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

High-Resolution Crystal Structures of Protein Helices Reconciled with Three-Centered Hydrogen Bonds and Multipole Electrostatics

PubMed Central

Kuster, Daniel J.; Liu, Chengyu; Fang, Zheng; Ponder, Jay W.; Marshall, Garland R.

2015-01-01

Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.613 α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.613/10-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding. PMID:25894612

High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics.

PubMed

Kuster, Daniel J; Liu, Chengyu; Fang, Zheng; Ponder, Jay W; Marshall, Garland R

2015-01-01

Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.6(13) α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.6(13/10)-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding.

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

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.

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

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.

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.

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.

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.

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.

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

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

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.

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).

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

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...

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

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.

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.

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.

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.

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

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

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

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

[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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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

(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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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].

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

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.

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

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.

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

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.

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.

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

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.

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

(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

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)°.

Inclined Fiber Pullout from a Cementitious Matrix: A Numerical Study

PubMed Central

Zhang, Hui; Yu, Rena C.

2016-01-01

It is well known that fibers improve the performance of cementitious composites by acting as bridging ligaments in cracks. Such bridging behavior is often studied through fiber pullout tests. The relation between the pullout force vs. slip end displacement is characteristic of the fiber-matrix interface. However, such a relation varies significantly with the fiber inclination angle. In the current work, we establish a numerical model to simulate the entire pullout process by explicitly representing the fiber, matrix and the interface for arbitrary fiber orientations. Cohesive elements endorsed with mixed-mode fracture capacities are implemented to represent the bond-slip behavior at the interface. Contact elements with Coulomb’s friction are placed at the interface to simulate frictional contact. The bond-slip behavior is first calibrated through pull-out curves for fibers aligned with the loading direction, then validated against experimental results for steel fibers oriented at 30∘ and 60∘. Parametric studies are then performed to explore the influences of both material properties (fiber yield strength, matrix tensile strength, interfacial bond) and geometric factors (fiber diameter, embedment length and inclination angle) on the overall pullout behavior, in particular on the maximum pullout load. The proposed methodology provides the necessary pull-out curves for a fiber oriented at a given angle for multi-scale models to study fracture in fiber-reinforced cementitious materials. The novelty lies in its capacity to capture the entire pullout process for a fiber with an arbitrary inclination angle. PMID:28773921

Inclined Fiber Pullout from a Cementitious Matrix: A Numerical Study.

PubMed

Zhang, Hui; Yu, Rena C

2016-09-26

It is well known that fibers improve the performance of cementitious composites by acting as bridging ligaments in cracks. Such bridging behavior is often studied through fiber pullout tests. The relation between the pullout force vs. slip end displacement is characteristic of the fiber-matrix interface. However, such a relation varies significantly with the fiber inclination angle. In the current work, we establish a numerical model to simulate the entire pullout process by explicitly representing the fiber, matrix and the interface for arbitrary fiber orientations. Cohesive elements endorsed with mixed-mode fracture capacities are implemented to represent the bond-slip behavior at the interface. Contact elements with Coulomb's friction are placed at the interface to simulate frictional contact. The bond-slip behavior is first calibrated through pull-out curves for fibers aligned with the loading direction, then validated against experimental results for steel fibers oriented at 30 ∘ and 60 ∘ . Parametric studies are then performed to explore the influences of both material properties (fiber yield strength, matrix tensile strength, interfacial bond) and geometric factors (fiber diameter, embedment length and inclination angle) on the overall pullout behavior, in particular on the maximum pullout load. The proposed methodology provides the necessary pull-out curves for a fiber oriented at a given angle for multi-scale models to study fracture in fiber-reinforced cementitious materials. The novelty lies in its capacity to capture the entire pullout process for a fiber with an arbitrary inclination angle.

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.

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

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.

N-[5-(Di­phenyl­phosphorylmeth­yl)-4-(4-fluoro­phen­yl)-6-iso­propyl­pyrimi­din-2-yl]-N-methyl­methane­sulfonamide

PubMed Central

Wu, Ya-Ming

2013-01-01

In the title compound, C28H29FN3O3PS, the pyrimidine ring is oriented at a dihedral angle of 50.9 (2)° with respect to the floro­benzene ring, while the two phenyl rings bonding to the same P atom are twisted with respect to each other, making a dihedral angle of 62.2 (2)°. In the crystal, mol­ecules are linked by weak C—H⋯O and C—H⋯F hydrogen bonds into a three-dimensional supra­molecular architecture. PMID:24454107

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.

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.

Characterization and reactivity of organic monolayers on gold and platinum surfaces

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

Wu, Chien-Ching

1995-12-06

Purpose is to understand how the mobilization, dielectric, orientation, composition, coverage, and structure of self-assembled organic monolayers on metal surfaces affects the surface reactivities and properties of these films in order to facilitate the construction of desired films. Two model systems were used: tiols at Au and aromatic acids at Pt. Surface analysis methods, including contact angle, electrochemistry, ellipsometry, infrared reflection absorption spectroscopy (IRRAS), and x-ray photospectroscopy, were used to study the self-assembled organic monolayers on Au and Pt. IRRAS, contact angle, and electrochemistry were used to determine the surface pK a of phenylcarboxylic acids and pyridylcarboxylic acids monolayers onmore » Pt. These techniques were also used to determine the orientation of polymethylene chain axis and the carboxylic follow the structural evolution of the chains and end group of the thiolate monolayers during formation. IRRAS was also used to assess the carboxylic acid group in terms of its possible existence as the non-hydrogen-bonded species, the hydrogen-bonded dimeric group, and the hydrogen-bonded polymeric group. These different forms of the end group were also followed vs coverage, as well as the reactivity vs solution pH. IRRAS and contact angle were used to calculate the rate constant of the esterification of carboxylic acid-terminated monolayers on Au.« less

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.

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

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.

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.

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.

(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

The Impact of Plasma Treatment of Cercon® Zirconia Ceramics on Adhesion to Resin Composite Cements and Surface Properties.

PubMed

Tabari, Kasra; Hosseinpour, Sepanta; Mohammad-Rahimi, Hossein

2017-01-01

Introduction: In recent years, the use of ceramic base zirconia is considered in dentistry for all ceramic restorations because of its chemical stability, biocompatibility, and good compressive as well as flexural strength. However, due to its chemical stability, there is a challenge with dental bonding. Several studies have been done to improve zirconia bonding but they are not reliable. The purpose of this research is to study the effect of plasma treatment on bonding strength of zirconia. Methods: In this in vitro study, 180 zirconia discs' (thickness was 0.85-0.9 mm) surfaces were processed with plasma of oxygen, argon, air and oxygen-argon combination with 90-10 and 80-20 ratio (n=30 for each group) after being polished by sandblast. Surface modifications were assessed by measuring the contact angle, surface roughness, and topographical evaluations. Cylindrical Panavia f2 resin-cement and Diafill were used for microshear strength bond measurements. The data analysis was performed by SPSS 20.0 software and one-way analysis of variance (ANOVA) and Tukey test as the post hoc. Results: Plasma treatment in all groups significantly reduces contact angle compare with control ( P =0.001). Topographic evaluations revealed coarseness promotion occurred in all plasma treated groups which was significant when compared to control ( P <0.05), except argon plasma treated group that significantly decreased surface roughness ( P <0.05). In all treated groups, microshear bond strength increased, except oxygen treated plasma group which decreased this strength. Air and argon-oxygen combination (both groups) significantly increased microshear bond strength ( P <0.05). Conclusion: According to this research, plasmatic processing with dielectric barrier method in atmospheric pressure can increase zirconia bonding strength.

Effects of N-vinylpyrrolidone (NVP) containing polyelectrolytes on surface properties of conventional glass-ionomer cements (GIC).

PubMed

Moshaverinia, Alireza; Roohpour, Nima; Ansari, Sahar; Moshaverinia, Maryam; Schricker, Scott; Darr, Jawwad A; Rehman, Ihtesham U

2009-10-01

It has been found that polyacids containing an N-vinylpyrrolidinone (NVP) comonomer produces a glass inomer cement with improved mechanical and handling properties. The objective of this study was to investigate the effect of NVP modified polyelectrolytes on the surface properties and shear bond strength to dentin of glass ionomer cements. Poly(acrylic acid (AA)-co-itaconic acid (IA)-co-N-vinylpyrrolidone) was synthesized by free radical polymerization. The terpolymer was characterized using (1)H NMR, FTIR spectroscopy and viscometry for solution properties. The synthesized polymers were used in glass ionomer cement formulations (Fuji II commercial GIC). Surface properties (wettability) of modified cements were studied by water contact angle measurements as a function of time. Work of adhesion values of different surfaces was also determined. The effect of NVP modified polyacid, on bond strength of glass-ionomer cement to dentin was also investigated. The mean data obtained from contact angle and bonding strength measurements were subjected to one- and two-way analysis of variance (ANOVA) at alpha=0.05. Results showed that NVP modified glass ionomer cements showed significantly lower contact angles (theta=47 degrees) and higher work of adhesion (WA=59.4 erg/cm(2)) in comparison to commercially available Fuji II GIC (theta=60 degrees and WA=50.3 erg/cm(2), respectively). The wettability of dentin surfaces conditioned with NVP containing terpolymer was higher (theta=21 degrees, WA=74.2 erg/cm(2)) than dentin conditioned with Fuji conditioner (theta=30 degrees, WA=69 erg/cm(2)). The experimental cement also showed higher but not statistically significant values for shear bond strength to dentin (7.8 MPa), when compared to control group (7.3 MPa). It was concluded that NVP containing polyelectrolytes are better dentin conditioners than the commercially available dentin conditioner (Fuji Cavity Conditioner, GC). NVP containing terpolymers can enhance the surface properties of GICs and also increase their bond strength to the dentin.

Prism Window for Optical Alignment

NASA Technical Reports Server (NTRS)

Tang, Hong

2008-01-01

A prism window has been devised for use, with an autocollimator, in aligning optical components that are (1) required to be oriented parallel to each other and/or at a specified angle of incidence with respect to a common optical path and (2) mounted at different positions along the common optical path. The prism window can also be used to align a single optical component at a specified angle of incidence. Prism windows could be generally useful for orienting optical components in manufacture of optical instruments. "Prism window" denotes an application-specific unit comprising two beam-splitter windows that are bonded together at an angle chosen to obtain the specified angle of incidence.

The Effect of Bond Albedo on Venus' Atmospheric and Surface Temperatures

NASA Astrophysics Data System (ADS)

Bullock, M. A.; Limaye, S. S.; Grinspoon, D. H.; Way, M.

2017-12-01

In spite of Venus' high planetary albedo, sufficient solar energy reaches the surface to drive a powerful greenhouse effect. The surface temperature is three times higher than it would be without an atmosphere. However, the details of the energy balance within Venus' atmosphere are poorly understood. Half of the solar energy absorbed within the clouds, where most of the solar energy is absorbed, is due to an unknown agent. One of the challenges of modeling Venus' atmosphere has been to account for all the sources of opacity sufficient to generate a globally averaged surface temperature of 735 K, when only 2% of the incoming solar energy is deposited at the surface. The wavelength and spherically integrated albedo, or Bond albedo, has typically been cited as between 0.7 and 0.82 (Colin 1983). Yet, recent photometry of Venus at extended phase angles between 2 and 179° indicate a Bond albedo of 0.90 (Mallama et al., 2006). The authors note an increase in cloud top brightness at phase angles < 2°, which effectively increases the spherically integrated albedo. They suggest that forward scattering by the H2SO4/H2O aerosols of the upper cloud is responsible for Venus' high albedo at very low phase angles. The present work investigates the implications of such a high albedo for understanding and modeling the energy balance of Venus' atmosphere. Using the successful 1D radiative transfer model SimVenus that incorporates the opacity due to 9 major gases in Venus' atmosphere, as well as multiple scattering calculations of radiation within the clouds, the sensitivity of surface temperature was studied as a function of Bond albedo. Results of these model calculations are shown in Fig. 1. Figure 1a (left). Venus' atmospheric temperature profile for different values of Bond albedo. The structure and radiative effects of the clouds are fixed. Figure 1b (right). Venus surface temperature as Bond Albedo changes. Radiative-convective equilibrium models predict the correct globally averaged surface temperature at a=0.81. Calculations here show that a Bond albedo of a=0.9 would yield a surface temperature of 666.4 K, about 70 K too low, unless there is additional thermal absorption within the atmosphere that is not understood. Colin, L.,, Venus, University of Arizona Press, Tucson, 1983, pp 10-26. Mallama, A., et al., 2006. Icarus. 182, 10-22.

[Effect of sandblasting particle sizes on bonding strength between porcelain and titanium fabricated by rapid laser forming].

PubMed

Zhang, Li-jun; Wang, Zhong-yi; Gao, Bo; Gao, Yang; Zhang, Chun-bao

2009-11-01

To evaluate the effect of sandblasting particle sizes of Al2O3 on the bonding strength between porcelain and titanium fabricated by laser rapid forming (LRF). The thermal expansion coefficient, roughness (Ra), contact angle, surface morphology of titanium surface and the bonding strength between titanium and porcelain were evaluated after the titanium surface being sandblasted using different sizes of Al2O3 (50 microm, 120 microm, 250 microm) at a pressure of 0.5 MPa. The cast titanium specimens were used as control, and were sandblasted with 50 microm Al2O3 at the same pressure. The thermal expansion coefficient of cast titanium [(9.84 +/- 0.42) x 10(-6)/ degrees C] and LRF Ti [(9.79 +/- 0.31) x 10(-6)/ degrees C) matched that of Noritake Ti-22 dentin porcelain [(8.93 +/- 0.36) x 10(-6)/ degrees C). When larger size of Al2O3 was used, the value of Ra and contact angle increased as well. There was no significant difference in bonding strength between the LRF Ti-50 microm [(25.91 +/- 1.02) MPa] and cast titanium [(26.42 +/- 1.65) MPa]. Significantly lower bonding strength was found in LRF Ti-120 microm [(21.86 +/- 1.64) MPa] and LRF Ti-250 microm [(19.96 +/- 1.03) MPa]. The bond strength between LRF Ti and Noritake Ti-22 dentin porcelain was above the lower limit value in the ISO 9693 (25 MPa) after using 50 microm Al2O3 sandblasting in 0.5MPa air pressure.

