κ3O,O':O;κ3O:O,O'-bis-[bis-(3-cyano-pyridine-κN1)(3-nitro-benzoato-κ2O,O')cadmium].

PubMed

Hökelek, Tuncer; Akduran, Nurcan; Özen, Azer; Uğurlu, Güventürk; Necefoğlu, Hacali

2017-03-01

The asymmetric unit of the title compound, [Cd 2 (C 7 H 4 NO 4 ) 4 (C 6 H 4 N 2 ) 4 ], contains one Cd II atom, two 3-nitro-benzoate (NB) anions and two 3-cyano-pyridine (CPy) ligands. The two CPy ligands act as monodentate N(pyridine)-bonding ligands, while the two NB anions act as bidentate ligands through the carboxyl-ate O atoms. The centrosymmetric dinuclear complex is generated by application of inversion symmetry, whereby the Cd II atoms are bridged by the carboxyl-ate O atoms of two symmetry-related NB anions, thus completing the distorted N 2 O 5 penta-gonal-bipyramidal coordination sphere of each Cd II atom. The benzene and pyridine rings are oriented at dihedral angles of 10.02 (7) and 5.76 (9)°, respectively. In the crystal, C-H⋯N hydrogen bonds link the mol-ecules, enclosing R 2 2 (26) ring motifs, in which they are further linked via C-H⋯O hydrogen bonds, resulting in a three-dimensional network. In addition, π-π stacking inter-actions between parallel benzene rings and between parallel pyridine rings of adjacent mol-ecules [shortest centroid-to-centroid distances = 3.885 (1) and 3.712 (1) Å, respectively], as well as a weak C-H⋯π inter-action, may further stabilize the crystal structure.

Accuracy of estimating Unicondylar Knee Replacement implant varus/valgus angles from antero-posterior radiographs.

PubMed

Khare, Rahul; Jaramaz, Branislav

2016-12-01

Unicondylar Knee Replacement (UKR) is an orthopedic surgical procedure to reduce pain and improve function in the knee. Load-bearing long-standing antero-posterior (AP) radiographs are typically used postoperatively to measure the leg alignment and assess the varus/valgus implant orientation. However, implant out-of-plane rotations, user variability, and X-ray acquisition parameters introduce errors in the estimation of the implant varus/valgus estimation. Previous work has explored the accuracy of various imaging modalities in this estimation. In this work, we explored the impact of out-of-plane rotations and X-ray acquisition parameters on the estimation of implant component varus/valgus angles. For our study, we used a single CT scan and positioned femoral and tibial implants under varying orientations within the CT volume. Then, a custom software application was used to obtain digitally reconstructed radiographs from the CT scan with implants under varying orientations. Two users were then asked to manually estimate the varus/valgus angles for the implants. We found that there was significant inter-user variability (p < 0.05) in the varus/valgus estimates for the two users. However, the 'ideal' measurements, obtained using actual implant orientations, showed small errors due to variations in implant orientation. We also found that variation in the projection center does not have a statistically significant impact (p < 0.01) on the estimation of implant varus/valgus angles. We conclude that manual estimates of UKR implant varus/valgus orientations are unreliable.

Measurement of local deformations on thermoformed composite parts under different process conditions

NASA Astrophysics Data System (ADS)

Vanclooster, K.; Lomov, S. V.; Willems, A.; Verpoest, I.

2007-04-01

The growing use of thermoplastic composites demands tools to analyze the deformed parts accurately. Intraply shear is the most pronounced deformation mode that occurs when a 2D fabric is draped into a complex 3D shape. The paper uses a 3D image correlation method to investigate the intraply shear deformation of a woven fabric reinforced composite. The thickness distribution of the formed ply is determined by using a dial indicator. The fabric is deformed by non-isothermal stamping into a matched "half-salami" shaped mould. The influence of processing conditions, especially pre-heating temperature, stamp speed and the blankholder force is investigated. The effect of the ply-orientation on the shear angle distribution is discussed. The measured shear angles are compared with a kinematical drape model. It was concluded that the local deformations are not influenced by the processing conditions. For 0 and 90° ply-orientation, the draping model adequately predicts the shear angle up to about 40°; for higher angles the shear is overestimated. In case of other ply orientations the model was unable to predict the correct shear angles.

Identification and Characterization of Molecular Bonding Structures by ab initio Quasi-Atomic Orbital Analyses.

PubMed

West, Aaron C; Duchimaza-Heredia, Juan J; Gordon, Mark S; Ruedenberg, Klaus

2017-11-22

The quasi-atomic analysis of ab initio electronic wave functions in full valence spaces, which was developed in preceding papers, yields oriented quasi-atomic orbitals in terms of which the ab initio molecular wave function and energy can be expressed. These oriented quasi-atomic orbitals are the rigorous ab initio counterparts to the conceptual bond forming atomic hybrid orbitals of qualitative chemical reasoning. In the present work, the quasi-atomic orbitals are identified as bonding orbitals, lone pair orbitals, radical orbitals, vacant orbitals and orbitals with intermediate character. A program determines the bonding characteristics of all quasi-atomic orbitals in a molecule on the basis of their occupations, bond orders, kinetic bond orders, hybridizations and local symmetries. These data are collected in a record and provide the information for a comprehensive understanding of the synergism that generates the bonding structure that holds the molecule together. Applications to a series of molecules exhibit the complete bonding structures that are embedded in their ab initio wave functions. For the strong bonds in a molecule, the quasi-atomic orbitals provide quantitative ab initio amplifications of the Lewis dot symbols. Beyond characterizing strong bonds, the quasi-atomic analysis also yields an understanding of the weak interactions, such as vicinal, hyperconjugative and radical stabilizations, which can make substantial contributions to the molecular bonding structure.

Mid-section of a can-annular gas turbine engine with an improved rotation of air flow from the compressor to the turbine

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

Little, David A.; Schilp, Reinhard; Ross, Christopher W.

A midframe portion (313) of a gas turbine engine (310) is presented and includes a compressor section with a last stage blade to orient an air flow (311) at a first angle (372). The midframe portion (313) further includes a turbine section with a first stage blade to receive the air flow (311) oriented at a second angle (374). The midframe portion (313) further includes a manifold (314) to directly couple the air flow (311) from the compressor section to a combustor head (318) upstream of the turbine section. The combustor head (318) introduces an offset angle in the airmore » flow (311) from the first angle (372) to the second angle (374) to discharge the air flow (311) from the combustor head (318) at the second angle (374). While introducing the offset angle, the combustor head (318) at least maintains or augments the first angle (372).« less

Contact angles and wettability of ionic liquids on polar and non-polar surfaces†

PubMed Central

Sousa, Filipa L.; Silva, Nuno J. O.; Lopes-da-Silva, José A.; Coutinho, João A. P.; Freire, Mara G.

2016-01-01

Many applications involving ionic liquids (ILs) require the knowledge of their interfacial behaviour, such as wettability and adhesion. In this context, herein, two approaches were combined aiming at understanding the impact of the IL chemical structures on their wettability on both polar and non-polar surfaces, namely: (i) the experimental determination of the contact angles of a broad range of ILs (covering a wide number of anions of variable polarity, cations, and cation alkyl side chain lengths) on polar and non-polar solid substrates (glass, Al-plate, and poly-(tetrafluoroethylene) (PTFE)); and (ii) the correlation of the experimental contact angles with the cation–anion pair interaction energies generated by the Conductor-like Screening Model for Real Solvents (COSMO-RS). The combined results reveal that the hydrogen-bond basicity of ILs, and thus the IL anion, plays a major role through their wettability on both polar and non-polar surfaces. The increase of the IL hydrogen-bond accepting ability leads to an improved wettability of more polar surfaces (lower contact angles) while the opposite trend is observed on non-polar surfaces. The cation nature and alkyl side chain lengths have however a smaller impact on the wetting ability of ILs. Linear correlations were found between the experimental contact angles and the cation–anion hydrogen-bonding and cation ring energies, estimated using COSMO-RS, suggesting that these features primarily control the wetting ability of ILs. Furthermore, two-descriptor correlations are proposed here to predict the contact angles of a wide variety of ILs on glass, Al-plate, and PTFE surfaces. A new extended list is provided for the contact angles of ILs on three surfaces, which can be used as a priori information to choose appropriate ILs before a given application. PMID:26554705

Contact angles and wettability of ionic liquids on polar and non-polar surfaces.

PubMed

Pereira, Matheus M; Kurnia, Kiki A; Sousa, Filipa L; Silva, Nuno J O; Lopes-da-Silva, José A; Coutinho, João A P; Freire, Mara G

2015-12-21

Many applications involving ionic liquids (ILs) require the knowledge of their interfacial behaviour, such as wettability and adhesion. In this context, herein, two approaches were combined aiming at understanding the impact of the IL chemical structures on their wettability on both polar and non-polar surfaces, namely: (i) the experimental determination of the contact angles of a broad range of ILs (covering a wide number of anions of variable polarity, cations, and cation alkyl side chain lengths) on polar and non-polar solid substrates (glass, Al-plate, and poly-(tetrafluoroethylene) (PTFE)); and (ii) the correlation of the experimental contact angles with the cation-anion pair interaction energies generated by the Conductor-like Screening Model for Real Solvents (COSMO-RS). The combined results reveal that the hydrogen-bond basicity of ILs, and thus the IL anion, plays a major role through their wettability on both polar and non-polar surfaces. The increase of the IL hydrogen-bond accepting ability leads to an improved wettability of more polar surfaces (lower contact angles) while the opposite trend is observed on non-polar surfaces. The cation nature and alkyl side chain lengths have however a smaller impact on the wetting ability of ILs. Linear correlations were found between the experimental contact angles and the cation-anion hydrogen-bonding and cation ring energies, estimated using COSMO-RS, suggesting that these features primarily control the wetting ability of ILs. Furthermore, two-descriptor correlations are proposed here to predict the contact angles of a wide variety of ILs on glass, Al-plate, and PTFE surfaces. A new extended list is provided for the contact angles of ILs on three surfaces, which can be used as a priori information to choose appropriate ILs before a given application.

Visualizing Bent Bonds in Cyclopropane

ERIC Educational Resources Information Center

Bertolini, Thomas M.

2004-01-01

A two-minute overhead demonstration using a molecular model kit is employed for illustrating the unique binding of cyclopropane. It is reported that most model kits, much like an sp (super 3) hybridized carbon atom, resist forming 60-degree bond angles.

Modeling spatial tuning of adaptation of the angular vestibulo-ocular reflex

PubMed Central

Yakushin, Sergei B.

2012-01-01

Gain adaptation of the yaw angular vestibular ocular reflex (aVOR) induced in side-down positions has gravity-independent (global) and -dependent (localized) components. When the head oscillation angles are small during adaptation, localized gain changes are maximal in the approximate position of adaptation. Concurrently, polarization vectors of canal–otolith vestibular neurons adapt their orientations during these small-angle adaptation paradigms. Whether there is orientation adaptation with large amplitude head oscillations, when the head is not localized to a specific position, is unknown. Yaw aVOR gains were decreased by oscillating monkeys about a yaw axis in a side-down position in a subject–stationary visual surround for 2 h. Amplitudes of head oscillation ranged from 15° to 180°. The yaw aVOR gain was tested in darkness at 0.5 Hz, with small angles of oscillation (±15°) while upright and in tilted positions. The peak value of the gain change was highly tuned for small angular oscillations during adaptation and significantly broadened with larger oscillation angles during adaptation. When the orientation of the polarization vectors associated with the gravity-dependent component of the neural network model was adapted toward the direction of gravity, it predicted the localized learning for small angles and the broadening when the orientation adaptation was diminished. The model-based analysis suggests that the otolith orientation adaptation plays an important role in the localized behavior of aVOR as a function of gravity and in regulating the relationship between global and localized adaptation. PMID:22660376

Stereodynamical Origin of Anti-Arrhenius Kinetics: Negative Activation Energy and Roaming for a Four-Atom Reaction.

PubMed

Coutinho, Nayara D; Silva, Valter H C; de Oliveira, Heibbe C B; Camargo, Ademir J; Mundim, Kleber C; Aquilanti, Vincenzo

2015-05-07

The OH + HBr → H2O + Br reaction, prototypical of halogen-atom liberating processes relevant to mechanisms for atmospheric ozone destruction, attracted frequent attention of experimental chemical kinetics: the nature of the unusual reactivity drop from low to high temperatures eluded a variety of theoretical efforts, ranking this one among the most studied four-atom reactions. Here, inspired by oriented molecular-beams experiments, we develop a first-principles stereodynamical approach. Thermalized sets of trajectories, evolving on a multidimensional potential energy surface quantum mechanically generated on-the-fly, provide a map of most visited regions at each temperature. Visualizations of rearrangements of bonds along trajectories and of the role of specific angles of reactants' mutual approach elucidate the mechanistic change from the low kinetic energy regime (where incident reactants reorient to find the propitious alignment leading to reaction) to high temperature (where speed hinders adjustment of directionality and roaming delays reactivity).

The IR Absorption Spectra of Aqueous Solutions of Dimethylsulfoxide over the Frequency Range 50-300 cm-1 and the Mobility of Water Molecules

NASA Astrophysics Data System (ADS)

Klemenkova, Z. S.; Novskova, T. A.; Lyashchenko, A. K.

2008-04-01

The IR absorption spectra of aqueous solutions of dimethylsulfoxide (DMSO) with concentrations from 100% H2O to 100% DMSO were recorded over the frequency range 50-500 cm-1. The absorption spectra were described using the theoretical scheme of hindered rotators. A model was developed according to which orientation relaxation in solution was related to separate rotations of H2O and DMSO molecules through fixed small and (or) large angles in a unified network of H-bonds consisting of several subsystems ordered to various degrees. The calculated absorption spectra were in agreement with the experimental data in the far IR region. Elementary motions of molecules were found to slow down in the passage from pure dimethylsulfoxide to its aqueous solutions. The special features of the hydrophilic and hydrophobic hydration of DMSO polar and nonpolar groups were considered.

Crystal structure of [propane-1,3-diylbis(piperidine-4,1-di-yl)]bis-[(pyridin-4-yl)methanone]-4,4'-oxydi-benzoic acid (1/1).

PubMed

Low, Emily M; LaDuca, Robert L

2014-09-01

In the title co-crystal, C25H32N4O2·C14H10O5, mol-ecules are connected into supra-molecular chains aligned along [102] by O-H⋯N hydrogen bonding. These aggregate into supra-molecular layers oriented parallel to (20-1) by C-H⋯O inter-actions. These layers then stack in an ABAB pattern along the c crystal direction to give the full three-dimensional crystal structure. The central chain in the dipyridylamide has an anti-anti conformation. The dihedral angle between the aromatic ring planes is 29.96 (3)°. Disorder is noted in some of the residues in the structure and this is manifested in two coplanar dispositions of one statistically disordered carb-oxy-lic acid group.

Polarized IR-microscope spectra of guanidinium hydrogenselenate single crystal.

PubMed

Drozd, M; Baran, J

2005-10-01

The polarized IR-microscope spectra of C(NH2)3.HSeO4 small single crystal samples were measured at room temperature. The spectra are discussed with the framework of oriented gas model approximation and group theory. The stretching nuOH vibration of the hydrogen bond with the O...O distance of 2.616 A gives characteristic broad AB-type absorption in the IR spectra. The changes of intensity of the AB bands in function of polarizer angle are described. Detailed assignment for bands derived from stretching and bending modes of selenate anions and guanidinium cations were performed. The observed intensities of these bands in polarized infrared spectra were correlated with theoretical calculation of directional cosines of selected transition dipole moments for investigated crystal. The vibrational studies seem to be helpful in understanding of physical and chemical properties of described compound and also in design of new complexes with exactly defined behaviors.

Polarised IR-microscope spectra of guanidinium hydrogensulphate single crystal.

PubMed

Drozd, M; Baran, J

2006-07-01

Polarised IR-microscope spectra of C(NH(2))(3)*HSO(4) small single crystal samples were measured at room temperature. The spectra are discussed on the basis of oriented gas model approximation and group theory. The stretching nuOH vibration of the hydrogen bond with the Ocdots, three dots, centeredO distance of 2.603A gives characteristic broad AB-type absorption in the IR spectra. The changes of intensity of the AB bands in function of polariser angle are described. Detailed assignments for bands derived from stretching and bending modes of sulphate anions and guanidinium cations were performed. The observed intensities of these bands in polarised infrared spectra were correlated with theoretical calculation of directional cosines of selected transition dipole moments for investigated crystal. The vibrational studies seem to be helpful in understanding of physical and chemical properties of described compound and also in design of new complexes with exactly defined behaviors.

New insights into the adsorption of 3-(trimethoxysilyl)propylmethacrylate on hydroxylated ZnO nanopowders.

PubMed

Bressy, Christine; Ngo, Van Giang; Ziarelli, Fabio; Margaillan, André

2012-02-14

Functionalization of zinc oxide (ZnO) nano-objects by silane grafting is an attractive method to provide nanostructured materials with a variety of surface properties. Active hydroxyl groups on the oxide surface are one of the causes governing the interfacial bond strength in nanohybrid particles. Here, "as-prepared" and commercially available zinc oxide nanopowders with a wide range of surface hydroxyl density were functionalized by a well-known polymerizable silane coupling agent, i.e., 3-(trimethoxysilyl)propylmethacrylate (MPS). Fourier transform infrared (FTIR) and solid-state (13)C and (29)Si nuclear magnetic resonance (NMR) spectroscopic investigations demonstrated that the silane coupling agent was fully hydrolyzed and linked to the hydroxyl groups already present on the particle surface through covalent and hydrogen bonds. Due to a basic catalyzed condensation of MPS with water, a siloxane layer was shown to be anchored to the nanoparticles through mono- and tridentate structures. Quantitative investigations were performed by thermogravimetric (TGA) and elemental analyses. The amount of silane linked to ZnO particles was shown to be affected by the amount of isolated hydroxyl groups available to react on the particle surface. For as-prepared ZnO nanoparticles, the number of isolated and available hydroxyl groups per square nanometer was up to 3 times higher than the one found on commercially available ZnO nanoparticles, leading to higher amounts of polymerizable silane agent linked to the surface. The MPS molecules were shown to be mainly oriented perpendicular to the oxide surface for all the as-prepared ZnO nanoparticles, whereas a parallel orientation was found for the preheated commercially ZnO nanopowders. In addition, ZnO nanoparticles were shown to be hydrophobized by the MPS treatment with water contact angles higher than 60°.

Graphene-Based Polymer Nanocomposites

DTIC Science & Technology

2015-03-31

Raman band I(δ) X - ray scattering intensity in the azimuthal scan I(r) Raman band intensity within laser spot I(ω...Krenchel orientation factor Θ Angle between the incident and the scattering X - ray θ Angle between the surface normal of graphene and sample λ...Wavelength of laser or X - ray λ2/λ4 Parameter in orientation distribution function µ Molecular dipole moment

Rotated grating coupled surface plasmon resonance on wavelength-scaled shallow rectangular gratings

NASA Astrophysics Data System (ADS)

Szalai, A.; Szekeres, G.; Balázs, J.; Somogyi, A.; Csete, Maria

2013-09-01

Theoretical investigation of rotated grating coupling phenomenon was performed on a multilayer comprising 416-nmperiodic shallow rectangular polymer grating on bimetal film made of gold and silver layers. During the multilayer illumination by 532 nm wavelength p-polarized light the polar and azimuthal angles were varied. In presence of 0-35 nm, 0-50 nm and 15-50 nm thick polymer-layers at the valleys and hills splitting was observed on the dual-angle dependent reflectance in two regions: (i) close to 0° azimuthal angle corresponding to incidence plane parallel to the periodic pattern (P-orientation); and (ii) around ~33.5°/29°/30° azimuthal angle (C-orientation), in agreement with our previous experimental studies. The near-field study revealed that in P-orientation the E-field is enhanced at the glass side with p/2 periodicity at the first minimum appearing at 49°/50°/52° polar angles, and comprises maxima below both the valleys and hills; while E-field enhancement is observable both at the glass and polymer side with p-periodicity at the second minimum developing at 55°/63/64° tilting, comprising maxima intermittently below the valleys or above the hills. In Corientation coupled plasmonic modes are observable, involving modes propagating along the valleys at the secondary maxima appearing at ~35°/32°/32° azimuthal and ~49°/51°/56° polar angles, while modes confined along the polymer hills are observable at the primary minima, which are coupled most strongly at the ~31.5°/25°/28° azimuthal and ~55°/63°/66° polar angles. The secondary peak observable in C-orientation is proposed for biosensing applications, since the supported modes are confined along the valleys, where biomolecules prefer to attach.

Investigation of Regional Influence of Magic-Angle Effect on T2 in Human Articular Cartilage with Osteoarthritis at 3 T

PubMed Central

Wang, Ligong; Regatte, Ravinder R.

2014-01-01

Rationale and Objectives The objectives of this research study were to determine the magic-angle effect on different subregions of in vivo human femoral cartilage through the quantitative assessment of the effect of static magnetic field orientation (B0) on transverse (T2) relaxation time at 3.0 T. Materials and Methods Healthy volunteers (n = 5l; mean age, 36.4 years) and clinical patients (n = 5; mean age, 64 years) with early osteoarthritis (OA) were scanned at 3.0-T magnetic resonance using an 8-channel phased-array knee coil (transmit-receive). Results The T2 maps revealed significantly greater values in ventral than in dorsal regions. When the cartilage regions were oriented at 55° to B0 (magic angle), the longest T2 values were detected in comparison with the neighboring regions oriented 90° and 180° (0°) to B0. The subregions oriented 180° (0°) to B0 showed the lowest T2 values. Conclusions The differences in T2 values of different subregions suggest that magic-angle effect needs to be considered when interpreting cartilage abnormalities in OA patients. PMID:25481517

Determining the orientation of a chiral substrate using full-hemisphere angle-resolved photoelectron spectroscopy.

PubMed

Tadich, A; Riley, J; Thomsen, L; Cowie, B C C; Gladys, M J

2011-10-21

Chiral interfaces and substrates are of increasing importance in the field of enantioselective chemistry. To fully understand the enantiospecific interactions between chiral adsorbate molecules and the chiral substrate, it is vital that the chiral orientation of the substrate is known. In this Letter we demonstrate that full-hemisphere angle-resolved photoemission permits straightforward identification of the orientation of a chiral surface. The technique can be applied to any solid state system for which photoemission measurements are possible. © 2011 American Physical Society

Increasing FSW join strength by optimizing feed rate, rotating speed and pin angle

NASA Astrophysics Data System (ADS)

Darmadi, Djarot B.; Purnowidodo, Anindito; Siswanto, Eko

2017-10-01

Principally the join in Friction Stir Welding (FSW) is formed due to mechanical bonding. At least there are two factors determines the quality of this join, first is the temperature in the area around the interface and secondly the intense of mixing forces in nugget zone to create the mechanical bonding. The adequate temperature creates good flowability of the nugget zone and an intensive mixing force produces homogeneous strong bonding. Based on those two factors in this research the effects of feed rate, rotating speed and pin angle of the FSW process to the tensile strength of resulted join are studied. The true experimental method was used. Feed rate was varied at 24, 42, 55 and 74 mm/minutes and from the experimental results, it can be concluded that the higher feed rate decreases the tensile strength of weld join and it is believed due to the lower heat embedded in the material. Inversely, the higher rotating speed increases the join’s tensile strength as a result of higher heat embedded in base metal and higher mixing force in the nugget zone. The rotating speed were 1842, 2257 and 2904 RPMs. The pin angle determines the direction of mixing force. With variation of pin angle: 0°, 4°, 8° and 12° the higher pin angle generally increases the tensile strength because of more intensive mixing force. For 12° pin angle the lower tensile strength is found since the force tends to push out the nugget area from the joint gap.

When the beachhopper looks at the moon: The moon compass hypothesis

NASA Technical Reports Server (NTRS)

Enright, J. T.

1972-01-01

The function of moon position for shoreline orientation by talitrids is investigated. Three major results were found: (1) Observed cases of compensation for changes in the direction of the moon are based on physiological rhythm with a period of about 25 hours which can persist for at least several days under constant conditions. (2) The zeitgeber for physiological rhythm may be either moonlight or some other factor associated with the tides. (3) If talitrids are long removed from environmental entrainment, either artifically or naturally, the internal rhythm no longer exerts an appreciable influence on the angle of lunar orientation; in such cases the system deteriorates into constant angle orientation, with an angle which is determined by the beach orgin, but may be modified by lighting conditions.

Energy States of Molecules

ERIC Educational Resources Information Center

Hollenberg, J. Leland

1970-01-01

Discusses molecular spectroscopy arising from transitions within rotational, vibrational, and electronic energy states. Using quantum mechanical formuli, the author describes how these spectroscopic methods can be used to determine internuclear distances, bond energies, bond angles, dipole moments, and other details. Concludes with a selected…

Interplay between Peptide Bond Geometrical Parameters in Nonglobular Structural Contexts

PubMed Central

Esposito, Luciana; De Simone, Alfonso; Vitagliano, Luigi

2013-01-01

Several investigations performed in the last two decades have unveiled that geometrical parameters of protein backbone show a remarkable variability. Although these studies have provided interesting insights into one of the basic aspects of protein structure, they have been conducted on globular and water-soluble proteins. We report here a detailed analysis of backbone geometrical parameters in nonglobular proteins/peptides. We considered membrane proteins and two distinct fibrous systems (amyloid-forming and collagen-like peptides). Present data show that in these systems the local conformation plays a major role in dictating the amplitude of the bond angle N-Cα-C and the propensity of the peptide bond to adopt planar/nonplanar states. Since the trends detected here are in line with the concept of the mutual influence of local geometry and conformation previously established for globular and water-soluble proteins, our analysis demonstrates that the interplay of backbone geometrical parameters is an intrinsic and general property of protein/peptide structures that is preserved also in nonglobular contexts. For amyloid-forming peptides significant distortions of the N-Cα-C bond angle, indicative of sterical hidden strain, may occur in correspondence with side chain interdigitation. The correlation between the dihedral angles Δω/ψ in collagen-like models may have interesting implications for triple helix stability. PMID:24455689

Interplay between peptide bond geometrical parameters in nonglobular structural contexts.

PubMed

Esposito, Luciana; Balasco, Nicole; De Simone, Alfonso; Berisio, Rita; Vitagliano, Luigi

2013-01-01

Several investigations performed in the last two decades have unveiled that geometrical parameters of protein backbone show a remarkable variability. Although these studies have provided interesting insights into one of the basic aspects of protein structure, they have been conducted on globular and water-soluble proteins. We report here a detailed analysis of backbone geometrical parameters in nonglobular proteins/peptides. We considered membrane proteins and two distinct fibrous systems (amyloid-forming and collagen-like peptides). Present data show that in these systems the local conformation plays a major role in dictating the amplitude of the bond angle N-C(α)-C and the propensity of the peptide bond to adopt planar/nonplanar states. Since the trends detected here are in line with the concept of the mutual influence of local geometry and conformation previously established for globular and water-soluble proteins, our analysis demonstrates that the interplay of backbone geometrical parameters is an intrinsic and general property of protein/peptide structures that is preserved also in nonglobular contexts. For amyloid-forming peptides significant distortions of the N-C(α)-C bond angle, indicative of sterical hidden strain, may occur in correspondence with side chain interdigitation. The correlation between the dihedral angles Δω/ψ in collagen-like models may have interesting implications for triple helix stability.

Ab initio Hartree-Fock investigation of 1- H-pyrrolo[3,2- b]pyridine-3-yl acetic acid

NASA Astrophysics Data System (ADS)

Ramek, Michael; Tomić, Sanja

2001-09-01

The potential energy surface of 1- H-pyrrolo[3,2- b]pyridine-3-yl acetic acid has been investigated via RIIF/6-31G* calculations. The stationary points and reaction paths for syn orientation of the COOH group were determined and are compared with those of the derivatives of 3-indole acetic acid, which act as plant growth hormones. 1- H-pyrrolo[3,2- b]pyridine-3-yl acetic acid forms a kinetically stable conformer with a strong intramolecular hydrogen bond, in which the COOH group is in anti orientation. The influence of this hydrogen bond on bond lengths and vibration frequencies is described.

Bond-bending isomerism of Au 2I 3 -: Competition between covalent bonding and aurophilicity

DOE PAGES

Li, Wan -Lu; Liu, Hong -Tao; Jian, Tian; ...

2015-10-13

We report a joint photoelectron spectroscopy and theoretical investigation of the gaseous Au 2I 3 – cluster, which is found to exhibit two types of isomers due to competition between Au–I covalent bonding and Au–Au aurophilic interactions. The covalent bonding favors a bent IAuIAuI – structure with an obtuse Au–I–Au angle (100.7°), while aurophilic interactions pull the two Au atoms much closer, leading to an acutely bent structure (72.0°) with an Au–Au distance of 3.08 Å. The two isomers are separated by a small barrier and are nearly degenerate with the obtuse isomer being slightly more stable. At low temperature,more » only the obtuse isomer is observed; distinct experimental evidence is observed for the co-existence of a combination of isomers with both acute and obtuse bending angles at room temperature. As a result, the two bond-bending isomers of Au 2I 3 – reveal a unique example of one molecule being able to oscillate between different structures as a result of two competing chemical forces.« less

Bond-bending isomerism of Au 2I 3 -: Competition between covalent bonding and aurophilicity

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

Li, Wan -Lu; Liu, Hong -Tao; Jian, Tian

We report a joint photoelectron spectroscopy and theoretical investigation of the gaseous Au 2I 3 – cluster, which is found to exhibit two types of isomers due to competition between Au–I covalent bonding and Au–Au aurophilic interactions. The covalent bonding favors a bent IAuIAuI – structure with an obtuse Au–I–Au angle (100.7°), while aurophilic interactions pull the two Au atoms much closer, leading to an acutely bent structure (72.0°) with an Au–Au distance of 3.08 Å. The two isomers are separated by a small barrier and are nearly degenerate with the obtuse isomer being slightly more stable. At low temperature,more » only the obtuse isomer is observed; distinct experimental evidence is observed for the co-existence of a combination of isomers with both acute and obtuse bending angles at room temperature. As a result, the two bond-bending isomers of Au 2I 3 – reveal a unique example of one molecule being able to oscillate between different structures as a result of two competing chemical forces.« less

Parametrization of a force field for metals complexed to biomacromolecules: applications to Fe(II), Cu(II) and Pb(II)

NASA Astrophysics Data System (ADS)

David, Laurent; Amara, Patricia; Field, Martin J.; Major, François

2002-08-01

Although techniques for the simulation of biomolecules, such as proteins and RNAs, have greatly advanced in the last decade, modeling complexes of biomolecules with metal ions remains problematic. Precise calculations can be done with quantum mechanical methods but these are prohibitive for systems the size of macromolecules. More qualitative modeling can be done with molecular mechanical potentials but the parametrization of force fields for metals is often difficult, particularly if the bonding between the metal and the groups in its coordination shell has significant covalent character. In this paper we present a method for deriving bond and bond-angle parameters for metal complexes from experimental bond and bond-angle distributions obtained from the Cambridge Structural Database. In conjunction with this method, we also introduce a non-standard energy term of gaussian form that allows us to obtain a stable description of the coordination about a metal center during a simulation. The method was evaluated on Fe(II)-porphyrin complexes, on simple Cu(II) ion complexes and a number of complexes of the Pb(II) ion.

Orientation of X Lines in Asymmetric Magnetic Reconnection-Mass Ratio Dependency

NASA Technical Reports Server (NTRS)

Liu, Yi-Hsin; Hesse, M.; Kuznetsova, M.

2015-01-01

Using fully kinetic simulations, we study the X line orientation of magnetic reconnection in an asymmetric configuration. A spatially localized perturbation is employed to induce a single X line, which has sufficient freedom to choose its orientation in three-dimensional systems. The effect of ion to electron mass ratio is investigated, and the X line appears to bisect the magnetic shear angle across the current sheet in the large mass ratio limit. The orientation can generally be deduced by scanning through the corresponding 2-D simulations to find the reconnection plane that maximizes the peak reconnection electric field. The deviation from the bisection angle in the lower mass ratio limit is consistent with the orientation shift of the most unstable linear tearing mode in an electron-scale current sheet.

Structural and optical characteristics of in-situ sputtered highly oriented 15R-SiC thin films on different substrates

NASA Astrophysics Data System (ADS)

Mourya, Satyendra; Jaiswal, Jyoti; Malik, Gaurav; Kumar, Brijesh; Chandra, Ramesh

2018-01-01

In this work, we have reported the in-situ fabrication of nanocrystalline rhombohedral silicon carbide (15R-SiC) thin films by RF-magnetron sputtering at 800 °C substrate temperature. The structural and optical properties were investigated for the films grown on four different substrates (ZrO2, MgO, SiC, and Si). The contact angle measurement was performed on all the substrates to investigate the role of interfacial surface energy in nucleation and growth of the films. The XRD measurement revealed the growth of (1 0 10) orientation for all the samples and demonstrated better crystallinity on Si substrate, which was further corroborated by the TEM results. The Raman spectroscopy confirmed the growth of rhombohedral phase with 15R polytype. Surface characteristics of the films have been investigated by energy dispersive x-ray spectroscopy, FTIR, and atomic force microscope (AFM) to account for chemical composition, bonding, and root mean square surface roughness (δrms). The optical dispersion behavior of 15R-SiC thin films was examined by variable angle spectroscopic ellipsometry in the wide spectral range (246-1688 nm), including the surface characteristics in the optical model. The non-linear optical parameters (χ3 and n2) of the samples have been calculated by the Tichy and Ticha relation using a single effective oscillator model of Wemple and Didomenico. Additionally, our optical results provided an alternative way to measure the ratio of carrier concentration to the effective mass (N/m*). These investigated optical parameters allow one to design and fabricate optoelectronic, photonic, and telecommunication devices for deployment in extreme environment.