Atomic bonding effects in annular dark field scanning transmission electron microscopy. II. Experiments

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

Odlyzko, Michael L.; Held, Jacob T.; Mkhoyan, K. Andre, E-mail: mkhoyan@umn.edu

2016-07-15

Quantitatively calibrated annular dark field scanning transmission electron microscopy (ADF-STEM) imaging experiments were compared to frozen phonon multislice simulations adapted to include chemical bonding effects. Having carefully matched simulation parameters to experimental conditions, a depth-dependent bonding effect was observed for high-angle ADF-STEM imaging of aluminum nitride. This result is explained by computational predictions, systematically examined in the preceding portion of this study, showing the propagation of the converged STEM beam to be highly sensitive to net interatomic charge transfer. Thus, although uncertainties in experimental conditions and simulation accuracy remain, the computationally predicted experimental bonding effect withstands the experimental testing reportedmore » here.« less

Fiber reinforced solids possessing great fracture toughness: The role of interfacial strength

NASA Technical Reports Server (NTRS)

Atkins, A. G.

1975-01-01

The results of angle-ply investigations for strength and toughness of brittle fiber/brittle filament composites are presented. General results are discussed for both unidirectional and angle-ply intermittently bonded boron/epoxy composites as affected by soaking and freezing water environments. A description of and the operating instructions are included for the modified 230 mm (9 inch) wide intermittent coating tape making apparatus.

Modeling the IR spectra of aqueous metal carboxylate complexes: correlation between bonding geometry and stretching mode wavenumber shifts.

PubMed

Sutton, Catherine C R; da Silva, Gabriel; Franks, George V

2015-04-27

A widely used principle is that shifts in the wavenumber of carboxylate stretching modes upon bonding with a metal center can be used to infer if the geometry of the bonding is monodentate or bidentate. We have tested this principle with ab initio modeling for aqueous metal carboxylate complexes and have shown that it does indeed hold. Modeling of the bonding of acetate and formate in aqueous solution to a range of cations was used to predict the infrared spectra of the metal-carboxylate complexes, and the wavenumbers of the symmetric and antisymmetric vibrational modes are reported. Furthermore, we have shown that these shifts in wavenumber occur primarily due to how bonding with the metal changes the carboxylate C-O bond lengths and O-C-O angle. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hydrogen bonds and twist in cellulose microfibrils.

PubMed

Kannam, Sridhar Kumar; Oehme, Daniel P; Doblin, Monika S; Gidley, Michael J; Bacic, Antony; Downton, Matthew T

2017-11-01

There is increasing experimental and computational evidence that cellulose microfibrils can exist in a stable twisted form. In this study, atomistic molecular dynamics (MD) simulations are performed to investigate the importance of intrachain hydrogen bonds on the twist in cellulose microfibrils. We systematically enforce or block the formation of these intrachain hydrogen bonds by either constraining dihedral angles or manipulating charges. For the majority of simulations a consistent right handed twist is observed. The exceptions are two sets of simulations that block the O2-O6' intrachain hydrogen bond, where no consistent twist is observed in multiple independent simulations suggesting that the O2-O6' hydrogen bond can drive twist. However, in a further simulation where exocyclic group rotation is also blocked, right-handed twist still develops suggesting that intrachain hydrogen bonds are not necessary to drive twist in cellulose microfibrils. Copyright © 2017 Elsevier Ltd. All rights reserved.

Fused silica GRISMs manufactured by hydrophilic direct bonding at moderate heating

NASA Astrophysics Data System (ADS)

Kalkowski, G.; Grabowski, K.; Harnisch, G.; Flügel-Paul, T.; Zeitner, U.; Risse, S.

2017-12-01

For high-resolution spectroscopy in space, GRISM elements—obtained by patterning gratings onto a prism surface—find increasing applications. We report on GRISM manufacturing by joining the individual functional elements—prisms and gratings—to suitable components by the technology of hydrophilic direct bonding. Fused silica was used as a substrate material and binary gratings were fabricated by standard e-beam lithography and dry etching. Alignment of the grating dispersion direction to the prism angle was realized by passive adjustment on dedicated bonding gear matched to the substrate geometry. Materials adapted bonds of high transmission, stiffness, and strength were obtained after heat treatment at temperatures of about 200 °C in vacuum. Examples for bonding uncoated as well as coated grating surfaces are given. The results illustrate the great potential of hydrophilic glass direct bonding for manufacturing transmission optics to be used in space or other heavy duty applications.

Crystal structure of (pyridine-κN)bis(quinolin-2-olato-κ2 N,O)copper(II) monohydrate

PubMed Central

Hawks, Benjamin; Yan, Jingjing; Basa, Prem; Burdette, Shawn

2015-01-01

The title complex, [Cu(C9H6NO)2(C5H4N)]·H2O, adopts a slightly distorted square-pyramidal geometry in which the axial pyridine ligand exhibits a long Cu—N bond of 2.305 (3) Å. The pyridine ligand forms dihedral angles of 79.5 (5) and 88.0 (1)° with the planes of the two quinolin-2-olate ligands, while the dihedral angle between the quinoline groups of 9.0 (3)° indicates near planarity. The water mol­ecule connects adjacent copper complexes through O—H⋯O hydrogen bonds to phenolate O atoms, forming a network inter­connecting all the complexes in the crystal lattice. PMID:25878845

Formation of a 1,4-diamino-2,3-disila-1,3-butadiene derivative.

PubMed

Mondal, Kartik Chandra; Roesky, Herbert W; Dittrich, Birger; Holzmann, Nicole; Hermann, Markus; Frenking, Gernot; Meents, Alke

2013-10-30

A 1,4-diamino-2,3-disila-1,3-butadiene derivative of composition (Me2-cAAC)2(Si2Cl2) (Me2-cAAC = :C(CMe2)2(CH2)N-2,6-iPr2C6H3) was synthesized by reduction of the Me2-cAAC:SiCl4 adduct with KC8. This compound is stable at 0 °C for 3 months in an inert atmosphere. Theoretical studies reveal that the silicon atoms exhibit pyramidal coordination, where the Cl-Si-Si-Cl dihedral angle is twisted by 43.3° (calcd 45.9°). The two silicon-carbon bonds are intermediates between single and double Si-C bonds due to twisting of the C-Si-Si-C dihedral angle (163.6°).

Synthesis and crystal structure of the rhodium(I) cyclooctadiene complex with bis(3-tert-butylimidazol-2-ylidene)borate ligand

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

Chen, F.; Shao, K.-J.; Xiao, Y.-C.

2015-12-15

The rhodium(I) cyclooctadiene complex with the bis(3-tert-butylimidazol-2-ylidene)borate ligand [H{sub 2}B(Im{sup t}Bu){sup 2}]Rh(COD) C{sup 22}H{sup 36}BN{sup 4}Rh, has been prepared, and its crystal structure is determined by X-ray diffraction. Complex exhibits slightly distorted square planar configurations around the metal center, which is coordinated by the bidentate H{sup 2}B(Im{sup t}Bu){sub 2} and one cyclooctadiene group. The Rh–C{sub carbene} bond lengths are 2.043(4) and 2.074(4) Å, and the bond angle C–Rh1–C is 82.59°. The dihedral angle between two imidazol-2-ylidene rings is 67.30°.

Influences of the cold atmospheric plasma jet treatment on the properties of the demineralized dentin surfaces

NASA Astrophysics Data System (ADS)

Xiaoming, ZHU; Heng, GUO; Jianfeng, ZHOU; Xiaofei, ZHANG; Jian, CHEN; Jing, LI; Heping, LI; Jianguo, TAN

2018-04-01

Improvement of the bonding strength and durability between the dentin surface and the composite resin is a challenging job in dentistry. In this paper, a radio-frequency atmospheric-pressure glow discharge (RF-APGD) plasma jet is employed for the treatment of the acid-etched dentin surfaces used for the composite restoration. The properties of the plasma treated dentin surfaces and the resin-dentin interfaces are analyzed using the x-ray photoemission spectroscopy, contact angle goniometer, scanning electron microscope and microtensile tester. The experimental results show that, due to the abundant chemically reactive species existing in the RF-APGD plasma jet under a stable and low energy input operating mode, the contact angle of the plasma-treated dentin surfaces decreases to a stable level with the increase of the atomic percentage of oxygen in the specimens; the formation of the long resin tags in the scattered clusters and the hybrid layers at the resin-dentin interfaces significantly improve the bonding strength and durability. These results indicate that the RF-APGD plasma jet is an effective tool for modifying the chemical properties of the dentin surfaces, and for improving the immediate bonding strength and the durability of the resin-dentin bonding in dentistry.

The Influence of Pd-Doped Au Wire Bonding on HAZ Microstructure and Looping Profile in Micro-Electromechanical Systems (MEMS) Packaging

NASA Astrophysics Data System (ADS)

Ismail, Roslina; Omar, Ghazali; Jalar, Azman; Majlis, Burhanuddin Yeop

2015-07-01

Wire bonding processes has been widely adopted in micro-electromechanical systems (MEMS) packaging especially in biomedical devices for the integration of components. In the first process sequence in wire bonding, the zone along the wire near the melted tips is called the heat-affected zone (HAZ). The HAZ plays an important factor that influenced the looping profiles of wire bonding process. This paper investigates the effect of dopants on microstructures in the HAZ. One precent palladium (Pd) was added to the as-drawn 4N gold wire and annealed at 600°C. The addition of Pd was able to moderate the grain growth in the HAZ by retarding the heat propagation to the wire. In the formation of the looping profile, the first bending point of the looping is highly associated with the length of the HAZ. The alloyed gold wire (2N gold) has a sharp angle at a distance of about 30 m from the neck of the wire with a measured bending radius of about 40 mm and bending angle of about 40° clockwise from vertical axis, while the 4N gold wire bends at a longer distance. It also shows that the HAZ for 4N gold is longer than 2N gold wire.

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

Nahum, T.; Dodiuk, H.; Dotan, A.

Superhydrophobic surfaces with contact angle (CA) >150 and sliding angle (SA) <10 have been aroused curiosity over the years due to their various applications. Superhydrophobicity can be obtained tailoring the chemistry and the roughness of the surface, mimicking the Lotus flower. Most superhydrophobic surfaces based on secondary bonding lose their roughness in harsh conditions and are unsuitable for practical applications. Photoreactive SiO{sub 2} nanoparticles (NPs) based on benzophenone (BP) can be a very effective tool for formation of reactive species that function as a molecular bridge by covalent bonding between the NP and any polymer matrix with C-C and C-Hmore » bonds. The present work focused on thermoset radiation curing urethane acrylate. Upon UV irradiation reactive excited nπ* triplet benzophenone species are formed and react through hydrogen abstraction to form ketyl radicals which interact with a radicals from the UV irradiated polymer matrix to yield covalent bonding. Roughness was achieved by dipping the substrate in SiO{sub 2}@BPs NPs dispersion followed by irradiation. Fluoroalkylsilane was used to obtain hydrophobic top layer. AFM nano manipulation was used to verify the immobilization of NPs. Evaluation of durability was made using air flow at 300 km/hr. Preliminary results indicate the formation of super hydrophobic surfaces (CA>150 and SA<10) with improved stability.« less

Size-induced changes of structural and ferromagnetic properties in La1-xSrxMnO3 nanoparticles

NASA Astrophysics Data System (ADS)

Hintze, Cornelia E.; Fuchs, Dirk; Merz, Michael; Amari, Houari; Kübel, Christian; Huang, Meng-Jie; Powell, Annie; v. Löhneysen, Hilbert

2017-06-01

La1-xSrxMnO3 nanocrystals were grown using a microemulsion approach with different water-to-surfactant ratios Rw resulting in diameters between 20 and 40 nm. The variation of Rw entails a variation in the Sr concentrations between x = 0.35 and 0.50. This technique allows the controlled growth of structurally well-defined nanoparticles using the same calcination conditions. With decreasing particle size, the unit-cell volume increases together with the Mn-O bond length, while the Mn-O-Mn bond angle was found to decrease. The size-dependent change of structural properties is possibly related to surface effects or disorder. With the decrease in particle size, the ferromagnetic ordering temperature TC decreases significantly by up to 20%. The reduction of TC can be well understood with respect to the structural changes: the increase of Mn-O bond length and the decrease of Mn-O-Mn bond angle weaken the double-exchange coupling and hence reduce T C . In addition the intrinsic finite-size effect reduces T C . The observed size-induced change of magnetic properties may allow for a controlled manipulation of magnetism in La1-xSrxMnO3 nanoparticles by varying the particle size.

Wetting behaviour of carbon nitride nanostructures grown by plasma enhanced chemical vapour deposition technique

NASA Astrophysics Data System (ADS)

Ahmad Kamal, Shafarina Azlinda; Ritikos, Richard; Abdul Rahman, Saadah

2015-02-01

Tuning the wettability of various coating materials by simply controlling the deposition parameters is essential for various specific applications. In this work, carbon nitride (CNx) films were deposited on silicon (1 1 1) substrates using radio-frequency plasma enhanced chemical vapour deposition employing parallel plate electrode configuration. Effects of varying the electrode distance (DE) on the films' structure and bonding properties were investigated using Field emission scanning electron microscopy, Atomic force microscopy, Fourier transform infrared and X-ray photoemission spectroscopy. The wettability of the films was analyzed using water contact angle measurements. At high DE, the CNx films' surface was smooth and uniform. This changed into fibrous nanostructures when DE was decreased. Surface roughness of the films increased with this morphological transformation. Nitrogen incorporation increased with decrease in DE which manifested the increase in both relative intensities of Cdbnd N to Cdbnd C and Nsbnd H to Osbnd H bonds. sp2-C to sp3-C ratio increased as DE decreased due to greater deformation of sp2 bonded carbon at lower DE. The films' characteristics changed from hydrophilic to super-hydrophobic with the decrease in DE. Roughness ratio, surface porosity and surface energy calculated from contact angle measurements were strongly dependent on the morphology, surface roughness and bonding properties of the films.

A new silica-infiltrated Y-TZP obtained by the sol-gel method.