Crystal structure of allyl­ammonium hydrogen succinate at 100 K

PubMed Central

Dziuk, Błażej; Zarychta, Bartosz; Ejsmont, Krzysztof

2014-01-01

The asymmetric unit of the title compound, C2H8N+·C4H5O4 −, consists of two allyl­ammonium cations and two hydrogen succinate anions (Z′ = 2). One of the cations has a near-perfect syn-periplanar (cis) conformation with an N—C—C—C torsion angle of 0.4 (3)°, while the other is characterized by a gauche conformation and a torsion angle of 102.5 (3)°. Regarding the anions, three out of four carboxilic groups are twisted with respect to the central C–CH2–CH2–C group [dihedral angles = 24.4 (2), 31.2 (2) and 40.4 (2)°], the remaining one being instead almost coplanar, with a dihedral angle of 4.0 (2)°. In the crystal, there are two very short, near linear O—H⋯O hydrogen bonds between anions, with the H atoms shifted notably from the donor O towards the O⋯O midpoint. These O—H⋯O hydrogen bonds form helical chains along the [011] which are further linked to each other through N—H⋯O hydrogen bonds (involving all the available NH groups), forming layers lying parallel to (100). PMID:25309251

Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 from Escherichia coli.

PubMed

Sun, Chang; Taguchi, Alexander T; Vermaas, Josh V; Beal, Nathan J; O'Malley, Patrick J; Tajkhorshid, Emad; Gennis, Robert B; Dikanov, Sergei A

2016-10-11

The respiratory cytochrome bo 3 ubiquinol oxidase from Escherichia coli has a high-affinity ubiquinone binding site that stabilizes the one-electron reduced ubisemiquinone (SQ H ), which is a transient intermediate during the electron-mediated reduction of O 2 to water. It is known that SQ H is stabilized by two strong hydrogen bonds from R71 and D75 to ubiquinone carbonyl oxygen O1 and weak hydrogen bonds from H98 and Q101 to O4. In this work, SQ H was investigated with orientation-selective Q-band (∼34 GHz) pulsed 1 H electron-nuclear double resonance (ENDOR) spectroscopy on fully deuterated cytochrome (cyt) bo 3 in a H 2 O solvent so that only exchangeable protons contribute to the observed ENDOR spectra. Simulations of the experimental ENDOR spectra provided the principal values and directions of the hyperfine (hfi) tensors for the two strongly coupled H-bond protons (H1 and H2). For H1, the largest principal component of the proton anisotropic hfi tensor T z' = 11.8 MHz, whereas for H2, T z' = 8.6 MHz. Remarkably, the data show that the direction of the H1 H-bond is nearly perpendicular to the quinone plane (∼70° out of plane). The orientation of the second strong hydrogen bond, H2, is out of plane by ∼25°. Equilibrium molecular dynamics simulations on a membrane-embedded model of the cyt bo 3 Q H site show that these H-bond orientations are plausible but do not distinguish which H-bond, from R71 or D75, is nearly perpendicular to the quinone ring. Density functional theory calculations support the idea that the distances and geometries of the H-bonds to the ubiquinone carbonyl oxygens, along with the measured proton anisotropic hfi couplings, are most compatible with an anionic (deprotonated) ubisemiquinone.

Effect of acetabular cup abduction angle on wear of ultrahigh-molecular-weight polyethylene in hip simulator testing.

PubMed

Korduba, Laryssa A; Essner, Aaron; Pivec, Robert; Lancin, Perry; Mont, Michael A; Wang, Aiguo; Delanois, Ronald E

2014-10-01

The effect of acetabular component positioning on the wear rates of metal-on-polyethylene articulations has not been extensively studied. Placement of acetabular cups at abduction angles of more than 40° has been noted as a possible reason for early failure caused by increased wear. We conducted a study to evaluate the effects of different acetabular cup abduction angles on polyethylene wear rate, wear area, contact pressure, and contact area. Our in vitro study used a hip joint simulator and finite element analysis to assess the effects of cup orientation at 4 angles (0°, 40°, 50°, 70°) on wear and contact properties. Polyethylene bearings with 28-mm cobalt-chrome femoral heads were cycled in an environment mimicking in vivo joint fluid to determine the volumetric wear rate after 10 million cycles. Contact pressure and contact area for each cup abduction angle were assessed using finite element analysis. Results were correlated with cup abduction angles to determine if there were any differences among the 4 groups. The inverse relationship between volumetric wear rate and acetabular cup inclination angle demonstrated less wear with steeper cup angles. The largest abduction angle (70°) had the lowest contact area, largest contact pressure, and smallest head coverage. Conversely, the smallest abduction angle (0°) had the most wear and most head coverage. Polyethylene wear after total hip arthroplasty is a major cause of osteolysis and aseptic loosening, which may lead to premature implant failure. Several studies have found that high wear rates for cups oriented at steep angles contributed to their failure. Our data demonstrated that larger cup abduction angles were associated with lower, not higher, wear. However, this potentially "protective" effect is likely counteracted by other complications of steep cup angles, including impingement, instability, and edge loading. These factors may be more relevant in explaining why implants fail at a higher rate if cups are oriented at more than 40° of abduction.

System analysis through bond graph modeling

NASA Astrophysics Data System (ADS)

McBride, Robert Thomas

2005-07-01

Modeling and simulation form an integral role in the engineering design process. An accurate mathematical description of a system provides the design engineer the flexibility to perform trade studies quickly and accurately to expedite the design process. Most often, the mathematical model of the system contains components of different engineering disciplines. A modeling methodology that can handle these types of systems might be used in an indirect fashion to extract added information from the model. This research examines the ability of a modeling methodology to provide added insight into system analysis and design. The modeling methodology used is bond graph modeling. An investigation into the creation of a bond graph model using the Lagrangian of the system is provided. Upon creation of the bond graph, system analysis is performed. To aid in the system analysis, an object-oriented approach to bond graph modeling is introduced. A framework is provided to simulate the bond graph directly. Through object-oriented simulation of a bond graph, the information contained within the bond graph can be exploited to create a measurement of system efficiency. A definition of system efficiency is given. This measurement of efficiency is used in the design of different controllers of varying architectures. Optimal control of a missile autopilot is discussed within the framework of the calculated system efficiency.

The electronic structure of oriented poly[2-methoxy-5-(2'-ethyl-hexyloxy)- 1,4-phenylene-vinylene

NASA Astrophysics Data System (ADS)

Chambers, D. K.; Karanam, S.; Qi, D.; Selmic, S.; Losovyj, Y. B.; Rosa, L. G.; Dowben, P. A.

2005-02-01

Poly[2-methoxy-5-(2’-ethyl-hexyloxy)-1,4-phenylene-vinylene] (MEH-PPV) adopts a preferential orientation on indium tin oxide. Although the basic building block of this polymer provides a negligible overall point-group symmetry, the polymer MEH-PPV packs with sufficient order to exhibit band structure. The polymer is fragile with bond cleavage evident following both argon-ion impact and ultraviolet radiation, but annealing leads to the restoration of much of the bond order.

A structural insight into mechanical strength of graphene-like carbon and carbon nitride networks

NASA Astrophysics Data System (ADS)

Rahaman, Obaidur; Mortazavi, Bohayra; Dianat, Arezoo; Cuniberti, Gianaurelio; Rabczuk, Timon

2017-02-01

Graphene, one of the strongest materials ever discovered, triggered the exploration of many 2D materials in the last decade. However, the successful synthesis of a stable nanomaterial requires a rudimentary understanding of the relationship between its structure and strength. In the present study, we investigate the mechanical properties of eight different carbon-based 2D nanomaterials by performing extensive density functional theory calculations. The considered structures were just recently either experimentally synthesized or theoretically predicted. The corresponding stress-strain curves and elastic moduli are reported. They can be useful in training force field parameters for large scale simulations. A comparative analysis of these results revealed a direct relationship between atomic density per area and elastic modulus. Furthermore, for the networks that have an armchair and a zigzag orientation, we observed that they were more stretchable in the zigzag direction than the armchair direction. A critical analysis of the angular distributions and radial distribution functions suggested that it could be due to the higher ability of the networks to suppress the elongations of the bonds in the zigzag direction by deforming the bond angles. The structural interpretations provided in this work not only improve the general understanding of a 2D material’s strength but also enables us to rationally design them for higher qualities.

(E)-2-[(2,4,6-Tri-meth-oxy-benzyl-idene)amino]-phenol.

PubMed

Kaewmanee, Narissara; Chantrapromma, Suchada; Boonnak, Nawong; Quah, Ching Kheng; Fun, Hoong-Kun

2014-01-01

There are two independent mol-ecules in the asymmetric unit of the title compound, C16H17NO4, with similar conformations but some differences in their bond angles. Each mol-ecule adopts a trans configuration with respect to the methyl-idene C=N bond and is twisted with a dihedral angle between the two substituted benzene rings of 80.52 (7)° in one mol-ecule and 83.53 (7)° in the other. All meth-oxy groups are approximately coplanar with the attached benzene rings, with Cmeth-yl-O-C-C torsion angles ranging from -6.7 (2) to 5.07 (19)°. In the crystal, independent mol-ecules are linked together by O-H⋯N and O-H⋯O hydrogen bonds and a π-π inter-action [centroid-centroid distance of 3.6030 (9) Å], forming a dimer. The dimers are further linked by weak C-H⋯O inter-actions and another π-π inter-action [centroid-centroid distance of 3.9452 (9) Å] into layers lying parallel to the ab plane.

Synthesis, structural characterization, and DFT calculations of 3-buthyl-4-(3-methyl-3-mesitylcyclobut-1-yl)-1,3-thiazole-2(3H)-thione

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

Şen, B.; Barim, E.; Kirilmis, C.

2016-03-15

The title compound, C{sub 21}H{sub 29}NS{sub 2}, has been synthesized and its crystal structure has been determined from single crystal X-ray diffraction data. Crystals are monoclinic, a = 11.4923(8), b = 13.1842(7), c = 14.6583(8) Å, β = 109.983(6)°, sp. gr. P2{sub 1}/c, Z = 4. Mesityl and thiazole groups are in cis positions with respect to the cyclobutane ring. The cyclobutane ring is puckered, with a dihedral angle of 26.6(2)° between the two three-atom planes. The crystal structure involves one weak intermolecular C–H···S hydrogen-bond. The molecular geometry was also optimized using density functional theory (DFT/B3LYP) method with the 6-311G(d,more » p) basis set in ground state. Geometric parameters (bond lengths, bond angles and torsion angles) and vibrational assignments have been calculated theoretically and compared with the experimental data.« less

Bis[2-(hy-droxy-imino-meth-yl)phenolato]nickel(II): a second monoclinic polymorph.

PubMed

Rusanova, Julia A; Buvaylo, Elena A; Rusanov, Eduard B

2011-01-15

The title compound, [Ni(C(7)H(6)NO(2))(2)], (I), is a second monoclinic polymorph of the compound, (II), reported by Srivastava et al. [Acta Cryst. (1967), 22, 922] and Mereiter [Private communication (2002) CCDC refcode NISALO01]. The bond lengths and angles are similar in both structures. The mol-ecule in both structures lies on a crystallographic inversion center and both have an inter-nal hydrogen bond. The title compound crystallizes in the space group P2(1)/c (Z = 2), whereas compound (II) is in the space group P2(1)/n (Z = 2) with a similar cell volume but different cell parameters. In both polymorphs, mol-ecules are arranged in the layers but in contrast to the previously published compound (II) where the dihedral angle between the layers is 86.3°, in the title polymorph the same dihedral angle is 29.4°. The structure of (I) is stabilized by strong intra-molecular O-H⋯O hydrogen bonding between the O-H group and the phenolate O atom.

Comparison of fiber orientation and tensile-stiffness orientation measurements in paper

Treesearch

David W. Vahey; John M. Considine; Andy Kahra; Mark Scotch

2008-01-01

We have had the opportunity to subject cross-machine paper strips from two mills to both ultrasound and optical "fiber-orientation" tests to examine the relationships between the results. Both determine an orientation angle, in degrees. Both measure sheet anisotropy as an MD/CD orientation ratio. The optical test has no counterpart to the ultrasonic...

The atomic nature of polymer-metal interactions in adhesion, friction and wear

NASA Technical Reports Server (NTRS)

Buckley, D. H.; Brainard, W. A.

1973-01-01

Adhesion experiments with polytetra-fluoroethylene (PTFE) and polyimide contacting tungsten indicate that the polymers bond chemically to the clean metal surface. Polymer chain fragments which transfer to the surface of tungsten in field ion microscopy adhesion studies are highly oriented. Auger emission spectroscopy of PTFE transfer films to various metal surfaces indicates that the PTFE is bonded to the metal surface via the carbon atom. With PTFE in sliding contact with different orientations of aluminum, metal orientation is found to influence surfaces in sliding. The lowest friction and least amount of surface damage is detected on the highest atomic density (111) plane. The friction process itself can initiate polymer film formation from simple organic molecules.

The Effect of Local Orientation Change on the Detection of Contours Defined by Constant Curvature: Psychophysics and Image Statistics.

PubMed

Khuu, Sieu K; Cham, Joey; Hayes, Anthony

2016-01-01

In the present study, we investigated the detection of contours defined by constant curvature and the statistics of curved contours in natural scenes. In Experiment 1, we examined the degree to which human sensitivity to contours is affected by changing the curvature angle and disrupting contour curvature continuity by varying the orientation of end elements. We find that (1) changing the angle of contour curvature decreased detection performance, while (2) end elements oriented in the direction (i.e., clockwise) of curvature facilitated contour detection regardless of the curvature angle of the contour. In Experiment 2 we further established that the relative effect of end-element orientation on contour detection was not only dependent on their orientation (collinear or cocircular), but also their spatial separation from the contour, and whether the contour shape was curved or not (i.e., C-shaped or S-shaped). Increasing the spatial separation of end-elements reduced contour detection performance regardless of their orientation or the contour shape. However, at small separations, cocircular end-elements facilitated the detection of C-shaped contours, but not S-shaped contours. The opposite result was observed for collinear end-elements, which improved the detection of S- shaped, but not C-shaped contours. These dissociative results confirmed that the visual system specifically codes contour curvature, but the association of contour elements occurs locally. Finally, we undertook an analysis of natural images that mapped contours with a constant angular change and determined the frequency of occurrence of end elements with different orientations. Analogous to our behavioral data, this image analysis revealed that the mapped end elements of constantly curved contours are likely to be oriented clockwise to the angle of curvature. Our findings indicate that the visual system is selectively sensitive to contours defined by constant curvature and that this might reflect the properties of curved contours in natural images.

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

NASA Astrophysics Data System (ADS)

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

2005-06-01

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

Interaction between benzenedithiolate and gold: classical force field for chemical bonding.

PubMed

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

2005-06-22

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

The Effect of Bracket Base Pylon Orientation on the Shear Bond Strength of the ODP ANCHOR-LOCK Bracket Pad

DTIC Science & Technology

2013-06-06

El Banna MS, Elsaka SE. Twelve-month bracket failure rate with amorphous calcium phosphate bonding system. Eur J Orthod 2012; doi:10.1093/ejo...material, Cambridge University Press. 1993;3. Willems G, Carels CEL, Verbeke G. In vitro peel /shear bond strength evaluation of orthodontic bracket

The Role of Financial Sector in Providing Sustainable Development Goals

NASA Astrophysics Data System (ADS)

Tokareva, G. F.; Shalina, O. I.; Barkova, E. E.

2018-01-01

The article contains the analysis of the current ecological situation in the Republic of Bashkortostan as an oil production region of Russia. It was emerged that the decrease in emissions from means of transport caused by change in the calculation methodology. The statistical data on environmental control costs and payments for the use of natural resources in the Russian Federation for the period from 2008 to 2016 years have been analyzed. The measures aimed to create favorable conditions for the sustainable social and economic development of the region have been determined. The authors proposed alternative sources of financing the environmental protection: the issuance of ecological («green») bonds and the attraction of ecological deposits to finance environment-oriented investment projects. The main significant investment directions of the funds, obtained due to the emission of domestic ecological loan bonds, corporate ecological bonds and concessional environment-oriented bonds have been identified.

First principles study of the electronic properties and band gap modulation of two-dimensional phosphorene monolayer: Effect of strain engineering

NASA Astrophysics Data System (ADS)

Phuc, Huynh V.; Hieu, Nguyen N.; Ilyasov, Victor V.; Phuong, Le T. T.; Nguyen, Chuong V.

2018-06-01

The effect of strain on the structural and electronic properties of monolayer phosphorene is studied by using first-principle calculations based on the density functional theory. The intra- and inter-bond length and bond angle for monolayer phosphorene is also evaluated. The intra- and inter-bond length and the bond angle for phosphorene show an opposite tendency under different directions of the applied strain. At the equilibrium state, monolayer phosphorene is a semiconductor with a direct band gap at the Γ-point of 0.91 eV. A direct-indirect band gap transition is found in monolayer phosphorene when both the compression and tensile strain are simultaneously applied along both zigzag and armchair directions. Under the applied compression strain, a semiconductor-metal transition for monolayer phosphorene is observed at -13% and -10% along armchair and zigzag direction, respectively. The direct-indirect and phase transition will largely constrain application of monolayer phosphorene to electronic and optical devices.

Terahertz spectroscopic analysis of crystal orientation in polymers

NASA Astrophysics Data System (ADS)

Azeyanagi, Chisato; Kaneko, Takuya; Ohki, Yoshimichi

2018-05-01

Terahertz time-domain spectroscopy (THz-TDS) is attracting keen attention as a new spectroscopic tool for characterizing various materials. In this research, the possibility of analyzing the crystal orientation in a crystalline polymer by THz-TDS is investigated by measuring angle-resolved THz absorption spectra for sheets of poly(ethylene terephthalate), poly(ethylene naphthalate), and poly(phenylene sulfide). The resultant angle dependence of the absorption intensity of each polymer is similar to that of the crystal orientation examined using pole figures of X-ray diffraction. More specifically, THz-TDS can indicate the alignment of molecules in polymers.

Recording polarization gratings with a standing spiral wave

NASA Astrophysics Data System (ADS)

Vernon, Jonathan P.; Serak, Svetlana V.; Hakobyan, Rafik S.; Aleksanyan, Artur K.; Tondiglia, Vincent P.; White, Timothy J.; Bunning, Timothy J.; Tabiryan, Nelson V.

2013-11-01

A scalable and robust methodology for writing cycloidal modulation patterns of optical axis orientation in photosensitive surface alignment layers is demonstrated. Counterpropagating circularly polarized beams, generated by reflection of the input beam from a cholesteric liquid crystal, direct local surface orientation in a photosensitive surface. Purposely introducing a slight angle between the input beam and the photosensitive surface normal introduces a grating period/orientation that is readily controlled and templated. The resulting cycloidal diffractive waveplates offer utility in technologies requiring diffraction over a broad range of angles/wavelengths. This simple methodology of forming polarization gratings offers advantages over conventional fabrication techniques.

Three-Dimensional Geometry of Collagenous Tissues by Second Harmonic Polarimetry.

PubMed

Reiser, Karen; Stoller, Patrick; Knoesen, André

2017-06-01

Collagen is a biological macromolecule capable of second harmonic generation, allowing label-free detection in tissues; in addition, molecular orientation can be determined from the polarization dependence of the second harmonic signal. Previously we reported that in-plane orientation of collagen fibrils could be determined by modulating the polarization angle of the laser during scanning. We have now extended this method so that out-of-plane orientation angles can be determined at the same time, allowing visualization of the 3-dimensional structure of collagenous tissues. This approach offers advantages compared with other methods for determining out-of-plane orientation. First, the orientation angles are directly calculated from the polarimetry data obtained in a single scan, while other reported methods require data from multiple scans, use of iterative optimization methods, application of fitting algorithms, or extensive post-optical processing. Second, our method does not require highly specialized instrumentation, and thus can be adapted for use in almost any nonlinear optical microscopy setup. It is suitable for both basic and clinical applications. We present three-dimensional images of structurally complex collagenous tissues that illustrate the power of such 3-dimensional analyses to reveal the architecture of biological structures.

Three-Dimensional Geometry of Collagenous Tissues by Second Harmonic Polarimetry

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

Reiser, Karen; Stoller, Patrick; Knoesen, André

Collagen is a biological macromolecule capable of second harmonic generation, allowing label-free detection in tissues; in addition, molecular orientation can be determined from the polarization dependence of the second harmonic signal. Previously we reported that in-plane orientation of collagen fibrils could be determined by modulating the polarization angle of the laser during scanning. We have now extended this method so that out-of-plane orientation angles can be determined at the same time, allowing visualization of the 3-dimensional structure of collagenous tissues. This approach offers advantages compared with other methods for determining out-of-plane orientation. First, the orientation angles are directly calculated frommore » the polarimetry data obtained in a single scan, while other reported methods require data from multiple scans, use of iterative optimization methods, application of fitting algorithms, or extensive post-optical processing. Second, our method does not require highly specialized instrumentation, and thus can be adapted for use in almost any nonlinear optical microscopy setup. It is suitable for both basic and clinical applications. We present three-dimensional images of structurally complex collagenous tissues that illustrate the power of such 3-dimensional analyses to reveal the architecture of biological structures.« less

Three-Dimensional Geometry of Collagenous Tissues by Second Harmonic Polarimetry

DOE PAGES

Reiser, Karen; Stoller, Patrick; Knoesen, André

2017-06-01

Collagen is a biological macromolecule capable of second harmonic generation, allowing label-free detection in tissues; in addition, molecular orientation can be determined from the polarization dependence of the second harmonic signal. Previously we reported that in-plane orientation of collagen fibrils could be determined by modulating the polarization angle of the laser during scanning. We have now extended this method so that out-of-plane orientation angles can be determined at the same time, allowing visualization of the 3-dimensional structure of collagenous tissues. This approach offers advantages compared with other methods for determining out-of-plane orientation. First, the orientation angles are directly calculated frommore » the polarimetry data obtained in a single scan, while other reported methods require data from multiple scans, use of iterative optimization methods, application of fitting algorithms, or extensive post-optical processing. Second, our method does not require highly specialized instrumentation, and thus can be adapted for use in almost any nonlinear optical microscopy setup. It is suitable for both basic and clinical applications. We present three-dimensional images of structurally complex collagenous tissues that illustrate the power of such 3-dimensional analyses to reveal the architecture of biological structures.« less

Application of the bond valence method in the non-isovalent semiconductor alloy (GaN) 1–x (ZnO) x

DOE PAGES

Liu, Jian

2016-09-29

This paper studies the bond valence method (BVM) and its application in the non-isovalent semiconductor alloy (GaN) 1-x(ZnO) x. Particular attention is paid to the role of short-range order (SRO). A physical interpretation based on atomic orbital interaction is proposed and examined by density-functional theory (DFT) calculations. Combining BVM with Monte-Carlo simulations and a DFT-based cluster expansion model, bond-length distributions and bond-angle variations are predicted. The correlation between bond valence and bond stiffness is also revealed. Lastly the concept of bond valence is extended into the modelling of an atomistic potential.

[Spectral Study on the Effects of Angle-Tuned Filter Wedge Angle Parameter to Reflecting Characteristics].

PubMed

Yu, Kan; Huang, De-xiu; Yin, Juan-juan; Bao, Jia-qi

2015-08-01

Three-port tunable optical filter is a key device in the all-optic intelligent switching network and dense wavelength division multiplexing system. The characteristics of the reflecting spectrum, especially the reflectivity and the isolation degree are very important to the three-port filter. Angle-tuned thin film filter is widely used as a three-port tunable filter for its high rectangular degree and good temperature stability. The characteristics of the reflecting spectrum are greatly influenced not only by the incident angle, but also by the wedge angle parameter of the non-paralleled wedge thin film filter. In the present paper, the influences of the wedge angle parameter to the reflectivity and the half bandwidth are analyzed, and the reflecting spectrum characterstics are simulationed in different wedge angle parameter and polarity. The wedge angle-tuned thin film filter with 0.8° wedge angle parameter is fabricated. The experimental results show that keeping the wedge angle the same orientation to the incident angle will worsen the reflectivity and the rectangular degree of the reflecting spectrum. However, keeping the wedge angle orientation reverse to the incident angle will enhance the reflectivity and decrease the bandwidth, which will give higher reflectivity and isolation degree to the three-port filter than that of high parallel degree angle-tuned thin film filter.

The increase in conductance of a gold single atom chain during elastic elongation

NASA Astrophysics Data System (ADS)

Tavazza, F.; Barzilai, S.; Smith, D. T.; Levine, L. E.

2013-02-01

The conductance of monoatomic gold wires has been studied using ab initio calculations and the transmission was found to vary with the elastic strain. Counter-intuitively, the conductance was found to increase for the initial stages of the elongation, where the structure has a zigzag shape and the bond angles increase from ≈140° toward ≈160°. After a certain elongation limit, where the angles are relatively high, the bond length elongation associated with a Peierls distortion reverses this trend and the conductance decreases. These simulations are in good agreement with previously unexplained experimental results.

Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations.

PubMed

Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B; Jain, Abhinandan; Vaidehi, Nagarajan

2016-01-28

The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential energy distortions encountered in constrained ICMD simulations of peptide molecules.

Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B.; Jain, Abhinandan; Vaidehi, Nagarajan

2016-01-01

The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential energy distortions encountered in constrained ICMD simulations of peptide molecules.

Strain-relaxed structure in (001)/(100)-oriented epitaxial PbTiO3 films grown on (100) SrTiO3 substrates by metal organic chemical vapor deposition

NASA Astrophysics Data System (ADS)

Nakaki, Hiroshi; Kim, Yong Kwan; Yokoyama, Shintaro; Ikariyama, Rikyu; Funakubo, Hiroshi; Nishida, Ken; Saito, Keisuke

2007-09-01

The authors grew (001)- and (001)/(100)-oriented epitaxial PbTiO3 films with various thicknesses on (100)SrTiO3 substrates. They used x-ray diffraction to measure the angles between surface normal [001] of (001)-oriented domains and [100] of (100)-oriented domains. The angles were found to be approximately 3.6° when the film thickness exceeded 1100nm. This value is consistent with the value obtained by a geometric calculation for strain-free PbTiO3. This result suggests that thick epitaxial PbTiO3 films grown on (100)SrTiO3 substrates have a fully strain-relaxed structure.

Artificial photosynthetic systems: assemblies of slipped cofacial porphyrins and phthalocyanines showing strong electronic coupling.

PubMed

Satake, Akiharu; Kobuke, Yoshiaki

2007-06-07

This paper reviews selected types of structurally well defined assemblies of porphyrins and phthalocyanines with strong electronic coupling. Face-to-face, head-to-tail, slipped cofacial, and non-parallel dimeric motifs constructed by covalent and non-covalent bonds are compared in the earlier sections. Their molecular orientation, electronic overlap, and absorption and fluorescence properties are discussed with a view towards the development of artificial photosynthetic systems and molecular electronics. Complementary coordination dimers are fully satisfactory in terms of structural stability, orientation factor, pi-electronic overlap, and zero fluorescence quenching. In later sections, several polymeric and macrocyclic porphyrin assemblies constructed by a combination of covalent bonds and complementary coordination bonds are discussed from the viewpoint of light-harvesting antenna functions.

Orientation and Order of the Amide Group of Sphingomyelin in Bilayers Determined by Solid-State NMR

PubMed Central

Matsumori, Nobuaki; Yamaguchi, Toshiyuki; Maeta, Yoshiko; Murata, Michio

2015-01-01

Sphingomyelin (SM) and cholesterol (Chol) are considered essential for the formation of lipid rafts; however, the types of molecular interactions involved in this process, such as intermolecular hydrogen bonding, are not well understood. Since, unlike other phospholipids, SM is characterized by the presence of an amide group, it is essential to determine the orientation of the amide and its order in the lipid bilayers to understand the nature of the hydrogen bonds in lipid rafts. For this study, 1′-13C-2-15N-labeled and 2′-13C-2-15N-labeled SMs were prepared, and the rotational-axis direction and order parameters of the SM amide in bilayers were determined based on 13C and 15N chemical-shift anisotropies and intramolecular 13C-15N dipole coupling constants. Results revealed that the amide orientation was minimally affected by Chol, whereas the order was enhanced significantly in its presence. Thus, Chol likely promotes the formation of an intermolecular hydrogen-bond network involving the SM amide without significantly changing its orientation, providing a higher order to the SM amide. To our knowledge, this study offers new insight into the significance of the SM amide orientation with regard to molecular recognition in lipid rafts, and therefore provides a deeper understanding of the mechanism of their formation. PMID:26083921

The Strengths of High-Achieving Black High School Students in a Racially Diverse Setting

ERIC Educational Resources Information Center

Marsh, Kris; Chaney, Cassandra; Jones, Derrick

2012-01-01

Robert Hill (1972) identified strengths of Black families: strong kinship bonds, strong work orientation, adaptability of family roles, high achievement orientation, and religious orientation. Some suggest these strengths sustain the physical, emotional, social, and spiritual needs of Blacks. This study used narratives and survey data from a…

A Conditioned Visual Orientation Requires the Ellipsoid Body in "Drosophila"

ERIC Educational Resources Information Center

Guo, Chao; Du, Yifei; Yuan, Deliang; Li, Meixia; Gong, Haiyun; Gong, Zhefeng; Liu, Li

2015-01-01

Orientation, the spatial organization of animal behavior, is an essential faculty of animals. Bacteria and lower animals such as insects exhibit taxis, innate orientation behavior, directly toward or away from a directional cue. Organisms can also orient themselves at a specific angle relative to the cues. In this study, using…

Structure and spectra of H/sub 2/O in hydrated. beta. -alumina

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

Bates, J.B.; Dudney, N.J.; Brown, G.M.

1982-11-15

The structure and spectra of hydrated Li and Na ..beta..-alumina were investigated using neutron diffraction, infrared absorption, and Raman scattering. The dimensions of the hexagonal unit cell of a hydrated Li ..beta..-alumina crystal containing 1.55 H/sub 2/O molecules per unit cell are a = 5.591 A and c = 22.715 A. The oxygen atoms of the water molecules are located in the conduction plane between the mO, and the aBR sites; the protons, located above the below the plane, form bent hydrogen bonds with the O(4) oxygen ions. The HOH bond angle of water in Li ..beta..-alumina is 114/sup 0/more » and the Vertical BarO--HVertical Bar bond distance is 0.992 A. Based on polarized infrared spectra, H/sub 2/O adopts a similar structure and orientation in Na ..beta..-alumina. Spectra of absorbed H/sub 2/O, D/sub 2/O, and HDO species show that water molecules dissociate in Li ..beta..-alumina to form OH/sup -/ and H(H/sub 2/O)/sup +//sub n/ species. No evidence was found for the dissociation of water in Na ..beta..-alumina. The absorption coefficients determined for OH/sup -/ and H/sub 2/O in Li ..beta..-alumina include local field corrections. A large local field anisotropy at the protons of H/sub 2/O is responsible for the large ratio of the intensities of ..nu../sub 3/ and ..nu../sub 1/ observed for water in Li and Na ..beta..-alumina.« less

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

Graf, J.; d'Astuto, M.; Jozwiak, C.

We report the first measurement of the Cu-O bond stretching phonon dispersion in optimally doped Bi{sub 2}Sr{sub 1.6}La{sub 0.4}Cu{sub 2}O{sub 6+{delta}} using inelastic x-ray scattering. We found a softening of this phonon at q = ({approx} 0.25, 0, 0) from 76 to 60 meV, similar to the one reported in other cuprates. A comparison with angle-resolved photoemission data on the same sample revealed an excellent agreement in terms of energy and momentum between the angle-resolved photoemission nodal kink and the soft part of the bond stretching phonon. Indeed, we find that the momentum space where a 63 {+-} 5 meVmore » kink is observed can be connected with a vector q = ({zeta}, 0, 0) with {zeta} {ge} 0.22, corresponding exactly to the soft part of the bond stretching phonon.« less

Benzamide-picric acid (1/1).

PubMed

Sivaramkumar, M S; Velmurugan, R; Sekar, M; Ramesh, P; Ponnuswamy, M N

2010-06-26

In the title compound, C(7)H(7)NO·C(6)H(3)N(3)O(7), one of the nitro groups of the picric acid mol-ecule lies in the plane of the attached benzene ring [dihedral angle = 1.4 (1)°] while the other two are twisted away by 9.9 (1) and 30.3 (1)°. In the benzamide mol-ecule, the amide group is almost coplanar with the benzene ring [dihedral angle = 4.4 (1)°]. An intra-molecular O-H⋯O hydrogen bond generates an S6 ring motif. In the crystal, mol-ecules are linked into a ribbon-like structure along the b axis by O-H⋯O and N-H⋯O inter-molecular hydrogen bonds. In addition, C-H⋯O hydrogen bonds and short O⋯O contacts [2.828 (2) Å] are observed.

Neutral Hydrogen Structures Trace Dust Polarization Angle: Implications for Cosmic Microwave Background Foregrounds.

PubMed

Clark, S E; Hill, J Colin; Peek, J E G; Putman, M E; Babler, B L

2015-12-11

Using high-resolution data from the Galactic Arecibo L-Band Feed Array HI (GALFA-Hi) survey, we show that linear structure in Galactic neutral hydrogen (Hi) correlates with the magnetic field orientation implied by Planck 353 GHz polarized dust emission. The structure of the neutral interstellar medium is more tightly coupled to the magnetic field than previously known. At high Galactic latitudes, where the Planck data are noise dominated, the Hi data provide an independent constraint on the Galactic magnetic field orientation, and hence the local dust polarization angle. We detect strong cross-correlations between template maps constructed from estimates of dust intensity combined with either Hi-derived angles, starlight polarization angles, or Planck 353 GHz angles. The Hi data thus provide a new tool in the search for inflationary gravitational wave B-mode polarization in the cosmic microwave background, which is currently limited by dust foreground contamination.

Mechanical aspects of degree of cement bonding and implant wedge effect.

PubMed

Yoon, Yong-San; Oxland, Thomas R; Hodgson, Antony J; Duncan, Clive P; Masri, Bassam A; Choi, Donok

2008-11-01

The degree of bonding between the femoral stem and cement in total hip replacement remains controversial. Our objective was to determine the wedge effect by debonding and stem taper angle on the structural behavior of axisymmetric stem-cement-bone cylinder models. Stainless steel tapered plugs with a rough (i.e. bonded) or smooth (i.e. debonded) surface finish were used to emulate the femoral stem. Three different stem taper angles (5 degrees , 7.5 degrees , 10 degrees ) were used for the debonded constructs. Non-tapered and tapered (7.5 degrees ) aluminum cylindrical shells were used to emulate the diaphyseal and metaphyseal segments of the femur. The cement-aluminum cylinder interface was designed to have a shear strength that simulated bone-cement interfaces ( approximately 8MPa). The test involved applying axial compression at a rate of 0.02mm/s until failure. Six specimens were tested for each combination of the variables. Finite element analysis was used to enhance the understanding of the wedge effect. The debonded stems sustained about twice as much load as the bonded stem, regardless of taper angle. The metaphyseal model carried 35-50% greater loads than the diaphyseal models and the stem taper produced significant differences. Based on the finite element analysis, failure was most probably by shear at the cement-bone interface. Our results in this simplified model suggest that smooth (i.e. debonded) stems have greater failure loads and will incur less slippage or shear failure at the cement-bone interface than rough (i.e. bonded) stems.

The natural angle between the hand and handle and the effect of handle orientation on wrist radial/ulnar deviation during maximal push exertions.

PubMed

Young, Justin G; Lin, Jia-Hua; Chang, Chien-Chi; McGorry, Raymond W

2013-01-01

The purpose of this experiment was to quantify the natural angle between the hand and a handle, and to investigate three design factors: handle rotation, handle tilt and between-handle width on the natural angle as well as resultant wrist radial/ulnar deviation ('RUD') for pushing tasks. Photographs taken of the right upper limb of 31 participants (14 women and 17 men) performing maximal seated push exertions on different handles were analysed. Natural hand/handle angle and RUD were assessed. It was found that all of the three design factors significantly affected natural handle angle and wrist RUD, but participant gender did not. The natural angle between the hand and the cylindrical handle was 65 ± 7°. Wrist deviation was reduced for handles that were rotated 0° (horizontal) and at the narrow width (31 cm). Handles that were tilted forward 15° reduced radial deviation consistently (12-13°) across handle conditions. Manual materials handling (MMH) tasks involving pushing have been related to increased risk of musculoskeletal injury. This study shows that handle orientation influences hand and wrist posture during pushing, and suggests that the design of push handles on carts and other MMH aids can be improved by adjusting their orientation to fit the natural interface between the hand and handle.

Determination of 3D optic axis orientation in cartilage by polarization-sensitive optical coherence tomography

NASA Astrophysics Data System (ADS)

Ugryumova, Nadya; Bonesi, Marco; Matcher, Stephen J.

2008-02-01

Polarization-sensitive optical coherence tomography has been used to solve fast-axis fibre orientation in three dimension space. Previously we have demonstrated that the apparent variations in polar angle orientation of collagen fibers along sagittal ridge of equine third metacarpophalangeal joint exist. A quantitative method based on multiple angles of illumination has been proposed to determine the polar angle of the collagen fibers. This method however ignored the full 3D structure by assuming that the collagen fibers long-axis lay within the plane of incidence. A new quantitative method based on the theory of light propagation in uniaxial materials is described which avoids this assumption. To test this method we have performed control experiments on a sample of equine tendon (this tissue has well defined c-axis lying along the long-axis of the tendon). Several samples of tendon were cut to achieve a planar surface inclined at -20° to the long axis. Additional 30° rotation provided non-zero azimuthal angle. The surface was then imaged using incident beam angles -40°, -20°, 0, +20°, +40° in two orthogonal planes. Values for both the polar and azimuthal angles were then derived using a numerical optimisation procedure. Results agreed qualitatively with the nominal values but suggested that the accuracy was limited by our method of determining the apparent birefringence.

Determination of 3D optic axis orientation in cartilage by polarization-sensitive optical coherence tomography

NASA Astrophysics Data System (ADS)

Ugryumova, Nadya; Matcher, Stephen J.

2007-02-01

Polarization-sensitive optical coherence tomography has been used to solve fast-axis fibre orientation in three dimension space. Previously we have demonstrated that the apparent variations in polar angle orientation of collagen fibers along sagittal ridge of equine third metacarpophalangeal joint exist. A quantitative method based on multiple angles of illumination has been proposed to determine the polar angle of the collagen fibers. This method however ignored the full 3-D structure by assuming that the collagen fibers long-axis lay within the plane of incidence. A new quantitative method based on the theory of light propagation in uniaxial materials is described which avoids this assumption. To test this method we have performed control experiments on a sample of equine tendon (this tissue has well defined c-axis lying along the long-axis of the tendon). Several samples of tendon were cut to achieve a planar surface inclined at -20° to the long axis. Additional 30° rotation provided non-zero azimuthal angle. The surface was then imaged using incident beam angles -40°, -20°, 0, +20°, +40° in two orthogonal planes. Values for both the polar and azimuthal angles were then derived using a numerical optimisation procedure. Results agreed qualitatively with the nominal values but suggested that the accuracy was limited by our method of determining the apparent birefringence.

The Uncertainty of Local Background Magnetic Field Orientation in Anisotropic Plasma Turbulence

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

Gerick, F.; Saur, J.; Papen, M. von, E-mail: felix.gerick@uni-koeln.de

In order to resolve and characterize anisotropy in turbulent plasma flows, a proper estimation of the background magnetic field is crucially important. Various approaches to calculating the background magnetic field, ranging from local to globally averaged fields, are commonly used in the analysis of turbulent data. We investigate how the uncertainty in the orientation of a scale-dependent background magnetic field influences the ability to resolve anisotropy. Therefore, we introduce a quantitative measure, the angle uncertainty, that characterizes the uncertainty of the orientation of the background magnetic field that turbulent structures are exposed to. The angle uncertainty can be used asmore » a condition to estimate the ability to resolve anisotropy with certain accuracy. We apply our description to resolve the spectral anisotropy in fast solar wind data. We show that, if the angle uncertainty grows too large, the power of the turbulent fluctuations is attributed to false local magnetic field angles, which may lead to an incorrect estimation of the spectral indices. In our results, an apparent robustness of the spectral anisotropy to false local magnetic field angles is observed, which can be explained by a stronger increase of power for lower frequencies when the scale of the local magnetic field is increased. The frequency-dependent angle uncertainty is a measure that can be applied to any turbulent system.« less

Energy monitoring and analysis during deformation of bedded-sandstone: use of acoustic emission.

PubMed

Wasantha, P L P; Ranjith, P G; Shao, S S

2014-01-01

This paper investigates the mechanical behaviour and energy releasing characteristics of bedded-sandstone with bedding layers in different orientations, under uniaxial compression. Cylindrical sandstone specimens (54 mm diameter and 108 mm height) with bedding layers inclined at angles of 10°, 20°, 35°, 55°, and 83° to the minor principal stress direction, were produced to perform a series of Uniaxial Compressive Strength (UCS) tests. One of the two identical sample sets was fully-saturated with water before testing and the other set was tested under dry conditions. An acoustic emission system was employed in all the testing to monitor the acoustic energy release during the whole deformation process of specimens. From the test results, the critical joint orientation was observed as 55° for both dry and saturated samples and the peak-strength losses due to water were 15.56%, 20.06%, 13.5%, 13.2%, and 13.52% for the bedding orientations 10°, 20°, 35°, 55°, and 83°, respectively. The failure mechanisms for the specimens with bedding layers in 10°, 20° orientations showed splitting type failure, while the specimens with bedding layers in 55°, 83° orientations were failed by sliding along a weaker bedding layer. The failure mechanism for the specimens with bedding layers in 35° orientation showed a mixed failure mode of both splitting and sliding types. Analysis of the acoustic energy, captured from the acoustic emission detection system, revealed that the acoustic energy release is considerably higher in dry specimens than that of the saturated specimens at any bedding orientation. In addition, higher energy release was observed for specimens with bedding layers oriented in shallow angles (which were undergoing splitting type failures), whereas specimens with steeply oriented bedding layers (which were undergoing sliding type failures) showed a comparatively less energy release under both dry and saturated conditions. Moreover, a considerable amount of energy dissipation before the ultimate failure was observed for specimens with bedding layers oriented in shallow angles under both dry and saturated conditions. These results confirm that when rock having bedding layers inclined in shallow angles the failures could be more violent and devastative than the failures of rock with steeply oriented bedding layers. Copyright © 2013 Elsevier B.V. All rights reserved.

Fixman compensating potential for general branched molecules

NASA Astrophysics Data System (ADS)

Jain, Abhinandan; Kandel, Saugat; Wagner, Jeffrey; Larsen, Adrien; Vaidehi, Nagarajan

2013-12-01

The technique of constraining high frequency modes of molecular motion is an effective way to increase simulation time scale and improve conformational sampling in molecular dynamics simulations. However, it has been shown that constraints on higher frequency modes such as bond lengths and bond angles stiffen the molecular model, thereby introducing systematic biases in the statistical behavior of the simulations. Fixman proposed a compensating potential to remove such biases in the thermodynamic and kinetic properties calculated from dynamics simulations. Previous implementations of the Fixman potential have been limited to only short serial chain systems. In this paper, we present a spatial operator algebra based algorithm to calculate the Fixman potential and its gradient within constrained dynamics simulations for branched topology molecules of any size. Our numerical studies on molecules of increasing complexity validate our algorithm by demonstrating recovery of the dihedral angle probability distribution function for systems that range in complexity from serial chains to protein molecules. We observe that the Fixman compensating potential recovers the free energy surface of a serial chain polymer, thus annulling the biases caused by constraining the bond lengths and bond angles. The inclusion of Fixman potential entails only a modest increase in the computational cost in these simulations. We believe that this work represents the first instance where the Fixman potential has been used for general branched systems, and establishes the viability for its use in constrained dynamics simulations of proteins and other macromolecules.

Hydrophobic fluorine mediated switching of the hydrogen bonding site as well as orientation of water molecules in the aqueous mixture of monofluoroethanol: IR, molecular dynamics and quantum chemical studies.

PubMed

Mondal, Saptarsi; Biswas, Biswajit; Nandy, Tonima; Singh, Prashant Chandra

2017-09-20

The local structures between water-water, alcohol-water and alcohol-alcohol have been investigated for aqueous mixtures of ethanol (ETH) and monofluoroethanol (MFE) by the deconvolution of IR bands in the OH stretching region, molecular dynamics simulation and quantum chemical calculations. It has been found that the addition of a small amount of ETH into the aqueous medium increases the strength of the hydrogen bonds between water molecules. In an aqueous mixture of MFE, the substitution of a single fluorine induces a change in the orientation as well as the hydrogen bonding site of water molecules from the oxygen to the fluorine terminal of MFE. The switching of the hydrogen bonding site of water in the aqueous mixture of MFE results in comparatively strong hydrogen bonds between MFE and water molecules as well as less clustering of water molecules, unlike the case of the aqueous mixture of ETH. These findings about the modification of a hydrogen bond network by the hydrophobic fluorine group probably make fluorinated molecules useful for pharmaceutical as well as biological applications.

Optical performance effects of the misalignment of nonimaging optics solar collectors

NASA Astrophysics Data System (ADS)

Ferry, Jonathan; Ricketts, Melissa; Winston, Roland

2017-09-01

The use of non-imaging optics in the application of high temperature solar thermal collectors can be extremely advantageous in eliminating the need to track the sun. The stationary nature of non-imaging optics collectors, commonly called compound parabolic concentrators (CPC's), present a unique design challenge when orienting them to collect sunlight. Many facilities throughout the world that adopt CPCs are not situated to orient the collectors in the ideal angle facing the sun. This East-West misalignment can adversely affect the optical and power performance of the CPC collector. To characterize how this misalignment effects CPCs, reverse raytracing simulations are conducted for varying offset angles of the collectors from solar South. Optical performance is analyzed for an ideal East-West oriented CPC with a 40-degree acceptance angle. Direction cosine plots are used to develop a ratio of annual solar collection by the CPC over the total annual solar input. From these simulations, average annual collector performance is given for offset angles ranging from 0 to 90 degrees for different Earth Latitudes in 10 degree increments.

An analytical method on the surface residual stress for the cutting tool orientation

NASA Astrophysics Data System (ADS)

Li, Yueen; Zhao, Jun; Wang, Wei

2010-03-01

The residual stress is measured by choosing 8 kinds orientations on cutting the H13 dies steel on the HSM in the experiment of this paper. The measured data shows on that the residual stress exists periodicity for the different rake angle (β) and side rake angle (θ) parameters, further study find that the cutting tool orientations have closed relationship with the residual stresses, and for the original of the machined residual stress on the surface from the cutting force and the axial force, it can be gained the simply model of tool-workpiece force, using the model it can be deduced the residual stress model, which is feasible to calculate the size of residual stress. And for almost all the measured residual stresses are compressed stress, the compressed stress size and the direction could be confirmed by the input data for the H13 on HSM. As the result, the residual stress model is the key for optimization of rake angle (β) and side rake angle (θ) in theory, using the theory the more cutting mechanism can be expressed.

Oppugning the assumptions of spatial averaging of segment and joint orientations.

PubMed

Pierrynowski, Michael Raymond; Ball, Kevin Arthur

2009-02-09

Movement scientists frequently calculate "arithmetic averages" when examining body segment or joint orientations. Such calculations appear routinely, yet are fundamentally flawed. Three-dimensional orientation data are computed as matrices, yet three-ordered Euler/Cardan/Bryant angle parameters are frequently used for interpretation. These parameters are not geometrically independent; thus, the conventional process of averaging each parameter is incorrect. The process of arithmetic averaging also assumes that the distances between data are linear (Euclidean); however, for the orientation data these distances are geodesically curved (Riemannian). Therefore we question (oppugn) whether use of the conventional averaging approach is an appropriate statistic. Fortunately, exact methods of averaging orientation data have been developed which both circumvent the parameterization issue, and explicitly acknowledge the Euclidean or Riemannian distance measures. The details of these matrix-based averaging methods are presented and their theoretical advantages discussed. The Euclidian and Riemannian approaches offer appealing advantages over the conventional technique. With respect to practical biomechanical relevancy, examinations of simulated data suggest that for sets of orientation data possessing characteristics of low dispersion, an isotropic distribution, and less than 30 degrees second and third angle parameters, discrepancies with the conventional approach are less than 1.1 degrees . However, beyond these limits, arithmetic averaging can have substantive non-linear inaccuracies in all three parameterized angles. The biomechanics community is encouraged to recognize that limitations exist with the use of the conventional method of averaging orientations. Investigations requiring more robust spatial averaging over a broader range of orientations may benefit from the use of matrix-based Euclidean or Riemannian calculations.

Anisotropic perception of visual angle: implications for the horizontal-vertical illusion, overconstancy of size, and the moon illusion.

PubMed

Higashiyama, A

1992-03-01

Three experiments investigated anisotropic perception of visual angle outdoors. In Experiment 1, scales for vertical and horizontal visual angles ranging from 20 degrees to 80 degrees were constructed with the method of angle production (in which the subject reproduced a visual angle with a protractor) and the method of distance production (in which the subject produced a visual angle by adjusting viewing distance). In Experiment 2, scales for vertical and horizontal visual angles of 5 degrees-30 degrees were constructed with the method of angle production and were compared with scales for orientation in the frontal plane. In Experiment 3, vertical and horizontal visual angles of 3 degrees-80 degrees were judged with the method of verbal estimation. The main results of the experiments were as follows: (1) The obtained angles for visual angle are described by a quadratic equation, theta' = a + b theta + c theta 2 (where theta is the visual angle; theta', the obtained angle; a, b, and c, constants). (2) The linear coefficient b is larger than unity and is steeper for vertical direction than for horizontal direction. (3) The quadratic coefficient c is generally smaller than zero and is negatively larger for vertical direction than for horizontal direction. And (4) the obtained angle for visual angle is larger than that for orientation. From these results, it was possible to predict the horizontal-vertical illusion, over-constancy of size, and the moon illusion.

Force-field parameters of the Psi and Phi around glycosidic bonds to oxygen and sulfur atoms.

PubMed

Saito, Minoru; Okazaki, Isao

2009-12-01

The Psi and Phi torsion angles around glycosidic bonds in a glycoside chain are the most important determinants of the conformation of a glycoside chain. We determined force-field parameters for Psi and Phi torsion angles around a glycosidic bond bridged by a sulfur atom, as well as a bond bridged by an oxygen atom as a preparation for the next study, i.e., molecular dynamics free energy calculations for protein-sugar and protein-inhibitor complexes. First, we extracted the Psi or Phi torsion energy component from a quantum mechanics (QM) total energy by subtracting all the molecular mechanics (MM) force-field components except for the Psi or Phi torsion angle. The Psi and Phi energy components extracted (hereafter called "the remaining energy components") were calculated for simple sugar models and plotted as functions of the Psi and Phi angles. The remaining energy component curves of Psi and Phi were well represented by the torsion force-field functions consisting of four and three cosine functions, respectively. To confirm the reliability of the force-field parameters and to confirm its compatibility with other force-fields, we calculated adiabatic potential curves as functions of Psi and Phi for the model glycosides by adopting the Psi and Phi force-field parameters obtained and by energetically optimizing other degrees of freedom. The MM potential energy curves obtained for Psi and Phi well represented the QM adiabatic curves and also these curves' differences with regard to the glycosidic oxygen and sulfur atoms. Our Psi and Phi force-fields of glycosidic oxygen gave MM potential energy curves that more closely represented the respective QM curves than did those of the recently developed GLYCAM force-field. (c) 2009 Wiley Periodicals, Inc.

Muscle Fiber Orientation Angle Dependence of the Tensile Fracture Behavior of Frozen Fish Muscle

NASA Astrophysics Data System (ADS)

Hagura, Yoshio; Okamoto, Kiyoshi; Suzuki, Kanichi; Kubota, Kiyoshi

We have proposed a new cutting method for frozen fish named "cryo-cutting". This method applied tensile fracture force or bending fracture force to the frozen fish at appropriate low temperatures. In this paper, to clarify cryo-cutting mechanism, we analyzed tensile fracture behavior of the frozen fish muscle. In the analysis, the frozen fish muscle was considered unidirectionally fiber-reinforced composite material which consisted of fiber (muscle fiber) and matrix (connective tissue). Fracture criteria (maximum stress criterion, Tsai-Hill criterion) for the unidirectionally fiber-reinforced composite material were used. The following results were obtained: (1) By using Tsai-Hill criterion, muscle fiber orientation angle dependence of the tensile fracture stress could be calculated. (2) By using the maximum stress theory jointly with Tsai-Hill criterion, muscle fiber orientation angle dependence of the fracture mode of the frozen fish muscle could be estimated.

2D simulations of orthogonal cutting of CFRP: Effect of tool angles on parameters of cut and chip morphology

NASA Astrophysics Data System (ADS)

Benhassine, Mehdi; Rivière-Lorphèvre, Edouard; Arrazola, Pedro-Jose; Gobin, Pierre; Dumas, David; Madhavan, Vinay; Aizpuru, Ohian; Ducobu, François

2018-05-01

Carbon-fiber reinforced composites (CFRP) are attractive materials for lightweight designs in applications needing good mechanical properties. Machining of such materials can be harder than metals due to their anisotropic behavior. In addition, the combination of the fibers and resin mechanical properties must also include the fiber orientation. In the case of orthogonal cutting, the tool inclination, rake angle or cutting angle usually influence the cutting process but such a detailed investigation is currently lacking in a 2D configuration. To address this issue, a model has been developed with Abaqus Explicit including Hashin damage. This model has been validated with experimental results from the literature. The effects of the tool parameters (rake angle, clearance angle) on the tool cutting forces, CFRP chip morphology and surface damage are herewith studied. It is shown that 90° orientation for the CFRP increases the surface damage. The rake angle has a minimal effect on the cutting forces but modifies the chip formation times. The feed forces are increased with increasing rake angle.

Methyl 6-eth-oxy-3-phenyl-3a,4-dihydro-3H-chromeno[4,3-c]isoxazole-3a-car-boxylate.

PubMed

Suresh, G; Srinivasan, J; Bakthadoss, M; Aravindhan, S

2013-02-01

In the title compound, C(20)H(19)NO(5), the dihedral angle between the mean plane of the pyran ring (which has a half-chair conformation) and the benzene ring of the chromeno ring system is 7.21 (7)°. The dihedral angle between the mean plane of the chromeno ring system and the isoxazole ring is 21.78 (6)°, while the isoxazole ring forms a dihedral angle of 72.60 (8)° with the attached phenyl ring. In the crystal, mol-ecules are linked via pairs of C-H⋯O hydrogen bonds, forming inversion dimers with an R(2) (2)(10) ring motif. These dimers are linked via C-H⋯N hydrogen bonds, forming chains along [001].

Building relationships with physicians. Internal marketing efforts help strengthen organizational bonds at a rural health care clinic.

PubMed

Peltier, J W; Boyt, T; Westfall, J E

1997-01-01

Physician turnover is costly for health care organizations, especially for rural organizations. One approach management can take to reduce turnover is to promote physician loyalty by treating them as an important customer segment. The authors develop an information--oriented framework for generating physician loyalty and illustrate how this framework has helped to eliminate physician turnover at a rural health care clinic. Rural health care organizations must develop a more internal marketing orientation in their approach to establishing strong relationship bonds with physicians.

Calculation of the structure of carbon clusters based on fullerene-like C24 and C48 molecules

NASA Astrophysics Data System (ADS)

Krylova, K. A.; Baimova, Yu. A.; Dmitriev, S. V.; Mulyukov, R. R.

2016-02-01

Equilibrium structures obtained by linking with valence bonds the carbon carcasses of two fullerene-like molecules have been studied by molecular dynamics simulation. In free fullerene, carbon atoms form sp 2 hybridized bonds, but at places of links between fullerenes, sp 3 hybridized bonds are formed, which determines the changes in the properties of such structures. In the literature, the topology of diamond-like phases is described, but equilibrium clusters based on fullerene-like molecules are underexplored. The right angles between the C-C bonds are energetically unfavorable, and the reduction in the energy of clusters in the process of relaxation is connected with the optimization of valence angles, which leads to a reduction in the symmetry of clusters and, in a number of cases, even to disruption of some valence bonds. It is shown that different fashions of linking two fullerenes result in the formation of clusters with different structures and energies. Different initial conditions can lead to different configurations of clusters with the same topology. Among the analyzed clusters, a structure with the minimum potential energy per atom was found. The results of this work contribute to the study of the real structure of carbon clusters.

Controlled Contamination of Epoxy Composites with PDMS and Removal by Laser Ablation

NASA Technical Reports Server (NTRS)

Palmieri, Frank; Ledesma, Rodolfo; Cataldo, Daniel; Lin, Yi; Wohl, Christopher; Gupta, Mool; Connell, John

2016-01-01

Surface preparation is critical to the performance of adhesively bonded composites. During manufacturing, minute quantities of mold release compounds are inevitably deposited on faying surfaces and may compromise bond performance. To ensure safety, mechanical fasteners and other crack arrest features must be installed in the bondlines of primary structures, which negates some advantages of adhesively bonded construction. Laser ablation is an automated, repeatable, and scalable process with high potential for the surface preparation of metals and composites in critical applications such as primary airframe structures. In this study, laser ablation is evaluated on composite surfaces for the removal of polydimethylsiloxane (PDMS), a common mold release material. Composite panels were contaminated uniformly with PDMS film thicknesses as low as 6.0 nm as measured by variable angle spectroscopic ellipsometry. Bond performance was assessed by mechanical testing using a 250 F cure, epoxy adhesive and compared with pre-bond surface inspection results. Water contact angle, optically stimulated electron emission, and laser induced breakdown spectroscopy were used to characterize contaminated and laser ablated surfaces. The failure mode obtained from double cantilever beam tests correlated well with surface characterization data. The test results indicated that even low levels of PDMS were not completely removed by laser ablation.

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

Shojaee, S. A.; Qi, Y.; Wang, Y. Q.

Ion irradiation is an alternative to heat treatment for transforming organic-inorganic thin films to a ceramic state. One major shortcoming in previous studies of ion-irradiated films is the assumption that constituent phases in ion-irradiated and heat-treated films are identical and that the ion irradiation effect is limited to changes in composition. Here, we investigate the effects of ion irradiation on both the composition and structure of constituent phases and use the results to explain the measured elastic modulus of the films. Our results indicated that the microstructure of the irradiated films consisted of carbon clusters within a silica matrix. Itmore » was found that carbon was present in a non-graphitic sp 2-bonded configuration. It was also observed that ion irradiation caused a decrease in the Si-O-Si bond angle of silica, similar to the effects of applied pressure. A phase transformation from tetrahedrally bonded to octahedrally bonded silica was also observed. The results indicated the incorporation of carbon within the silica network. Finally, a combination of the decrease in Si-O-Si bond angle and an increase in the carbon incorporation within the silica network was found to be responsible for the increase in the elastic modulus of the films.« less

Mach-like capillary-gravity wakes.

PubMed

Moisy, Frédéric; Rabaud, Marc

2014-08-01

We determine experimentally the angle α of maximum wave amplitude in the far-field wake behind a vertical surface-piercing cylinder translated at constant velocity U for Bond numbers Bo(D)=D/λ(c) ranging between 0.1 and 4.2, where D is the cylinder diameter and λ(c) the capillary length. In all cases the wake angle is found to follow a Mach-like law at large velocity, α∼U(-1), but with different prefactors depending on the value of Bo(D). For small Bo(D) (large capillary effects), the wake angle approximately follows the law α≃c(g,min)/U, where c(g,min) is the minimum group velocity of capillary-gravity waves. For larger Bo(D) (weak capillary effects), we recover a law α∼√[gD]/U similar to that found for ship wakes at large velocity [Rabaud and Moisy, Phys. Rev. Lett. 110, 214503 (2013)]. Using the general property of dispersive waves that the characteristic wavelength of the wave packet emitted by a disturbance is of order of the disturbance size, we propose a simple model that describes the transition between these two Mach-like regimes as the Bond number is varied. We show that the new capillary law α≃c(g,min)/U originates from the presence of a capillary cusp angle (distinct from the usual gravity cusp angle), along which the energy radiated by the disturbance accumulates for Bond numbers of order of unity. This model, complemented by numerical simulations of the surface elevation induced by a moving Gaussian pressure disturbance, is in qualitative agreement with experimental measurements.

Phi ({Phi}) and psi ({Psi}) angles involved in malarial peptide bonds determine sterile protective immunity

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

Patarroyo, Manuel E., E-mail: mepatarr@gmail.com; Universidad Nacional de Colombia, Bogota; Moreno-Vranich, Armando

Highlights: Black-Right-Pointing-Pointer Phi ({Phi}) and psi ({Psi}) angles determine sterile protective immunity. Black-Right-Pointing-Pointer Modified peptide's tendency to assume a regular conformation related to a PPII{sub L}. Black-Right-Pointing-Pointer Structural modifications in mHABPs induce Ab and protective immunity. Black-Right-Pointing-Pointer mHABP backbone atom's interaction with HLA-DR{beta}1{sup Asterisk-Operator} is stabilised by H-bonds. -- Abstract: Modified HABP (mHABP) regions interacting with HLA-DR{beta}1{sup Asterisk-Operator} molecules have a more restricted conformation and/or sequence than other mHABPs which do not fit perfectly into their peptide binding regions (PBR) and do not induce an acceptable immune response due to the critical role of their {Phi} and {Psi} torsion angles.more » These angle's critical role was determined in such highly immunogenic, protection-inducing response against experimental malaria using the conformers (mHABPs) obtained by {sup 1}H-NMR and superimposed into HLA-DR{beta}1{sup Asterisk-Operator }-like Aotus monkey molecules; their phi ({Phi}) and psi ({Psi}) angles were measured and the H-bond formation between these molecules was evaluated. The aforementioned mHABP propensity to assume a regular conformation similar to a left-handed polyproline type II helix (PPII{sub L}) led to suggesting that favouring these conformations according to their amino acid sequence would lead to high antibody titre production and sterile protective immunity induction against malaria, thereby adding new principles or rules for vaccine development, malaria being one of them.« less

Electron backscatter diffraction studies of focused ion beam induced phase transformation in cobalt

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

Jones, H.G., E-mail: helen.jones@npl.co.uk

A focused ion beam microscope was used to induce cubic to hexagonal phase transformation in a cobalt alloy, of similar composition to that of the binder phase in a hardmetal, in a controlled manner at 0°, 45° and 80° ion incident angles. The cobalt had an average grain size of ~ 20 μm, allowing multiple orientations to be studied, exposed to a range of doses between 6 × 10{sup 7} and 2 × 10{sup 10} ions/μm{sup 2}. Electron backscatter diffraction (EBSD) was used to determine the original and induced phase orientations, and area fractions, before and after the ion beammore » exposure. On average, less phase transformation was observed at higher incident angles and after lower ion doses. However there was an orientation effect where grains with an orientation close to (111) planes were most susceptible to phase transformation, and (101) the least, where grains partially and fully transformed at varying ion doses. - Highlights: •Ion-induced phase change in FCC cobalt was observed at multiple incidence angles. •EBSD was used to study the relationship between grain orientation and transformation. •Custom software analysed ion dose and phase change with respect to grain orientation. •A predictive capability of ion-induced phase change in cobalt was enabled.« less

Electromagnetic wave extinction within a forested canopy

NASA Technical Reports Server (NTRS)

Karam, M. A.; Fung, A. K.

1989-01-01

A forested canopy is modeled by a collection of randomly oriented finite-length cylinders shaded by randomly oriented and distributed disk- or needle-shaped leaves. For a plane wave exciting the forested canopy, the extinction coefficient is formulated in terms of the extinction cross sections (ECSs) in the local frame of each forest component and the Eulerian angles of orientation (used to describe the orientation of each component). The ECSs in the local frame for the finite-length cylinders used to model the branches are obtained by using the forward-scattering theorem. ECSs in the local frame for the disk- and needle-shaped leaves are obtained by the summation of the absorption and scattering cross-sections. The behavior of the extinction coefficients with the incidence angle is investigated numerically for both deciduous and coniferous forest. The dependencies of the extinction coefficients on the orientation of the leaves are illustrated numerically.

Genetic analysis of the gravitropic set-point angle in lateral roots of Arabidopsis

NASA Technical Reports Server (NTRS)

Mullen, J. L.; Hangarter, R. P.; Kiss, J. Z. (Principal Investigator)

2003-01-01

Research on gravity responses in plants has mostly focused on primary roots and shoots, which typically orient to a vertical orientation. However, the distribution of lateral organs and their characteristically non-vertical growth orientation are critical for the determination of plant form. For example, in Arabidopsis, when lateral roots emerge from the primary root, they grow at a nearly horizontal orientation. As they elongate, the roots slowly curve until they eventually reach a vertical orientation. The regulation of this lateral root orientation is an important component affecting overall root system architecture. We found that this change in orientation is not simply due to the onset of gravitropic competence, as non-vertical lateral roots are capable of both positive and negative gravitropism. Thus, the horizontal growth of new lateral roots appears to be determined by what is called the gravitropic set-point angle (GSA). This developmental control of the GSA of lateral roots in Arabidopsis provides a useful system for investigating the components involved in regulating gravitropic responses. Using this system, we have identified several Arabidopsis mutants that have altered lateral root orientations but maintain normal primary root orientation. c2003 COSPAR. Published by Elsevier Ltd. All rights reserved.

Spatial orientation and mechanical properties of the human trachea: a computed tomography study.