PubMed

Campos, T M B; Ramos, N C; Machado, J P B; Bottino, M A; Souza, R O A; Melo, R M

2016-05-01

The aim of this study was to evaluate silica infiltration into dental zirconia (VITA In-Ceram 2000 YZ, Vita Zahnfabrik) and its effects on zirconia's surface characteristics, structural homogeneity and bonding to a resin cement. Infiltration was performed by immersion of the pre-sintered zirconia specimens in silica sols for five days (ZIn). Negative (pure zirconia specimens, ZCon-) and positive controls (specimens kept in water for 5 days, ZCon+) were also performed. After sintering, the groups were evaluated by X-ray diffraction (XRD), grazing angle X-ray diffraction (DRXR), scanning electron microscopy (SEM), contact angle measurements, optical profilometry, biaxial flexural test and shear bonding test. Weibull analysis was used to determine the Weibull modulus (m) and characteristic strength (σ0) of all groups. There were no major changes in strength for the infiltrated group, and homogeneity (m) was also increased. A layer of ZrSiO4 was formed on the surface. The bond strength to resin cement was improved after zirconia infiltration, acid conditioning and the use of an MDP primer. The sol-gel method is an efficient and simple method to increase the homogeneity of zirconia. Infiltration also improved bonding to resin cement. The performance of a zirconia infiltrated by silica gel improved in at least two ways: structural homogeneity and bonding to resin cement. The infiltration is simple to perform and can be easily managed in a prosthesis laboratory. Copyright © 2016 Elsevier Ltd. All rights reserved.

The estimation of H-bond and metal ion-ligand interaction energies in the G-Quadruplex ⋯ Mn+ complexes

NASA Astrophysics Data System (ADS)

Mostafavi, Najmeh; Ebrahimi, Ali

2018-06-01

In order to characterize various interactions in the G-quadruplex ⋯ Mn+ (G-Q ⋯ Mn+) complexes, the individual H-bond (EHB) and metal ion-ligand interaction (EMO) energies have been estimated using the electron charge densities (ρs) calculated at the X ⋯ H (X = N and O) and Mn+ ⋯ O (Mn+ is an alkaline, alkaline earth and transition metal ion) bond critical points (BCPs) obtained from the atoms in molecules (AIM) analysis. The estimated values of EMO and EHB were evaluated using the structural parameters, results of natural bond orbital analysis (NBO), aromaticity indexes and atomic charges. The EMO value increase with the ratio of ionic charge to radius, e/r, where a linear correlation is observed between EMO and e/r (R = 0.97). Meaningful relationships are also observed between EMO and indexes used for aromaticity estimation. The ENH value is higher than EOH in the complexes; this is in complete agreement with the trend of N⋯Hsbnd N and O⋯Hsbnd N angles, the E (2) value of nN → σ*NH and nO → σ*NH interactions and the difference between the natural charges on the H-bonded atom and the hydrogen atom of guanine (Δq). In general, the O1MO2 angle becomes closer to 109.5° with the increase in EMO and decrease in EHB in the presence of metal ion.

Comparative structural and vibrational study of the four lowest energy conformers of serotonin

NASA Astrophysics Data System (ADS)

Jha, Omkant; Yadav, T. K.; Yadav, R. A.

2017-02-01

A computational investigation of all possible lowest energy conformers of serotonin was carried out at the B3LYP/6-311 ++G** level. Out of the 14 possible lowest energy conformers, the first 4 conformers were investigated thoroughly for the optimized geometries, fundamental frequencies, the potential energy distributions, APT and natural charges, natural bond orbital (NBO) analysis, MEP, Contour map, total density array, HOMO, LUMO energies. The second third and fourth conformers are energetically at higher temperatures of 78, 94 and 312 K respectively with respect to the first one. Bond angles and bond lengths do not show significant variations while the dihedral angles vary significantly in going from one conformer to the other. Some of the vibrational modes of the indole moiety are conformation dependent to some extent whereas most of the normal modes of vibration of amino-ethyl side chain vary significantly in going from one conformer to conformer. The MEP for the four conformers suggested that the sites of the maximum positive and negative ESP change on changing the conformation. The charges at some atomic sites also change significantly from conformer to conformer.

(E)-2-[2-(4-Carb­oxy­phen­yl)ethen­yl]-8-hydroxy­quinolin-1-ium chloride ethanol monosolvate

PubMed Central

Schulze, Mathias M.; Seichter, Wilhelm; Weber, Edwin

2013-01-01

In the title compound, C18H14NO3 +·Cl−·CH3CH2OH, the dihedral angle formed by the mean planes of the quinolinium and benzene rings is 3.4 (1)°, while the carb­oxy substituent is tilted at an angle of 4.8 (1)° with respect to the benzene ring. There is a short N—H⋯O contact in the cation. In the crystal, due to the planar mol­ecular geometry, two-dimensional aggregates are formed parallel to (221) via C—H⋯O, C—H⋯Cl, O—H⋯Cl and N—H⋯Cl hydrogen bonds. Inter­layer association is accomplished by O—Hethanol⋯Cl and O—H⋯Oethanol hydrogen bonds and π–π stacking inter­actions [centroid–centroid distances vary from 3.6477 (12) to 3.8381 (11) Å]. A supra­molecular three-dimensional architecture results from a stacked arrangement of layers comprising the ionic and hydrogen-bonded components. PMID:24454221

3,3′′-Bis(9-hy­droxy­fluoren-9-yl)-1,1′:3′,1′′-terphen­yl

PubMed Central

Skobridis, Konstantinos; Theodorou, Vassiliki; Paraskevopoulos, Georgios; Seichter, Wilhelm; Weber, Edwin

2013-01-01

The asymmetric unit of the title compound, C44H30O2, contains two independent mol­ecules in which the terminal rings of the terphenyl element are inclined at angles of 36.3 (1) and 22.5 (1)° with respect to the central ring and the dihedral angles between the fluorenyl units are 72.3 (1) and 62.8 (1)°. In the crystal, pairs of O—H⋯O hydrogen bonds link the mol­ecules into inversion dimers. The hy­droxy H atoms not involved in these hydrogen bonds form O—H⋯π inter­actions in which the central terphenyl rings act as acceptors. Weak C—H⋯O contacts and π–π [centroid–centroid distance = 4.088 (2) Å] stacking inter­actions also occur. Taking into account directed non-covalent bonding between the molecules, the crystal is constructed of supramolecular strands extending along the a-axis direction. PMID:24098206

Elastomeric member and method of manufacture therefor

DOEpatents

Hoppie, Lyle O.

1985-01-01

An energy storage device (10) is disclosed consisting of a stretched elongated elastomeric member (16) disposed within a tubular housing (14), which elastomeric member (16) is adapted to be torsionally stressed to store energy. The elastomeric member (16) is configured in the relaxed state with a uniform diameter body section (74), and transition end sections (76, 78), attached to rigid end piece assemblies (22, 24) of a lesser diameter. The profile and deflection characteristic of the transition sections (76, 78) are such that upon stretching of the elastomeric member (16), a substantially uniform diameter assembly results, to minimize the required volume of the surrounding housing (14). Each of the transition sections (76, 78) are received within and bonded to a woven wire mesh sleeve (26, 28) having helical windings at a particular helix angle to control the deflection of the transition section. Each sleeve (26, 28) also contracts with the contraction of the associated transition section to maintain the bond therebetween. During manufacture, the sleeves (26, 28) are forced against a forming surface and bonded to the associated transition section (76, 78) to provide the correct profile and helix angle.

Elastomeric member

DOEpatents

Hoppie, Lyle O.

1985-01-01

An energy storage device (10) is disclosed consisting of a stretched elongated elastomeric member (16) disposed within a tubular housing (14), which elastomeric member (16) is adapted to be torsionally stressed to store energy. The elastomeric member (16) is configured in the relaxed state with a uniform diameter body section (74), and transition end sections (76, 78), attached to rigid end piece assemblies (22, 24) of a lesser diameter. The profile and deflection characteristic of the transition sections (76, 78) are such that upon stretching of the elastomeric member (16), a substantially uniform diameter assembly results, to minimize the required volume of the surrounding housing (14). Each of the transition sections (76, 78) are received within and bonded to a woven wire mesh sleeve (26, 28) having helical windings at a particular helix angle to control the deflection of the transition section. Each sleeve (26, 28) also contracts with the contraction of the associated transition section to maintain the bond therebetween. During manufacture, the sleeves (26, 28) are forced against a forming surface and bonded to the associated transition section (76, 78) to provide the correct profile and helix angle.

FT-Raman, FT-IR spectra and total energy distribution of 3-pentyl-2,6-diphenylpiperidin-4-one: DFT method.

PubMed

Subashchandrabose, S; Saleem, H; Erdogdu, Y; Rajarajan, G; Thanikachalam, V

2011-11-01

FT-Raman and FT-IR spectra were recorded for 3-pentyl-2,6-diphenylpiperidin-4-one (PDPO) sample in solid state. The equilibrium geometries, harmonic vibrational frequencies, infrared and the Raman scattering intensities were computed using DFT/6-31G(d,p) level. Results obtained at this level of theory were used for a detailed interpretation of the infrared and Raman spectra, based on the total energy distribution (TED) of the normal modes. Molecular parameters such as bond lengths, bond angles and dihedral angles were calculated and compared with X-ray diffraction data. This comparison was good agreement. The intra-molecular charge transfer was calculated by means of natural bond orbital analysis (NBO). Hyperconjugative interaction energy was more during the π-π* transition. Energy gap of the molecule was found using HOMO and LUMO calculation, hence the less band gap, which seems to be more stable. Atomic charges of the carbon, nitrogen and oxygen were calculated using same level of calculation. Copyright © 2011 Elsevier B.V. All rights reserved.

Ab initio study on the structural and electronic properties of water surrounding a multifunctional nanoprobe

NASA Astrophysics Data System (ADS)

Xia, Xiuli; Shao, Yuanzhi

2018-02-01

We report the magneto-electric behavior of a dual-modality biomedical nanoprobe, a ternary nanosystem consisting of gold and gadolinia clusters and water molecules, with the effect of both nanoclusters on the structural and electronic properties of water. The hydrogen-oxygen bond lengths and angles as well as electronic charges of water molecules surrounding both nanoclusters were calculated using Hubbard U corrected density functional theory aided by molecular dynamics approach. The calculations reveal existence of a magneto-electric interaction between gold and gadolinium oxide nanoclusters, which influences the physical properties of surrounding water remarkably. A broader (narrower) distribution of Hsbnd O bond lengths (Hsbnd Osbnd H bond angles) was observed at the presence of either gold or gadolinia nanoclusters. The presence of Gd6O9 cluster leads to the larger charges of neighbour oxygen atoms. The distribution of oxygen atom charges becomes border when both Gd6O9 and Au13 clusters coexist. Ab initio calculation provides a feasible approach to explore the most essential interactions among functional components of a multimodal nanoprobe applied in aqueous environment.

Selenium carboxylic acids betaine; 3,3‧,3″-selenotris(propanoic acid) betaine, Se(CH2CH2COOH)2(CH2CH2COO)

NASA Astrophysics Data System (ADS)

Doudin, Khalid; Törnroos, Karl W.

2017-06-01

Attempts to prepare [Se(CH2CH2COOH)3]+Cl- from Se(CH2CH2COOH)2 and H2Cdbnd CHCOOH in concentrated hydrochloric acid, for the corresponding sulfonium salt, led exclusively to the Se-betaine, Se(CH2CH2COOH)2(CH2CH2COO). The Se-betaine crystallises in the space group P2l/c with the cell dimensions at 223 K, a = 5.5717(1), b = 24.6358(4), c = 8.4361(1) Å, β = 104.762(1)°, V = 1119.74(3) Å3, Z = 4, Dcalc = 1.763 Mgm- 3, μ = 3.364 Mm-1. The structure refined to RI = 0.0223 for 2801 reflections with Fo > 4σ(Fo). In the crystalline state the molecule is intermolecularly linked to neighbouring molecules by a number of hydrogen bonds; a very strong carboxylic-carboxylate bond with an O⋯O distance of 2.4435(16) Å, a medium strong carboxylic-carboxylate bond with an O⋯O distance of 2.6431(16) Å and several weak O⋯H(CH2) with O⋯C distances between 3.2 and 3.3 Å. In the carboxylic group involved in the very strong hydrogen bond the O⋯H bond is antiperiplanar to the Cdbnd O bond while the Osbnd H bond is periplanar to the Cdbnd O bond in the second carboxylic group. Based upon the Csbnd O bond lengths and the elongation of the Osbnd H bond involved in the strong hydrogen bond one may describe the compound as strongly linked units of Se(CH2CH2COOH)(CH2CH2COO)2 rather than Se(CH2CH2COOH)2(CH2CH2COO). The selenium atom forms two strong intramolecular 1,5-Se⋯O contacts, with a carboxylate oxygen atom, 2.9385(12) Å, and with a carboxylic oxygen atom, 2.8979(11) Å. To allow for these contacts the two organic fragments have been forced into the periplanar conformation. The molecule is only slightly asymmetric with regard to the Csbnd Sesbnd C bond angles but is very asymmetric with regard to the torsion angles.

(E)-N′-[1-(Thio­phen-2-yl)ethyl­idene]isonicotinohydrazide

PubMed Central

Dileep, C. S.; Abdoh, M. M. M; Chakravarthy, M. P.; Mohana, K. N.; Sridhar, M. A.

2012-01-01

In the title compound, C12H11N3OS, the dihedral angle between the pyridine and thio­phene 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. PMID:23125752

Structure of Poly(dialkylsiloxane) Melts:  Comparisons of Wide-Angle X-ray Scattering, Molecular Dynamics Simulations, and Integral Equation Theory

DOE PAGES

Habenschuss, Anton; Tsige, Mesfin; Curro, John G.; ...