PubMed

Zanella, Alberto; Cressoni, Massimo; Ferlicca, Daniela; Chiurazzi, Chiara; Epp, Myra; Rovati, Cristina; Chiumello, Davide; Pesenti, Antonio; Gattinoni, Luciano; Kolobow, Theodor

2015-04-01

The literature generally describes the trachea as oriented toward the right and back, but there is very little detailed characterization. Therefore, the aim of this study was to precisely determine the spatial orientation and to better characterize the physical properties of the human trachea. We analyzed lung computed tomography scans of 68 intubated and mechanically ventilated subjects suffering from acute lung injury/ARDS at airway pressures (Paw) of 5, 15, and 45 cm H2O. At each Paw, the inner edge of the trachea from the subglottal space to the carina was captured. Tracheal length and diameter were measured. Tracheal orientation and compliance were estimated from processing barycenter and surface tracheal sections. Tracheal orientation at a Paw of 5 cm H2O showed a 4.2 ± 5.3° angle toward the right and a 20.6 ± 6.9° angle downward toward the back, which decreased significantly while increasing Paw (19.4 ± 6.9° at 15 cm H2O and 17.1 ± 6.8° at 45 cm H2O, P < .001). Tracheal compliance was 0.0113 ± 0.0131 mL/cm H2O/cm of trachea length from 5 to 15 cm H2O and 0.004 ± 0.0041 mL/cm H2O/cm of trachea length from 15 to 45 cm H2O (P < .001). Tracheal diameter was 19.6 ± 3.4 mm on the medial-lateral axis and 21.0 ± 4.3 mm on the sternal-vertebral axis. The trachea is oriented downward toward the back at a 20.6 ± 6.9° angle and slightly toward the right at a 4.2 ± 5.3° angle. Understanding tracheal orientation may help in enhancing postural drainage and respiratory physiotherapy, and knowing the physical properties of the trachea may aid in endotracheal tube cuff design. Copyright © 2015 by Daedalus Enterprises.

Linear-to-λ-Shape P-O-P Bond Transmutation in Polyphosphates with Infinite (PO3)∞ Chain.

PubMed

Wang, Ying; Li, Lin; Han, Shujuan; Lei, Bing-Hua; Abudoureheman, Maierhaba; Yang, Zhihua; Pan, Shilie

2017-09-05

A new metal polyphosphate, α-CsBa 2 (PO 3 ) 5 , exhibiting the first example of a linear P-O-P bond angle in a one-dimensional (PO 3 ) ∞ chain has been reported. Interestingly, α → β phase transition occurs in CsBa 2 (PO 3 ) 5 along with the P-O-P bonds varying from linear to λ-shape, suggesting that α-CsBa 2 (PO 3 ) 5 with unfavorable linear P-O-P bonds is more stable at ambient temperature.

Modeling and Control of Needles with Torsional Friction

PubMed Central

Reed, Kyle B.; Okamura, Allison M.; Cowan, Noah J.

2010-01-01

A flexible needle can be accurately steered by robotically controlling the bevel tip orientation as the needle is inserted into tissue. Friction between the long, flexible needle shaft and the tissue can cause a significant discrepancy between the orientation of the needle tip and the orientation of the base where the needle angle is controlled. Our experiments show that several common phantom tissues used in needle steering experiments impart substantial friction forces to the needle shaft, resulting in a lag of over 45° for a 10 cm insertion depth in some phantoms; clinical studies report torques large enough to cause similar errors during needle insertions. Such angle discrepancies will result in poor performance or failure of path planners and image-guided controllers, since the needles used in percutaneous procedures are too small for state-of-the-art imaging to accurately measure the tip angle. To compensate for the angle discrepancy, we develop an estimator using a mechanics-based model of the rotational dynamics of a needle being inserted into tissue. Compared to controllers that assume a rigid needle in a frictionless environment, our estimator-based controller improves the tip angle convergence time by nearly 50% and reduces the path deviation of the needle by 70%. PMID:19695979

Calculated Hydride Donor Abilities of Five-Coordinate Transition Metal Hydrides [HM(diphosphine)2] (+) (M = Ni, Pd, Pt) as a Function of the Bite Angle and Twist Angle of Diphosphine Ligands

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

Nimlos, Mark R.; Chang, Christopher H.; Curtis, Calvin J.

2008-07-07

Density functional theory (BLYP and B3LYP) and the polarized continuum model (PCM-UA0) for solvation have been used to investigate the effect of bite angle (P-M-P) of diphosphine ligands and the dihedral or twist angle between diphosphine ligands on the hydride donor abilities of Ni, Pd, and Pt [HM(diphosphine)2]+ complexes. It is found that an increased bite angle for a given transition metal atom results in poorer hydride donor abilities. However, hydride donor abilities for these complexes also decrease as the size of the alkyl side groups on the phosphorus atom increase (Et > Me > H) and with the lengthmore » of the metal phosphorus bond (Ni > Pd = Pt). These trends correlate with an increase in the twist angle between the two diphosphine ligands, which increases from 0° for a square-planar configuration to 90° for a tetrahedral geometry. Shorter M-P bonds, larger substituents on the diphosphine ligands, and larger bite angles all result in increased steric interactions between diphosphine ligands and larger dihedral or twist angles between the diphosphine ligands. The twist angle correlates much more strongly with hydride donor abilities than do bite angles alone. As the twist angle increases, the hydride donor ability decreases in a linear fashion. A frontier orbital analysis has been carried out, and it is shown that the hydride donor ability of [HM(diphosphine)2]+ complexes is largely determined by the energy of the lowest unoccupied molecular orbital of the corresponding [M(diphosphine)2]2+ complex. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.« less

Calculated Hydride Donor Abilities of Five-Coordinate Transition Metal Hydrides [HM(diphosphine)2]+ (M = Ni, Pd, Pt) as a Function of the Bite Angle and Twist Angle of Diphosphine Ligands

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

Nimlos, Mark; Chang, Christopher H.; Curtis, Calvin J.

2008-06-23

Density functional theory (BLYP and B3LYP) and the polarized continuum model (PCM-UA0) for solvation have been used to investigate the effect of bite angle (P-M-P) of diphosphine ligands and the dihedral or twist angle between diphosphine ligands on the hydride donor abilities of Ni, Pd, and Pt [HM(diphosphine)2]+ complexes. It is found that an increased bite angle for a given transition metal atom results in poorer hydride donor abilities. However, hydride donor abilities for these complexes also decrease as the size of the alkyl side groups on the phosphorus atom increase (Et > Me > H) and with the lengthmore » of the metal phosphorus bond (Ni > Pd = Pt). These trends correlate with an increase in the twist angle between the two diphosphine ligands, which increases from 0° for a square-planar configuration to 90° for a tetrahedral geometry. Shorter M-P bonds, larger substituents on the diphosphine ligands, and larger bite angles all result in increased steric interactions between diphosphine ligands and larger dihedral or twist angles between the diphosphine ligands. The twist angle correlates much more strongly with hydride donor abilities than do bite angles alone. As the twist angle increases, the hydride donor ability decreases in a linear fashion. A frontier orbital analysis has been carried out, and it is shown that the hydride donor ability of [HM(diphosphine)2]+ complexes is largely determined by the energy of the lowest unoccupied molecular orbital of the corresponding [M(diphosphine)2]2+ complex. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.« less

HIFiRE-1 and HIFiRE-5 Test Results

DTIC Science & Technology

2014-02-01

From AFRL and NASA BETs ....................................................................................................... 12 Figure 10 Roll ...34 Figure 31 Roll Angle and PLBW3 Pressure Trace Versus Flight Time During Reentry ........................... 34 Figure...vehicle orientation in flight is described by the velocity-referenced coordinate system shown in Figure 10. Roll angle, Φ, is defined as the angle

The Age-Related Orientational Changes of Human Semicircular Canals.

PubMed

Lyu, Hui-Ying; Chen, Ke-Guang; Yin, Dong-Ming; Hong, Juan; Yang, Lin; Zhang, Tian-Yu; Dai, Pei-Dong

2016-06-01

Some changes are found in the labyrinth anatomy during postnatal development. Although the spatial orientation of semicircular canals was thought to be stable after birth, we investigated the age-related orientational changes of human semicircular canals during development. We retrospectively studied the computed tomography (CT) images of both ears of 76 subjects ranged from 1 to 70 years old. They were divided into 4 groups: group A (1-6 years), group B (7-12 years), group C (13-18 years), and group D (>18 years). The anatomical landmarks of the inner ear structures were determined from CT images. Their coordinates were imported into MATLAB software for calculating the semicircular canals orientation, angles between semicircular canal planes and the jugular bulb (JB) position. Differences between age groups were analyzed using multivariate statistics. Relationships between variables were analyzed using Pearson analysis. The angle between the anterior semicircular canal plane and the coronal plane, and the angle between the horizontal semicircular canal plane and the coronal plane were smaller in group D than those in group A (P<0.05). The JB position, especially the anteroposterior position of right JB, correlated to the semicircular canals orientation (P<0.05). However, no statistically significant differences in the angles between ipsilateral canal planes among different age groups were found. The semicircular canals had tendencies to tilt anteriorly simultaneously as a whole with age. The JB position correlated to the spatial arrangement of semicircular canals, especially the right JB. Our calculation method helps detect developmental and pathological changes in vestibular anatomy.

Crystal structure of methyl (4R)-4-(4-meth-oxy-benzo-yl)-4-{[(1R)-1-phenyl-eth-yl]carbamo-yl}butano-ate.

PubMed

Manchado, Alejandro; Salgado, Mateo M; Vicente, Álvaro; Díez, David; Sanz, Francisca; Garrido, Narciso M

2017-04-01

The title compound, C 22 H 25 NO 5 , was prepared by CAN [cerium(IV) ammonium nitrate] oxidation of the corresponding β-lactam. The dihedral angle between the benzene rings is 13.3 (4)° and the C-N-C(=O)-C torsion angle is 176.1 (6)°. In the crystal, amide- C (4) N-H⋯O and reinforcing C-H⋯O hydrogen bonds link the mol-ecules into infinite [010] chains. Further C-H⋯O hydrogen bonds cross-link the chains in the c -axis direction.

Fast modification on wheat straw outer surface by water vapor plasma and its application on composite material.

PubMed

Chen, Weimin; Xu, Yicheng; Shi, Shukai; Cao, Yizhong; Chen, Minzhi; Zhou, Xiaoyan

2018-02-02

The presence of non-poplar extracts, cutin, and wax layer in the wheat straw outer surface (WOS) greatly limit its application in bio-composite preparation. In this study, a dielectric-barrier-discharge plasma using water vapor as feeding gas was used to fast modify the WOS. The morphology, free radical concentrations, surface chemical components, and contact angles of WOS before and after plasma modification were investigated. Wheat straw was further prepared into wheat straw-based composites (WSC) and its bonding strength was evaluated by a paper tension meter. The results showed that water vapor plasma leads to the appearance of surface roughness, the generation of massive free radicals, and the introduction of oxygen-containing groups. In addition, both initial and equilibrium contact angle and the surface total free energy were significantly increased after plasma modification. These results synergistically facilitate the spread and permeation of adhesive onto the WOS and thus improve the bonding strength of all prepared WSCs. A good linear relationship between bonding strength and surface roughness parameters, contact angles, and total free energy were observed. In general, this study provided a time-saving and cost-effective modification method to realize WSC manufacture.

Disentangling neighbors and extended range density oscillations in monatomic amorphous semiconductors.

PubMed

Roorda, S; Martin, C; Droui, M; Chicoine, M; Kazimirov, A; Kycia, S

2012-06-22

High energy x-ray diffraction measurements of pure amorphous Ge were made and its radial distribution function (RDF) was determined at high resolution, revealing new information on the atomic structure of amorphous semiconductors. Fine structure in the second peak in the RDF provides evidence that a fraction of third neighbors are closer than some second neighbors; taking this into account leads to a narrow distribution of tetrahedral bond angles, (8.5 ± 0.1)°. A small peak which appears near 5 Å upon thermal annealing shows that some ordering in the dihedral bond-angle distribution takes place during structural relaxation. Extended range order is detected (in both a-Ge and a-Si) which persists to beyond 20 Å, and both the periodicity and its decay length increase upon thermal annealing. Previously, the effect of structural relaxation was only detected at intermediate range, involving reduced tetrahedral bond-angle distortions. These results enhance our understanding of the atomic order in continuous random networks and place significantly more stringent requirements on computer models intending to describe these networks, or their alternatives which attempt to describe the structure in terms of an arrangement of paracrystals.

Noncovalent Organocatalysis Based on Hydrogen Bonding: Elucidation of Reaction Paths by Computational Methods

NASA Astrophysics Data System (ADS)

Etzenbach-Effers, Kerstin; Berkessel, Albrecht

In this article, the functions of hydrogen bonds in organocatalytic reactions are discussed on atomic level by presenting DFT studies of selected examples. Theoretical investigation provides a detailed insight in the mechanism of substrate activation and orientation, and the stabilization of transition states and intermediates by hydrogen bonding (e.g. oxyanion hole). The examples selected comprise stereoselective catalysis by bifunctional thioureas, solvent catalysis by fluorinated alcohols in epoxidation by hydrogen peroxide, and intramolecular cooperative hydrogen bonding in TADDOL-type catalysts.

Segmentation decreases the magnitude of the tilt illusion

PubMed Central

Qiu, Cheng; Kersten, Daniel; Olman, Cheryl A.

2013-01-01

In the tilt illusion, the perceived orientation of a target grating depends strongly on the orientation of a surround. When the orientations of the center and surround gratings differ by a small angle, the center grating appears to tilt away from the surround orientation (repulsion), whereas for a large difference in angle, the center appears to tilt toward the surround orientation (attraction). In order to understand how segmentation/perceptual grouping of the center and surround affect the magnitude of the tilt illusion, we conducted three psychophysical experiments in which we measured observers' perception of center orientation as a function of center-surround relative contrast, relative disparity depth, and geometric features such as occlusion and collinearity. All of these manipulations affected the strength of perceived orientation bias in the center. Our results suggest that if stronger segmentation/perceptual grouping is induced between the center and surround, the tilt repulsion bias decreases/increases. A grouping-dependent tilt illusion plays an important role in visual search and detection by enhancing the sensitivity of our visual system to feature discrepancies, especially in relatively homogenous environments. PMID:24259671

Effects of consumption-oriented versus trophy-oriented fisheries on Muskellunge population size structure in northern Wisconsin

USGS Publications Warehouse

Faust, Matthew D.; Hansen, Michael J.

2016-01-01

To determine whether a consumption-oriented fishery was compatible with a trophy-oriented fishery for Muskellunge Esox masquinongy, we modeled effects of a spearing fishery and recreational angling fishery on population size structure (i.e., numbers of fish ≥ 102, 114, and 127 cm) in northern Wisconsin. An individual-based simulation model was used to quantify the effect of harvest mortality at currently observed levels of recreational angling and tribal spearing fishery exploitation, along with simulated increases in exploitation, for three typical growth potentials (i.e., low, moderate, and high) of Muskellunge in northern Wisconsin across a variety of minimum length limits (i.e., 71, 102, 114, and 127 cm). Populations with moderate to high growth potential and minimum length limits ≥ 114 cm were predicted to have lower declines in numbers of trophy Muskellunge when subjected to angling-only and mixed fisheries at observed and increased levels of exploitation, which suggested that fisheries with disparate motivations may be able to coexist under certain conditions such as restrictive length limits and low levels of exploitation. However, for most Muskellunge populations in northern Wisconsin regulated by a 102-cm minimum length limit, both angling and spearing fisheries may reduce numbers of trophy Muskellunge as larger declines were predicted across all growth potentials. Our results may be useful if Muskellunge management options in northern Wisconsin are re-examined in the future.

Three-dimensional orientation and location-dependent varying rules of radiographic angles of the acetabular cup.

PubMed

Zhao, Jing-Xin; Su, Xiu-Yun; Zhao, Zhe; Xiao, Ruo-Xiu; Zhang, Li-Cheng; Tang, Pei-Fu

2018-02-17

The aim of this study is to demonstrate the varying rules of radiographic angles following varying three-dimensional (3D) orientations and locations of cup using an accurate mathematical model. A cone model is established to address the quantitative relationship between the opening circle of cup and its ellipse projection on radiograph. The varying rules of two-dimensional (2D) radiographic anteversion (RA) and inclination (RI) angles can be analyzed. When the centre of cup is located above X-ray source, with proper 3D RI/RA angles, 2D RA angle can be equal to its 3D counterpart, and 2D RI angle is usually greater than its 3D counterpart. Except for the original point on hip-centered anterior-posterior radiograph, there is no area on radiograph where both 2D RA and RI angles are equal to their 3D counterparts simultaneously. This study proposes an innovative model for accurately explaining how 2D RA/RI angles of cup are varying following different 3D RA/RI angles and location of cup. The analysis results provide clinicians an intuitive grasp of knowledge about 2D RA/RI angles greater or smaller than their 3D counterparts post-operatively. The established model may allow determining the effects of pelvic rotations on 2D radiographic angles of cup.

Improved ultrasonic TV images achieved by use of Lamb-wave orientation technique

NASA Technical Reports Server (NTRS)

Berger, H.

1967-01-01

Lamb-wave sample orientation technique minimizes the interference from standing waves in continuous wave ultrasonic television imaging techniques used with thin metallic samples. The sample under investigation is oriented such that the wave incident upon it is not normal, but slightly angled.

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

Smedskjaer, Morten M., E-mail: mos@bio.aau.dk; Bauchy, Mathieu; Mauro, John C.

The properties of glass are determined not only by temperature, pressure, and composition, but also by their complete thermal and pressure histories. Here, we show that glasses of identical composition produced through thermal annealing and through quenching from elevated pressure can result in samples with identical density and mean interatomic distances, yet different bond angle distributions, medium-range structures, and, thus, macroscopic properties. We demonstrate that hardness is higher when the density increase is obtained through thermal annealing rather than through pressure-quenching. Molecular dynamics simulations reveal that this arises because pressure-quenching has a larger effect on medium-range order, while annealing hasmore » a larger effect on short-range structures (sharper bond angle distribution), which ultimately determine hardness according to bond constraint theory. Our work could open a new avenue towards industrially useful glasses that are identical in terms of composition and density, but with differences in thermodynamic, mechanical, and rheological properties due to unique structural characteristics.« less

Synthesis and crystal structure of the iridium(I) carbene complex with a pair of hydrogen wing tips

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

Huang, H.-Y.; Chen, Z.-M.; Wang, Y.

The iridium(I) cyclooctadiene complex with two (3-tert-butylimidazol-2-ylidene) ligands [(H-Im{sup t}Bu){sub 2}Ir(COD)]{sup +}PF{sub 6}{sup −} (C{sub 22}H{sub 32}PF{sub 6}IrN{sub 4}) has been prepared, and its crystal structure is determined by X-ray diffraction. Complex exhibits slightly distorted square planar configurations around the metal atom, which is coordinated by two H-Im{sup t}Bu ligands and one cyclooctadiene group. The new iridium carbene complex has a pair of hydrogen wing tips. The Ir−C{sub carbene} bond lengths are 2.066(5) and 2.052(5) Å, and the bond angle C−Ir−C between these bonds is 95.54(19)°. The dihedral angle between two imidazol-2-ylidene rings is 86.42°.

Crystal structure of (E)-2-hy-droxy-4'-meth-oxy-aza-stilbene.

PubMed

Chantrapromma, Suchada; Kaewmanee, Narissara; Boonnak, Nawong; Chantrapromma, Kan; Ghabbour, Hazem A; Fun, Hoong-Kun

2015-06-01

The title aza-stilbene derivative, C14H13NO2 {systematic name: (E)-2-[(4-meth-oxy-benzyl-idene)amino]-phenol}, is a product of the condensation reaction between 4-meth-oxy-benzaldehyde and 2-amino-phenol. The mol-ecule adopts an E conformation with respect to the azomethine C=N bond and is almost planar, the dihedral angle between the two substituted benzene rings being 3.29 (4)°. The meth-oxy group is coplanar with the benzene ring to which it is attached, the Cmeth-yl-O-C-C torsion angle being -1.14 (12)°. There is an intra-molecular O-H⋯N hydrogen bond generating an S(5) ring motif. In the crystal, mol-ecules are linked via C-H⋯O hydrogen bonds, forming zigzag chains along [10-1]. The chains are linked via C-H⋯π inter-actions, forming a three-dimensional structure.

Nanostructure of cellulose microfibrils in spruce wood.

PubMed

Fernandes, Anwesha N; Thomas, Lynne H; Altaner, Clemens M; Callow, Philip; Forsyth, V Trevor; Apperley, David C; Kennedy, Craig J; Jarvis, Michael C

2011-11-22

The structure of cellulose microfibrils in wood is not known in detail, despite the abundance of cellulose in woody biomass and its importance for biology, energy, and engineering. The structure of the microfibrils of spruce wood cellulose was investigated using a range of spectroscopic methods coupled to small-angle neutron and wide-angle X-ray scattering. The scattering data were consistent with 24-chain microfibrils and favored a "rectangular" model with both hydrophobic and hydrophilic surfaces exposed. Disorder in chain packing and hydrogen bonding was shown to increase outwards from the microfibril center. The extent of disorder blurred the distinction between the I alpha and I beta allomorphs. Chains at the surface were distinct in conformation, with high levels of conformational disorder at C-6, less intramolecular hydrogen bonding and more outward-directed hydrogen bonding. Axial disorder could be explained in terms of twisting of the microfibrils, with implications for their biosynthesis.

Benzamide–picric acid (1/1)

PubMed Central

Sivaramkumar, M. S.; Velmurugan, R.; Sekar, M.; Ramesh, P.; Ponnuswamy, M. N.

2010-01-01

In the title compound, C7H7NO·C6H3N3O7, one of the nitro groups of the picric acid mol­ecule lies in the plane of the attached benzene ring [dihedral angle = 1.4 (1)°] while the other two are twisted away by 9.9 (1) and 30.3 (1)°. In the benzamide mol­ecule, the amide group is almost coplanar with the benzene ring [dihedral angle = 4.4 (1)°]. An intra­molecular O—H⋯O hydrogen bond generates an S6 ring motif. In the crystal, mol­ecules are linked into a ribbon-like structure along the b axis by O—H⋯O and N—H⋯O inter­molecular hydrogen bonds. In addition, C—H⋯O hydrogen bonds and short O⋯O contacts [2.828 (2) Å] are observed. PMID:21588027

Bonding Properties of Basalt Fiber and Strength Reduction According to Fiber Orientation

PubMed Central

Choi, Jeong-Il; Lee, Bang Yeon

2015-01-01

The basalt fiber is a promising reinforcing fiber because it has a relatively higher tensile strength and a density similar to that of a concrete matrix as well as no corrosion possibility. This study investigated experimentally the bonding properties of basalt fiber with cementitious material as well as the effect of fiber orientation on the tensile strength of basalt fiber for evaluating basalt fiber’s suitability as a reinforcing fiber. Single fiber pullout tests were performed and then the tensile strength of fiber was measured according to fiber orientation. The test results showed that basalt fiber has a strong chemical bond with the cementitious matrix, 1.88 times higher than that of polyvinyl alcohol fibers with it. However, other properties of basalt fiber such as slip-hardening coefficient and strength reduction coefficient were worse than PVA and polyethylene fibers in terms of fiber bridging capacity. Theoretical fiber-bridging curves showed that the basalt fiber reinforcing system has a higher cracking strength than the PVA fiber reinforcing system, but the reinforcing system showed softening behavior after cracking. PMID:28793595

Bonding Properties of Basalt Fiber and Strength Reduction According to Fiber Orientation.

PubMed

Choi, Jeong-Il; Lee, Bang Yeon

2015-09-30

The basalt fiber is a promising reinforcing fiber because it has a relatively higher tensile strength and a density similar to that of a concrete matrix as well as no corrosion possibility. This study investigated experimentally the bonding properties of basalt fiber with cementitious material as well as the effect of fiber orientation on the tensile strength of basalt fiber for evaluating basalt fiber's suitability as a reinforcing fiber. Single fiber pullout tests were performed and then the tensile strength of fiber was measured according to fiber orientation. The test results showed that basalt fiber has a strong chemical bond with the cementitious matrix, 1.88 times higher than that of polyvinyl alcohol fibers with it. However, other properties of basalt fiber such as slip-hardening coefficient and strength reduction coefficient were worse than PVA and polyethylene fibers in terms of fiber bridging capacity. Theoretical fiber-bridging curves showed that the basalt fiber reinforcing system has a higher cracking strength than the PVA fiber reinforcing system, but the reinforcing system showed softening behavior after cracking.

N-(1,3-Thia­zol-2-yl)benzamide

PubMed Central

Zonouzi, Afsaneh; Mirzazadeh, Roghieh; Rahmani, Hossein; Ng, Seik Weng

2009-01-01

The title compound, C10H8N2OS, features a nonplanar mol­ecule [dihedral angle between the two aromatic rings = 43.6 (1)°]. Two mol­ecules are linked by N—H⋯N hydrogen bonds about a centre of inversion, giving rise to a hydrogen-bonded dimer. PMID:21582538

Control Mechanisms of Photoisomerization in Protonated Schiff Bases.

PubMed

Vuković, Lela; Burmeister, Carl F; Král, Petr; Groenhof, Gerrit

2013-03-21

We performed ab initio excited-state molecular dynamics simulations of a gas-phase photoexcited protonated Schiff base (C1-N2═C3-C4═C5-C6) to search for control mechanisms of its photoisomerization. The excited molecule twists by ∼90° around either the N2C3 bond or the C4C5 bond and relaxes to the ground electronic state through a conical intersection with either a trans or cis outcome. We show that a large initial distortion of several dihedral angles and a specific normal vibrational mode combining pyramidalization and double-bond twisting can lead to a preferential rotation of atoms around the C4C5 bond. We also show that selective pretwisting of several dihedral angles in the initial ground state thermal ensemble (by analogy to a protein pocket) can significantly increase the fraction of photoreactive (cis → trans) trajectories. We demonstrate that new ensembles with higher degrees of control over the photoisomerization reaction can be obtained by a computational directed evolution approach on the ensembles of molecules with the pretwisted geometries.

Crystal structure of benzyl 3-(3-methyl-phen-yl)di-thio-carbazate.

PubMed

Aziz, NurFadhilah Abdul; Yusof, Enis Nadia Md; Ravoof, Thahira Begum S A; Tiekink, Edward R T

2015-04-01

In the title compound, C15H16N2S2, the central CN2S2 residue is almost planar (r.m.s. deviation = 0.0354 Å) and forms dihedral angles of 56.02 (4) and 75.52 (4)° with the phenyl and tolyl rings, respectively; the dihedral angle between the aromatic rings is 81.72 (5)°. The conformation about the N-N bond is gauche [C-N-N-C = -117.48 (15)°]. Overall, the mol-ecule has the shape of the letter L. In the crystal packing, supra-molecular chains along the a axis are formed by N-H⋯S(thione) hydrogen bonds whereby the thione S atom accepts two such bonds. The hydrogen bonding leads to alternating edge-shared eight-membered {⋯HNCS}2 and 10-membered {⋯HNNH⋯S}2 synthons. The chains are connected into layers by phen-yl-tolyl C-H⋯π inter-actions; the layers stack along the c axis with no specific inter-actions between them.

Recrystallization texture in nickel heavily deformed by accumulative roll bonding

NASA Astrophysics Data System (ADS)

Mishin, O. V.; Zhang, Y. B.; Godfrey, A.

2017-07-01

The recrystallization behavior of Ni processed by accumulative roll bonding to a total accumulated von Mises strain of 4.8 has been examined, and analyzed with respect to heterogeneity in the deformation microstructure. The regions near the bonding interface are found to be more refined and contain particle deformation zones around fragments of the steel wire brush used to prepare the surface for bonding. Sample-scale gradients are also observed, manifested as differences between the subsurface, intermediate and central layers, where the distributions of texture components are different. These heterogeneities affect the progress of recrystallization. While the subsurface and near-interface regions typically contain lower frequencies of cube-oriented grains than anywhere else in the sample, a strong cube texture forms in the sample during recrystallization, attributed to both a high nucleation rate and fast growth rate of cube-oriented grains. The observations highlight the sensitivity of recrystallization to heterogeneity in the deformation microstructure and demonstrate the importance of characterizing this heterogeneity over several length scales.

Dynamic mechanical analysis of fiber reinforced composites

NASA Technical Reports Server (NTRS)

Reed, K. E.

1979-01-01

Dynamic mechanical and thermal properties were determined for unidirectional epoxy/glass composites at various fiber orientation angles. Resonant frequency and relative logarithmic decrement were measured as functions of temperature. In low angle and longitudinal specimens a transition was observed above the resin glass transition temperature which was manifested mechanically as an additional damping peak and thermally as a change in the coefficient of thermal expansion. The new transition was attributed to a heterogeneous resin matrix induced by the fiber. The temperature span of the glass-rubber relaxation was found to broaden with decreasing orientation angle, reflecting the growth of fiber contribution and exhibiting behavior similar to that of Young's modulus. The change in resonant frequency through the glass transition was greatest for samples of intermediate fiber angle, demonstrating behavior similar to that of the longitudinal shear modulus.

Low phosphate alters lateral root setpoint angle and gravitropism.

PubMed

Bai, Hanwen; Murali, Bhavna; Barber, Kevin; Wolverton, Chris

2013-01-01

Lateral roots, responsible for water and nutrient uptake, maintain nonvertical angles throughout development. Soil phosphate is one limiting nutrient for plant growth that is known to induce changes to root system architecture, such as increased lateral root formation. This study seeks to determine whether phosphate concentration affects lateral root orientation in addition to its previously described influences on root architecture. Images of intact Arabidopsis root systems were recorded for 24 h, and lateral root tip angles were measured for wild-type and mutant pgm-1 and pin3-1 roots on a full or low phosphate medium. Setpoint angles of unstimulated root systems were determined, as were gravitropic responses of lateral roots over time. The root system setpoint angles of wild-type and mutant pin3-1 roots showed a shift toward a more vertical orientation on low orthophosphate (Pi) medium. The gravitropic responses of both pgm-1 and pin3-1 roots on low Pi medium was elevated relative to control Pi medium. Mutations in two phosphate transporters with high levels of expression in the root showed a gravitropic response similar to wild-type roots grown on low Pi, supporting a role for Pi status in regulating lateral root gravitropism. Lateral root orientation and gravitropism are affected by Pi status and may provide an important additional parameter for describing root responses to low Pi. The data also support the conclusion that gravitropic setpoint angle reacts to nutrient status and is under dynamic regulation.

Remeasuring tree heights on permanent plots using rectangular coordinates and one angle per tree

Treesearch

Robert L. Neal

1973-01-01

Heights of permanent sample trees with tops visible from any point can be measured from that point with any clinometer, measuring one vertical angle per tree. Two horizontal angles and one additional vertical angle per observation point are necessary to orient the point to the plot. Permanently recorded coordinates and elevations of tree locations are used with the...

A Global Orientation Map in the Primary Visual Cortex (V1): Could a Self Organizing Model Reveal Its Hidden Bias?

PubMed Central

Philips, Ryan T.; Chakravarthy, V. Srinivasa

2017-01-01

A remarkable accomplishment of self organizing models is their ability to simulate the development of feature maps in the cortex. Additionally, these models have been trained to tease out the differential causes of multiple feature maps, mapped on to the same output space. Recently, a Laterally Interconnected Synergetically Self Organizing Map (LISSOM) model has been used to simulate the mapping of eccentricity and meridional angle onto orthogonal axes in the primary visual cortex (V1). This model is further probed to simulate the development of the radial bias in V1, using a training set that consists of both radial (rectangular bars of random size and orientation) as well as non-radial stimuli. The radial bias describes the preference of the visual system toward orientations that match the angular position (meridional angle) of that orientation with respect to the point of fixation. Recent fMRI results have shown that there exists a coarse scale orientation map in V1, which resembles the meridional angle map, thereby providing a plausible neural basis for the radial bias. The LISSOM model, trained for the development of the retinotopic map, on probing for orientation preference, exhibits a coarse scale orientation map, consistent with these experimental results, quantified using the circular cross correlation (rc). The rc between the orientation map developed on probing with a thin annular ring containing sinusoidal gratings with a spatial frequency of 0.5 cycles per degree (cpd) and the corresponding meridional map for the same annular ring, has a value of 0.8894. The results also suggest that the radial bias goes beyond the current understanding of a node to node correlation between the two maps. PMID:28111542

A Global Orientation Map in the Primary Visual Cortex (V1): Could a Self Organizing Model Reveal Its Hidden Bias?

PubMed

Philips, Ryan T; Chakravarthy, V Srinivasa

2016-01-01

A remarkable accomplishment of self organizing models is their ability to simulate the development of feature maps in the cortex. Additionally, these models have been trained to tease out the differential causes of multiple feature maps, mapped on to the same output space. Recently, a Laterally Interconnected Synergetically Self Organizing Map (LISSOM) model has been used to simulate the mapping of eccentricity and meridional angle onto orthogonal axes in the primary visual cortex (V1). This model is further probed to simulate the development of the radial bias in V1, using a training set that consists of both radial (rectangular bars of random size and orientation) as well as non-radial stimuli. The radial bias describes the preference of the visual system toward orientations that match the angular position (meridional angle) of that orientation with respect to the point of fixation. Recent fMRI results have shown that there exists a coarse scale orientation map in V1, which resembles the meridional angle map, thereby providing a plausible neural basis for the radial bias. The LISSOM model, trained for the development of the retinotopic map, on probing for orientation preference, exhibits a coarse scale orientation map, consistent with these experimental results, quantified using the circular cross correlation ( r c ). The r c between the orientation map developed on probing with a thin annular ring containing sinusoidal gratings with a spatial frequency of 0.5 cycles per degree (cpd) and the corresponding meridional map for the same annular ring, has a value of 0.8894. The results also suggest that the radial bias goes beyond the current understanding of a node to node correlation between the two maps.