2007-08-21

Here, wide-angle X-ray scattering, molecular dynamics (MD) simulations, and integral equation theory are used to study the structure of poly(diethylsiloxane) (PDES), poly(ethylmethylsiloxane) (PEMS), and poly(dimethylsiloxane) (PDMS) melts. The structure functions of PDES, PEMS, and PDMS are similar, but systematic trends in the intermolecular packing are observed. The local intramolecular structure is extracted from the experimental structure functions. The bond distances and bond angles obtained, including the large Si-O-Si angle, are in good agreement with the explicit atom (EA) and united atom (UA) potentials used in the simulations and theory and from other sources. Very good agreement is found between themore » MD simulations using the EA potentials and the experimental scattering results. Good agreement is also found between the polymer reference interaction site model (PRISM theory) and the UA MD simulations. The intermolecular structure is examined experimentally using an appropriately weighted radial distribution function and with theory and simulation using intermolecular site/site pair correlation functions. Finally, experiment, simulation, and theory show systematic increases in the chain/chain packing distances in the siloxanes as the number of sites in the pendant side chains is increased.« less

Composite drill pipe and method for forming same

DOEpatents

Leslie, James C; Leslie, II, James C; Heard, James; Truong, Liem; Josephson, Marvin

2014-04-15

Metal inner and outer fittings configured, the inner fitting configured proximally with an external flange and projecting distally to form a cylindrical barrel and stepped down-in-diameter to form an abutment shoulder and then projecting further distally to form a radially inwardly angled and distally extending tapered inner sleeve. An outer sleeve defining a torque tube is configured with a cylindrical collar to fit over the barrel and is formed to be stepped up in diameter in alignment with the first abutment shoulder to then project distally forming a radially outwardly tapered and distally extending bonding surface to cooperate with the inner sleeve to cooperate with the inner sleeve in forming a annular diverging bonding cavity to receive the extremity of a composite pipe to abut against the abutment shoulders and to be bonded to the respective bonding surfaces by a bond.

How strained are carbomeric-cycloalkanes?

PubMed

Wodrich, Matthew D; Gonthier, Jérôme F; Steinmann, Stephan N; Corminboeuf, Clémence

2010-06-24

The ring strain energies of carbomeric-cycloalkanes (molecules with one or more acetylene spacer units placed into carbon single bonds) are assessed using a series of isodesmic, homodesmotic, and hyperhomodesmotic chemical equations. Isodesmic bond separation reactions and other equations derived from the explicitly defined hierarchy of homodesmotic equations are insufficient for accurately determining these values, since not all perturbing effects (i.e., conjugation and hyperconjugation) are fully balanced. A set of homodesmotic reactions is proposed, which succeeds in balancing all stereoelectronic effects present within the carbomeric rings, allowing for a direct assessment of the strain energies. Values calculated from chemical equations are validated using an increment/additivity approach. The ring strain energy decreases as acetylene units are added, manifesting from the net stabilization gained by opening the C-CH(2)-C angle around the methylene groups and the destabilization arising from bending the C-C identical withC angles of the spacer groups. This destabilization vanishes with increasing parent ring size (i.e., the angle distortion is less in the carbomeric-cyclobutanes than in the carbomeric-cyclopropanes), leading to strain energies near zero for carbo(n)-cyclopentanes and carbo(n)-cyclohexanes.

Elevated temperature properties of boron/aluminum composites

NASA Technical Reports Server (NTRS)

Sullivan, P. G.

1978-01-01

The high temperature properties of boron/aluminum composites, fabricated by an air diffusion bonding technique utilizing vacuum-bonded monolayer tape are reported. Seventeen different combinations of matrix alloy, reinforcement diameter, reinforcement volume percent, angle-ply and matrix enhancement (i.e. titanium cladding and interleaves) were fabricated, inspected, and tested. It is shown that good to excellent mechanical properties could be obtained for air-bonded boron/aluminum composites and that these properties did not decrease significantly up to a test temperature of at least 260 C. Composites made with 8 mil B/W fiber show a much greater longitudinal strength dependence on volume percent fiber than composites made with 5.6 mil fiber. The addition of titanium caused difficulties in composite bonding and yielded composites with reduced strength.

1-(4-Methyl-1-naphth­yl)ethanone

PubMed Central

Hu, Yong-Hong; Zhao, Xiao-Lei; Yang, Wen-Ge; Yao, Jin-Feng; Lu, Xiu-Tao

2008-01-01

In the mol­ecule of the title compound, C13H12O, the two aromatic rings are oriented at a dihedral angle of 2.90 (3)°. An intra­molecular C—H⋯O hydrogen bond results in the formation of a non-planar six-membered ring, which adopts an envelope conformation. In the crystal structure, inter­molecular C—H⋯O hydrogen bonds link the mol­ecules. PMID:21581284

Ceramic Inlays: Effect of Mechanical Cycling and Ceramic Type on Restoration-dentin Bond Strength.

PubMed

Trindade, F Z; Kleverlaan, C J; da Silva, L H; Feilzer, A J; Cesar, P F; Bottino, M A; Valandro, L F

2016-01-01

This study aimed to evaluate the bond strength between dentin and five different ceramic inlays in permanent maxillary premolars, with and without mechanical cycling. One hundred permanent maxillary premolars were prepared and divided into 10 groups (n=10) according to the ceramic system (IPS e.Max Press; IPS e.Max CAD; Vita PM9; Vita Mark II; and Vita VM7) and the mechanical cycling factor (with and without [100 N, 2 Hz, 1.2×10(6) cycles]). The inlays were adhesively cemented, and all of the specimens were cut into microbars (1×1 mm, nontrimming method), which were tested under microtensile loading. The failure mode was classified and contact angle, roughness, and microtopographic analyses were performed on each ceramic surface. The mechanical cycling had a significant effect (p=0.0087) on the bond strength between dentin and IPS e.max Press. The Vita Mark II group had the highest bond strength values under both conditions, with mechanical cycling (9.7±1.8 MPa) and without (8.2±1.9 MPa), while IPS e.Max CAD had the lowest values (2.6±1.6 and 2.2±1.4, respectively). The adhesive failure mode at the ceramic/cement interface was the most frequent. Vita Mark II showed the highest value of average roughness. IPS e.max Press and Vita Mark II ceramics presented the lowest contact angles. In conclusion, the composition and manufacturing process of ceramics seem to have an influence on the ceramic surface and resin cement bond strength. Mechanical cycling did not cause significant degradation on the dentin and ceramic bond strength under the configuration used.

A novel bonding method for large scale poly(methyl methacrylate) micro- and nanofluidic chip fabrication

NASA Astrophysics Data System (ADS)

Qu, Xingtian; Li, Jinlai; Yin, Zhifu

2018-04-01

Micro- and nanofluidic chips are becoming increasing significance for biological and medical applications. Future advances in micro- and nanofluidics and its utilization in commercial applications depend on the development and fabrication of low cost and high fidelity large scale plastic micro- and nanofluidic chips. However, the majority of the present fabrication methods suffer from a low bonding rate of the chip during thermal bonding process due to air trapping between the substrate and the cover plate. In the present work, a novel bonding technique based on Ar plasma and water treatment was proposed to fully bond the large scale micro- and nanofluidic chips. The influence of Ar plasma parameters on the water contact angle and the effect of bonding conditions on the bonding rate and the bonding strength of the chip were studied. The fluorescence tests demonstrate that the 5 × 5 cm2 poly(methyl methacrylate) chip with 180 nm wide and 180 nm deep nanochannels can be fabricated without any block and leakage by our newly developed method.

Micromachined needles and lancets with design adjustable bevel angles

NASA Astrophysics Data System (ADS)

Sparks, Douglas; Hubbard, Timothy

2004-08-01

A new method of micromachining hollow needles and two-dimensional needle arrays from single crystal silicon is described. The process involves a combination of fusion bonding, photolithography and anisotropic plasma etching. The cannula produced with this process can have design adjustable bevel angles, wall thickness and channel dimensions. A subset of processing steps can be employed to produce silicon blades and lancets with design adjustable bevel angles and shaft dimensions. Applications for this technology include painless drug infusion, blood diagnosis, glucose monitoring, cellular injection and the manufacture of microkeratomes for ocular, vascular and neural microsurgery.

Flip-chip integration of tilted VCSELs onto a silicon photonic integrated circuit.

PubMed

Lu, Huihui; Lee, Jun Su; Zhao, Yan; Scarcella, Carmelo; Cardile, Paolo; Daly, Aidan; Ortsiefer, Markus; Carroll, Lee; O'Brien, Peter

2016-07-25

In this article we describe a cost-effective approach for hybrid laser integration, in which vertical cavity surface emitting lasers (VCSELs) are passively-aligned and flip-chip bonded to a Si photonic integrated circuit (PIC), with a tilt-angle optimized for optical-insertion into standard grating-couplers. A tilt-angle of 10° is achieved by controlling the reflow of the solder ball deposition used for the electrical-contacting and mechanical-bonding of the VCSEL to the PIC. After flip-chip integration, the VCSEL-to-PIC insertion loss is -11.8 dB, indicating an excess coupling penalty of -5.9 dB, compared to Fibre-to-PIC coupling. Finite difference time domain simulations indicate that the penalty arises from the relatively poor match between the VCSEL mode and the grating-coupler.

Structural and vibrational studies on 1-(5-methyl-[1,3,4] thiadiazol-2-yl)-pyrolidin-2-ol

NASA Astrophysics Data System (ADS)

Ramesh Babu, N.; Saleem, H.; Subashchandrabose, S.; Padusha, M. Syed Ali; Bharanidharan, S.

2016-01-01

FT-Raman and FT-IR spectra were recorded for1-(5-methyl-[1,3,4]thiadiazol-2-yl)-pyrolidin-2-ol (MTPN) sample in solid state. The equilibrium geometries, harmonic vibrational frequencies, IR and the Raman scattering intensities were computed using DFT/6-311++G (d,p) level. Results obtained at this level of theory were used for a detailed interpretation of the IR and Raman spectra, based on the TED of the normal modes. Molecular parameters such as bond lengths, bond angles and dihedral angles were calculated. The intra-molecular charge transfer was calculated by means of NBO. Hyperconjugative interaction energy was more during the π-π∗ transition. Energy gap of the molecule has been found using HOMO and LUMO calculation, hence the less band gap, which seems to be more stable.

Crystal structure of N-{[3-bromo-1-(phenyl-sulfon-yl)-1H-indol-2-yl]meth-yl}benzene-sulfonamide.

PubMed

Umadevi, M; Raju, P; Yamuna, R; Mohanakrishnan, A K; Chakkaravarthi, G

2015-10-01

In the title compound, C21H17BrN2O4S2, the indole ring system subtends dihedral angles of 85.96 (13) and 9.62 (16)° with the planes of the N- and C-bonded benzene rings, respectively. The dihedral angles between the benzene rings is 88.05 (17)°. The mol-ecular conformation is stabilized by intra-molecular N-H⋯O and C-H⋯O hydrogen bonds and an aromatic π-π stacking [centroid-to-centroid distance = 3.503 (2) Å] inter-action. In the crystal, short Br⋯O [2.9888 (18) Å] contacts link the mol-ecules into [010] chains. The chains are cross-linked by weak C-H⋯π inter-actions, forming a three-dimensional network.

Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement

DOE PAGES

Moriarty, Nigel W.; Tronrud, Dale E.; Adams, Paul D.; ...

2014-06-17

Ideal values of bond angles and lengths used as external restraints are crucial for the successful refinement of protein crystal structures at all but the highest of resolutions. The restraints in common usage today have been designed based on the assumption that each type of bond or angle has a single ideal value independent of context. However, recent work has shown that the ideal values are, in fact, sensitive to local conformation, and as a first step toward using such information to build more accurate models, ultra-high resolution protein crystal structures have been used to derive a conformation-dependent library (CDL)more » of restraints for the protein backbone (Berkholz et al. 2009. Structure. 17, 1316). Here, we report the introduction of this CDL into the Phenix package and the results of test refinements of thousands of structures across a wide range of resolutions. These tests show that use of the conformation dependent library yields models that have substantially better agreement with ideal main-chain bond angles and lengths and, on average, a slightly enhanced fit to the X-ray data. No disadvantages of using the backbone CDL are apparent. In Phenix usage of the CDL can be selected by simply specifying the cdl=True option. This successful implementation paves the way for further aspects of the context-dependence of ideal geometry to be characterized and applied to improve experimental and predictive modelling accuracy.« less

Atomic and molecular analysis highlights the biophysics of unprotonated and protonated retinal in UV and scotopic vision.

PubMed

Kubli-Garfias, Carlos; Vázquez-Ramírez, Ricardo; Cabrera-Vivas, Blanca M; Gómez-Reyes, Baldomero; Ramírez, Juan Carlos

2015-09-26

During the photoreaction of rhodopsin, retinal isomerizes, rotating the C11[double bond, length as m-dash]C12 π-bond from cis to an all-trans configuration. Unprotonated (UR) or protonated (PR) retinal in the Schiff's base (SB) is related to UV and light vision. Because the UR and PR have important differences in their physicochemical reactivities, we compared the atomic and molecular properties of these molecules using DFT calculations. The C10-C11[double bond, length as m-dash]C12-C13 dihedral angle was rotated from 0° to 180° in 45° steps, giving five conformers, and the following were calculated from them: atomic orbital (AO) contributions to the HOMO and LUMO, atomic charges, bond length, bond order, HOMO, LUMO, hardness, electronegativity, polarizability, electrostatic potential, UV-vis spectra and dipole moment (DM). Similarly, the following were analyzed: the energy profile, hybridization, pyramidalization and the hydrogen-out-of-plane (HOOP) wagging from the H11-C11[double bond, length as m-dash]C12-H12 dihedral angle. In addition, retinal with a water H-bond (HR) in the SB was included for comparison. Interestingly, in the PR, C11 and C12 are totally the LUMO and the HOMO, respectively, and have a large electronegativity difference, which predicts an electron jump in these atoms during photoexcitation. At the same time, the PR showed a longer bond length and lower bond order, with a larger DM, lower HOMO-LUMO gap, lower hardness and higher electronegativity. In addition, the AOs of -45° and -90° conformers changed significantly, from pz to py, during the rotation concomitantly with marked hybridization, smooth pyramidalization and lower HOOP activity. Clearly, the atomic and molecular differences between the UR and PR are overwhelming, including the rotational energy profile and light absorption spectra, which indicates that light absorption of UR and PR is already determined by the retinal characteristics of the SB protonation. The HR-model compared with UR shows a lower energy barrier and a discreet bathochromic effect in the UV region.

High Si-H local mode overtones in SiHD/sub 3/

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

Bernheim, R.A.; Lampe, F.W.; O'Keefe, J.F.

1984-01-01

Spectra for SiHD/sub 3/ obtained using a nonresonant photoacoustic cell mounted within the cavity of a CR490 tunable CW laser are reported herein. The symmetric top spectra exhibit partial rotational resolution. A relation for determining the Si-H bond distance is reported, and the Si-D bond distance is taken to be the same as the Si-H distance in the ground vibrational state. The bond angle is assumed to remain tetrahedral in both situations. The noted spectral vibrational band widths arise only from rotational structure with contributions from fast vibrational relaxation not being evident. 10 references, 2 figures, 1 table.

Methyl 4-amino-3-methyl­benzoate

PubMed Central

Li, Xiang; Yuan, Lian-Shan; Wang, Dan; Liu, Shan; Yao, Cheng

2008-01-01

In the mol­ecule of the title compound, C9H11NO2, the methyl C and amino N atoms bonded to the benzene ring lie in the ring plane. Intra­molecular C—H⋯O hydrogen bonding results in the formation of a five-membered planar ring, which is oriented at a dihedral angle of 2.73 (3)° with respect to the benzene ring, so they are nearly coplanar. In the crystal structure, inter­molecular N—H⋯O hydrogen bonds link the mol­ecules into chains elongated along the c axis and stacked along the b axis. PMID:21202370

The role of disulfide bond in hyperthermophilic endocellulase.

PubMed

Kim, Han-Woo; Ishikawa, Kazuhiko

2013-07-01

The hyperthermophilic endocellulase, EGPh (glycosyl hydrolase family 5) from Pyrococcus horikoshii possesses 4 cysteine residues forming 2 disulfide bonds, as identified by structural analysis. One of the disulfide bonds is located at the proximal region of the active site in EGPh, which exhibits a distinct pattern from that of the thermophilic endocellulase EGAc (glycosyl hydrolase family 5) of Acidothermus cellulolyticus despite the structural similarity between the two endocellulases. The structural similarity between EGPh and EGAc suggests that EGPh possesses a structure suitable for changing the position of the disulfide bond corresponding to that in EGAc. Introduction of this alternative disulfide bond in EGPh, while removing the original disulfide bond, did not result in a loss of enzymatic activity but the EGPh was no longer hyperthermostable. These results suggest that the contribution of disulfide bond to hyperthermostability at temperature higher than 100 °C is restrictive, and that its impact is dependent on the specific structural environment of the hyperthermophilic proteins. The data suggest that the structural position and environment of the disulfide bond has a greater effect on high-temperature thermostability of the enzyme than on the potential energy of the dihedral angle that contributes to disulfide bond cleavage.

N,N,N′,N′-Tetra­methyl­guanidinium tetra­phenyl­borate

PubMed Central

Tiritiris, Ioannis

2012-01-01

In the title salt, C5H14N3 +·C24H20B−, the C—N bond lengths in the central CN3 unit are 1.3322 (11), 1.3385 (12) and 1.3422 (12) Å, indicating partial double-bond character. The central C atom is bonded to the three N atoms in a nearly ideal trigonal-planar geometry [N—C—N angles = 119.51 (8), 119.81 (9) and 120.69 (8)°] and the positive charge is delocalized in the CN3 plane. The bond lengths between the N atoms and the terminal methyl groups all have values close to a typical single bond [1.4597 (12)–1.4695 (13) Å]. The crystal packing is caused by electrostatic inter­actions between cations and anions. PMID:23476307

Natural bond orbital analysis, electronic structure, non-linear properties and vibrational spectral analysis of L-histidinium bromide monohydrate: a density functional theory.

PubMed

Sajan, D; Joseph, Lynnette; Vijayan, N; Karabacak, M

2011-10-15

The spectroscopic properties of the crystallized nonlinear optical molecule L-histidinium bromide monohydrate (abbreviated as L-HBr-mh) have been recorded and analyzed by FT-IR, FT-Raman and UV techniques. The equilibrium geometry, vibrational wavenumbers and the first order hyperpolarizability of the crystal were calculated with the help of density functional theory computations. The optimized geometric bond lengths and bond angles obtained by using DFT (B3LYP/6-311++G(d,p)) show good agreement with the experimental data. The complete assignments of fundamental vibrations were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The natural bond orbital (NBO) analysis confirms the occurrence of strong intra and intermolecular N-H⋯O hydrogen bonding. Copyright © 2011 Elsevier B.V. All rights reserved.

Low-temperature direct copper-to-copper bonding enabled by creep on (111) surfaces of nanotwinned Cu

PubMed Central

Liu, Chien-Min; Lin, Han-Wen; Huang, Yi-Sa; Chu, Yi-Cheng; Chen, Chih; Lyu, Dian-Rong; Chen, Kuan-Neng; Tu, King-Ning

2015-01-01

Direct Cu-to-Cu bonding was achieved at temperatures of 150–250 °C using a compressive stress of 100 psi (0.69 MPa) held for 10–60 min at 10−3 torr. The key controlling parameter for direct bonding is rapid surface diffusion on (111) surface of Cu. Instead of using (111) oriented single crystal of Cu, oriented (111) texture of extremely high degree, exceeding 90%, was fabricated using the oriented nano-twin Cu. The bonded interface between two (111) surfaces forms a twist-type grain boundary. If the grain boundary has a low angle, it has a hexagonal network of screw dislocations. Such network image was obtained by plan-view transmission electron microscopy. A simple kinetic model of surface creep is presented; and the calculated and measured time of bonding is in reasonable agreement. PMID:25962757

Bonded half planes containing an arbitrarily oriented crack

NASA Technical Reports Server (NTRS)

Erdogan, F.; Aksogan, O.

1973-01-01

The plane elastostatic problem for two bonded half planes containing an arbitrarily oriented crack in the neighborhood of the interface is considered. Using Mellin transforms, the problem is formulated as a system of singular integral equations. The equations are solved for various crack orientations, material combinations, and external loads. The numerical results given include the stress intensity factors, tHe strain energy release rates, and tHe probable cleavage angles giving the direction of crack propagation.

Closed Loop Adaptive Refinement of Dynamical Models for Complex Chemical Reactions

DTIC Science & Technology

2008-06-26

rotational energy Erot , bond length, or bond angle of the products, the corresponding RS-HDMR component functions, cf. eq. (??), can be constructed from a...rotational energy ∆ Erot , and (3) the H2O vibrational energy ∆Evib. The usually strong Coriolis coupling, for example, between H2O rotational and...averaged vibrational energy) is usually considered after the collision. On the other hand, the corresponding internal energy Eint = Evib+ Erot will remain

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.

Chromophore orientation in bacteriorhodopsin determined from the angular dependence of deuterium nuclear magnetic resonance spectra of oriented purple membranes.

PubMed

Moltke, S; Nevzorov, A A; Sakai, N; Wallat, I; Job, C; Nakanishi, K; Heyn, M P; Brown, M F

1998-08-25

The orientation of prosthetic groups in membrane proteins is of considerable importance in understanding their functional role in energy conversion, signal transduction, and ion transport. In this work, the orientation of the retinylidene chromophore of bacteriorhodopsin (bR) was investigated using 2H NMR spectroscopy. Bacteriorhodopsin was regenerated with all-trans-retinal stereospecifically deuterated in one of the geminal methyl groups on C1 of the cyclohexene ring. A highly oriented sample, which is needed to obtain individual bond orientations from 2H NMR, was prepared by forming hydrated lamellar films of purple membranes on glass slides. A Monte Carlo method was developed to accurately simulate the 2H NMR line shape due to the distribution of bond angles and the orientational disorder of the membranes. The number of free parameters in the line shape simulation was reduced by independent measurements of the intrinsic line width (1.6 kHz from T2e experiments) and the effective quadrupolar coupling constant (38. 8-39.8 kHz from analysis of the line shape of a powder-type sample). The angle between the C1-(1R)-1-CD3 bond and the purple membrane normal was determined with high accuracy from the simultaneous analysis of a series of 2H NMR spectra recorded at different inclinations of the uniaxially oriented sample in the magnetic field at 20 and -50 degrees C. The value of 68.7 +/- 2.0 degrees in dark-adapted bR was used, together with the previously determined angle of the C5-CD3 bond, to calculate the possible orientations of the cyclohexene ring in the membrane. The solutions obtained from 2H NMR were then combined with additional constraints from linear dichroism and electron cryomicroscopy to obtain the allowed orientations of retinal in the noncentrosymmetric membrane structure. The combined data indicate that the methyl groups on the polyene chain point toward the cytoplasmic side of the membrane and the N-H bond of the Schiff base to the extracellular side, i.e., toward the side of proton release in the pump pathway.

4-[(E)-(2,4-Difluoro-phen-yl)(hydroxy-imino)meth-yl]piperidinium picrate.

PubMed

Jasinski, Jerry P; Butcher, Ray J; Yathirajan, H S; Mallesha, L; Mohana, K N

2009-09-05

The title compound, C(12)H(15)F(2)N(2)O(+)·C(6)H(2)N(3)O(7) (-), a picrate salt of 4-[(E)-(2,4-difluoro-phen-yl)(hydroxy-imino)meth-yl]piper-idine, crystallizes with two independent mol-ecules in a cation-anion pair in the asymmetric unit. In the cation, a methyl group is tris-ubstituted by hydroxy-imino, piperidin-4-yl and 2,4-difluoro-phenyl groups, the latter of which contains an F atom disordered over two positions in the ring [occupancy ratio 0.631 (4):0.369 (4)]. The mean plane of the hydr-oxy group is in a synclinical conformation nearly orthogonal [N-C-C-C = 72.44 (19)°] to the mean plane of the piperidine ring, which adopts a slightly distorted chair conformation. The dihedral angle between the mean plane of the 2,4-difluoro-phenyl and piperidin-4-yl groups is 60.2 (3)°. In the picrate anion, the mean planes of the two o-NO(2) and single p-NO(2) groups adopt twist angles of 5.7 (2), 25.3 (7) and 8.3 (6)°, respectively, with the attached planar benzene ring. The dihedral angle between the mean planes of the benzene ring in the picrate anion and those in the hydroxy-imino, piperidin-4-yl and 2,4-difluoro-phenyl groups in the cation are 84.9 (7), 78.9 (4) and 65.1 (1)°, respectively. Extensive hydrogen-bond inter-actions occur between the cation-anion pair, which help to establish the crystal packing in the unit cell. This includes dual three-center hydrogen bonds with the piperidin-4-yl group, the phenolate and o-NO(2) O atoms of the picrate anion at different positions in the unit cell, which form separate N-H⋯(O,O) bifurcated inter-molecular hydrogen-bond inter-actions. Also, the hydr-oxy group forms a separate hydrogen bond with a nearby piperidin-4-yl N atom, thus providing two groups of hydrogen bonds, which form an infinite two-dimensional network along (011).

Design of new anti-Alzheimer drugs: ring-expansion synthesis and synchrotron X-ray diffraction study of dimethyl 4-ethyl-11-fluoro-1,4,5,6,7,8-hexa­hydro­azonino[5,6-b]indole-2,3-di­carboxyl­ate

PubMed Central

Toze, Flavien A. A.; Listratova, Anna V.; Voskressensky, Leonid G.; Chernikova, Natalia Yu.; Lobanov, Nikolai N.; Bilyachenko, Alexey N.

2018-01-01

The title compound, C20H23FN2O4, is the product of a ring-expansion reaction from a seven-membered fluorinated hexa­hydro­azepine to a nine-membered azonine. The nine-membered azonine ring of the mol­ecule adopts a chair–boat conformation. The C=C and C—N bond lengths [1.366 (3) and 1.407 (3) Å, respectively] indicate the presence of conjugation within the enamine CH2—C=C—N—CH2 fragment. The substituent planes at the C=C double bond of this fragment are twisted by 16.0 (3)° as a result of steric effects. The amine N(Et) N atom has a trigonal–pyramidal configuration (sum of the bond angles = 346.3°). The inter­planar angle between the two carboxyl­ate substituents is 60.39 (8)°. In the crystal, mol­ecules form zigzag chains along [010] by inter­molecular N—H⋯O hydrogen-bonding inter­actions, which are further packed in stacks toward [100]. The title azonino­indole might be considered as a candidate for the design of new Alzheimer drugs. PMID:29765710

Synthesis, characterization and vibrational spectra analysis of ethyl (2Z)-2-(2-amino-4-oxo-1,3-oxazol-5(4H)-ylidene)-3-oxo-3-phenylpropanoate.

PubMed

Kıbrız, Ibrahim Evren; Sert, Yusuf; Saçmacı, Mustafa; Sahin, Ertan; Yıldırım, Ismail; Ucun, Fatih

2013-10-01

In the present study, the experimental and theoretical vibrational spectra of ethyl (2Z)-2-(2-amino-4-oxo-1,3-oxazol-5(4H)-ylidene)-3-oxo-3-phenylpropanoate (AOX) were investigated. The experimental FT-IR (400-4000 cm(-1)) and Laser-Raman spectra (100-4000 cm(-1)) of the molecule in the solid phase were recorded. Theoretical vibrational frequencies and geometric parameters (bond lengths, bond angles and torsion angles) were calculated using ab initio Hartree Fock (HF), Density Functional Theory (B3LYP and B3PW91) methods with 6-311++G(d,p) basis set by Gaussian 03 program, for the first time. The computed values of frequencies are scaled using a suitable scale factor to yield good coherence with the observed values. The assignments of the vibrational frequencies were performed by potential energy distribution (PED) analysis by using VEDA 4 program. The theoretical optimized geometric parameters and vibrational frequencies were compared with the corresponding experimental X-ray diffraction data, and they were seen to be in a good agreement with each other. The hydrogen bonding geometry of the molecule was also simulated to evaluate the effect of intermolecular hydrogen bonding on the vibrational frequencies. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies were found. Published by Elsevier B.V.