Molecular dynamics analysis of transitions between rotational isomers in polymethylene

NASA Astrophysics Data System (ADS)

Zúñiga, Ignacio; Bahar, Ivet; Dodge, Robert; Mattice, Wayne L.

1991-10-01

Molecular dynamics trajectories have been computed and analyzed for linear chains, with sizes ranging from C10H22 to C100H202, and for cyclic C100H200. All hydrogen atoms are included discretely. All bond lengths, bond angles, and torsion angles are variable. Hazard plots show a tendency, at very short times, for correlations between rotational isomeric transitions at bond i and i±2, in much the same manner as in the Brownian dynamics simulations reported by Helfand and co-workers. This correlation of next nearest neighbor bonds in isolated polyethylene chains is much weaker than the correlation found for next nearest neighbor CH-CH2 bonds in poly(1,4-trans-butadiene) confined to the channel formed by crystalline perhydrotriphenylene [Dodge and Mattice, Macromolecules 24, 2709 (1991)]. Less than half of the rotational isomeric transitions observed in the entire trajectory for C50H102 can be described as strongly coupled next nearest neighbor transitions. If correlated motions are identified with successive transitions, which occur within a time interval of Δt≤1 ps, only 18% of the transitions occur through cooperative motion of bonds i and i±2. An analysis of the entire data set of 2482 rotational isomeric state transitions, observed in a 3.7 ns trajectory for C50H102 at 400 K, was performed using a formalism that treats the transitions at different bonds as being independent. On time scales of 0.1 ns or longer, the analysis based on independent bonds accounts reasonably well for the results from the molecular dynamics simulations. At shorter times the molecular dynamics simulation reveals a higher mobility than implied by the analysis assuming independent bonds, presumably due to the influence of correlations that are important at shorter times.

A Method to Determine Angular Orientation of a Projectile Using a Polarization Scanning Reference Source

NASA Astrophysics Data System (ADS)

Kankipati, Venkata Varun

This thesis presents a method to determine the angular orientation of a projectile in flight, by mechanically scanning a linearly polarized, microwave reference source. In particular, the research focuses on real time measurement of the roll angle. A 10 GHz, linearly polarized electromagnetic wave is radiated toward the projectile by means of a 10 dB horn antenna. The projectile is equipped with a backward facing 10 dB horn antenna, which has orientation, namely roll angle, sensitivity. The response of the received signal follows a cosine law, producing a maximum when the receiver orientation is aligned with the transmitting polarization. As expected, the peak response shifts in response to the roll-angle, however, unambiguous recovery of the angle requires synchronization with the polarization orientation of the source. This has been achieved through the use of a unique transmitter power sequence, which includes a start-of-scan and end-of-scan time stamp. Based on the above concept, a complete system comprising a polarization scanning reference source, the receiving antenna mounted on a vehicle, and pertinent electronic components, has been tested for both line of sight and non-line of sight applications. The transmitter antenna, mounted on a computer controlled stepper motor allowed source polarization to be scanned from -90° to 90° in 0.3 seconds. The receiving antenna continuously samples the received electromagnetic background at the source frequency and uses a RF detector and a data acquisition system to record the subsequent time-varying voltage signal, which is processed to recover the roll-angle. Measurements in an anechoic chamber were used to confirm the efficacy of the system and field trials, using a transmitter power of 2 W, were successfully demonstrated over a distance of 0.15 miles. The distance limit can be extended by increasing the transmitter power, receiver sensitivity and increase source frequency.

N-(1-Allyl-1H-indazol-5-yl)-4-methyl-benzene-sulfonamide.

PubMed

Chicha, Hakima; Rakib, El Mostapha; Abderrafia, Hafid; Saadi, Mohamed; El Ammari, Lahcen

2013-11-30

The asymmetric unit of the title compound, C17H17N3O2S, contains two independent mol-ecules linked by an N-H⋯O hydrogen bond. The mol-ecules show different conformations. In the first mol-ecule, the fused five- and six-membered ring system is almost perpendicular to the plane through the atoms forming the allyl group, as indicated by the dihedral angle of 85.1 (4)°. The dihedral angle with the methyl-benzene-sulfonamide group is 78.8 (1)°. On the other hand, in the second mol-ecule, the dihedral angles between the indazole plane and the allyl and methyl-benzene-sulfonamide groups are 80.3 (3) and 41.5 (1)°, respectively. In the crystal, mol-ecules are further linked by N-H⋯N and C-H⋯O hydrogen bonds, forming a three-dimensional network.

Dibenzo-18-crown-6–picric acid–water (1/2/3)

PubMed Central

Saleh, Muhammad Idiris; Kusrini, Eny; Rosli, Mohd Mustaqim; Fun, Hoong-Kun

2008-01-01

In the crown ether ring of the title compound, C20H24O6·2C6H3N3O7·3H2O, the O—C(H2)—C(H2)—O torsion angles indicate a gauche conformation of the ethyl­eneoxy units, while the C—O—C—C torsion angles indicate planarity of these segments; the dihedral angle between the two benzene rings is 44.53 (13)°. In both picric acid mol­ecules, one of the nitro groups is twisted away from the attached ring. The mol­ecules are linked into chains along the b axis via inter­molecular O—H⋯O hydrogen bonds. In addition, the crystal structure is stabilized by C—H⋯O hydrogen bonds and π–π inter­actions [centroid–centroid distance between benzene rings = 3.5697 (16) Å]. PMID:21202944

Internal Coordinate Molecular Dynamics: A Foundation for Multiscale Dynamics

PubMed Central

2015-01-01

Internal coordinates such as bond lengths, bond angles, and torsion angles (BAT) are natural coordinates for describing a bonded molecular system. However, the molecular dynamics (MD) simulation methods that are widely used for proteins, DNA, and polymers are based on Cartesian coordinates owing to the mathematical simplicity of the equations of motion. However, constraints are often needed with Cartesian MD simulations to enhance the conformational sampling. This makes the equations of motion in the Cartesian coordinates differential-algebraic, which adversely impacts the complexity and the robustness of the simulations. On the other hand, constraints can be easily placed in BAT coordinates by removing the degrees of freedom that need to be constrained. Thus, the internal coordinate MD (ICMD) offers an attractive alternative to Cartesian coordinate MD for developing multiscale MD method. The torsional MD method is a special adaptation of the ICMD method, where all the bond lengths and bond angles are kept rigid. The advantages of ICMD simulation methods are the longer time step size afforded by freezing high frequency degrees of freedom and performing a conformational search in the more important low frequency torsional degrees of freedom. However, the advancements in the ICMD simulations have been slow and stifled by long-standing mathematical bottlenecks. In this review, we summarize the recent mathematical advancements we have made based on spatial operator algebra, in developing a robust long time scale ICMD simulation toolkit useful for various applications. We also present the applications of ICMD simulations to study conformational changes in proteins and protein structure refinement. We review the advantages of the ICMD simulations over the Cartesian simulations when used with enhanced sampling methods and project the future use of ICMD simulations in protein dynamics. PMID:25517406

Local orientational mobility in regular hyperbranched polymers.

PubMed

Dolgushev, Maxim; Markelov, Denis A; Fürstenberg, Florian; Guérin, Thomas

2016-07-01

We study the dynamics of local bond orientation in regular hyperbranched polymers modeled by Vicsek fractals. The local dynamics is investigated through the temporal autocorrelation functions of single bonds and the corresponding relaxation forms of the complex dielectric susceptibility. We show that the dynamic behavior of single segments depends on their remoteness from the periphery rather than on the size of the whole macromolecule. Remarkably, the dynamics of the core segments (which are most remote from the periphery) shows a scaling behavior that differs from the dynamics obtained after structural average. We analyze the most relevant processes of single segment motion and provide an analytic approximation for the corresponding relaxation times. Furthermore, we describe an iterative method to calculate the orientational dynamics in the case of very large macromolecular sizes.

Vibrational spectral investigation and natural bond orbital analysis of pharmaceutical compound 7-Amino-2,4-dimethylquinolinium formate - DFT approach

NASA Astrophysics Data System (ADS)

Suresh, D. M.; Amalanathan, M.; Sebastian, S.; Sajan, D.; Hubert Joe, I.; Bena Jothy, V.; Nemec, Ivan

2013-11-01

The molecular geometry, the normal mode frequencies and corresponding vibrational assignments, natural bond orbital analysis and the HOMO-LUMO analysis of 7-Amino-2,4-dimethylquinolinium formate in the ground state were performed by B3LYP levels of theory using the 6-31G(d) basis set. The optimised bond lengths and bond angles are in good agreement with the X-ray data. The vibrational spectra of the title compound which is calculated by DFT method, reproduces vibrational wave numbers and intensities with an accuracy which allows reliable vibrational assignments. The possibility of N-H⋯O hydrogen bonding was identified using NBO analysis. Natural bond orbital analysis confirms the presence of intramolecular charge transfer and the hydrogen bonding interaction.

In Vitro Comparison of the Bond Strength between Ceramic Repair Systems and Ceramic Materials and Evaluation of the Wettability.

PubMed

Kocaağaoğlu, Hasan; Manav, Taha; Albayrak, Haydar

2017-04-01

When fracture of an all-ceramic restoration occurs, it can be necessary to repair without removing the restoration. Although there are many studies about the repair of metal-ceramic restorations, there are few about all-ceramic restorations. The aim of this study was to evaluate the shear bond strength between ceramic repair systems and esthetic core materials and to evaluate the wettability of all-ceramic core materials. Disk-like specimens (N = 90) made of three dental ceramic infrastructure materials (zirconia ceramic, alumina ceramic, glass ceramic) were polished with silicon carbide paper, prepared for bonding (abrasion with 30 μm diamond rotary cutting instrument). Thirty specimens of each infrastructure were obtained. Each infrastructure group was divided into three subgroups; they were bonded using 3 repair systems: Bisco Intraoral Repair Kit, Cimara & Cimara Zircon Repair System, and Clearfil Repair System. After 1200 thermocycles, shear bond strength was measured in a universal testing machine at a 0.5 mm/min crosshead speed. In addition, the contact angle values of the infrastructures after surface treatments were examined for wettability. Data were analyzed by using ANOVA and Tukey post hoc tests. Although there were no significant differences among the repair systems (p > 0.05) in the glass ceramic and zirconia groups, a significant difference was found among the repair systems in alumina infrastructure (p < 0.001). There were no statistically significant differences among the infrastructures (p > 0.05); however, a statistically significant difference was found among the repair systems (p < 0.05). No difference was found among the infrastructures and repair systems in terms of contact angle values. Cimara & Cimara Zircon Repair System had higher bond strength values than the other repair systems. Although no difference was found among the infrastructures and repair systems, contact wettability angle was decreased by surface treatments compared with polished surfaces. © 2015 by the American College of Prosthodontists.

(E)-1-(2-Amino­phen­yl)-3-(3,4,5-trimeth­oxy­phen­yl)prop-2-en-1-one

PubMed Central

Chantrapromma, Suchada; Ruanwas, Pumsak; Fun, Hoong-Kun

2011-01-01

In the asymmetric unit of the title chalcone derivative, C18H19NO4, there are three crystallographically independent mol­ecules (mol­ecules A, B and C). In mol­ecule A, the dihedral angle between two benzene rings is 12.22 (10)° and the plane of the central prop-2-en-1-one unit makes dihedral angles of 11.02 (13) and 2.64 (12)° with the two adjacent benzene rings. The corresponding angles in mol­ecule B are 12.35 (10), 18.78 (12) and 7.29 (12)°, respectively, and those in mol­ecule C are 15.40 (10), 15.62 (3) and 3.19 (13)°. In each mol­ecule, an intra­molecular N—H⋯O hydrogen bond generates an S(6) ring motif. In the crystal structure, the mol­ecules B are linked by inter­molecular N—H⋯O hydrogen bonds into a zigzag chain along the c axis, while the mol­ecules A and C are linked together via an N—H⋯O hydrogen bond into a dimer. Adjacent dimers are further connected by N—H⋯N hydrogen bonds into a three-dimensional network. Weak C—H⋯O and C—H⋯π inter­actions are also observed. PMID:22064816

Research and Development of High-Performance Axial-Flow Turbomachinery

DTIC Science & Technology

1968-05-01

following conditions: 1. At any orientation of the turbocompressor in a zero to 0.18-g accelera- tion field; 2. At any angle between zero and 180...degrees shaft angle (where zero would correspond to a vertically oriented shaft with the compressor-end up and 180 degrees would be vertical with the...rpm. Hence, the absolute values of bearing forces in the vicinity of the rigid body criticals are approximate. Over the range of 40,000 to 60,000 rpm

Incident flux angle induced crystal texture transformation in nanostructured molybdenum films

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

Chen, L.; Lu, T.-M.; Wang, G.-C.

2012-07-15

Molybdenum films were observed to undergo a dramatic change in crystal texture orientation when the incident flux angle was varied in an oblique angle sputter deposition on amorphous substrates. Reflection high-energy electron diffraction pole figure and scanning electron microscopy were used to analyze in detail the texture orientation of the films. The normal incident deposition resulted in a fiber texture film with the minimum energy (110) crystal plane parallel to the substrate surface. A (110)[110] biaxial texture was observed for the samples grown with low incident angles of less than 45 Degree-Sign , with respect to the surface normal. Onmore » the other hand, for an oblique angle deposition of larger than 60 Degree-Sign , a (111)[112] biaxial texture was observed and appeared to be consistent with a zone T structure where the geometrically fastest growth [001] direction of a crystal plays a dominant role in defining the texture. We argue that a structural transition had occurred when the incident flux was varied from near normal incidence to a large angle.« less

Alignment between Protostellar Outflows and Filamentary Structure

NASA Astrophysics Data System (ADS)

Stephens, Ian W.; Dunham, Michael M.; Myers, Philip C.; Pokhrel, Riwaj; Sadavoy, Sarah I.; Vorobyov, Eduard I.; Tobin, John J.; Pineda, Jaime E.; Offner, Stella S. R.; Lee, Katherine I.; Kristensen, Lars E.; Jørgensen, Jes K.; Goodman, Alyssa A.; Bourke, Tyler L.; Arce, Héctor G.; Plunkett, Adele L.

2017-09-01

We present new Submillimeter Array (SMA) observations of CO(2-1) outflows toward young, embedded protostars in the Perseus molecular cloud as part of the Mass Assembly of Stellar Systems and their Evolution with the SMA (MASSES) survey. For 57 Perseus protostars, we characterize the orientation of the outflow angles and compare them with the orientation of the local filaments as derived from Herschel observations. We find that the relative angles between outflows and filaments are inconsistent with purely parallel or purely perpendicular distributions. Instead, the observed distribution of outflow-filament angles are more consistent with either randomly aligned angles or a mix of projected parallel and perpendicular angles. A mix of parallel and perpendicular angles requires perpendicular alignment to be more common by a factor of ˜3. Our results show that the observed distributions probably hold regardless of the protostar’s multiplicity, age, or the host core’s opacity. These observations indicate that the angular momentum axis of a protostar may be independent of the large-scale structure. We discuss the significance of independent protostellar rotation axes in the general picture of filament-based star formation.

Surface diffusion of CO on silica-supported Ru particles: 13C nuclear magnetic resonance studies

NASA Astrophysics Data System (ADS)

Duncan, T. M.; Thayer, A. M.; Root, T. W.

1990-02-01

Portions of CO adsorbed on Ru particles, selected by the orientation of the C-O bond relative to an external magnetic field, are labeled by inversion of the 13C nuclear magnetic dipole. Changes in the orientation of the CO bond of these labeled molecules are then observed with 13C NMR spectroscopy. The temperature dependence and rate of reorientation are consistent with surface diffusion on Ru particles with small numbers of flat faces. The insensitivity to CO pressure in the range 0.5-100 Torr discounts stimulated desorption by gas-phase CO.

The influence of lathe check depth and orientation on the bond quality of phenol-formaldehyde-bonded birch plywood

Treesearch

Anti Rohumaa; Christopher G. Hunt; Mark Hughes; Charles R. Frihart; Janne Logren

2013-01-01

During the rotary peeling of veneer for plywood or the laminated veneer lumber manufacture, checks are formed in the veneer that are as deep as 70 – 80 % of the veneer thickness. The results of this study show that, during adhesive bond testing, deep lathe checks in birch (Betula pendula Roth.) veneer significantly reduce the shear strength and the...

(E)-1,3-Bis(2,3,4,5,6-penta­fluoro­phen­yl)prop-2-en-1-one

PubMed Central

Schwarzer, Anke; Weber, Edwin

2010-01-01

In the title compound, C15H2F10O, the two perfluorinated arene rings are tilted at an angle of 66.08 (5)° with respect to each other. The olefinic double bond adopts an E configuration and the single bond between the olefinic and carbonyl double bonds has an s-trans conformation. The carbonyl group is not in a coplanar alignment with respect to the neighbouring arene ring (0.963 Å from aryl plane) while being coplanar with regard to the olefinic double bond (0.0805 Å from olefinic bond). The crystal packing does not feature significant hydrogen-bond-type or stacking inter­actions. PMID:21588260

Electric-regulated enhanced in-plane uniaxial anisotropy in FeGa/PMN-PT composite using oblique pulsed laser deposition

NASA Astrophysics Data System (ADS)

Zhang, Yi; Huang, Chaojuan; Turghun, Mutellip; Duan, Zhihua; Wang, Feifei; Shi, Wangzhou

2018-04-01

The FeGa film with in-plane uniaxial magnetic anisotropy was fabricated onto different oriented single-crystal lead magnesium niobate-lead titanate using oblique pulsed laser deposition. An enhanced in-plane uniaxial magnetic anisotropy field of FeGa film can be adjusted from 18 Oe to 275 Oe by tuning the oblique angle and polarizing voltage. The competitive relationship of shape anisotropy and strain anisotropy has been discussed, which was induced by oblique angle and polarizing voltage, respectively. The (100)-oriented and (110)-oriented PMN-PT show completely different characters on voltage-dependent magnetic properties, which could be attributed to various anisotropy directions depended on different strain directions.

The neural code for face orientation in the human fusiform face area.

PubMed

Ramírez, Fernando M; Cichy, Radoslaw M; Allefeld, Carsten; Haynes, John-Dylan

2014-09-03

Humans recognize faces and objects with high speed and accuracy regardless of their orientation. Recent studies have proposed that orientation invariance in face recognition involves an intermediate representation where neural responses are similar for mirror-symmetric views. Here, we used fMRI, multivariate pattern analysis, and computational modeling to investigate the neural encoding of faces and vehicles at different rotational angles. Corroborating previous studies, we demonstrate a representation of face orientation in the fusiform face-selective area (FFA). We go beyond these studies by showing that this representation is category-selective and tolerant to retinal translation. Critically, by controlling for low-level confounds, we found the representation of orientation in FFA to be compatible with a linear angle code. Aspects of mirror-symmetric coding cannot be ruled out when FFA mean activity levels are considered as a dimension of coding. Finally, we used a parametric family of computational models, involving a biased sampling of view-tuned neuronal clusters, to compare different face angle encoding models. The best fitting model exhibited a predominance of neuronal clusters tuned to frontal views of faces. In sum, our findings suggest a category-selective and monotonic code of face orientation in the human FFA, in line with primate electrophysiology studies that observed mirror-symmetric tuning of neural responses at higher stages of the visual system, beyond the putative homolog of human FFA. Copyright © 2014 the authors 0270-6474/14/3412155-13$15.00/0.

Evaluation of regression-based 3-D shoulder rhythms.

PubMed

Xu, Xu; Dickerson, Clark R; Lin, Jia-Hua; McGorry, Raymond W

2016-08-01

The movements of the humerus, the clavicle, and the scapula are not completely independent. The coupled pattern of movement of these bones is called the shoulder rhythm. To date, multiple studies have focused on providing regression-based 3-D shoulder rhythms, in which the orientations of the clavicle and the scapula are estimated by the orientation of the humerus. In this study, six existing regression-based shoulder rhythms were evaluated by an independent dataset in terms of their predictability. The datasets include the measured orientations of the humerus, the clavicle, and the scapula of 14 participants over 118 different upper arm postures. The predicted orientations of the clavicle and the scapula were derived from applying those regression-based shoulder rhythms to the humerus orientation. The results indicated that none of those regression-based shoulder rhythms provides consistently more accurate results than the others. For all the joint angles and all the shoulder rhythms, the RMSE are all greater than 5°. Among those shoulder rhythms, the scapula lateral/medial rotation has the strongest correlation between the predicted and the measured angles, while the other thoracoclavicular and thoracoscapular bone orientation angles only showed a weak to moderate correlation. Since the regression-based shoulder rhythm has been adopted for shoulder biomechanical models to estimate shoulder muscle activities and structure loads, there needs to be further investigation on how the predicted error from the shoulder rhythm affects the output of the biomechanical model. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Different electronic and charge-transport properties of four organic semiconductors Tetraazaperopyrenes derivatives

NASA Astrophysics Data System (ADS)

Shi, Yarui; Wei, Huiling; Liu, Yufang

2015-03-01

Tetraazaperopyrenes (TAPPs) derivatives are high-performance n-type organic semiconductor material families with the remarkable long-term stabilities. The charge carrier mobilities in TAPPs derivatives crystals were calculated by the density functional theory (DFT) method combined with the Marcus-Hush electron-transfer theory. The existence of considerable C-H…F-C bonding defines the conformation of the molecular structure and contributes to its stability. We illustrated how it is possible to control the electronic and charge-transport parameters of TAPPs derivatives as a function of the positions, a type of the substituents. It is found that the core substitution of TAPPs has a drastic influence on the charge-transport mobilities. The maximum electron mobility value of the core-brominated 2,9-bis (perfluoroalkyl)-substituted TAPPs is 0.521 cm2 V-1 s-1, which appear in the orientation angle 95° and 275°. The results demonstrate that the TAPPs with bromine substituents in ortho positions exhibit the best charge-transfer efficiency among the four different TAPP derivatives.

(E)-2-[4-(Diethyl­amino)­styr­yl]-1-methyl­pyridinium 4-chloro­benzene­sulfonate monohydrate

PubMed Central

Fun, Hoong-Kun; Kaewmanee, Narissara; Chanawanno, Kullapa; Karalai, Chatchanok; Chantrapromma, Suchada

2011-01-01

In the title hydrated mol­ecular salt, C18H23N2 +·C6H4ClO3S−·H2O, which shows moderate biological activity against methicillin-resistant Staphylococcus aureus (MRSA), one ethyl group of the 2-[4-(diethyl­amino)­styr­yl]-1-methyl­pyridinium cation is disordered over two orientations in a 0.604 (13):0.396 (13) ratio. The main part of the cation is nearly planar with a dihedral angle of 4.50 (10)° between the pyridinium and benzene rings. In the crystal, the components are linked by O—H⋯O hydrogen bonds and C—H⋯O weak inter­actions. Aromatic π–π stacking inter­actions with centroid–centroid separations of 3.7363 (12) and 3.7490 (13) Å also occur. PMID:22059040

Fishing for Northern Pike in Minnesota: A comparison of anglers and dark house spearers

USGS Publications Warehouse

Schroeder, Susan A.; Fulton, David C.

2014-01-01

In order to project fishing effort and demand of individuals targeting Northern Pike Esox lucius in Minnesota, it is important to understand the catch orientations, management preferences, and site choice preferences of those individuals. Northern Pike are specifically targeted by about 35% of the approximately 1.5 million licensed anglers in Minnesota and by approximately 14,000–15,000 dark house spearers. Dark house spearing is a traditional method of harvesting fish through the ice in winter. Mail surveys were distributed to three research strata: anglers targeting Northern Pike, dark house spearing license holders spearing Northern Pike, and dark house spearing license holders angling for Northern Pike. Dark house spearers, whether spearing or angling, reported a stronger orientation toward keeping Northern Pike than did anglers. Anglers reported a stronger orientation toward catching large Northern Pike than did dark house spearers when spearing or angling. Northern Pike regulations were the most important attribute affecting site choice for respondents in all three strata. Models for all strata indicated a preference for lakes without protected slot limits. However, protected slot limits had a stronger negative influence on lake preference for dark house spearing licensees (whether spearing or angling) than for anglers.

Influence of intramuscular fiber orientation on the Achilles tendon curvature using three-dimensional finite element modeling of contracting skeletal muscle.

PubMed

Kinugasa, Ryuta; Yamamura, Naoto; Sinha, Shantanu; Takagi, Shu

2016-10-03

Tendon curvature plays a key role in mechanical gain (amplifying the joint excursion relative to fiber length change) during joint motion, but the mechanism remains unresolved. A three-dimensional finite element (FE) model was used to investigate the influence of intramuscular fiber orientation upon the curvature pattern of the Achilles tendon during active muscular contraction. Two simulation models, with fiber pennation angles of θ = 25° and 47° were tested for the gastrocnemius and soleus muscles. A smaller pennation angle (25°) of the soleus muscle fibers was accompanied by a large change in curvature whereas a larger pennation angle (47°) of the soleus muscle was accompanied by small effects. These results suggest that the fiber pennation angle determines the curvature of the tendon, and the magnitude of the curvature varies along the length of the aponeurosis. Such FE modeling has the potential of determining changes in force output consequent to changes in intramuscular fiber orientation arising from resistance training or unloading, and provides mechanism for predicting the risk of Achilles tendon ruptures. Copyright © 2016 Elsevier Ltd. All rights reserved.

Experimental determination of torsion angles in the polypeptide backbone of the gramicidin A channel by solid state nuclear magnetic resonance.

PubMed

Teng, Q; Nicholson, L K; Cross, T A

1991-04-05

An analytical method for the determination of torsion angles from solid state 15N nuclear magnetic resonance (n.m.r.) spectroscopic data is demonstrated. Advantage is taken of the 15N-1H and 15N-13C dipolar interactions as well as the 15N chemical shift interaction in oriented samples. The membrane-bound channel conformation of gramicidin A has eluded an atomic resolution structure determination by more traditional approaches. Here, the torsion angles for the Ala3 site are determined by obtaining the n.m.r. data for both the Gly2-Ala3 and Ala3-Leu4 peptide linkages. Complete utilization of the orientational constraints derived from these orientation-dependent nuclear spin interactions in restricting the conformational space is most effectively achieved by utilizing spherical trigonometry. Two possible sets of torsion angles for the Ala3 site are obtained (phi, psi = -129 degrees, 153 degrees and -129 degrees, 122 degrees), both of which are consistent with a right-handed beta-helix. Other functional and computational evidence strongly supports the set for which the carbonyl oxygen atom of the Ala3-Leu4 linkage is rotated into the channel lumen.

Chemical bonding in TiSb(2) and VSb(2): a quantum chemical and experimental study.

PubMed

Armbrüster, Marc; Schnelle, Walter; Schwarz, Ulrich; Grin, Yuri

2007-08-06

The chemical bonding in the isostructural intermetallic compounds TiSb2 and VSb2, crystallizing in the CuAl2 type, was investigated by means of quantum chemical calculations, particularly the electron localization function (ELF), as well as by Raman spectroscopy, Hall effect and conductivity measurements on oriented single crystals, and high-pressure X-ray powder diffraction. The homogeneity ranges of the compounds were determined by powder X-ray diffraction, WDXS, and DSC measurements. TiSb2 exhibits no significant homogeneity range, while VSb2 shows a small homogeneity range of approximately 0.3 at. %. According to the ELF calculations, the Sb atoms form dumbbells via a two-center two-electron bond, while the T atoms (T = Ti, V) build up chains along the crystallographic c-axis. Both building units are connected by covalent T-Sb-T three-center bonds, thus forming a three-dimensional network. The strength of the bonds involving Sb was determined by fitting a force constant model to the vibrational mode frequencies observed by polarized Raman measurements on oriented single crystals. The resulting bond order of the Sb2 dumbbells is 1, while the strength of the three-center bonds resembles a bond order of 1.5. The weak pressure dependence of the c/a ratio confirms the slightly different bonding picture in TiSb2 compared to that in CuAl2. Electrical transport measurements show the presence of free charge carriers, as well as a metal-like temperature dependence of the electrical resistivity.

Quantifying resistances across nanoscale low- and high-angle interspherulite boundaries in solution-processed organic semiconductor thin films.

PubMed

Lee, Stephanie S; Mativetsky, Jeffrey M; Loth, Marsha A; Anthony, John E; Loo, Yueh-Lin

2012-11-27

The nanoscale boundaries formed when neighboring spherulites impinge in polycrystalline, solution-processed organic semiconductor thin films act as bottlenecks to charge transport, significantly reducing organic thin-film transistor mobility in devices comprising spherulitic thin films as the active layers. These interspherulite boundaries (ISBs) are structurally complex, with varying angles of molecular orientation mismatch along their lengths. We have successfully engineered exclusively low- and exclusively high-angle ISBs to elucidate how the angle of molecular orientation mismatch at ISBs affects their resistivities in triethylsilylethynyl anthradithiophene thin films. Conductive AFM and four-probe measurements reveal that current flow is unaffected by the presence of low-angle ISBs, whereas current flow is significantly disrupted across high-angle ISBs. In the latter case, we estimate the resistivity to be 22 MΩμm(2)/width of the ISB, only less than a quarter of the resistivity measured across low-angle grain boundaries in thermally evaporated sexithiophene thin films. This discrepancy in resistivities across ISBs in solution-processed organic semiconductor thin films and grain boundaries in thermally evaporated organic semiconductor thin films likely arises from inherent differences in the nature of film formation in the respective systems.

Phi (Φ) and psi (Ψ) angles involved in malarial peptide bonds determine sterile protective immunity.

PubMed

Patarroyo, Manuel E; Moreno-Vranich, Armando; Bermúdez, Adriana

2012-12-07

Modified HABP (mHABP) regions interacting with HLA-DRβ1(∗) molecules have a more restricted conformation and/or sequence than other mHABPs which do not fit perfectly into their peptide binding regions (PBR) and do not induce an acceptable immune response due to the critical role of their Φ and Ψ torsion angles. These angle's critical role was determined in such highly immunogenic, protection-inducing response against experimental malaria using the conformers (mHABPs) obtained by (1)H-NMR and superimposed into HLA-DRβ1(∗)-like Aotus monkey molecules; their phi (Φ) and psi (Ψ) angles were measured and the H-bond formation between these molecules was evaluated. The aforementioned mHABP propensity to assume a regular conformation similar to a left-handed polyproline type II helix (PPII(L)) led to suggesting that favouring these conformations according to their amino acid sequence would lead to high antibody titre production and sterile protective immunity induction against malaria, thereby adding new principles or rules for vaccine development, malaria being one of them. Copyright © 2012 Elsevier Inc. All rights reserved.

Crystal structure of 3-(2,5-di-meth-oxy-phen-yl)propionic acid.

PubMed

Bugenhagen, Bernhard; Al Jasem, Yosef; AlAzani, Mariam; Thiemann, Thies

2015-05-01

In the crystal of the title compound, C11H14O4, the aromatic ring is almost coplanar with the 2-position meth-oxy group with which it subtends a dihedral of 0.54 (2)°, while the 5-position meth-oxy group makes a corresponding dihedral angle of just 5.30 (2)°. The angle between the mean planes of the aromatic ring and the propionic acid group is 78.56 (2)°. The fully extended propionic side chain is in a trans configuration with a C-C-C-C torsion angle of -172.25 (7)°. In the crystal, hydrogen bonding is limited to dimer formation via R 2 (2)(8) rings. The hydrogen-bonded dimers are stacked along the b axis. The average planes of the two benzene rings in a dimer are parallel to each other, but at an offset of 4.31 (2) Å. Within neighbouring dimers along the [101] direction, the average mol-ecular benzene planes are almost perpendicular to each other, with a dihedral angle of 85.33 (2)°.

Correlation between superconductivity and bond angle of CrAs chain in non-centrosymmetric compounds A2Cr3As3 (A = K, Rb)

PubMed Central

Wang, Zhe; Yi, Wei; Wu, Qi; Sidorov, Vladimir A.; Bao, Jinke; Tang, Zhangtu; Guo, Jing; Zhou, Yazhou; Zhang, Shan; Li, Hang; Shi, Youguo; Wu, Xianxin; Zhang, Ling; Yang, Ke; Li, Aiguo; Cao, Guanghan; Hu, Jiangping; Sun, Liling; Zhao, Zhongxian

2016-01-01

Non-centrosymmetric superconductors, whose crystal structure is absent of inversion symmetry, have recently received special attentions due to the expectation of unconventional pairings and exotic physics associated with such pairings. The newly discovered superconductors A2Cr3As3 (A = K, Rb), featured by the quasi-one dimensional structure with conducting CrAs chains, belongs to such kind of superconductor. In this study, we are the first to report the finding that superconductivity of A2Cr3As3 (A = K, Rb) has a positive correlation with the extent of non-centrosymmetry. Our in-situ high pressure ac susceptibility and synchrotron x-ray diffraction measurements reveal that the larger bond angle of As-Cr-As (defined as α) in the CrAs chains can be taken as a key factor controlling superconductivity. While the smaller bond angle (defined as β) and the distance between the CrAs chains also affect the superconductivity due to their structural connections with the α angle. We find that the larger value of α-β, which is associated with the extent of the non-centrosymmetry of the lattice structure, is in favor of superconductivity. These results are expected to shed a new light on the underlying mechanism of the superconductivity in these Q1D superconductors and also to provide new perspective in understanding other non-centrosymmetric superconductors. PMID:27886268

Correlation between superconductivity and bond angle of CrAs chain in non-centrosymmetric compounds A2Cr3As3 (A = K, Rb).