Synthesis, characterization and vibrational spectra analysis of ethyl (2Z)-2-(2-amino-4-oxo-1,3-oxazol-5(4H)-ylidene)-3-oxo-3-phenylpropanoate

NASA Astrophysics Data System (ADS)

Kıbrız, İbrahim Evren; Sert, Yusuf; Saçmacı, Mustafa; Şahin, Ertan; Yıldırım, İsmail; Ucun, Fatih

2013-10-01

In the present study, the experimental and theoretical vibrational spectra of ethyl (2Z)-2-(2-amino-4-oxo-1,3-oxazol-5(4H)-ylidene)-3-oxo-3-phenylpropanoate (AOX) were investigated. The experimental FT-IR (400-4000 cm-1) and Laser-Raman spectra (100-4000 cm-1) of the molecule in the solid phase were recorded. Theoretical vibrational frequencies and geometric parameters (bond lengths, bond angles and torsion angles) were calculated using ab initio Hartree Fock (HF), Density Functional Theory (B3LYP and B3PW91) methods with 6-311++G(d,p) basis set by Gaussian 03 program, for the first time. The computed values of frequencies are scaled using a suitable scale factor to yield good coherence with the observed values. The assignments of the vibrational frequencies were performed by potential energy distribution (PED) analysis by using VEDA 4 program. The theoretical optimized geometric parameters and vibrational frequencies were compared with the corresponding experimental X-ray diffraction data, and they were seen to be in a good agreement with each other. The hydrogen bonding geometry of the molecule was also simulated to evaluate the effect of intermolecular hydrogen bonding on the vibrational frequencies. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies were found.

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

Structural characterization of 1,3-propanedithiols that feature carboxylic acids: Homologues of mercury chelating agents ✩

PubMed Central

Sattler, Wesley; Palmer, Joshua H.; Bridges, Christy C.; Joshee, Lucy; Zalups, Rudolfs K.; Parkin, Gerard

2013-01-01

The molecular structures of a series of 1,3-propanedithiols that contain carboxylic acid groups, namely rac- and meso-2,4-dimercaptoglutaric acid (H4DMGA) and 2-carboxy-1,3-propanedithiol (H3DMCP), have been determined by X-ray diffraction. Each compound exhibits two centrosymmetric intermolecular hydrogen bonding interactions between pairs of carboxylic acid groups, which result in a dimeric structure for H3DMCP and a polymeric tape-like structure for rac- and meso-H4DMGA. Significantly, the hydrogen bonding motifs observed for rac- and meso-H4DMGA are very different to those observed for the 1,2-dithiol, rac-2,3-dimercaptosuccinic acid (rac-H4DMSA), in which the two oxygen atoms of each carboxylic acid group hydrogen bond to two different carboxylic acid groups, thereby resulting in a hydrogen bonded sheet-like structure rather than a tape. Density functional theory calculations indicate that 1,3-dithiolate coordination to mercury results in larger S–Hg–S bond angles than does 1,2-dithiolate coordination, but these angles are far from linear. As such, κ2-S2 coordination of these dithiolate ligands is expected to be associated with mercury coordination numbers of greater than two. In vivo studies demonstrate that both rac-H4DMGA and H3DMCP reduce the renal burden of mercury in rats, although the compounds are not as effective as either 2,3-dimercaptopropane-1-sulfonic acid (H3DMPS) or meso-H4DMSA. PMID:24187425

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

PubMed

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

2017-11-29

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

Investigation on the mechanism of nitrogen plasma modified PDMS bonding with SU-8

NASA Astrophysics Data System (ADS)

Yang, Chengxin; Yuan, Yong J.

2016-02-01

Polydimethylsiloxane (PDMS) and SU-8 are both widely used for microfluidic system. However, it is difficult to permanently seal SU-8 microfluidic channels using PDMS with conventional methods. Previous efforts of combining these two materials mainly employed oxygen plasma modified PDMS. The nitrogen plasma modification of PDMS bonding with SU-8 is rarely studied in recent years. In this work, the mechanism of nitrogen plasma modified PDMS bonding with SU-8 was investigated. The fourier-transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS) and contact angle of a water droplet were used to analyze the nitrogen plasma modified surface and the hydrophilic stability of PDMS samples. Pull-off tests were used for estimating the bonding effect of interface between nitrogen plasma modified PDMS and SU-8.

Rapid and Clean Covalent Attachment of Methylsiloxane Polymers and Oligomers to Silica Using B(C6F5)3 Catalysis.

PubMed

Flagg, Daniel H; McCarthy, Thomas J

2017-08-22

The rapid, room-temperature covalent attachment of alkylhydridosilanes (R 3 Si-H) to silicon oxide surfaces to form monolayers using tris(pentafluorophenyl)borane (B(C 6 F 5 ) 3 , BCF) catalysis has recently been described. This method, unlike alternative routes to monolayers, produces only unreactive H 2 gas as a byproduct and reaches completion within minutes. We report the use of this selective reaction between surface silanols and hydridosilanes to prepare surface-grafted poly(dimethylsiloxane)s (PDMSs) with various graft architectures that are controlled by the placement of hydridosilane functionality at one end, both ends, or along the chain of PDMS samples of controlled molecular weight. We also report studies of model methylsiloxane monolayers prepared from pentamethyldisiloxane, heptamethyltrisiloxane (two isomers), heptamethylcyclotetrasiloxane, and tris(trimethylsiloxy)silane. These modified silica surfaces with structurally defined methylsiloxane groups are not accessible by conventional silane surface chemistry and proved to be useful in exploring the steric limitations of the reaction. Linear monohydride- and dihydride-terminated PDMS-grafted surfaces exhibit increasing thickness and decreasing contact angle hysteresis with increasing molecular weight up to a particular molecular weight value. Above this value, the hysteresis increases with increasing molecular weight of end-grafted polymers. Poly(hydridomethyl-co-dimethylsiloxane)s with varied hydride content (3-100 mol %) exhibit decreasing thickness, decreasing contact angle, and increasing contact angle hysteresis with increasing hydride content. These observations illustrate the importance of molecular mobility in three-phase contact line dynamics on low-hysteresis surfaces. To calibrate our preparative procedure against both monolayers prepared by conventional approaches as well as the recent reports, a series of trialkylsilane (mostly, n-alkyldimethylsilane) monolayers was prepared to determine the reaction time required to achieve the maximum bonding density using dynamic contact angle analysis. Monolayers prepared from hydridosilanes with BCF catalysis have lower bonding densities than those derived from chlorosilanes, and the reactions are more sensitive to alkyl group sterics. This lower bonding density renders greater flexibility to the n-alkyl groups in monolayers and can decrease the contact angle hysteresis.

Contamination and Surface Preparation Effects on Composite Bonding

NASA Technical Reports Server (NTRS)

Kutscha, Eileen O.; Vahey, Paul G.; Belcher, Marcus A.; VanVoast, Peter J.; Grace, William B.; Blohowiak, Kay Y.; Palmieri, Frank L.; Connell, John W.

2017-01-01

Results presented here demonstrate the effect of several prebond surface contaminants (hydrocarbon, machining fluid, latex, silicone, peel ply residue, release film) on bond quality, as measured by fracture toughness and failure modes of carbon fiber reinforced epoxy substrates bonded in secondary and co-bond configurations with paste and film adhesives. Additionally, the capability of various prebond surface property measurement tools to detect contaminants and potentially predict subsequent bond performance of three different adhesives is also shown. Surface measurement methods included water contact angle, Dyne solution wettability, optically stimulated electron emission spectroscopy, surface free energy, inverse gas chromatography, and Fourier transform infrared spectroscopy with chemometrics analysis. Information will also be provided on the effectiveness of mechanical and energetic surface treatments to recover a bondable surface after contamination. The benefits and drawbacks of the various surface analysis tools to detect contaminants and evaluate prebond surfaces after surface treatment were assessed as well as their ability to correlate to bond performance. Surface analysis tools were also evaluated for their potential use as in-line quality control of adhesive bonding parameters in the manufacturing environment.

Chemical intuition for high thermoelectric performance in monolayer black phosphorus, α-arsenene and aW-antimonene

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

Peng, Bo; Zhang, Hao; Shao, Hezhu

Identifying materials with intrinsically high thermoelectric performance remains a challenge even with the aid of a high-throughput search. Here, using a chemically intuitive approach based on the bond-orbital theory, three anisotropic 2D group-V materials (monolayer black phosphorus, α-arsenene, and aW-antimonene) are identified as candidates for high thermoelectric energy conversion efficiency. Concepts, such as bond length, bond angle, and bond strength, are used to explain the trends in their electronic properties, such as the band gap and the effective mass. Our first principles calculations confirm that high carrier mobilities and large Seebeck coefficients can be obtained at the same time inmore » these materials, due to complex Fermi surfaces originating from the anisotropic structures. An intuitive understanding of how the bonding character affects phonon transport is also provided with emphasis on the importance of bonding strength and bond anharmonicity. High thermoelectric performance is observed in these materials. In conclusion, our approach provides a powerful tool to identify new thermoelectric materials and evaluate their transport properties.« less

Chemical intuition for high thermoelectric performance in monolayer black phosphorus, α-arsenene and aW-antimonene

DOE PAGES

Peng, Bo; Zhang, Hao; Shao, Hezhu; ...

2017-11-21

Identifying materials with intrinsically high thermoelectric performance remains a challenge even with the aid of a high-throughput search. Here, using a chemically intuitive approach based on the bond-orbital theory, three anisotropic 2D group-V materials (monolayer black phosphorus, α-arsenene, and aW-antimonene) are identified as candidates for high thermoelectric energy conversion efficiency. Concepts, such as bond length, bond angle, and bond strength, are used to explain the trends in their electronic properties, such as the band gap and the effective mass. Our first principles calculations confirm that high carrier mobilities and large Seebeck coefficients can be obtained at the same time inmore » these materials, due to complex Fermi surfaces originating from the anisotropic structures. An intuitive understanding of how the bonding character affects phonon transport is also provided with emphasis on the importance of bonding strength and bond anharmonicity. High thermoelectric performance is observed in these materials. In conclusion, our approach provides a powerful tool to identify new thermoelectric materials and evaluate their transport properties.« less

Hyperspectral Analysis for Standoff Detection of Dimethyl ...

EPA Pesticide Factsheets

Journal Article Detecting organophosphates in indoor settings requires more efficient and faster methods of surveying large surface areas than conventional approaches, which sample small surface areas followed by extraction and analysis. This study examined a standoff detection technique utilizing hyperspectral imaging for analysis of building materials in near-real time. In this proof-of-concept study, dimethyl methylphosphonate (DMMP) was applied to stainless steel and laminate coupons and spectra were collected during active illumination. Absorbance bands at approximately 1275 cm-1 and 1050 cm-1 were associated with phosphorus-oxygen double bond (P=O) and phosphorus-oxygen-carbon (P-O-C) bond stretches of DMMP, respectively. The magnitude of these bands increased linearly (r2 = 0.93) with DMMP across the full absorbance spectrum, between ν1 = 877 cm-1 to ν2 = 1262 cm-1. Comparisons between bare and contaminated surfaces on stainless steel using the spectral contrast angle technique indicated that the bare samples showed no sign of contamination, with large uniformly distributed contrast angles of 45˚-55˚, while the contaminated samples had smaller spectral contact angles of 40° in the uncontaminated region. The laminate contaminated region exhibited contact angles of < 25°. To the best of our knowledge, this is the first report to demonstrate that hyperspectral imaging can be used to detect DMMP on building materials, with detection levels similar to c

Magnetic and magnetocaloric properties of Ba and Ti co-doped SrRuO{sub 3}

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

Sarkar, Babusona; Dalal, Biswajit; Dev Ashok, Vishal

2014-12-28

Temperature evolution of magnetic properties in Ba and Ti doped SrRuO{sub 3} has been investigated to observe the effects of larger ionic radius Ba at Sr site and isovalent nonmagnetic impurity Ti at Ru site. Ionic radius mismatch and different electronic configuration in comparison with Ru modify Sr(Ba)-O and Ru(Ti)-O bond lengths and Ru-O-Ru bond angle. The apical and basal Ru-O-Ru bond angles vary significantly with Ti doping. Ferromagnetic Curie temperature decreases from 161 K to 149 K monotonically with Ba (10%) and Ti (10%) substitutions at Sr and Ru sites. The zero field cooled (ZFC) magnetization reveals a prominent peak whichmore » shifts towards lower temperature with application of magnetic field. The substitution of tetravalent Ti with localized 3d{sup 0} orbitals for Ru with more delocalized 4d{sup 4} orbitals leads to a broad peak in ZFC magnetization. A spontaneous ZFC magnetization becomes negative below 160 K for all the compositions. The occurrence of both normal and inverse magnetocaloric effects in Ba and Ti co-doped SrRuO{sub 3} makes the system more interesting.« less

Structural modeling of djenkolic acid with sulfur replaced by selenium and tellurium.

PubMed

Melnikov, Petr; Nascimento, Valter A; Silva, Anderson F; Consolo, Lourdes Z Z

2014-04-17

The comparative structural modeling of djenkolic acid and its derivatives containing selenium and tellurium in chalcogen sites (Ch=Se, Te) has provided detailed information about the bond lengths and bond angles, filling the gap in what we know about the structural characteristics of these aminoacids. The investigation using the molecular mechanics technique with good approximation confirmed the available information on X-ray refinements for the related compounds methionine and selenomethionine, as well as for an estimate made earlier for telluromethionine. It was shown that the Ch-C(3) and Ch-C(4) bond lengths grow in parallel with the increasing anionic radii. Although the distances C-C, C-O, and C-N are very similar, the geometry of conformers is quite different owing to the possibility of rotation about four carbon atoms, hence the remarkable variability observed in dihedral angles. It was shown that the compounds contain a rigid block with two Ch atoms connected through a methylene group. The standard program Gaussian 03 with graphical interface Gaussview 4.1.2 has proved to be satisfactory tool for the structural description of less-common bioactive compositions when direct X-ray results are absent.

Structural confirmation and spectroscopic study of a biomolecule: Norepinephrine.

PubMed

Yadav, T; Mukherjee, V

2018-05-21

The present work deals with the conformational and vibrational spectroscopic study of an important bio-molecule named norepinephrine in gas phase. The FTIR and FTRaman spectrum of norepinephrine in amorphous form were recorded in wavenumber range 4000-400 cm -1 and 4000-50 cm -1 respectively. We have investigated twenty-seven stable conformational structures of norepinephrine molecule. All the calculations have been done using Density Functional Theory with exchange functional B3LYP incorporated with the 6-31++G(d, p) basis set. The effect of hydrochloride on different bond lengths, bond angles and dihedral angles in the most stable conformer has also been studied. The total potential energy distribution for both the most stable conformer and the most stable conformer in hydrochloride was performed with the help Normal coordinate analysis method. Most of the calculated vibrational frequencies are in good agreement with the experimental frequencies. The natural bond orbital analysis was also performed to ensure the stability of electronic structures of norepinephrine. To know chemical reactivity of norepinephrine molecule we have calculated the energy gap between HOMO and LUMO orbitals and it has found above 5 eV in all the conformers. Copyright © 2018 Elsevier B.V. All rights reserved.