PubMed

Wang, Zhe; Yi, Wei; Wu, Qi; Sidorov, Vladimir A; Bao, Jinke; Tang, Zhangtu; Guo, Jing; Zhou, Yazhou; Zhang, Shan; Li, Hang; Shi, Youguo; Wu, Xianxin; Zhang, Ling; Yang, Ke; Li, Aiguo; Cao, Guanghan; Hu, Jiangping; Sun, Liling; Zhao, Zhongxian

2016-11-25

Non-centrosymmetric superconductors, whose crystal structure is absent of inversion symmetry, have recently received special attentions due to the expectation of unconventional pairings and exotic physics associated with such pairings. The newly discovered superconductors A 2 Cr 3 As 3 (A = K, Rb), featured by the quasi-one dimensional structure with conducting CrAs chains, belongs to such kind of superconductor. In this study, we are the first to report the finding that superconductivity of A 2 Cr 3 As 3 (A = K, Rb) has a positive correlation with the extent of non-centrosymmetry. Our in-situ high pressure ac susceptibility and synchrotron x-ray diffraction measurements reveal that the larger bond angle of As-Cr-As (defined as α) in the CrAs chains can be taken as a key factor controlling superconductivity. While the smaller bond angle (defined as β) and the distance between the CrAs chains also affect the superconductivity due to their structural connections with the α angle. We find that the larger value of α-β, which is associated with the extent of the non-centrosymmetry of the lattice structure, is in favor of superconductivity. These results are expected to shed a new light on the underlying mechanism of the superconductivity in these Q1D superconductors and also to provide new perspective in understanding other non-centrosymmetric superconductors.

Bond-orientational analysis of hard-disk and hard-sphere structures.

PubMed

Senthil Kumar, V; Kumaran, V

2006-05-28

We report the bond-orientational analysis results for the thermodynamic, random, and homogeneously sheared inelastic structures of hard-disks and hard-spheres. The thermodynamic structures show a sharp rise in the order across the freezing transition. The random structures show the absence of crystallization. The homogeneously sheared structures get ordered at a packing fraction higher than the thermodynamic freezing packing fraction, due to the suppression of crystal nucleation. On shear ordering, strings of close-packed hard-disks in two dimensions and close-packed layers of hard-spheres in three dimensions, oriented along the velocity direction, slide past each other. Such a flow creates a considerable amount of fourfold order in two dimensions and body-centered-tetragonal (bct) structure in three dimensions. These transitions are the flow analogs of the martensitic transformations occurring in metals due to the stresses induced by a rapid quench. In hard-disk structures, using the bond-orientational analysis we show the presence of fourfold order. In sheared inelastic hard-sphere structures, even though the global bond-orientational analysis shows that the system is highly ordered, a third-order rotational invariant analysis shows that only about 40% of the spheres have face-centered-cubic (fcc) order, even in the dense and near-elastic limits, clearly indicating the coexistence of multiple crystalline orders. When layers of close-packed spheres slide past each other, in addition to the bct structure, the hexagonal-close-packed (hcp) structure is formed due to the random stacking faults. Using the Honeycutt-Andersen pair analysis and an analysis based on the 14-faceted polyhedra having six quadrilateral and eight hexagonal faces, we show the presence of bct and hcp signatures in shear ordered inelastic hard-spheres. Thus, our analysis shows that the dense sheared inelastic hard-spheres have a mixture of fcc, bct, and hcp structures.

Head angle and elevation in classroom environments: implications for amplification.

PubMed

Ricketts, Todd Andrew; Galster, Jason

2008-04-01

The purpose of this study was to examine children's head orientation relative to the arrival angle of competing signals and the sound source of interest in actual school settings. These data were gathered to provide information relative to the potential for directional benefit. Forty children, 4-17 years of age, with and without hearing loss, completed the study. Deviation in head angle and elevation relative to the direction of sound sources of interest were measured in 40 school environments. Measurements were made on the basis of physical data and videotapes from 3 cameras placed within each classroom. The results revealed similarly accurate head orientation across children with and without hearing loss when focusing on the 33% proportion of time in which children were most accurate. Orientation accuracy was not affected by age. The data also revealed that children with hearing loss were significantly more likely to orient toward brief utterances made by secondary talkers than were children with normal hearing. These data are consistent with the hypothesized association between hearing loss and increased visual monitoring. In addition, these results suggest that age does not limit the potential for signal-to-noise improvements from directivity-based interventions in noisy environments.

A dense and strong bonding collagen film for carbon/carbon composites

NASA Astrophysics Data System (ADS)

Cao, Sheng; Li, Hejun; Li, Kezhi; Lu, Jinhua; Zhang, Leilei

2015-08-01

A strong bonding collagen film was successfully prepared on carbon/carbon (C/C) composites. The surface conditions of the modified C/C composites were detected by contact angle measurements, scanning electron microscope (SEM), X-ray photoelectron spectroscopy (XPS) and Raman spectra. The roughness, optical morphology, bonding strength and biocompatibility of collagen films at different pH values were detected by confocal laser scanning microscope (CLSM), universal test machine and cytology tests in vitro. After a 4-h modification in 30% H2O2 solution at 100 °C, the contact angle on the surface of C/C composites was decreased from 92.3° to 65.3°. Large quantities of hydroxyl, carboxyl and carbonyl functional groups were formed on the surface of the modified C/C composites. Then a dense and continuous collagen film was prepared on the modified C/C substrate. Bonding strength between collagen film and C/C substrate was reached to 8 MPa level when the pH value of this collagen film was 2.5 after the preparing process. With 2-day dehydrathermal treatment (DHT) crosslinking at 105 °C, the bonding strength was increased to 12 MPa level. At last, the results of in vitro cytological test showed that this collagen film made a great improvement on the biocompatibility on C/C composites.

Ion irradiation induced structural modifications and increase in elastic modulus of silica based thin films

PubMed Central

Shojaee, S. A.; Qi, Y.; Wang, Y. Q.; Mehner, A.; Lucca, D. A.

2017-01-01

Ion irradiation is an alternative to heat treatment for transforming organic-inorganic thin films to a ceramic state. One major shortcoming in previous studies of ion-irradiated films is the assumption that constituent phases in ion-irradiated and heat-treated films are identical and that the ion irradiation effect is limited to changes in composition. In this study, we investigate the effects of ion irradiation on both the composition and structure of constituent phases and use the results to explain the measured elastic modulus of the films. The results indicated that the microstructure of the irradiated films consisted of carbon clusters within a silica matrix. It was found that carbon was present in a non-graphitic sp2-bonded configuration. It was also observed that ion irradiation caused a decrease in the Si-O-Si bond angle of silica, similar to the effects of applied pressure. A phase transformation from tetrahedrally bonded to octahedrally bonded silica was also observed. The results indicated the incorporation of carbon within the silica network. A combination of the decrease in Si-O-Si bond angle and an increase in the carbon incorporation within the silica network was found to be responsible for the increase in the elastic modulus of the films. PMID:28071696

Ion irradiation induced structural modifications and increase in elastic modulus of silica based thin films

DOE PAGES

Shojaee, S. A.; Qi, Y.; Wang, Y. Q.; ...

2017-01-10

Ion irradiation is an alternative to heat treatment for transforming organic-inorganic thin films to a ceramic state. One major shortcoming in previous studies of ion-irradiated films is the assumption that constituent phases in ion-irradiated and heat-treated films are identical and that the ion irradiation effect is limited to changes in composition. Here, we investigate the effects of ion irradiation on both the composition and structure of constituent phases and use the results to explain the measured elastic modulus of the films. Our results indicated that the microstructure of the irradiated films consisted of carbon clusters within a silica matrix. Itmore » was found that carbon was present in a non-graphitic sp 2-bonded configuration. It was also observed that ion irradiation caused a decrease in the Si-O-Si bond angle of silica, similar to the effects of applied pressure. A phase transformation from tetrahedrally bonded to octahedrally bonded silica was also observed. The results indicated the incorporation of carbon within the silica network. Finally, a combination of the decrease in Si-O-Si bond angle and an increase in the carbon incorporation within the silica network was found to be responsible for the increase in the elastic modulus of the films.« less

Real-space identification of intermolecular bonding with atomic force microscopy.

PubMed

Zhang, Jun; Chen, Pengcheng; Yuan, Bingkai; Ji, Wei; Cheng, Zhihai; Qiu, Xiaohui

2013-11-01

We report a real-space visualization of the formation of hydrogen bonding in 8-hydroxyquinoline (8-hq) molecular assemblies on a Cu(111) substrate, using noncontact atomic force microscopy (NC-AFM). The atomically resolved molecular structures enable a precise determination of the characteristics of hydrogen bonding networks, including the bonding sites, orientations, and lengths. The observation of bond contrast was interpreted by ab initio density functional calculations, which indicated the electron density contribution from the hybridized electronic state of the hydrogen bond. Intermolecular coordination between the dehydrogenated 8-hq and Cu adatoms was also revealed by the submolecular resolution AFM characterization. The direct identification of local bonding configurations by NC-AFM would facilitate detailed investigations of intermolecular interactions in complex molecules with multiple active sites.

Reusable Launch Vehicle Control in Multiple Time Scale Sliding Modes

NASA Technical Reports Server (NTRS)

Shtessel, Yuri

1999-01-01

A reusable launch vehicle control problem during ascent is addressed via multiple-time scaled continuous sliding mode control. The proposed sliding mode controller utilizes a two-loop structure and provides robust, de-coupled tracking of both orientation angle command profiles and angular rate command profiles in the presence of bounded external disturbances and plant uncertainties. Sliding mode control causes the angular rate and orientation angle tracking error dynamics to be constrained to linear, de-coupled, homogeneous, and vector valued differential equations with desired eigenvalues placement. The dual-time scale sliding mode controller was designed for the X-33 technology demonstration sub-orbital launch vehicle in the launch mode. 6DOF simulation results show that the designed controller provides robust, accurate, de-coupled tracking of the orientation angle command profiles in presence of external disturbances and vehicle inertia uncertainties. It creates possibility to operate the X-33 vehicle in an aircraft-like mode with reduced pre-launch adjustment of the control system.

Investigation of dynamic properties of a polymer matrix composite with different angles of fiber orientations

NASA Astrophysics Data System (ADS)

Kadioglu, F.; Coskun, T.; Elfarra, M.

2018-05-01

For the dynamic values of fiber-reinforced polymer matrix composite materials, elastic modulus and damping values are emphasized, and the two are desired to be high as much as possible, as the first is related to load bearing capacity, the latter provides the capability of energy absorption. In the composites, while fibers are usually utilized for reinforcement providing high elastic modulus and so high strength, matrix introduces a medium for high damping. Correct measurement of damping values is a critical step in designing composite materials. The aim of the current study is to measure the dynamic values of a glass fiber-reinforced polymer matrix composite, Hexply 913/33%/UD280, produced by Hexcel, using a vibrating beam technique. The specimens with different angles of fiber orientations (0, ±10°, ±20°, ±35, ±45°, ±55°, ±70, ±80 and 90) were manufactured from the composite prepreg and subjected to the clamped-free boundary conditions. Two different methods, the half power bandwidth and the logarithmic free decay, were used to measure the damping values to be able to compare the results. It has been revealed that the dynamic values are affected by the fiber orientations; for high flexural modulus the specimens with small angles of orientation, but for high damping those with large angles of orientation should be preferred. In general, the results are comparable, and the free decay method gave smaller values compared to the bandwidth method, with a little exception. It is suggested that the results (data) obtained from the test can be used for modal analysis reliably.

Development of a Coordinate Transformation method for direct georeferencing in map projection frames

NASA Astrophysics Data System (ADS)

Zhao, Haitao; Zhang, Bing; Wu, Changshan; Zuo, Zhengli; Chen, Zhengchao

2013-03-01

This paper develops a novel Coordinate Transformation method (CT-method), with which the orientation angles (roll, pitch, heading) of the local tangent frame of the GPS/INS system are transformed into those (omega, phi, kappa) of the map projection frame for direct georeferencing (DG). Especially, the orientation angles in the map projection frame were derived from a sequence of coordinate transformations. The effectiveness of orientation angles transformation was verified through comparing with DG results obtained from conventional methods (Legat method and POSPac method) using empirical data. Moreover, the CT-method was also validated with simulated data. One advantage of the proposed method is that the orientation angles can be acquired simultaneously while calculating position elements of exterior orientation (EO) parameters and auxiliary points coordinates by coordinate transformation. These three methods were demonstrated and compared using empirical data. Empirical results show that the CT-method is both as sound and effective as Legat method. Compared with POSPac method, the CT-method is more suitable for calculating EO parameters for DG in map projection frames. DG accuracy of the CT-method and Legat method are at the same level. DG results of all these three methods have systematic errors in height due to inconsistent length projection distortion in the vertical and horizontal components, and these errors can be significantly reduced using the EO height correction technique in Legat's approach. Similar to the results obtained with empirical data, the effectiveness of the CT-method was also proved with simulated data. POSPac method: The method is presented by Applanix POSPac software technical note (Hutton and Savina, 1997). It is implemented in the POSEO module of POSPac software.

Device orientation of a leadless pacemaker and subcutaneous implantable cardioverter-defibrillator in canine and human subjects and the effect on intrabody communication.

PubMed

Quast, Anne-Floor B E; Tjong, Fleur V Y; Koop, Brendan E; Wilde, Arthur A M; Knops, Reinoud E; Burke, Martin C

2018-02-14

The development of communicating modular cardiac rhythm management systems relies on effective intrabody communication between a subcutaneous implantable cardioverter-defibrillator (S-ICD) and a leadless pacemaker (LP), using conducted communication. Communication success is affected by the LP and S-ICD orientation. This study is designed to evaluate the orientation of the LP and S-ICD in canine subjects and measure success and threshold of intrabody communication. To gain more human insights, we will explore device orientation in LP and S-ICD patients. Canine subjects implanted with a prototype S-ICD and LP (both Boston Scientific, MA, USA) with anterior-posterior fluoroscopy images were included in this analysis. For comparison, a retrospective analysis of human S-ICD and LP patients was performed. The angle of the long axis of the LP towards the vertical axis of 0°, and distance between the coil and LP were measured. Twenty-three canine subjects were analysed. Median angle of the LP was 29° and median distance of the S-ICD coil to LP was 0.8 cm. All canine subjects had successful communication. The median communicating threshold was 2.5 V. In the human retrospective analysis, 72 LP patients and 100 S-ICD patients were included. The mean angle of the LP was 56° and the median distance between the S-ICD coil and LP was 4.6 cm. Despite the less favourable LP orientation in canine subjects, all communication attempts were successful. In the human subjects, we observed a greater and in theory more favourable LP angle towards the communication vector. These data suggests suitability of human anatomy for conductive intrabody communication.

An extended N-H bond, driven by a conserved second-order interaction, orients the flavin N5 orbital in cholesterol oxidase

NASA Astrophysics Data System (ADS)

Golden, Emily; Yu, Li-Juan; Meilleur, Flora; Blakeley, Matthew P.; Duff, Anthony P.; Karton, Amir; Vrielink, Alice

2017-01-01

The protein microenvironment surrounding the flavin cofactor in flavoenzymes is key to the efficiency and diversity of reactions catalysed by this class of enzymes. X-ray diffraction structures of oxidoreductase flavoenzymes have revealed recurrent features which facilitate catalysis, such as a hydrogen bond between a main chain nitrogen atom and the flavin redox center (N5). A neutron diffraction study of cholesterol oxidase has revealed an unusual elongated main chain nitrogen to hydrogen bond distance positioning the hydrogen atom towards the flavin N5 reactive center. Investigation of the structural features which could cause such an unusual occurrence revealed a positively charged lysine side chain, conserved in other flavin mediated oxidoreductases, in a second shell away from the FAD cofactor acting to polarize the peptide bond through interaction with the carbonyl oxygen atom. Double-hybrid density functional theory calculations confirm that this electrostatic arrangement affects the N-H bond length in the region of the flavin reactive center. We propose a novel second-order partial-charge interaction network which enables the correct orientation of the hydride receiving orbital of N5. The implications of these observations for flavin mediated redox chemistry are discussed.

The gonial angle stripper: an instrument for the treatment of prominent gonial angle.

PubMed

Kyutoku, S; Yanagida, A; Kusumoto, K; Ogawa, Y

1994-12-01

In the Orient, a prominent gonial angle, so-called benign masseteric hypertrophy, is rather common and considered unattractive. Therefore, its surgical correction is one of the most popular forms of facial skeletal contouring. For accurate and safe osteotomy of the mandibular angle region, a gonial angle stripper was specially invented. It has a small projection that will ease identification of the osteotomy line in a narrow operative field. The tool has been clinically used in eight patients to prove its usefulness, especially for a posteriorly developed mandibular angle.

Surface Modification by Atmospheric Pressure Plasma for Improved Bonding

NASA Astrophysics Data System (ADS)

Williams, Thomas Scott

An atmospheric pressure plasma source operating at temperatures below 150?C and fed with 1.0-3.0 volume% oxygen in helium was used to activate the surfaces of the native oxide on silicon, carbon-fiber reinforced epoxy composite, stainless steel type 410, and aluminum alloy 2024. Helium and oxygen were passed through the plasma source, whereby ionization occurred and ˜10 16 cm-3 oxygen atoms, ˜1015 cm -3 ozone molecules and ˜1016 cm-3 metastable oxygen molecules (O21Deltag) were generated. The plasma afterglow was directed onto the substrate material located 4 mm downstream. Surface properties of the plasma treated materials have been investigated using water contact angle (WCA), atomic force microscopy (AFM), infrared spectroscopy (IR), and x-ray photoelectron spectroscopy (XPS). The work presented herein establishes atmospheric-pressure plasma as a surface preparation technique that is well suited for surface activation and enhanced adhesive bond strength in a variety of materials. Atmospheric plasma activation presents an environmentally friendly alternative to wet chemical and abrasive methods of surface preparation. Attenuated total internal reflection infrared spectroscopy was used to study the aging mechanism of the native oxide on silicon. During storage at ambient conditions, the water contact angle of a clean surface increased from <5° to 40° over a period of 12 hours. When stored under a nitrogen purge, the water contact angle of a clean surface increased from <5° to 30° over a period of 40-60 hours. The change in contact angle resulted from the adsorption of nonanal onto the exposed surface hydroxyl groups. The rate of adsorption of nonanal under a nitrogen purged atmosphere ranged from 0.378+/-0.011 hr-1 to 0.182+/-0.008 hr -1 molecules/(cm2•s), decreasing as the fraction of hydrogen-bonded hydroxyl groups increased from 49% to 96% on the SiO 2 surface. The adsorption of the organic contaminant could be suppressed indefinitely by storing the silicon wafers in the presence of activated carbon or in a freezer at -22°C. The enhancement of adhesive bond strength and durability for carbon-fiber reinforced epoxy composite, stainless steel type 410, and aluminum alloy 2024 was demonstrated with the atmospheric pressure helium-oxygen plasma. All surfaces studied were converted from a hydrophobic state with a water contact angle of 65° to 80° into a hydrophilic state with a water contact angle between 20° and 40° within 5 seconds of plasma exposure. X-ray photoelectron spectroscopy confirmed that the carbon atoms on the carbon-fiber/epoxy composite were oxidized, yielding 17 atom% carboxylic acid groups, 10% ketones or aldehydes and 9% alcohols. Analysis of stainless steel and aluminum by XPS illustrate oxidation of the metal surface and an increase in the concentration of hydroxyl groups in the oxide film. Following plasma activation, the total hydroxyl species concentration on stainless steel increased from 31% to 57%, while aluminum exhibited an increase from 4% to 16% hydroxyl species. Plasma activation of the surface led to an increase in bond strength of the different surfaces by up to 150% when using Cytec FM300 and FM300-2 epoxy adhesives. Wedge crack extension tests following plasma activation revealed cohesive failure percentages of 97% for carbon-fiber/epoxy composite bonded to stainless steel, and 96% for aluminum bonded to itself. The bond strength and durability of the substrates correlated with changes in the specific surface chemistry, not the wetting angle or the morphological properties of the material. This suggests that enhanced chemical bonding at the interface was responsible for the improvement in mechanical properties following plasma activation. The surface preparation of polymers and composites using atmospheric pressure plasmas is a promising technique for replacing traditional methods of surface preparation by sanding, grit blasting or peel ply. After oxygen plasma activation and joining the materials together with epoxy, one observes 100% cohesive failure within the cured film adhesive. Depending on the material, the lap shear strength can be increased several fold over that achieved by either solvent wiping or abrasion. The trends in adhesion with plasma exposure time do not correlate well with surface wetting or roughness; instead they correlate with the fraction of the polymer surface sites that are converted into carboxylic acid groups.

Control of concerted two bond versus single bond dissociation in CH(3)Co(CO)(4) via an intermediate state using pump-dump laser pulses.

PubMed

Ambrosek, David; González, Leticia

2007-10-07

Wavepacket propagations on ab initio multiconfigurational two-dimensional potential energy surfaces for CH(3)Co(CO)(4) indicate that after irradiation to the lowest first and second electronic excited states, concerted dissociation of CH(3) and the axial CO ligand takes place. We employ a pump-dump sequence of pulses with appropriate frequencies and time delays to achieve the selective breakage of a single bond by controlling the dissociation angle. The pump and dump pulse sequence exploits the unbound surface where dissociation occurs in a counterintuitive fashion; stretching of one bond in an intermediate state enhances the single dissociation of the other bond.

1,5-Bis[1-(2,4-dihy­droxy­phen­yl)ethyl­idene]carbonohydrazide dimethyl­formamide disolvate

PubMed Central

He, Qing-Peng; Tan, Bo; Lu, Ze-Hua

2010-01-01

In the title compound, C17H18N4O5·2C3H7NO, two solvent mol­ecules are linked to the main mol­ecule via N—H⋯O and O—H⋯O hydrogen bonds, forming a hydrogen-bonded trimer. Intra­molecular O—H⋯N hydrogen bonds influence the mol­ecular conformation of the main mol­ecule, and the two benzene rings form a dihedral angle of 10.55 (18)°. In the crystal, inter­molecular O—H⋯O hydrogen bonds link hydrogen-bonded trimers into ribbons extending along the b axis. PMID:21589135

Methods and system for controlled laser-driven explosive bonding

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

Rubenchik, Alexander M.; Farmer, Joseph C.; Hackel, Lloyd

A technique for bonding two dissimilar materials includes positioning a second material over a first material at an oblique angle and applying a tamping layer over the second martial. A laser beam is directed at the second material that generates a plasma at the location of impact on the second material. The plasma generates pressure that accelerates a portion of the second material to a very high velocity and towards the first material. The second material impacts the first material causing bonding of the two materials.

A critical study of the role of the surface oxide layer in titanium bonding

NASA Technical Reports Server (NTRS)

Dias, S.; Wightman, J. P.

1982-01-01

The molecular understanding of the role which the surface oxide layer of the adherend plays in titanium bonding is studied. The effects of Ti6-4 adherends pretreatment, bonding conditions, and thermal aging of the lap shear specimens were studied. The use of the SEM/EDAX and ESCA techniques to study surface morphology and surface composition was emphasized. In addition, contact angles and both infrared and visible reflection spectroscopy were used in ancillary studies.

Chemically modified graphene/polyimide composite films based on utilization of covalent bonding and oriented distribution.

PubMed

Huang, Ting; Lu, Renguo; Su, Chao; Wang, Hongna; Guo, Zheng; Liu, Pei; Huang, Zhongyuan; Chen, Haiming; Li, Tongsheng

2012-05-01

Herein, we have developed a rather simple composite fabrication approach to achieving molecular-level dispersion and planar orientation of chemically modified graphene (CMG) in the thermosetting polyimide (PI) matrix as well as realizing strong adhesion at the interfacial regions between reinforcing filler and matrix. The covalent adhesion of CMG to PI matrix and oriented distribution of CMG were carefully confirmed and analyzed by detailed investigations. Combination of covalent bonding and oriented distribution could enlarge the effectiveness of CMG in the matrix. Efficient stress transfer was found at the CMG/PI interfaces. Significant improvements in the mechanical performances, thermal stability, electrical conductivity, and hydrophobic behavior were achieved by addition of only a small amount of CMG. Furthermore, it is noteworthy that the hydrophilic-to-hydrophobic transition and the electrical percolation were observed at only 0.2 wt % CMG in this composite system. This facile methodology is believed to afford broad application potential in graphene-based polymer nanocomposites, especially other types of high-performance thermosetting systems.

Glass polymorphism in amorphous germanium probed by first-principles computer simulations

NASA Astrophysics Data System (ADS)

Mancini, G.; Celino, M.; Iesari, F.; Di Cicco, A.

2016-01-01

The low-density (LDA) to high-density (HDA) transformation in amorphous Ge at high pressure is studied by first-principles molecular dynamics simulations in the framework of density functional theory. Previous experiments are accurately reproduced, including the presence of a well-defined LDA-HDA transition above 8 GPa. The LDA-HDA density increase is found to be about 14%. Pair and bond-angle distributions are obtained in the 0-16 GPa pressure range and allowed us a detailed analysis of the transition. The local fourfold coordination is transformed in an average HDA sixfold coordination associated with different local geometries as confirmed by coordination number analysis and shape of the bond-angle distributions.

Extended Friedberg-Lee hidden symmetries, quark masses,and CP violation with four generations

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

Bar-Shalom, S.; Soni, A.; Oaknin, D.

2009-07-16

Motivated in part by the several observed anomalies involving CP asymmetries of B and B{sub s} decays, we consider the standard model with a 4th sequential family (SM4) which seems to offer a rather simple resolution. We initially assume T-invariance by taking the up and down-quark 4 x 4 mass matrix to be real. Following Friedberg and Lee (FL), we then impose a hidden symmetry on the unobserved (hidden) up and down-quark SU(2) states. The hidden symmetry for four generations ensures the existence of two zero-mass eigenstates, which we take to be the (u,c) and (d,s) states in the upmore » and down-quark sectors, respectively. Then, we simultaneously break T-invariance and the hidden symmetry by introducing two phase factors in each sector. This breaking mechanism generates the small quark masses m{sub u}, m{sub c} and m{sub d}, m{sub s}, which, along with the orientation of the hidden symmetry, determine the size of CP-violation in the SM4. For illustration we choose a specific physical picture for the hidden symmetry and the breaking mechanism that reproduces the observed quark masses, mixing angles and CP-violation, and at the same time allows us to further obtain very interesting relations/predictions for the mixing angles of t and t'. For example, with this choice we get V{sub td} {approx} (V{sub cb}/V{sub cd}-V{sub ts}/V{sub us}) + O({lambda}{sup 2}) and V{sub t'b}{approx}V{sub t'd{sm_bullet}}(V{sub cb}/V{sub cd}), V{sub tb'}V{sub t'd{sm_bullet}}(V{sub ts}/V{sub us}), implying that V{sub t'd} > V{sub t'b}, V{sub tb'}. We furthermore find that the Cabibbo angle is related to the orientation of the hidden symmetry and that the key CP-violating quantity of our model at high energies, J{sub SM4} {triple_bond} Im(V{sub tb}V{sub t'b*}V{sub t'b{prime}}V{sub tb'*}), which is the high-energy analogue of the Jarlskog invariant of the SM, is proportional to the light-quark masses and the measured Cabibbo-Kobayashi-Maskawa quark-mixing matrix angles: |J{sub SM4}|A{sup 3}{lambda}{sup 5} x ({radical}(m{sub u}/m{sub t}) + {radical}m{sub c}/m{sub t'}-{radical}(m{sub d}/m{sub b}) + {radical}m{sub s}/m{sub b'}) {approx} 10{sup -5}, where A {approx} 0.81 and {lambda} = 0.2257 are the Wolfenstein parameters. Other choices for the orientation of the hidden symmetry and/or the breaking mechanism may lead to different physical outcomes. A general solution, obtained numerically, will be presented in a forthcoming paper.« less

Challenges of Roll Orientation with Respect to Vehicle Heading at Touchdown for the Orion Command Module

NASA Technical Reports Server (NTRS)

Gay, Robert S.; Bihari, Brian D.

2008-01-01

Due to mass constraints, the Orion Command Module landing attention system requires that the capsule be oriented in a specific direction with respect to the horizontal surface-relative velocity (Heading) at touchdown in order to keep crew and vehicle loads within specifications. These constraints apply to both land and water landings. In fact, water landings are even more constrained with the addition of impact angle requirements necessary to slice through the water. There are two primary challenges with achieving this touchdown orientation: 1. Navigation knowledge of velocity (needed to determine Heading) with and without GPS, including the effects of the Heading angle itself becoming undefined as horizontal velocity decreases, and 2. Controlling to the desired orientation in the presences of chute torque and wind gusts that may change the Heading just prior to touchdown. This paper will discuss the design and performance of the current Orion navigation and control system used to achieve the desired orientation at touchdown.

Anomalous refraction of light through slanted-nanoaperture arrays on metal surface

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

Kim, Myungji; Jung, Yun Suk; Xi, Yonggang

2015-09-07

We report a nanoapertured metal surface that demonstrates anomalous refraction of light for a wide range of incident angles. A nanoslit aperture is designed to serve as a tilted vertical-dipole whose radiation pattern orients to a glancing angle direction to substrate. An array of such slanted nanoslits formed in a metal film redirects an incident beam into the direction of negative refraction angle: the aperture-transmitted wave makes a far-field propagation to the tilt-oriented direction of radiation pattern. The thus-designed nanoaperture array demonstrates the −1st order diffraction (i.e., to the negative refraction-angle direction) with well-suppressed background transmission (the zero-order direct transmissionmore » and other higher-order diffractions). Engineering the radiation pattern of nanoaperture offers an approach to overcoming the limits of conventional diffractive/refractive optics and complementing metasurface-based nano-optics.« less

Optic axis determination by fibre-based polarization-sensitive swept-source optical coherence tomography

NASA Astrophysics Data System (ADS)

Lu, Zenghai; Kasaragod, Deepa K.; Matcher, Stephen J.

2011-02-01

We describe a fibre-based variable-incidence angle (VIA) polarization-sensitive swept-source optical coherence tomography (PS-SS-OCT) system to determine the 3D optical axis of birefringent biological tissues. Single-plane VIA-PS-OCT is also explored which requires measurement of the absolute fast-axis orientation. A state-of-the-art PS-SS-OCT system with some improvements both in hardware and software was used to determine the apparent optical birefringence of equine tendon for a number of different illumination directions. Polar and azimuthal angles of cut equine tendon were produced by the VIA method and compared with the nominal values. A quarter waveplate (QWP) and equine tendon were used as test targets to validate the fast-axis measurements using the system. Polar and azimuthal angles of cut equine tendon broadly agreed with the expected values within about 8% of the nominal values. A theoretical and experimental analysis of the effect of the sample arm fibre on determination of optical axis orientation using a proposed definition based on the orientation of the eigenpolarization ellipse experimentally confirms that this algorithm only works correctly for special settings of the sample arm fibre. A proposed algorithm based on the angle between Stokes vectors on the Poincaré sphere is confirmed to work for all settings of the sample arm fibre. A calibration procedure is proposed to remove the sign ambiguity of the measured orientation and was confirmed experimentally by using the QWP.

Optic axis determination by fiber-based polarization-sensitive swept-source optical coherence tomography

NASA Astrophysics Data System (ADS)

Lu, Zenghai; Kasaragod, Deepa K.; Matcher, Stephen J.

2011-03-01

We describe a fiber-based variable-incidence-angle (VIA) polarization-sensitive swept-source optical coherence tomography (PS-SS-OCT) system to determine the 3-D optical axis of birefringent biological tissues. Single-plane VIAPS- OCT is also explored which requires measurement of the absolute fast-axis orientation. A state-of-the-art PS-SS-OCT system with some improvements both in hardware and software was used to determine the apparent optical birefringence of equine tendon for a number of different illumination directions. Polar and azimuthal angles of cut equine tendon were produced by VIA method and compared with the nominal values. A quarter waveplate (QWP) and equine tendon were used as test targets to validate the fast-axis measurements using the system. Polar and azimuthal angles of cut equine tendon broadly agreed with the expected values within about 8% of the nominal values. A theoretical and experimental analysis of the effect of the sample arm fiber on determination of optical axis orientation using a proposed definition based on the orientation of the eigenpolarization ellipse experimentally confirms that this algorithm only works correctly for special settings of the sample arm fiber. A proposed algorithm based on the angle between Stokes vectors on the Poincaré sphere is confirmed to work for all settings of the sample arm fiber. A calibration procedure is proposed to remove the sign ambiguity of the measured orientation and was confirmed experimentally by using the QWP.