3-[4-Bromo-α( R*)-methoxybenzyl]-6-chloro-3( S*),4( S*)-dihydroxychroman: X-ray and DFT Studies

NASA Astrophysics Data System (ADS)

Sepay, Nayim; Mondal, Rina; Guha, Chayan; Mallik, Asok K.

2018-05-01

Sodium borohydride reduction of E-3-benzylidenechromanone epoxides in dry methanol has afforded 3( S*), 4( S*)-dihydroxy-3-[α( R*)-methoxybenzyl]chromans as an interesting class of products, the structures of which have been assigned mainly from spectral data and consideration of the mechanistic aspects. X-ray diffraction study of one of them, 3-[4-bromo-α( R*)-methoxybenzyl]-6-chloro-3( S*),4( S*)- dihydroxychroman, is performed. The title compound crystallizes in the monoclinic sp. gr. P21/ n, with a = 13.336(6) Å, b = 10.866(5) Å, c = 27.166(11) Å, β = 95.193(6)°, V = 3920(3) Å3, and Z = 8. Supramolecular construction of the compound involves O-H···O intermolecular hydrogen bonds as well as three other types of non-covalent interactions which are responsible for crystal packing. Density functional theory was applied for geometry optimization, molecular orbital calculations, and prediction of UV spectral features. The geometric parameters (bond lengths, bond angles, and dihedral angles) for the representative compound obtained from density functional theory with B3LY6-31G basis set were in good agreement with experimental values.

Conformation-dependent restraints for polynucleotides: I. Clustering of the geometry of the phosphodiester group

PubMed Central

Kowiel, Marcin; Brzezinski, Dariusz; Jaskolski, Mariusz

2016-01-01

The refinement of macromolecular structures is usually aided by prior stereochemical knowledge in the form of geometrical restraints. Such restraints are also used for the flexible sugar-phosphate backbones of nucleic acids. However, recent highly accurate structural studies of DNA suggest that the phosphate bond angles may have inadequate description in the existing stereochemical dictionaries. In this paper, we analyze the bonding deformations of the phosphodiester groups in the Cambridge Structural Database, cluster the studied fragments into six conformation-related categories and propose a revised set of restraints for the O-P-O bond angles and distances. The proposed restraints have been positively validated against data from the Nucleic Acid Database and an ultrahigh-resolution Z-DNA structure in the Protein Data Bank. Additionally, the manual classification of PO4 geometry is compared with geometrical clusters automatically discovered by machine learning methods. The machine learning cluster analysis provides useful insights and a practical example for general applications of clustering algorithms for automatic discovery of hidden patterns of molecular geometry. Finally, we describe the implementation and application of a public-domain web server for automatic generation of the proposed restraints. PMID:27521371

(E)-N′-(4-Meth­oxy­benzyl­idene)pyridine-3-carbohydrazide dihydrate

PubMed Central

Novina, J. Josephine; Vasuki, G.; Suresh, M.; Padusha, M. Syed Ali

2013-01-01

In the title compound, C14H13N3O2·2H2O, the hydrazone mol­ecule adopts an E conformation with respect to the C=N bond. The dihedral angle between the benzene and pyridine rings is 8.55 (10)°. The methyl­idene–hydrazide [–C(=O)–N–N=C–] fragment is essentially planar, with a maximum deviation of 0.0375 (13) Å. The mean planes of the benzene and pyridine rings make dihedral angles of 2.71 (14) and 11.25 (13)°, respectively, with mean plane of the methyl­idene-hydrazide fragment. In the crystal, the benzohydrazide and water mol­ecules are linked by N—H⋯O, O—H⋯O and O—H⋯N hydrogen bonds into a three-dimensional network. PMID:24046719

Crystal structure of (E)-N′-{[(1R,3R)-3-isopropyl-1-methyl-2-oxo­cyclo­pent­yl]methyl­idene}-4-methyl­benzene­sulfono­hydrazide

PubMed Central

Tymann, David; Dragon, Dina Christina; Golz, Christopher; Preut, Hans; Strohmann, Carsten; Hiersemann, Martin

2015-01-01

The title compound, C17H24N2O3S, was synthesized in order to determine the relative configuration of the corresponding β-keto aldehyde. In the U-shaped mol­ecule, the five-membered ring approximates an envelope with the methyl­ene atom adjacent to the quaternary C atom being the flap. The dihedral angles between the four nearly coplanar atoms of the five-membered ring and the flap and the aromatic ring are 38.8 (4) and 22.9 (2)°, respectively. The bond angles around the S atom are in the range 104.11 (16)–119.95 (16)°. In the crystal, mol­ecules are linked via N—H⋯O by hydrogen bonds, forming a chain along the a-axis direction. PMID:25878892

Synthesis, spectroscopic investigation and computational study of 3-(1-(((methoxycarbonyl)oxy)imino)ethyl)-2H-chromen-2-one

NASA Astrophysics Data System (ADS)

Gokula Krishnan, K.; Sivakumar, R.; Thanikachalam, V.; Saleem, H.; Arockia doss, M.

2015-06-01

The molecular structure and vibrational modes of 3-acetylcoumarin oxime carbonate (abbreviated as 3-ACOC) have been investigated by FT-IR, FT-Raman, NMR spectra and also by computational methods using HF and B3LYP with 6-311++G(d,p) basis set. The optimized geometric parameters (bond lengths, bond angles and dihedral angles) were in good agreement with the corresponding experimental values of 3-ACOC. The calculated vibrational frequencies of normal modes from DFT method matched well with the experimental values. The complete assignments were made on the basis of the total energy distribution (TED) of the vibrational modes. NMR (1H and 13C) chemical shifts were calculated by GIAO method and the results were compared with the experimental values. The other parameters like dipole moment, polarizability, first order hyperpolarizability, zero-point vibrational energy, EHOMO, ELUMO, heat capacity and entropy have also been computed.

Porus electrode comprising a bonded stack of pieces of corrugated metal foil

NASA Technical Reports Server (NTRS)

Mccallum, J. (Inventor)

1973-01-01

An electrode suitable for use in an electrochemical cell is described. The electrode is composed of a porous conductive support with a bonded stack of pieces of thin corrugated nickel foil where the corrugations are oriented approximately perpendicular to the sides of the electrode and form an array of passages through the electrode. Active material such as cadmium hydroxide or nickel hydroxide is uniformly distributed within the passages. The support may comprise also a piece of thin flat nickel foil between adjacent pieces of the corrugated foil, forming a barrier between the passages formed on each side of it. Typically the corrugations in the odd corrugated layers are oriented at a small angle from the perpendicular in one direction and the corrugations in the even corrugated layers are oriented at a small angle from the perpendicular in the opposite direction.

3β,5α,6β-Trihy­droxy­androstan-17-one

PubMed Central

Andrade, L.C.R.; de Almeida, M.J.B.M.; Paixão, J.A.; Carvalho, J.F.S.; Sá e Melo, M.L.

2011-01-01

The title compound, C19H30O4, is an androstan-17-one derivative synthesized from the dehydro­epiandrosterone through a sequential addition of an oxidant, followed by a trans-diaxial opening of the epoxide generated, with Bi(OTf)3 (OTf is trifluoro­methane­sulfonate). The six-membered rings have a slightly flattened chair conformation, while the five-membered ring adopts a 14-α envelope conformation. All rings are trans fused. In the crystal, the mol­ecules are connected by O—H⋯O hydrogen bonds involving the hydroxyl and carbonyl groups, forming a three-dimensional network. A quantum mechanical ab initio Roothan Hartree–Fock calculation of the free mol­ecule gives bond lengths, valency angles and ring torsion angles of the free molecule at equilibrium geometry (energy minimum) close to the experimental values. PMID:21754383

N-(2-Allyl-4-chloro-2H-indazol-5-yl)-4-meth­oxy­benzene­sulfonamide hemi­hydrate

PubMed Central

Chicha, Hakima; Kouakou, Assoman; Rakib, El Mostapha; Saadi, Mohamed; El Ammari, Lahcen

2013-01-01

The fused five- and six-membered rings in the title compound, C17H16ClN3O3S·0.5H2O, are practically coplanar, with the maximum deviation from the mean plane being 0.057 (3) Å for the C atom bound to the exocyclic N atom. The indazole system makes a dihedral angle of 66.18 (12)° with the plane through the benzene ring, and it is nearly perpendicular to the allyl group, as indicated by the N—N—C—C torsion angle of 79.2 (3)°. In the crystal, the water mol­ecule, lying on a twofold axis, forms O—H⋯N and accepts N—H⋯O hydrogen bonds. Additional C—H⋯O hydrogen bonds contribute to the formation of a chain along the b-axis direction. PMID:24109418

N-(2-Allyl-4-chloro-2H-indazol-5-yl)-4-meth-oxy-benzene-sulfonamide hemi-hydrate.

PubMed

Chicha, Hakima; Kouakou, Assoman; Rakib, El Mostapha; Saadi, Mohamed; El Ammari, Lahcen

2013-01-01

The fused five- and six-membered rings in the title compound, C17H16ClN3O3S·0.5H2O, are practically coplanar, with the maximum deviation from the mean plane being 0.057 (3) Å for the C atom bound to the exocyclic N atom. The indazole system makes a dihedral angle of 66.18 (12)° with the plane through the benzene ring, and it is nearly perpendicular to the allyl group, as indicated by the N-N-C-C torsion angle of 79.2 (3)°. In the crystal, the water mol-ecule, lying on a twofold axis, forms O-H⋯N and accepts N-H⋯O hydrogen bonds. Additional C-H⋯O hydrogen bonds contribute to the formation of a chain along the b-axis direction.

The notion of a plastic material spin in atomistic simulations

NASA Astrophysics Data System (ADS)

Dickel, D.; Tenev, T. G.; Gullett, P.; Horstemeyer, M. F.

2016-12-01

A kinematic algorithm is proposed to extend existing constructions of strain tensors from atomistic data to decouple elastic and plastic contributions to the strain. Elastic and plastic deformation and ultimately the plastic spin, useful quantities in continuum mechanics and finite element simulations, are computed from the full, discrete deformation gradient and an algorithm for the local elastic deformation gradient. This elastic deformation gradient algorithm identifies a crystal type using bond angle analysis (Ackland and Jones 2006 Phys. Rev. B 73 054104) and further exploits the relationship between bond angles to determine the local deformation from an ideal crystal lattice. Full definitions of plastic deformation follow directly using a multiplicative decomposition of the deformation gradient. The results of molecular dynamics simulations of copper in simple shear and torsion are presented to demonstrate the ability of these new discrete measures to describe plastic material spin in atomistic simulation and to compare them with continuum theory.

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

Identification of non-classical C-H···M interactions in early and late transition metal complexes containing the CH(ArO)3 ligand.

PubMed

Lein, Matthias; Harrison, John A; Nielson, Alastair J

2013-08-14

The fully optimised DFT structure of the d(0) complex [{CH(ArO)3}Ti(NEt2)] (2) at the B3LYP level compares well with the distorted tetrahedral geometry shown by the X-ray crystal structure. QTAIM analysis of the electron density associated with the C-H···Ti interaction shows a well defined bond critical point, a bond path between the hydrogen and titanium centres and a negative value for the energy density indicative of covalency. A natural bond orbital (NBO) picture of the interaction shows that the C-H σ bond electron density donates to a d hybrid orbital on the metal in a linear fashion. Calculated IR and NMR data for the components of the interaction are consistent with experiment. The computed structures for [{CH(ArO)3}Ti(OPh)] (3), [{CH(ArO)3}Zr(NEt2)] (4), [{CH(ArO)3}Hf(NEt2)] (5), show tetrahedral geometries and QTAIM and NBO properties similar to (2). [{CH(ArO)3}Mo(NEt2)] (6) shows distortion of the tripodal ligand and a reduced C-H···M bond angle with properties more consistent with a C-H···M side-on donor interaction. In [{CH(ArO)3}Fe(NEt2)] (7) the C-H···M bond angle is linear and involves a donor interaction. An energy minimised structure maintaining the three fold coordination to the tripodal ligand was not obtained for [{CH(ArO)3}Ni(NEt2)](2-) but changing from a diethyl amide ligand to phenolato gave energy minimised [{CH(ArO)3}Ni(OPh)](2-) (8). This structure shows a distorted square planar geometry with a substantially bent phenoxo ligand and a near linear C-H···M covalent interaction with donor and back bonding properties. The work shows that linear C-H···M interactions can have both agostic and weak hydrogen bond-like covalency.

Systematic oxidation of polystyrene by ultraviolet-ozone, characterized by near-edge X-ray absorption fine structure and contact angle.

PubMed

Klein, Robert J; Fischer, Daniel A; Lenhart, Joseph L

2008-08-05

The process of implanting oxygen in polystyrene (PS) via exposure to ultraviolet-ozone (UV-O) was systematically investigated using the characterization technique of near-edge X-ray absorption fine structure (NEXAFS). Samples of PS exposed to UV-O for 10-300 s and washed with isopropanol were analyzed using the carbon and oxygen K-edge NEXAFS partial electron yields, using various retarding bias voltages to depth-profile the oxygen penetration into the surface. Evaluation of reference polymers provided a scale to quantify the oxygen concentration implanted by UV-O treatment. We find that ozone initially reacts with the double bonds on the phenyl rings, forming carbonyl groups, but within 1 min of exposure, the ratio of double to single oxygen bonds stabilizes at a lower value. Oxygen penetrates the film with relative ease, creating a fairly uniform distribution of oxygen within at least the first 4 nm (the effective depth probed by NEXAFS here). Before oxygen accumulates in large concentrations, however, it preferentially degrades the uppermost layer of the film by removing oxygenated low-molecular-weight oligomers. The failure to accumulate high concentrations of oxygen is seen in the nearly constant carbon edge jump, the low concentration of oxygen even at 5 min exposure (58% of that in poly(4-acetoxystyrene), the polymer with the most similarities to UV-O-treated PS), and the relatively high contact angles. At 5 min exposure the oxygen concentration contains ca. 7 atomic % oxygen. The oxygen species that are implanted consist predominantly of single O-C bonds and double O=C bonds but also include a small fraction of O-H. UV-O treatment leads a plateau after 2 min exposure in the water contact angle hysteresis, at a value of 67 +/- 2 degrees , due primarily to chemical heterogeneity. Annealing above T(g) allows oxygenated species to move short distances away from the surface but not diffuse further than 1-2 nm.