RELATIVISTIC DOPPLER BEAMING AND MISALIGNMENTS IN AGN JETS

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

Singal, Ashok K., E-mail: asingal@prl.res.in

Radio maps of active galactic nuclei often show linear features, called jets, on both parsec and kiloparsec scales. These jets supposedly possess relativistic motion and are oriented close to the line of sight of the observer, and accordingly the relativistic Doppler beaming makes them look much brighter than they really are in their respective rest frames. The flux boosting due to the relativistic beaming is a very sensitive function of the jet orientation angle, as seen by the observer. Sometimes, large bends are seen in these jets, with misalignments being 90° or more, which might imply a change in themore » orientation angle that should cause a large change in the relativistic beaming factor. Hence, if relativistic beaming does play an important role in these jets such large bends should usually show high contrast in the brightness of the jets before and after the bend. It needs to be kept in mind that sometimes a small intrinsic change in the jet angle might appear as a much larger misalignment due to the effects of geometrical projection, especially when seen close to the line of sight. What really matters are the initial and final orientation angles of the jet with respect to the observer’s line of sight. Taking the geometrical projection effects properly into account, we calculate the consequences of the presumed relativistic beaming and demonstrate that there ought to be large brightness ratios in jets before and after the observed misalignments.« less

From reaching to reach-to-grasp: the arm posture difference and its implications on human motion control strategy.

PubMed

Li, Zhi; Milutinović, Dejan; Rosen, Jacob

2017-05-01

Reach-to-grasp arm postures differ from those in pure reaching because they are affected by grasp position/orientation, rather than simple transport to a position during a reaching motion. This paper investigates this difference via an analysis of experimental  data collected on reaching and reach-to-grasp motions. A seven-degree-of-freedom (DOFs) kinematic arm model with the swivel angle is used for the motion analysis. Compared to a widely used anatomical arm model, this model distinguishes clearly the four grasping-relevant DOFs (GR-DOFs) that are affected by positions and orientations of the objects to be grasped. These four GR-DOFs include the swivel angle that measures the elbow rotation about the shoulder-wrist axis, and three wrist joint angles. For each GR-DOF, we quantify position vs orientation task-relevance bias that measures how much the DOF is affected by the grasping position vs orientation. The swivel angle and forearm supination have similar bias, and the analysis of their motion suggests two hypotheses regarding the synergistic coordination of the macro- and micro-structures of the human arm (1) DOFs with similar task-relevance are synergistically coordinated; and (2) such synergy breaks when a task-relevant DOF is close to its joint limit without necessarily reaching the limit. This study provides a motion analysis method to reduce the control complexity for reach-to-grasp tasks, and suggests using dynamic coupling to coordinate the hand and arm of upper-limb exoskeletons.

Relativistic Doppler Beaming and Misalignments in AGN Jets

NASA Astrophysics Data System (ADS)

Singal, Ashok K.

2016-08-01

Radio maps of active galactic nuclei often show linear features, called jets, on both parsec and kiloparsec scales. These jets supposedly possess relativistic motion and are oriented close to the line of sight of the observer, and accordingly the relativistic Doppler beaming makes them look much brighter than they really are in their respective rest frames. The flux boosting due to the relativistic beaming is a very sensitive function of the jet orientation angle, as seen by the observer. Sometimes, large bends are seen in these jets, with misalignments being 90° or more, which might imply a change in the orientation angle that should cause a large change in the relativistic beaming factor. Hence, if relativistic beaming does play an important role in these jets such large bends should usually show high contrast in the brightness of the jets before and after the bend. It needs to be kept in mind that sometimes a small intrinsic change in the jet angle might appear as a much larger misalignment due to the effects of geometrical projection, especially when seen close to the line of sight. What really matters are the initial and final orientation angles of the jet with respect to the observer’s line of sight. Taking the geometrical projection effects properly into account, we calculate the consequences of the presumed relativistic beaming and demonstrate that there ought to be large brightness ratios in jets before and after the observed misalignments.

Functional Implications of Ubiquitous Semicircular Canal Non-Orthogonality in Mammals

PubMed Central

Berlin, Jeri C.; Kirk, E. Christopher; Rowe, Timothy B.

2013-01-01

The ‘canonical model’ of semicircular canal orientation in mammals assumes that 1) the three ipsilateral canals of an inner ear exist in orthogonal planes (i.e., orthogonality), 2) corresponding left and right canal pairs have equivalent angles (i.e., angle symmetry), and 3) contralateral synergistic canals occupy parallel planes (i.e., coplanarity). However, descriptions of vestibular anatomy that quantify semicircular canal orientation in single species often diverge substantially from this model. Data for primates further suggest that semicircular canal orthogonality varies predictably with the angular head velocities encountered in locomotion. These observations raise the possibility that orthogonality, symmetry, and coplanarity are misleading descriptors of semicircular canal orientation in mammals, and that deviations from these norms could have significant functional consequences. Here we critically assess the canonical model of semicircular canal orientation using high-resolution X-ray computed tomography scans of 39 mammal species. We find that substantial deviations from orthogonality, angle symmetry, and coplanarity are the rule for the mammals in our comparative sample. Furthermore, the degree to which the semicircular canals of a given species deviate from orthogonality is negatively correlated with estimated vestibular sensitivity. We conclude that the available comparative morphometric data do not support the canonical model and that its overemphasis as a heuristic generalization obscures a large amount of functionally relevant variation in semicircular canal orientation between species. PMID:24260256

Laser Surface Preparation for Adhesive Bonding of Aerospace Structural Composites

NASA Technical Reports Server (NTRS)

Belcher, M. A.; Wohl, C. J.; Hopkins, J. W.; Connell, J. W.

2010-01-01

Adhesive bonds are critical to the integrity of built-up structures. Disbonds can often be detected but the strength of adhesion between surfaces in contact is not obtainable without destructive testing. Typically the number one problem in a bonded structure is surface contamination, and by extension, surface preparation. Standard surface preparation techniques, including grit blasting, manual abrasion, and peel ply, are not ideal because of variations in their application. Etching of carbon fiber reinforced plastic (CFRP) panels using a neodymium-doped yttrium aluminum garnet (Nd:YAG) laser appears to be a highly precise and promising way to both clean a composite surface prior to bonding and provide a bond-promoting patterned surface akin to peel ply without the inherent drawbacks from the same (i.e., debris and curvature). CFRP surfaces prepared using laser patterns conducive to adhesive bonding were compared to typical pre-bonding surface treatments through optical microscopy, contact angle goniometry, and post-bonding mechanical testing.

Crystal structure, vibrational spectra and DFT studies of hydrogen bonded 1,2,4-triazolium hydrogenselenate

NASA Astrophysics Data System (ADS)

Arjunan, V.; Thirunarayanan, S.; Marchewka, M. K.; Mohan, S.

2017-10-01

The new hydrogen bonded molecular complex 1,2,4-triazolium hydrogenselenate (THS) is prepared by the reaction of 1H-1,2,4-triazole and selenic acid. This complex is stabilised by N-H⋯O and C-H⋯O hydrogen bonding and electrostatic attractive forces between 1H and 1,2,4-triazolium cations and hydrogen selenate anions. The XRD studies revealed that intermolecular proton transfer occur from selenic acid to 1H-1,2,4-triazole molecule, results in the formation of 1,2,4-triazolium hydrogenselenate which contains 1,2,4-triazolium cations and hydrogenselenate anions. The molecular structure of THS crystal has also been optimised by using Density Functional Theory (DFT) using B3LYP/cc-pVTZ and B3LYP/6-311++G** methods in order to find the whole characteristics of the molecular complex. The theoretical structural parameters such as bond length, bond angle and dihedral angle determined by DFT methods are well agreed with the XRD parameters. The atomic charges and thermodynamic properties are also calculated and analysed. The energies of frontier molecular orbitals HOMO, LUMO, HOMO-1, LUMO+1 and LUMO-HUMO energy gap are calculated to understand the kinetic stability and chemical reactivity of the molecular complex. The natural bond orbital analysis (NBO) has been performed in order to study the intramolecular bonding interactions and delocalisation of electrons. These intra molecular charge transfer may induce biological activities such as antimicrobials, antiinflammatory, antifungal etc. The complete vibrational assignments of THS have been performed by using FT-IR and FT-Raman spectra.

Universal connectors for joining stringers

NASA Technical Reports Server (NTRS)

Harrison, Jr., Ernest (Inventor)

1987-01-01

This invention is a lightweight, universal connector that joins stringers at various angles. The connectors 10 are fabricated from fiber-epoxy resin strips that wrap around stringers 30 and have ends, tabs 16 and 18, which extend in one general direction. The inside surface of the first tab 16 lies on a plane defined by the stringers being joined, and the second tab 18 is separated from the first tab 16 by a distance equal to their thickness. Stringers 30 of different shapes and sizes are joined by alternately bonding the first tab 16 of one connector between the first 16 and second 18 tabs of another connector. Tee-joints are formed by using web elements 41 and 42 which each partially wrap around a stringer 3010 and have tabs 411 and 421 which are offset, and are bonded between tabs 16 and 18 of universal connectors 109 and 1010 bonded to another stringer 309. Sharp corners are trimmed from the tabs so that a gusset area remains between the stringers for support. Acute angle through obtuse angle joints are formed by trimming those edges of the tabs which lie against the stringers. A specific application of the invention is a Walker 60, utilized by handicapped individuals, fabricated from composite materials that is 40% lighter than similar metallic structures.

Computational study of the interplay between intermolecular interactions and CO2 orientations in type I hydrates.

PubMed

Pérez-Rodríguez, M; Vidal-Vidal, A; Míguez, J M; Blas, F J; Torré, J-P; Piñeiro, M M

2017-01-25

Carbon dioxide (CO 2 ) molecules show a rich orientation landscape when they are enclathrated in type I hydrates. Previous studies have described experimentally their preferential orientations, and some theoretical works have explained, but only partially, these experimental results. In the present paper, we use classical molecular dynamics and electronic density functional theory to advance in the theoretical description of CO 2 orientations within type I hydrates. Our results are fully compatible with those previously reported, both theoretical and experimental, the geometric shape of the cavities in hydrate being, and therefore, the steric constraints, responsible for some (but not all) preferential angles. In addition, our calculations also show that guest-guest interactions in neighbouring cages are a key factor to explain the remaining experimental angles. Besides the implication concerning equation of state hydrate modeling approximations, the conclusion is that these guest-guest interactions should not be neglected, contrary to the usual practice.

Shear Bond Strength of Bracket Bases to Adhesives Based on Bracket Base Design

DTIC Science & Technology

2016-04-13

moving in the right direction. And to my wife, Allyson, I’m forever grateful for your patience and support, enabling me to pursue dreams as we begin... intrusion and extrusion in Angle and post Angle eras. As a result, the strength and precision of systems to apply forces through teeth have also

2'-Chloro-4-meth-oxy-3-nitro-benzil.

PubMed

Nithya, G; Thanuja, B; Chakkaravarthi, G; Kanagam, Charles C

2011-06-01

In the title compound, C(15)H(10)ClNO(5), the dihedral angle between the aromatic rings is 87.99 (5)°. The O-C-C-O torsion angle between the two carbonyl units is -119.03 (16)°. The crystal structure is stabilized by a weak intermolecular C-H⋯O hydrogen bond.

Effect of gold wire bonding process on angular correlated color temperature uniformity of white light-emitting diode.

PubMed

Wu, Bulong; Luo, Xiaobing; Zheng, Huai; Liu, Sheng

2011-11-21

Gold wire bonding is an important packaging process of lighting emitting diode (LED). In this work, we studied the effect of gold wire bonding on the angular uniformity of correlated color temperature (CCT) in white LEDs whose phosphor layers were coated by freely dispersed coating process. Experimental study indicated that different gold wire bonding impacts the geometry of phosphor layer, and it results in different fluctuation trends of angular CCT at different spatial planes in one LED sample. It also results in various fluctuating amplitudes of angular CCT distributions at the same spatial plane for samples with different wire bonding angles. The gold wire bonding process has important impact on angular uniformity of CCT in LED package. © 2011 Optical Society of America

The orientation distribution of tunneling-related quantities

NASA Astrophysics Data System (ADS)

Seif, W. M.; Refaie, A. I.; Botros, M. M.

2018-03-01

In the nuclear tunneling processes involving deformed nuclei, most of the tunneling-related quantities depend on the relative orientations of the participating nuclei. In the presence of different multipole deformations, we study the variation of a few relevant quantities for the α-decay and the sub-barrier fusion processes, in an orientation degree of freedom. The knocking frequency and the penetration probability are evaluated within the Wentzel-Kramers-Brillouin approximation. The interaction potential is calculated with Skyrme-type nucleon-nucleon interaction. We found that the width of the potential pocket, the Coulomb barrier radius, the penetration probability, the α-decay width, and the fusion cross-section follow consistently the orientation-angle variation of the radius of the deformed nucleus. The orientation distribution patterns of the pocket width, the barrier radius, the logarithms of the penetrability, the decay width, and the fusion cross-section are found to be highly analogous to pattern of the deformed-nucleus radius. The curve patterns of the orientation angle distributions of the internal pocket depth, the Coulomb barrier height and width, as well as the knocking frequency simulate inversely the variation of the deformed nucleus radius. The predicted orientation behaviors will be of a special interest in predicting the optimum orientations for the tunneling processes.

Structural transformations of carbon and boron nitride nanoscrolls at high impact collisions

NASA Astrophysics Data System (ADS)

Woellner, C. F.; Machado, L. D.; Autreto, P. A. S.; de Sousa, J. M.; Galvao, D. S.

The behavior of nanostructures under high strain-rate conditions has been object of theoretical and experimental investigations in recent years. For instance, it has been shown that carbon and boron nitride nanotubes can be unzipped into nanoribbons at high velocity impacts. However, the response of many nanostructures to high strain-rate conditions is still not completely understood. In this work we have investigated through fully atomistic reactive (ReaxFF) molecular dynamics (MD) simulations the mechanical behavior of carbon (CNS) and boron nitride nanoscrolls (BNS) colliding against solid targets at high velocities,. CNS (BNS) nanoscrolls are graphene (boron nitride) membranes rolled up into papyrus-like structures. Their open-ended topology leads to unique properties not found in close-ended analogues, such as nanotubes. Our results show that the collision products are mainly determined by impact velocities and by two impact angles, which define the position of the scroll (i) axis and (ii) open edge relative to the target. Our MD results showed that for appropriate velocities and orientations large-scale deformations and nanoscroll fracture can occur. We also observed unscrolling (scrolls going back to quasi-planar membranes), scroll unzipping into nanoribbons, and significant reconstruction due to breaking and/or formation of new chemical bonds. For particular edge orientations and velocities, conversion from open to close-ended topology is also possible, due to the fusion of nanoscroll walls.

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

van Veelen, Arjen; Bargar, John R.; Law, Gareth T. W.

Polarization-dependent grazing incidence X-ray absorption spectroscopy (XAS) measurements were completed on oriented single crystals of magnesite [MgCO 3] and brucite [Mg(OH) 2] reacted with aqueous uranyl chloride above and below the solubility boundaries of schoepite (500, 50, and 5 ppm) at pH 8.3 and at ambient (P CO2 = 10 –3.5) or reduced partial pressures of carbon dioxide (P CO2 = 10 –4.5). X-ray absorption near edge structure (XANES) spectra show a striking polarization dependence (χ = 0° and 90° relative to the polarization plane of the incident beam) and consistently demonstrated that the uranyl molecule was preferentially oriented withmore » its O axial = U(VI) = O axial linkage at high angles (60–80°) to both magnesite (101¯4) and brucite (0001). Extended X-ray absorption fine structure (EXAFS) analysis shows that the “effective” number of U(VI) axial oxygens is the most strongly affected fitting parameter as a function of polarization. Furthermore, axial tilt in the surface thin films (thickness ~ 21 Å) is correlated with surface roughness [σ]. Our results show that hydrated uranyl(-carbonate) complexes polymerize on all of our experimental surfaces and that this process is controlled by surface hydroxylation. Lastly, these results provide new insights into the bonding configuration expected for uranyl complexes on the environmentally significant carbonate and hydroxide mineral surfaces.« less

Uranium immobilization and nanofilm formation on magnesium-rich minerals

DOE PAGES

van Veelen, Arjen; Bargar, John R.; Law, Gareth T. W.; ...

2016-03-18

Polarization-dependent grazing incidence X-ray absorption spectroscopy (XAS) measurements were completed on oriented single crystals of magnesite [MgCO 3] and brucite [Mg(OH) 2] reacted with aqueous uranyl chloride above and below the solubility boundaries of schoepite (500, 50, and 5 ppm) at pH 8.3 and at ambient (P CO2 = 10 –3.5) or reduced partial pressures of carbon dioxide (P CO2 = 10 –4.5). X-ray absorption near edge structure (XANES) spectra show a striking polarization dependence (χ = 0° and 90° relative to the polarization plane of the incident beam) and consistently demonstrated that the uranyl molecule was preferentially oriented withmore » its O axial = U(VI) = O axial linkage at high angles (60–80°) to both magnesite (101¯4) and brucite (0001). Extended X-ray absorption fine structure (EXAFS) analysis shows that the “effective” number of U(VI) axial oxygens is the most strongly affected fitting parameter as a function of polarization. Furthermore, axial tilt in the surface thin films (thickness ~ 21 Å) is correlated with surface roughness [σ]. Our results show that hydrated uranyl(-carbonate) complexes polymerize on all of our experimental surfaces and that this process is controlled by surface hydroxylation. Lastly, these results provide new insights into the bonding configuration expected for uranyl complexes on the environmentally significant carbonate and hydroxide mineral surfaces.« less

Uranium Immobilization and Nanofilm Formation on Magnesium-Rich Minerals.

PubMed

van Veelen, Arjen; Bargar, John R; Law, Gareth T W; Brown, Gordon E; Wogelius, Roy A

2016-04-05

Polarization-dependent grazing incidence X-ray absorption spectroscopy (XAS) measurements were completed on oriented single crystals of magnesite [MgCO3] and brucite [Mg(OH)2] reacted with aqueous uranyl chloride above and below the solubility boundaries of schoepite (500, 50, and 5 ppm) at pH 8.3 and at ambient (PCO2 = 10(-3.5)) or reduced partial pressures of carbon dioxide (PCO2 = 10(-4.5)). X-ray absorption near edge structure (XANES) spectra show a striking polarization dependence (χ = 0° and 90° relative to the polarization plane of the incident beam) and consistently demonstrated that the uranyl molecule was preferentially oriented with its Oaxial═U(VI)═Oaxial linkage at high angles (60-80°) to both magnesite (101̅4) and brucite (0001). Extended X-ray absorption fine structure (EXAFS) analysis shows that the "effective" number of U(VI) axial oxygens is the most strongly affected fitting parameter as a function of polarization. Furthermore, axial tilt in the surface thin films (thickness ∼ 21 Å) is correlated with surface roughness [σ]. Our results show that hydrated uranyl(-carbonate) complexes polymerize on all of our experimental surfaces and that this process is controlled by surface hydroxylation. These results provide new insights into the bonding configuration expected for uranyl complexes on the environmentally significant carbonate and hydroxide mineral surfaces.

Anisotropic Tribological Properties of Silicon Carbide

NASA Technical Reports Server (NTRS)

Miyoshi, K.; Buckley, D. H.

1980-01-01

The anisotropic friction, deformation and fracture behavior of single crystal silicon carbide surfaces were investigated in two categories. The categories were called adhesive and abrasive wear processes, respectively. In the adhesive wear process, the adhesion, friction and wear of silicon carbide were markedly dependent on crystallographic orientation. The force to reestablish the shearing fracture of adhesive bond at the interface between silicon carbide and metal was the lowest in the preferred orientation of silicon carbide slip system. The fracturing of silicon carbide occurred near the adhesive bond to metal and it was due to primary cleavages of both prismatic (10(-1)0) and basal (0001) planes.

Evaporation of nanoscale water on a uniformly complete wetting surface at different temperatures.

PubMed

Guo, Yuwei; Wan, Rongzheng

2018-05-03

The evaporation of nanoscale water films on surfaces affects many processes in nature and industry. Using molecular dynamics (MD) simulations, we show the evaporation of a nanoscale water film on a uniformly complete wetting surface at different temperatures. With the increase in temperature, the growth of the water evaporation rate becomes slow. Analyses show that the hydrogen bond (H-bond) lifetimes and orientational autocorrelation times of the outermost water film decrease slowly with the increase in temperature. Compared to a thicker water film, the H-bond lifetimes and orientational autocorrelation times of a monolayer water film are much slower. This suggests that the lower evaporation rate of the monolayer water film on a uniformly complete wetting surface may be caused by the constriction of the water rotation due to the substrate. This finding may be helpful for controlling nanoscale water evaporation within a certain range of temperatures.

Adhesives with wood materials : bond formation and performance

Treesearch

Charles R. Frihart; Christopher G. Hunt

2010-01-01

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

Ceramic microstructure and adhesion

NASA Technical Reports Server (NTRS)

Buckley, D. H.

1984-01-01

When a ceramic is brought into contact with a ceramic, a polymer, or a metal, strong bond forces can develop between the materials. The bonding forces will depend upon the state of the surfaces, cleanliness and the fundamental properties of the two solids, both surface and bulk. Adhesion between a ceramic and another solid are discussed from a theoretical consideration of the nature of the surfaces and experimentally by relating bond forces to interface resulting from solid state contact. Surface properties of ceramics correlated with adhesion include, orientation, reconstruction and diffusion as well as the chemistry of the surface specie. Where a ceramic is in contact with a metal their interactive chemistry and bond strength is considered. Bulk properties examined include elastic and plastic behavior in the surficial regions, cohesive binding energies, crystal structures and crystallographic orientation. Materials examined with respect to interfacial adhesive interactions include silicon carbide, nickel zinc ferrite, manganese zinc ferrite, and aluminum oxide. The surfaces of the contacting solids are studied both in the atomic or molecularly clean state and in the presence of selected surface contaminants.

Ceramic microstructure and adhesion

NASA Technical Reports Server (NTRS)

Buckley, D. H.

1985-01-01

When a ceramic is brought into contact with a ceramic, a polymer, or a metal, strong bond forces can develop between the materials. The bonding forces will depend upon the state of the surfaces, cleanliness and the fundamental properties of the two solids, both surface and bulk. Adhesion between a ceramic and another solid are discussed from a theoretical consideration of the nature of the surfaces and experimentally by relating bond forces to interface resulting from solid state contact. Surface properties of ceramics correlated with adhesion include, orientation, reconstruction and diffusion as well as the chemistry of the surface specie. Where a ceramic is in contact with a metal their interactive chemistry and bond strength is considered. Bulk properties examined include elastic and plastic behavior in the surficial regions, cohesive binding energies, crystal structures and crystallographic orientation. Materials examined with respect to interfacial adhesive interactions include silicon carbide, nickel zinc ferrite, manganese zinc ferrite, and aluminum oxide. The surfaces of the contacting solids are studied both in the atomic or molecularly clean state and in the presence of selected surface contaminants.

Z-direction fiber orientation in paperboard

Treesearch

John M. Considine; David W. Vahey; Roland Gleisner; Alan Rudie; Sabine Rolland du Roscoat; Jean-Francis Bloch

2010-01-01

This work evaluated the use of conventional tests to show beneficial attributes of z-direction fiber orientation (ZDFO) for structural paperboards. A survey of commercial linerboards indicated the presence of ZDFO in one material that had higher Taber stiffness, out-of-plane shear strength, directional dependence of Scott internal bond strength and directional...

Oriental nose elongation using an L-shaped polyethylene sheet implant for combined septal spreading and extension.

PubMed

Zhou, Jia; Huang, Xiaolu; Zheng, Danning; Li, Haizhou; Herrler, Tanja; Li, Qingfeng

2014-04-01

The currently recommended strategies for short nose elongation were designed primarily for the Caucasian nasal framework. For Oriental patients, more elongation often is required because a hypoplastic septal cartilage requires more elongation, resulting in a higher risk of complications. This report proposes a modified technique for Oriental nose elongation, which adjusts the pressure points after nasal elongation using an L-shaped implant. Between January 2007 and December 2009, 58 patients underwent Oriental nose elongation using an L-shaped, porous, high-density polyethylene sheet implant. Augmentation rhinoplasty and conchal cartilage shield grafts were performed depending on the nasal shape. Pre- and postoperative nasal length, height, and projection as well as columella-labial angle, columella-lobular angle, and nasal tip angle were measured and compared. A patient satisfaction survey was performed postoperatively. All occurring complications were recorded. The postoperative nasal length was significantly elongated from 47.0±10.4 mm to 49.3±10.1 mm (p=0.003), and the nasal height increased significantly from 48.5±9.1 mm to 50.4±8.5 mm (p=0.011). The initially obtuse columella-labial angle improved significantly from 100.8°±12.1° to 92.5°±15.5° (p=0.014). No significant changes were found regarding nasal projection, nasal tip angle, or columella-lobular angle. The majority of the patients (91.3%) were highly satisfied or satisfied with the aesthetic results. A major complication in terms of implant exposure was observed in one case. The minor complications included stiffness of the nasal tip (3 patients) and tip redness (1 patient). In Oriental nose elongation, the use of an L-shaped graft is a feasible and safe treatment option that allows for an excellent aesthetic outcome and reduces the incidence of complications. This journal requires that authors assign a level of evidence to each submission to which Evidence-Based Medicine rankings are applicable. This excludes Review Articles, Book Reviews, and manuscripts that concern Basic Science, Animal Studies, Cadaver Studies, and Experimental Studies. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

N′-[(E)-3-Chloro-2-fluoro­benzyl­idene]-6-methyl­nicotinohydrazide monohydrate

PubMed Central

Fun, Hoong-Kun; Quah, Ching Kheng; Shyma, P. C.; Kalluraya, Balakrishna; Vidyashree, J. H. S.

2012-01-01

The title compound, C14H11ClFN3O·H2O, exists in an E conformation with respect to the N=C bond. The pyridine ring forms a dihedral angle of 5.00 (9)° with the benzene ring. In the crystal, the ketone O atom accepts one O—H⋯O and one C—H⋯O hydrogen bond, the water O atom accepts one N—H⋯O and two C—H⋯O hydrogen bonds and the pyridine N atom accepts one O—H⋯N hydrogen bond, forming layers parallel to the ab plane. PMID:22798798

Elastomeric member and method of manufacture therefor

DOEpatents

Hoppie, L.O.

1985-12-10

An energy storage device is disclosed consisting of a stretched elongated elastomeric member disposed within a tubular housing, which elastomeric member is adapted to be torsionally stressed to store energy. The elastomeric member is configured in the relaxed state with a uniform diameter body section, and transition end sections, attached to rigid end piece assemblies of a lesser diameter. The profile and deflection characteristic of the transition sections are such that upon stretching of the elastomeric member, a substantially uniform diameter assembly results, to minimize the required volume of the surrounding housing. Each of the transition sections are received within and bonded to a woven wire mesh sleeve having helical windings at a particular helix angle to control the deflection of the transition section. Each sleeve also contracts with the contraction of the associated transition section to maintain the bond therebetween. During manufacture, the sleeves are forced against a forming surface and bonded to the associated transition section to provide the correct profile and helix angle. 12 figs.

Elastomeric member

DOEpatents

Hoppie, L.O.

1985-07-30

An energy storage device is disclosed consisting of a stretched elongated elastomeric member disposed within a tubular housing, which elastomeric member is adapted to be torsionally stressed to store energy. The elastomeric member is configured in the relaxed state with a uniform diameter body section, and transition end sections, attached to rigid end piece assemblies of a lesser diameter. The profile and deflection characteristic of the transition sections are such that upon stretching of the elastomeric member, a substantially uniform diameter assembly results, to minimize the required volume of the surrounding housing. Each of the transition sections are received within and bonded to a woven wire mesh sleeve having helical windings at a particular helix angle to control the deflection of the transition section. Each sleeve also contracts with the contraction of the associated transition section to maintain the bond there between. During manufacture, the sleeves are forced against a forming surface and bonded to the associated transition section to provide the correct profile and helix angle. 12 figs.

B-spline tight frame based force matching method

NASA Astrophysics Data System (ADS)

Yang, Jianbin; Zhu, Guanhua; Tong, Dudu; Lu, Lanyuan; Shen, Zuowei

2018-06-01

In molecular dynamics simulations, compared with popular all-atom force field approaches, coarse-grained (CG) methods are frequently used for the rapid investigations of long time- and length-scale processes in many important biological and soft matter studies. The typical task in coarse-graining is to derive interaction force functions between different CG site types in terms of their distance, bond angle or dihedral angle. In this paper, an ℓ1-regularized least squares model is applied to form the force functions, which makes additional use of the B-spline wavelet frame transform in order to preserve the important features of force functions. The B-spline tight frames system has a simple explicit expression which is useful for representing our force functions. Moreover, the redundancy of the system offers more resilience to the effects of noise and is useful in the case of lossy data. Numerical results for molecular systems involving pairwise non-bonded, three and four-body bonded interactions are obtained to demonstrate the effectiveness of our approach.

Capillary forces exerted by liquid drops caught between crossed cylinders. A 3-D meniscus problem with free contact line

NASA Technical Reports Server (NTRS)

Patzek, T. W.; Scriven, L. E.

1982-01-01

The Young-Laplace equation is solved for three-dimensional menisci between crossed cylinders, with either the contact line fixed or the contact angle prescribed, by means of the Galerkin/finite element method. Shapes are computed, and with them the practically important quantities: drop volume, wetted area, capillary pressure force, surface tension force, and the total force exerted by the drop on each cylinder. The results show that total capillary force between cylinders increases with decreasing contact angle, i.e. with better wetting. Capillary force is also increases with decreasing drop volume, approaching an asymptotic limit. However, the wetted area on each cylinder decreases with decreasing drop volume, which raises the question of the optimum drop volume to strive for, when permanent bonding is sought from solidified liquid. For then the strength of the bond is likely to depend upon the area of contact, which is the wetted area when the bonding agent was introduced in liquid form.

Alignment between Protostellar Outflows and Filamentary Structure

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

Stephens, Ian W.; Dunham, Michael M.; Myers, Philip C.

2017-09-01

We present new Submillimeter Array (SMA) observations of CO(2–1) outflows toward young, embedded protostars in the Perseus molecular cloud as part of the Mass Assembly of Stellar Systems and their Evolution with the SMA (MASSES) survey. For 57 Perseus protostars, we characterize the orientation of the outflow angles and compare them with the orientation of the local filaments as derived from Herschel observations. We find that the relative angles between outflows and filaments are inconsistent with purely parallel or purely perpendicular distributions. Instead, the observed distribution of outflow-filament angles are more consistent with either randomly aligned angles or a mixmore » of projected parallel and perpendicular angles. A mix of parallel and perpendicular angles requires perpendicular alignment to be more common by a factor of ∼3. Our results show that the observed distributions probably hold regardless of the protostar’s multiplicity, age, or the host core’s opacity. These observations indicate that the angular momentum axis of a protostar may be independent of the large-scale structure. We discuss the significance of independent protostellar rotation axes in the general picture of filament-based star formation.« less

3D Printing of 316L Stainless Steel and Its Effect on Microstructure and Mechanical Properties

NASA Astrophysics Data System (ADS)

Rawn, Penn

Laser powder bed fusion or 3D printing is a potential candidate for net shape forming and manufacturing complex shapes. Understanding of how various parameters affect build quality is necessary. Specimens were made from 316L stainless steel at 0°, 30°, 60°, and 90° angles measured from the build plate. Three tensile and four fatigue specimens at each angle were produced. Fracture morphology investigation was performed to determine the fracture mode of specimens at each build angle. Microstructural analysis was performed on one of each orientation. The average grain size of the samples was marginally influenced by the build angle orientation. Tensile yield strength was the highest for 0° and decreased in the order of 60°, 30°, and 90° angles; all had higher yield strength than wrought. Unlike with the tensile results, the 60° had the highest fatigue strength followed by the 0°, then the 30°, and the 90° build angle had the lowest fatigue strength. Tensile specimens all failed predominantly by ductile fracture, with a few locations of brittle fracture suspected to be caused by delamination. Fatigue fracture always initiated at void space.

Powder collection apparatus/method

DOEpatents

Anderson, I.E.; Terpstra, R.L.; Moore, J.A.

1994-01-11

Device for separating and collecting ultrafine atomized powder from the gas stream of a gas atomizing apparatus comprises a housing having an interior wall oriented at an angle relative to horizontal so as to form a downwardly converging, conical expansion chamber, an inlet conduit communicated to the expansion chamber proximate an upper region thereof for receiving the gas stream, and an outlet proximate a lower region of the expansion chamber. The inlet conduit is oriented at a compound inclined angle (with respect to horizontal) selected to promote separation and collection of powder from the gas stream in the expansion chamber. The compound angle comprises a first entrance angle that is greater than the angle of repose of the powder on the housing interior wall such that any powder accumulation in the inlet conduit tends to flow down the wall toward the outlet. The second angle is selected generally equal to the angle of the housing interior wall measured from the same horizontal plane so as to direct the gas stream into the expansion chamber generally tangent to the housing interior wall to establish a downward swirling gas stream flow in the expansion chamber. A powder collection container is communicated to the outlet of the expansion chamber to collect the powder for further processing. 4 figures.

Powder collection apparatus/method

DOEpatents

Anderson, Iver E.; Terpstra, Robert L.; Moore, Jeffery A.

1994-01-11

Device for separating and collecting ultrafine atomized powder from the gas stream of a gas atomizing apparatus comprises a housing having an interior wall oriented at an angle relative to horizontal so as to form a downwardly converging, conical expansion chamber, an inlet conduit communicated to the expansion chamber proximate an upper region thereof for receiving the gas stream, and an outlet proximate a lower region of the expansion chamber. The inlet conduit is oriented at a compound inclined angle (with respect to horizontal) selected to promote separation and collection of powder from the gas stream in the expansion chamber. The compound angle comprises a first entrance angle that is greater than the angle of repose of the powder on the housing interior wall such that any powder accumulation in the inlet conduit tends to flow down the wall toward the outlet. The second angle is selected generally equal to the angle of the housing interior wall measured from the same horizontal plane so as to direct the gas stream into the expansion chamber generally tangent to the housing interior wall to establish a downward swirling gas stream flow in the expansion chamber. A powder collection container is communicated to the outlet of the expansion chamber to collect the powder for further processing.

Annealing texture of nanostructured IF steel

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

Jamaati, Roohollah, E-mail: jamaati@nit.ac.ir

In the present work, the evolution of annealing texture in nanostructured interstitial free steel fabricated via accumulative roll bonding (ARB) process was investigated. Textural evolution after post-annealing of ARB-processed samples was evaluated using X-ray diffraction. There were several texture transitions in the γ-fiber and ζ-fiber during ARB and post-annealing treatment. It was found that with increasing the number of ARB cycles, the volume fraction of the low angle grain boundary decreased and the high angle grain boundary fraction increased. Also, the shear texture was dominant after the first cycle, while for other samples, the rolling texture was dominant. The one-cyclemore » sample clearly indicated a weak α-fiber and γ-fiber and a relatively strong ζ-fiber. In addition, during the recrystallization and before the grain growth, the intensity of α-fiber and γ-fiber decreased, the intensity of ζ-fiber increased, and the intensity of (011)〈100〉 orientation in the ε-fiber and η-fiber increased. Moreover, it was concluded that the transition from the rolling texture to the shear one was a sign of occurrence of the recrystallization (before the grain growth). Finally, with increasing the number of ARB cycles, the intensity of rolling and shear textures saturated and a stable texture formed. - Highlights: • There were texture transitions in the γ-fiber and ζ-fiber. • When the number of cycles increased, the low angle grain boundaries decreased. • The shear texture was dominant after the first cycle. • Transition from rolling texture to shear one was a sign of recrystallization. • With increasing the number of ARB cycles, a stable texture formed.« less

The effects of target distance on pivot hip, trunk, pelvis, and kicking leg kinematics in Taekwondo roundhouse kicks.

PubMed

Kim, Jae-Woong; Kwon, Moon-Seok; Yenuga, Sree Sushma; Kwon, Young-Hoooo

2010-06-01

The study purpose was to investigate the effects of target distance on pivot hip, trunk, pelvis, and kicking leg movements in Taekwondo roundhouse kick. Twelve male black-belt holders executed roundhouse kicks for three target distances (Normal, Short, and Long). Linear displacements of the pivot hip and orientation angles of the pelvis, trunk, right thigh, and right shank were obtained through a three-dimensional video motion analysis. Select displacements, distances, peak orientation angles, and angle ranges were compared among the conditions using one-way repeated measure ANOVA (p < 0.05). Several orientation angle variables (posterior tilt range, peak right-tilted position, peak right-rotated position, peak left-rotated position, and left rotation range of the pelvis; peak hyperextended position and peak right-flexed position of the trunk; peak flexed position, flexion range and peak internal-rotated position of the hip) as well as the linear displacements of the pivot hip and the reach significantly changed in response to different target distances. It was concluded that the adjustment to different target distances was mainly accomplished through the pivot hip displacements, hip flexion, and pelvis left rotation. Target distance mainly affected the reach control function of the pelvis and the linear balance function of the trunk.

Orientation Dependence of Columnar Dendritic Growth with Sidebranching Behaviors in Directional Solidification: Insights from Phase-Field Simulations

NASA Astrophysics Data System (ADS)

Xing, Hui; Dong, Xianglei; Wang, Jianyuan; Jin, Kexin

2018-04-01

In this study, a thin-interface phase-field model was employed to study the orientation dependence of the columnar dendritic growth with sidebranching behaviors in directional solidification. It was found that the dimensionless tip undercooling increases with the increase of misorientation angle for three pulling velocities. The primary spacing is found to be a function of misorientation angle, and the dimensionless primary spacing with respect to the misorientation angle follows the orientation correction given by Gandin and Rappaz (Acta. Metall. 42:2233-2246, 1994). For the analysis of the dendritic tip, the two-dimensional (2-D) form of the nonaxisymmetric needle crystal was used to determine the radius of the tilted columnar dendrite. Based on the definitions of open side and constrained side of the dendrite, the analysis of the width active sidebranches and the dendritic area in 2-D with respect to the distance from the dendritic tip was carried out to investigate the asymmetrical dendrite envelop and sidebranching behaviors on the two sides in directional solidification. The obtained prefactor and exponent with respect to misorientation angle are discussed, showing that the sidebranching behaviors of a tilted columnar dendritic array obey a similar power-law relationship with that of a free dendritic growth.

Mineral crystal alignment in mineralized fracture callus determined by 3D small-angle X-ray scattering

NASA Astrophysics Data System (ADS)

Liu, Yifei; Manjubala, Inderchand; Roschger, Paul; Schell, Hanna; Duda, Georg N.; Fratzl, Peter

2010-10-01

Callus tissue formed during bone fracture healing is a mixture of different tissue types as revealed by histological analysis. But the structural characteristics of mineral crystals within the healing callus are not well known. Since two-dimensional (2D) scanning small-angle X-ray scattering (sSAXS) patterns showed that the size and orientation of callus crystals vary both spatially and temporally [1] and 2D electron microscopic analysis implies an anisotropic property of the callus morphology, the mineral crystals within the callus are also expected to vary in size and orientation in 3D. Three-dimensional small-angle X-ray scattering (3D SAXS), which combines 2D SAXS patterns collected at different angles of sample tilting, has been previously applied to investigate bone minerals in horse radius [2] and oim/oim mouse femur/tibia [3]. We implement a similar 3D SAXS method but with a different way of data analysis to gather information on the mineral alignment in fracture callus. With the proposed accurate yet fast assessment of 3D SAXS information, it was shown that the plate shaped mineral particles in the healing callus were aligned in groups with their predominant orientations occurring as a fiber texture.

Influence of hydrophilic pre-treatment on resin bonding to zirconia ceramics.

PubMed

Noro, Akio; Kameyama, Atsushi; Haruyama, Akiko; Takahashi, Toshiyuki

2015-01-01

Atmospheric plasma or ultraviolet (UV) treatment alters the surface characteristics of tetragonal zirconia polycrystal (TZP), increasing its hydrophilicity by reducing the contact angle against water to zero. This suggests that such treatment would increase the wettability of bonding resin. The purpose of this study was to determine how increasing the hydrophilicity of TZP through plasma irradiation, UV treatment, or application of ceramic primer affected initial bonding with resin composites. Here, the effect of each pre-treatment on the hydrophilicity of TZP surfaces was determined by evaluating change in shear bond strength. Plasma irradiation, UV, or ceramic primer pre-treatment showed no significant effect on bonding strength between TZP surfaces and resin composites. In addition, alumina blasting yielded no significant increase in bond strength. Plasma irradiation, UV treatment, or ceramic primer pre-treatment did not lead to significant increase in bond strength between TZP and resin composites.

Vibrational spectral investigation and natural bond orbital analysis of pharmaceutical compound 7-Amino-2,4-dimethylquinolinium formate - DFT approach.

PubMed

Suresh, D M; Amalanathan, M; Sebastian, S; Sajan, D; Hubert Joe, I; Bena Jothy, V; Nemec, Ivan

2013-11-01

The molecular geometry, the normal mode frequencies and corresponding vibrational assignments, natural bond orbital analysis and the HOMO-LUMO analysis of 7-Amino-2,4-dimethylquinolinium formate in the ground state were performed by B3LYP levels of theory using the 6-31G(d) basis set. The optimised bond lengths and bond angles are in good agreement with the X-ray data. The vibrational spectra of the title compound which is calculated by DFT method, reproduces vibrational wave numbers and intensities with an accuracy which allows reliable vibrational assignments. The possibility of N-H⋯O hydrogen bonding was identified using NBO analysis. Natural bond orbital analysis confirms the presence of intramolecular charge transfer and the hydrogen bonding interaction. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

Laser Surface Preparation and Bonding of Aerospace Structural Composites

NASA Technical Reports Server (NTRS)

Belcher, M. A.; Wohl, C. J.; Hopkins, J. W.; Connell, J. W.

2010-01-01

Adhesive bonds are critical to the integrity of built-up structures. Disbonds can often be detected but the strength of adhesion between surfaces in contact is not obtainable without destructive testing. Typically the number one problem in a bonded structure is surface contamination, and by extension, surface preparation. Standard surface preparation techniques, including grit blasting, manual abrasion, and peel ply, are not ideal because of variations in their application. Etching of carbon fiber reinforced plastic (CFRP) panels using a neodymium-doped yttrium aluminum garnet (Nd:YAG) laser appears to be a highly precise and promising way to both clean a composite surface prior to bonding and provide a bond-promoting patterned surface akin to peel ply without the inherent drawbacks from the same (i.e., debris and curvature). CFRP surfaces prepared using laser patterns conducive to adhesive bonding were compared to typical prebonding surface treatments through optical microscopy, contact angle goniometry, and post-bonding mechanical testing.

Making heads turn: the effect of familiarity and stimulus rotation on a gender-classification task.

PubMed

Stevenage, Sarah V; Osborne, Cara D

2006-01-01

Recent work has demonstrated that facial familiarity can moderate the influence of inversion when completing a configural processing task. Here, we examine whether familiarity interacts with intermediate angles of orientation in the same way that it interacts with inversion. Participants were asked to make a gender classification to familiar and unfamiliar faces shown at seven angles of orientation. Speed and accuracy of performance were assessed for stimuli presented (i) as whole faces and (ii) as internal features. When presented as whole faces, the task was easy, as revealed by ceiling levels of accuracy and no effect of familiarity or angle of rotation on response times. However, when stimuli were presented as internal features, an influence of facial familiarity was evident. Unfamiliar faces showed no increase in difficulty across angle of rotation, whereas familiar faces showed a marked increase in difficulty across angle, which was explained by significant linear and cubic trends in the data. Results were interpreted in terms of the benefit gained from a mental representation when face processing was impaired by stimulus rotation.

THE VIEWING ANGLES OF BROAD ABSORPTION LINE VERSUS UNABSORBED QUASARS

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

DiPompeo, M. A.; Brotherton, M. S.; De Breuck, C.

2012-06-10

It was recently shown that there is a significant difference in the radio spectral index distributions of broad absorption line (BAL) quasars and unabsorbed quasars, with an overabundance of BAL quasars with steeper radio spectra. This result suggests that source orientation does play into the presence or absence of BAL features. In this paper, we provide more quantitative analysis of this result based on Monte Carlo simulations. While the relationship between viewing angle and spectral index does indeed contain a lot of scatter, the spectral index distributions are different enough to overcome that intrinsic variation. Utilizing two different models ofmore » the relationship between spectral index and viewing angle, the simulations indicate that the difference in spectral index distributions can be explained by allowing BAL quasar viewing angles to extend about 10 Degree-Sign farther from the radio jet axis than non-BAL sources, though both can be seen at small angles. These results show that orientation cannot be the only factor determining whether BAL features are present, but it does play a role.« less

Crystallography and Molecular Arrangement of Polymorphic Monolayer J-Aggregates of a Cyanine Dye: Multiangle Polarized Light Fluorescence Optical Microscopy Study.

PubMed

Prokhorov, Valery V; Pozin, Sergey I; Perelygina, Olga M; Mal'tsev, Eugene I

2018-04-24

The molecular orientation in monolayer J-aggregates of 3,3-di(γ-sulfopropyl)-5,5-dichlorotiamonomethinecyanine dye has been precisely estimated using improved linear polarization measurements in the fluorescence microscope in which a multiangle set of polarization data is obtained using sample rotation. The estimated molecular orientation supplemented with the previously established crystallographic constraints based on the analysis of the well-developed two-dimensional J-aggregate shapes unambiguously indicate the staircase type of molecular arrangement for striplike J-aggregates with the staircases oriented along strips. The molecular transition dipoles are inclined at an angle of ∼25° to the strip direction, whereas the characteristic strip vertex angle ∼45° is formed by the [100] and [1-10] directions of the monoclinic unit cell. Measurements of the geometry of partially unwound tubes and their polarization properties support the model of tube formation by close-packed helical winding of flexible monolayer strips. In the tubes, the long molecular axes are oriented at a small angle in the range of 5-15° to the normal to the tube axis providing low bending energy. At a nanoscale, high-resolution atomic force microscopy imaging of J-aggregate monolayers reveals a complex quasi-one-dimensional organization.

Radiant energy during infrared neural stimulation at the target structure

NASA Astrophysics Data System (ADS)

Richter, Claus-Peter; Rajguru, Suhrud; Stafford, Ryan; Stock, Stuart R.

2013-03-01

Infrared neural stimulation (INS) describes a method, by which an infrared laser is used to stimulate neurons. The major benefit of INS over stimulating neurons with electrical current is its spatial selectivity. To translate the technique into a clinical application it is important to know the energy required to stimulate the neural structure. With this study we provide measurements of the radiant exposure, at the target structure that is required to stimulate the auditory neurons. Flat polished fibers were inserted into scala tympani so that the spiral ganglion was in front of the optical fiber. Angle polished fibers were inserted along scala tympani, and rotating the beveled surface of the fiber allowed the radiation beam to be directed perpendicular to the spiral ganglion. The radiant exposure for stimulation at the modiolus for flat and angle polished fibers averaged 6.78+/-2.15 mJ/cm2. With the angle polished fibers, a 90º change in the orientation of the optical beam from an orientation that resulted in an INS-evoked maximum response, resulted in a 50% drop in the response amplitude. When the orientation of the beam was changed by 180º, such that it was directed opposite to the orientation with the maxima, minimum response amplitude was observed.

Interfacial interaction track of amorphous solid dispersions established by water-soluble polymer and indometacin.

PubMed

Li, Jing; Fan, Na; Wang, Xin; Li, Chang; Sun, Mengchi; Wang, Jian; Fu, Qiang; He, Zhonggui

2017-08-30

The present work studied interfacial interactions of amorphous solid dispersions matrix of indometacin (IMC) that established using PVP K30 (PVP) and PEG 6000 (PEG) by focusing on their interaction forces and wetting process. Infrared spectroscopy (IR), raman spectroscopy, X-ray photoelectron spectra and contact angle instrument were used throughout the study. Hydrogen bond energy formed between PEG and IMC were stronger than that of PVP and IMC evidenced by molecular modeling measurement. The blue shift of raman spectroscopy confirmed that hydrogen bonding forces were formed between IMC and two polymers. The contact angle study can be used as an easy method to determine the dissolution mechanism of amorphous solid dispersions through fitting the profile of contact angle of water on a series of tablets. It is believed that the track of interfacial interactions will certainly become powerful tools to for designing and evaluating amorphous solid dispersions. Copyright © 2017 Elsevier B.V. All rights reserved.

N-(1-Allyl-1H-indazol-5-yl)-4-methyl­benzene­sulfonamide

PubMed Central

Chicha, Hakima; Rakib, El Mostapha; Abderrafia, Hafid; Saadi, Mohamed; El Ammari, Lahcen

2013-01-01

The asymmetric unit of the title compound, C17H17N3O2S, contains two independent mol­ecules linked by an N—H⋯O hydrogen bond. The mol­ecules show different conformations. In the first mol­ecule, the fused five- and six-membered ring system is almost perpendicular to the plane through the atoms forming the allyl group, as indicated by the dihedral angle of 85.1 (4)°. The dihedral angle with the methyl­benzene­sulfonamide group is 78.8 (1)°. On the other hand, in the second mol­ecule, the dihedral angles between the indazole plane and the allyl and methyl­benzene­sulfonamide groups are 80.3 (3) and 41.5 (1)°, respectively. In the crystal, mol­ecules are further linked by N—H⋯N and C—H⋯O hydrogen bonds, forming a three-dimensional network. PMID:24454264

3D visualization of molecular structures in the MOGADOC database

NASA Astrophysics Data System (ADS)

Vogt, Natalja; Popov, Evgeny; Rudert, Rainer; Kramer, Rüdiger; Vogt, Jürgen

2010-08-01

The MOGADOC database (Molecular Gas-Phase Documentation) is a powerful tool to retrieve information about compounds which have been studied in the gas-phase by electron diffraction, microwave spectroscopy and molecular radio astronomy. Presently the database contains over 34,500 bibliographic references (from the beginning of each method) for about 10,000 inorganic, organic and organometallic compounds and structural data (bond lengths, bond angles, dihedral angles, etc.) for about 7800 compounds. Most of the implemented molecular structures are given in a three-dimensional (3D) presentation. To create or edit and visualize the 3D images of molecules, new tools (special editor and Java-based 3D applet) were developed. Molecular structures in internal coordinates were converted to those in Cartesian coordinates.

2-({4-[4-(1H-Benzimidazol-2-yl)phen­yl]-1H-1,2,3-triazol-1-yl}meth­oxy)ethanol

PubMed Central

Ouahrouch, Abdelaaziz; Taourirte, Moha; Lazrek, Hassan B.; Bats, Jan W.; Engels, Joachim W.

2012-01-01

In the title molecule, C18H17N5O2, the dihedral angle between the benzene plane and the benzimidazole plane is 19.8 (1)° and the angle between the benzene plane and the triazole plane is 16.7 (1)°. In the crystal, mol­ecules are connected by O—H⋯N hydrogen bonds, forming zigzag chains along the c-axis direction. The chains are connected by bifurcated N—H⋯(N,N) hydrogen bonds into layers parallel to (100). These layers are connected along the a-axis direction by weak C—H⋯O contacts, forming a three-dimensional network. PMID:22719663

Nitriles as directionally tolerant hydrogen bond acceptors: IR-UV ion depletion spectroscopy of benzenepropanenitrile and its hydrate clusters

NASA Astrophysics Data System (ADS)

Robertson, Patrick A.; Lobo, Isabella A.; Wilson, David J. D.; Robertson, Evan G.

2016-09-01

Benzenepropanenitrile (BPN) and its hydrate clusters are studied by R2PI and IR-UV ion-depletion spectroscopy in the CH/OH stretch regions, aided by theoretical calculations. A single water molecule binds to the terminal nitrile 'lone-pair' of the anti-BPN host, but there is also evidence for a side-type structure with OH donating to the nitrile π-electrons. In the gauche-BPN cluster, water is located at an intermediate angle that facilitates O⋯HC(ortho) interaction. A wide range of attachment angles is possible, as the intrinsic preference for linear hydrogen bonding is mediated by additional CH⋯O interactions that depend on molecular geometry near the nitrile group.

CO adsorption on (111) and (100) surfaces of the Pt sub 3 Ti alloy. Evidence for parallel binding and strong activation of CO

NASA Technical Reports Server (NTRS)

Mehandru, S. P.; Anderson, A. B.; Ross, P. N.

1985-01-01

The CO adsorption on a 40 atom cluster model of the (111) surface and a 36 atom cluster model of the (100) surface of the Pt3Ti alloy was studied. Parallel binding to high coordinate sites associated with Ti and low CO bond scission barriers are predicted for both surfaces. The binding of CO to Pt sites occurs in an upright orientation. These orientations are a consequence of the nature of the CO pi donation interactions with the surface. On the Ti sites the orbitals donate to the nearly empty Ti 3d band and the antibonding counterpart orbitals are empty. On the Pt sites, however, they are in the filled Pt 5d region of the alloy band, which causes CO to bond in a vertical orientation by 5 delta donation from the carbon end.

Magnetic field effect on the structural properties of a peptide model: Molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Housaindokht, Mohammad Reza; Moosavi, Fatemeh

2018-06-01

The effect of magnetization on the properties of a system containing a peptide model is studied by molecular dynamics simulation at a range of 298-318 K. Two mole fractions of 0.001 and 0.002 of peptide were simulated and the variation of hydrogen bond number, orientational ordering parameter, gyration radius, mean square displacement, as well as radial distribution function, were under consideration. The results show that applying magnetic field will increase the number of hydrogen bonds between water molecules by clustering them and decreases the interaction of water and peptide. This reduction may cause more available free space and enhance the movement of the peptide. As a result, the diffusion coefficient of the peptide becomes greater and its conformation changes. Orientational ordering parameter besides radius of gyration demonstrates that peptide is expanded by static magnetic field and its orientational ordering parameter is affected.

(2E)-3-(6-methoxynaphthalen-2-yl)-1-(pyridin-3-yl)prop-2-en-1-one and its cyclocondensation product with guanidine, (4RS)-2-amino-4-(6-methoxynaphthalen-2-yl)-6-(pyridin-3-yl)-3,4-dihydropyrimidine monohydrate: two types of hydrogen-bonded sheet.

PubMed

Nayak, Prakash S; Narayana, Badiadka; Yathirajan, Hemmige S; Hosten, Eric C; Betz, Richard; Glidewell, Christopher

2014-11-01

The structures of a chalcone and of its cyclocondensation product with guanidine are reported. In (2E)-3-(6-methoxynaphthalen-2-yl)-1-(pyridin-3-yl)prop-2-en-1-one, C19H15NO2, (I), the planes of the pyridine and naphthalene units make dihedral angles with that of the central spacer unit of 23.61 (13) and 23.57 (15)°, respectively, and a dihedral angle of 47.24 (9)° with each other. The molecules of (I) are linked into sheets by a combination of C-H···O and C-H···π(arene) hydrogen bonds. In the cyclocondensation product (4RS)-2-amino-4-(6-methoxynaphthalen-2-yl)-6-(pyridin-3-yl)-3,4-dihydropyrimidine monohydrate, C20H18N4O·H2O, (II), the dihydropyrimidine ring adopts a conformation best described as a shallow boat. The molecular components are linked by two N-H···O hydrogen bonds, two O-H···N hydrogen bonds and one N-H···N hydrogen bond to form complex sheets, with the methoxynaphthalene interdigitated between inversion-related pairs of sheets.

Flexure mechanism-based parallelism measurements for chip-on-glass bonding

NASA Astrophysics Data System (ADS)

Jung, Seung Won; Yun, Won Soo; Jin, Songwan; Kim, Bo Sun; Jeong, Young Hun

2011-08-01

Recently, liquid crystal displays (LCDs) have played vital roles in a variety of electronic devices such as televisions, cellular phones, and desktop/laptop monitors because of their enhanced volume, performance, and functionality. However, there is still a need for thinner LCD panels due to the trend of miniaturization in electronic applications. Thus, chip-on-glass (COG) bonding has become one of the most important aspects in the LCD panel manufacturing process. In this study, a novel sensor was developed to measure the parallelism between the tooltip planes of the bonding head and the backup of the COG main bonder, which has previously been estimated by prescale pressure films in industry. The sensor developed in this study is based on a flexure mechanism, and it can measure the total pressing force and the inclination angles in two directions that satisfy the quantitative definition of parallelism. To improve the measurement accuracy, the sensor was calibrated based on the estimation of the total pressing force and the inclination angles using the least-squares method. To verify the accuracy of the sensor, the estimation results for parallelism were compared with those from prescale pressure film measurements. In addition, the influence of parallelism on the bonding quality was experimentally demonstrated. The sensor was successfully applied to the measurement of parallelism in the COG-bonding process with an accuracy of more than three times that of the conventional method using prescale pressure films.

Hydrogen-bonded turns in proteins: The case for a recount

PubMed Central

Panasik, Nick; Fleming, Patrick J.; Rose, George D.

2005-01-01

β-Turns are sites at which proteins change their overall chain direction, and they occur with high frequency in globular proteins. The Protein Data Bank has many instances of conformations that resemble β-turns but lack the characteristic N–H(i) → O=C(i − 3) hydrogen bond of an authentic β-turn. Here, we identify potential hydrogen-bonded β-turns in the coil library, a Web-accessible database utility comprised of all residues not in repetitive secondary structure, neither α-helix nor β-sheet (http://www.roselab.jhu.edu/coil). In particular, candidate turns were identified as four-residue segments satisfying highly relaxed geometric criteria but lacking a strictly defined hydrogen bond. Such candidates were then subjected to a minimization protocol to determine whether slight changes in torsion angles are sufficient to shift the conformation into reference-quality geometry without deviating significantly from the original structure. This approach of applying constrained minimization to known structures reveals a substantial population of previously unidentified, stringently defined, hydrogen-bonded β-turns. In particular, 33% of coil library residues were classified as β-turns prior to minimization. After minimization, 45% of such residues could be classified as β-turns, with another 8% in 310 helixes (which closely resemble type III β-turns). Of the remaining coil library residues, 37% have backbone dihedral angles in left-handed polyproline II structure. PMID:16251367

Hydrogen-bonded turns in proteins: the case for a recount.

PubMed

Panasik, Nick; Fleming, Patrick J; Rose, George D

2005-11-01

Beta-turns are sites at which proteins change their overall chain direction, and they occur with high frequency in globular proteins. The Protein Data Bank has many instances of conformations that resemble beta-turns but lack the characteristic N-H(i) --> O=C(i - 3) hydrogen bond of an authentic beta-turn. Here, we identify potential hydrogen-bonded beta-turns in the coil library, a Web-accessible database utility comprised of all residues not in repetitive secondary structure, neither alpha-helix nor beta-sheet (http://www.roselab.jhu.edu/coil). In particular, candidate turns were identified as four-residue segments satisfying highly relaxed geometric criteria but lacking a strictly defined hydrogen bond. Such candidates were then subjected to a minimization protocol to determine whether slight changes in torsion angles are sufficient to shift the conformation into reference-quality geometry without deviating significantly from the original structure. This approach of applying constrained minimization to known structures reveals a substantial population of previously unidentified, stringently defined, hydrogen-bonded beta-turns. In particular, 33% of coil library residues were classified as beta-turns prior to minimization. After minimization, 45% of such residues could be classified as beta-turns, with another 8% in 3(10) helixes (which closely resemble type III beta-turns). Of the remaining coil library residues, 37% have backbone dihedral angles in left-handed polyproline II structure.

(E)-N'-[1-(Thio-phen-2-yl)ethyl-idene]isonicotinohydrazide.

PubMed

Dileep, C S; Abdoh, M M M; Chakravarthy, M P; Mohana, K N; Sridhar, M A

2012-10-01

In the title compound, C(12)H(11)N(3)OS, the dihedral angle between the pyridine and thio-phene rings is 46.70 (9)° and the C-N-N-C torsion angle is 178.61 (15)°. In the crystal, inversion dimers linked by pairs of N-H⋯O hydrogen bonds generate R(2) (2)(8) loops.

2′-Chloro-4-meth­oxy-3-nitro­benzil

PubMed Central

Nithya, G.; Thanuja, B.; Chakkaravarthi, G.; Kanagam, Charles C.

2011-01-01

In the title compound, C15H10ClNO5, the dihedral angle between the aromatic rings is 87.99 (5)°. The O—C—C—O torsion angle between the two carbonyl units is −119.03 (16)°. The crystal structure is stabilized by a weak intermolecular C—H⋯O hydrogen bond. PMID:21754895

Why Is the Tetrahedral Bond Angle 109 Degrees? The Tetrahedron-in-a-Cube

ERIC Educational Resources Information Center

Lim, Kieran F.

2012-01-01

The common question of why the tetrahedral angle is 109.471 degrees can be answered using a tetrahedron-in-a-cube, along with some Year 10 level mathematics. The tetrahedron-in-a-cube can also be used to demonstrate the non-polarity of tetrahedral molecules, the relationship between different types of lattice structures, and to demonstrate that…

(E)-N′-(4-Chloro­benzyl­idene)-1-benzofuran-2-carbohydrazide monohydrate

PubMed Central

Fun, Hoong-Kun; Quah, Ching Kheng; Nitinchandra; Kalluraya, Balakrishna; Babu, M.

2012-01-01

The title compound, C16H11ClN2O2·H2O, exists in an E conformation with respect to the N=C bond. The benzofuran ring system forms a dihedral angle of 1.26 (4)° with the benzene ring. In the crystal, mol­ecules are linked via (N,C)—H⋯O bifurcated acceptor hydrogen bonds and (O,O,C)—H⋯O trifurcated acceptor hydrogen bonds, forming layers parallel to the bc plane. PMID:22798835

Metal oxide, Group V-VI chalcogenides and GaN/AlGaN photodetectors

NASA Astrophysics Data System (ADS)

Hasan, Md. Rezaul

In this work, a simple, low-cost and catalyst free one-step solution processing of onedimensional Sb2S3 nanostructures on polyimide substrates was done. This structure demonstrated its potential application as a photoconductor in the UV and visible regime. Using-field emission scanning electron microscopy (SEM), grazing incidence X-Ray diffraction, Raman spectra and transmission electron microscopy measurements, it was shown that the Sb 2S3 films have high crystallinity, uniform morphology and nearstoichiometric composition. Further, using tauc plot, it was found that the films have a direct bandgap of 1.67 eV. MSM photodetectors, fabricated using these films showed a clear photo response in both UV as well as visible wavelength. These devices showed UV on/off ratio as high as 160 under the light intensity of 30 mW/cm2 and a small rise time and fall time of 44 ms 28 ms respectively. The effect of geometry of metal pad and bonding wire orientation of a multi-channel FET on the coupling of THz radiation was studied. The spatial variation images were taken by raster scan with the resolution of 0.07 mm steps in both x and y directions. An effective gate bias, where the effect of noise is minimum and photoresponse is maximum, was used for imaging. By applying VGS =-2.8V and VDS =380mV, the images were taken for all different combinations of activated bonding wires and metal pads. It was observed that, effect of bonding wire orientation is negligible for the large source pad as the radiation is coupled basically between drain and gate pad. Effect of drain bonding wire on coupling depends on the maximum width or diameter of metal pad and the incoming wavelength. In this work, Position of activated Drain pad and orientation of respective bonding wire defined the image tilting angle. Voltage drop across the shorting metal between drain pads, also played a role in increasing the asymmetry by selectively exciting a certain portion of FET Channels more than the other portion. Position of gate pad defined the center point of the image without tilting the image as the geometry of the gate pads were parallel to each other. And there was no effect of gate pad bonding wire orientation because of the larger width of gate pads. For the GaN/AlGaNHEMT, the effect of Al mole fraction in AlGaN layer and the effect of gate oxide on the DC and low frequency noise characterization was studied. MOSHEMT with SiO2 improved the Id(on)/I d(off) ratio up to more than 8 orders, while it is only 10 times in conventional HEMT. It was shown that the gate leakage and isolation leakage suppression efficiency improved dramatically with the oxide. Subthreshold swing (SS) of MOS-HEMTs with different Al mole fraction (from 20% to 35%) vary slightly from 72 mV/decade to 79 mV/decade, but the conventional GaN/AlGaN HEMT showed SS of 2.4V/decade. Low frequency noise study revealed the difference in transport mechanism between HEMT and MOS-HEMTs. By using Carrier Number Fluctuation (CNF) model on the measured data, it was found that the noise is predominantly coming from the surface states. While generation-recombination is very prominent in conventional HEMT, it is very weak and insignificant in both MOS-HEMTs at much higher frequencies. This study reveals that very high number of surface states assisting the tunneling in schottky/AlGaN barrier is responsible for unusually high leakage and higher noise level in conventional HEMT. Leakage level is improved from mA/mm range for HEMT to pA/mm range for MOS-HEMTs. Leakage suppression improvement and minimization of noise level can be mainly attributed to high quality SiO2. Hooge's constant was in the order of 5-6x10-3 in MOS-HEMTs, which is 5x10 -2 for conventional HEMT indicating much lower noise level in the MOS-HEMTs. (Abstract shortened by ProQuest.).

Diurnal movements of cotton leaves expressed as thermodynamic work and entropy changes

NASA Technical Reports Server (NTRS)

Schutt, J. B.; Kimes, D. S.; Newcomb, W. W.

1985-01-01

It is pointed out that some important agricultural crops show heliotropic leaf movements. In these species, the proclivity of leaves to orient either perpendicularly or parallel or in some combination of these positions with respect to the sun is controlled by the leaf turgor and the availability of water. Such an orientational response is particularly noticeable for cotton. Schutt et al. (1985) have detailed leaf trajectories using three angles. The present investigation applies the three-angle representation to leaf trajectory mapping and to the calculation of the phase angle 'gamma' between the individual leaf normals and the solar direction. Using gamma, the thermodynamic work and entropy functions are evaluated and used to distinguish between the behavior of water-stressed and well watered cotton canopies.