2-[(2-Hy­droxy-4-meth­oxy­benzyl­idene)aza­nium­yl]benzoate monohydrate

PubMed Central

Hang, Zhi-Xi; Dong, Bo; Wang, Xing-Wen

2010-01-01

In the title compound, C15H13NO4·H2O, the Schiff base exists in a zwitterionic form and a bifurcated intra­molecular N—H⋯(O,O) hydrogen bond generates two S(6) rings. The dihedral angle between the two benzene rings is 25.8 (2)°. The crystal structure is stabilized by inter­molecular O—H⋯O hydrogen bonds. PMID:21587989

N′-[(E)-4-Hydr­oxy-3-methoxy­benzyl­idene]pyridine-4-carbohydrazide

PubMed Central

Shafiq, Zahid; Yaqub, Muhammad; Tahir, M. Nawaz; Hussain, Abid; Iqbal, M. Saeed

2009-01-01

In the title compound, C14H13N3O3, the two six-membered rings are oriented at a dihedral angle of 15.17 (11)° and an intra­molecular O—H⋯O hydrogen bond occurs. In the crystal, mol­ecules inter­act by way of N—H⋯O, O—H⋯N and C—H⋯O hydrogen bonds, thereby generating S(5) chain and R 2 1(7) ring motifs. PMID:21578481

(Z)-5-(4-Fluoro­benzyl­idene)-1,3-thia­zolidine-2,4-dione

PubMed Central

Sun, Hong-Shun; Xu, Ye-Ming; He, Wei; Tang, Shi-Gui; Guo, Cheng

2008-01-01

In the title compound, C10H6FNO2S, the benzene and thia­zolidine rings make a dihedral angle of 7.52 (3)°. Intra­molecular C—H⋯O and C—H⋯S hydrogen bonds result in the formation of nearly planar five- and six-membered rings; the adjacent rings are nearly coplanar. In the crystal structure, inter­molecular N—H⋯O hydrogen bonds link the mol­ecules. PMID:21201543

Quantum mechanics models of the methanol dimer: OH⋯O hydrogen bonds of β-d-glucose moieties from crystallographic data.

PubMed

Cintrón, Michael Santiago; Johnson, Glenn P; French, Alfred D

2017-04-18

The interaction of two methanol molecules, simplified models of carbohydrates and cellulose, was examined using a variety of quantum mechanics (QM) levels of theory. Energy plots for hydrogen bonding distance (H⋯O) and angle (OH⋯O) were constructed. All but two experimental structures were located in stabilized areas on the vacuum phase energy plots. Each of the 399 models was analyzed with Bader's atoms-in-molecules (AIM) theory, which showed a widespread ability by the dimer models to form OH⋯O hydrogen bonds that have bond paths and Bond Critical Points. Continuum solvation calculations suggest that a portion of the energy-stabilized structures could occur in the presence of water. A survey of the Cambridge Structural Database (CSD) for all donor-acceptor interactions in β-D-glucose moieties examined the similarities and differences among the hydroxyl groups and acetal oxygen atoms that participate in hydrogen bonds. Comparable behavior was observed for the O2H, O3H, O4H, and O6H hydroxyls, acting either as acceptors or donors. Ring O atoms showed distinct hydrogen bonding behavior that favored mid-length hydrogen bonds. Published by Elsevier Ltd.

Water: two liquids divided by a common hydrogen bond.

PubMed

Soper, Alan K

2011-12-08

The structure of water is the subject of a long and ongoing controversy. Unlike simpler liquids, where atomic interactions are dominated by strong repulsive forces at short distances and weaker attractive (van der Waals) forces at longer distances, giving rise to local atomic coordination numbers of order 12, water has pronounced and directional hydrogen bonds which cause the dense liquid close-packed structure to open out into a disordered and dynamic network, with coordination number 4-5. Here I show that water structure can be accurately represented as a mixture of two identical, interpenetrating, molecular species separated by common hydrogen bonds. Molecules of one type can form hydrogen bonds with molecules of the other type but cannot form hydrogen bonds with molecules of the same type. These hydrogen bonds are strong along the bond but weak with respect to changes in the angle between neighboring bonds. The observed pressure and temperature dependence of water structure and thermodynamic properties follow naturally from this choice of water model, and it also gives a simple explanation of the enduring claims based on spectroscopic evidence that water is a mixture of two components. © 2011 American Chemical Society

Crystal and mol-ecular structure of (2Z,5Z)-3-(2-meth-oxy-phen-yl)-2-[(2-meth-oxy-phen-yl)imino]-5-(4-nitro-benzyl-idene)thia-zolidin-4-one.

PubMed

Djafri, Ahmed; Chouaih, Abdelkader; Daran, Jean-Claude; Djafri, Ayada; Hamzaoui, Fodil

2017-04-01

In the title compound, C 24 H 19 N 3 O 5 S, the thia-zole ring (r.m.s. deviation = 0.012 Å) displays a planar geometry and is surrounded by three fragments, two meth-oxy-phenyl and one nitro-phenyl. The thia-zole ring is almost in the same plane as the nitro-phenyl ring, making a dihedral angle of 20.92 (6)°. The two meth-oxy-phenyl groups are perpendicular to the thia-zole ring [dihedral angles of 79.29 (6) and 71.31 (7)° and make a dihedral angle of 68.59 (7)°. The mol-ecule exists in an Z , Z conformation with respect to the C=N imine bond. In the crystal, a series of C-H⋯N, C-H⋯O and C-H⋯S hydrogen bonds, augmented by several π-π(ring) inter-actions, produce a three-dimensional architecture of mol-ecules stacked along the b -axis direction. The experimentally derived structure is compered with that calculated theoretically using DFT(B3YLP) methods.

Nanoscopic analysis of oxygen segregation at tilt boundaries in silicon ingots using atom probe tomography combined with TEM and ab initio calculations.

PubMed

Ohno, Y; Inoue, K; Fujiwara, K; Kutsukake, K; Deura, M; Yonenaga, I; Ebisawa, N; Shimizu, Y; Inoue, K; Nagai, Y; Yoshida, H; Takeda, S; Tanaka, S; Kohyama, M

2017-12-01

We have developed an analytical method to determine the segregation levels on the same tilt boundaries (TBs) at the same nanoscopic location by a joint use of atom probe tomography and scanning transmission electron microscopy, and discussed the mechanism of oxygen segregation at TBs in silicon ingots in terms of bond distortions around the TBs. The three-dimensional distribution of oxygen atoms was determined at the typical small- and large-angle TBs by atom probe tomography with a low impurity detection limit (0.01 at.% on a TB plane) simultaneously with high spatial resolution (about 0.4 nm). The three-dimensional distribution was correlated with the atomic stress around the TBs; the stress at large-angle TBs was estimated by ab initio calculations based on atomic resolution scanning transmission electron microscopy data and that at small-angle TBs were calculated with the elastic theory based on dark-field transmission electron microscopy data. Oxygen atoms would segregate at bond-centred sites under tensile stress above about 2 GPa, so as to attain a more stable bonding network by reducing the local stress. The number of oxygen atoms segregating in a unit TB area N GB (in atoms nm -2 ) was determined to be proportional to both the number of the atomic sites under tensile stress in a unit TB area n bc and the average concentration of oxygen atoms around the TB [O i ] (in at.%) with N GB ∼ 50 n bc [O i ]. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

Piperidine-1-carboximidamide

PubMed Central

Tiritiris, Ioannis

2012-01-01

In the title compound, C6H13N3, the C=N and C—N bond lengths in the CN3 unit are 1.3090 (17), and 1.3640 (17) (C–NH2) and 1.3773 (16) Å, indicating double- and single-bond character, respectively. The N—C—N angles are 116.82 (12), 119.08 (11) and 124.09 (11)°, showing a deviation of the CN3 plane from an ideal trigonal–planar geometry. The piperidine ring is in a chair conformation. In the crystal, mol­ecules are linked by N—H⋯N hydrogen bonds, forming a two-dimensional network along the ac plane. PMID:23284550

Correlated oxygen displacements and phonon mode changes in LaCoO3 single crystal

NASA Astrophysics Data System (ADS)

Sikolenko, V. V.; Molodtsov, S. L.; Izquierdo, M.; Troyanchuk, I. O.; Karpinsky, D.; Tiutiunnikov, S. I.; Efimova, E.; Prabhakaran, D.; Novoselov, D.; Efimov, V.

2018-05-01

X-ray diffraction and inelastic X-ray scattering studies have been performed across the spin ( 100 K) and semiconductor-metal ( 500 K) transitions in LaCoO3 single crystals. The quadratic increase with temperature of the oxygen displacement parameters parallel and perpendicular to the Co-O bond has been correlated with softening of the TO2 and hardening of the TO1 phonon branches along the [0 ξ ξ] high symmetry direction. The latter effect can be associated with the weakening of the Co-O bond strength derived from the increase of Co-O bond length and angle as expected upon increasing the high spin state population of the system with temperature.

Laser Surface Preparation for Adhesive Bonding of Ti-6Al-4V

NASA Technical Reports Server (NTRS)

Belcher, Marcus A.; List, Martina S.; Wohl, Christopher J.; Ghose, Sayata; Watson, Kent A.; Hopkins, John W.; Connell, John W.

2010-01-01

Adhesively bonded structures are potentially lighter in weight than mechanically fastened ones, but existing surface treatments are often considered unreliable. Two main problems in achieving reproducible and durable adhesive bonds are surface contamination and variability in standard surface preparation techniques. In this work three surface pretreatments were compared: laser etching with and without grit blasting and conventional Pasa-Jell treatment. Ti-6Al-4V surfaces were characterized by contact angle goniometry, optical microscopy, and X-ray photoelectron spectroscopy (XPS). Laser -etching was found to produce clean surfaces with precisely controlled surface topographies and PETI-5 lap shear strengths and durabilities were equivalent to those produced with Pasa-Jell.

Structural elucidation of antihemorrhage drug molecule Diethylammonium 2,5-dihydroxybenzene sulfonate - an insilico approach

NASA Astrophysics Data System (ADS)

Kumar, S. Anil; Bhaskar, BL

2018-02-01

Ab-initio computational study of antihemorrhage drug molecule diethylammonium 2,5-dihydroxybenzene sulfonate, popularly known as ethamsylate, has been attempted using Gaussian 09. The optimized molecular geometry has been envisaged using density functional theory method at B3LYP/6-311 basis set. Different geometrical parameters like bond lengths and bond angles were computed and compared against the experimental results available in literature. Fourier transform infrared scanning of the title molecule was performed and vibrational frequencies were also computed using Gaussian software. The presence of O-H---O hydrogen bonds between C6H5O5S- anions and N-H---O hydrogen bonds between anion and cation is evident in the computational studies also. In general, satisfactory agreement of concordance has been observed between computational and experimental results.

Constructing Cross-Linked Polymer Networks Using Monte Carlo Simulated Annealing Technique for Atomistic Molecular Simulations

DTIC Science & Technology

2014-10-01

the angles and dihedrals that are truly unique will be indicated by the user by editing NewAngleTypesDump and NewDihedralTypesDump. The program ...Atomistic Molecular Simulations 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Robert M Elder, Timothy W Sirk, and...Antechamber program in Assisted Model Building with Energy Refinement (AMBER) Tools to assign partial charges (using the Austin Model 1 [AM1]-bond charge

N-(3-Chloro-1H-indazol-5-yl)-4-meth-oxy-benzene-sulfonamide.

PubMed

Chicha, Hakima; Rakib, El Mostapha; Bouissane, Latifa; Saadi, Mohamed; El Ammari, Lahcen

2013-10-12

In the title compound, C14H12ClN3O3S, the fused five- and six-membered rings are folded slightly along the common edge, forming a dihedral angle of 3.2 (1)°. The mean plane through the indazole system makes a dihedral angle of 30.75 (7)° with the distant benzene ring. In the crystal, N-H⋯O hydrogen bonds link the mol-ecules, forming a two-dimensional network parallel to (001).

1-Allyl-3-chloro-5-nitro-1H-indazole

PubMed Central

Chicha, Hakima; Rakib, El Mostapha; Spinelli, Domenico; Saadi, Mohamed; El Ammari, Lahcen

2013-01-01

In the title compound, C10H8ClN3O2, the indazole ring system makes a dihedral angle of 7.9 (3)° with the plane through the nitro group. The allyl group is rotated out of the plane of the indazole ring system [N—N—C—C torsion angle = 104.28 (19)°]. In the crystal, mol­ecules are linked by C—H⋯O hydrogen bonds, forming zigzag chains propagating along the b-axis direction. PMID:24427047

1-Allyl-3-chloro-5-nitro-1H-indazole.

PubMed

Chicha, Hakima; Rakib, El Mostapha; Spinelli, Domenico; Saadi, Mohamed; El Ammari, Lahcen

2013-01-01

In the title compound, C10H8ClN3O2, the indazole ring system makes a dihedral angle of 7.9 (3)° with the plane through the nitro group. The allyl group is rotated out of the plane of the indazole ring system [N-N-C-C torsion angle = 104.28 (19)°]. In the crystal, mol-ecules are linked by C-H⋯O hydrogen bonds, forming zigzag chains propagating along the b-axis direction.

Di-μ-acetato-bis­[(acetato-κ2 O,O′)bis­(iso­nicotinamide-κN)copper(II)

PubMed Central

Perec, Mireille; Baggio, Ricardo

2010-01-01

The title centrosymmetric bimetallic complex, [Cu2(C2H3O2)4(C6H6N2O)4], is composed of two copper(II) cations, four acetate anions and four isonicotinamide (INA) ligands. The asymmetric unit contains one copper cation to which two acetate units bind asymmetrically; one of the Cu—O distances is rather long [2.740 (2) Å], almost at the limit of coordination. These Cu—O bonds define an equatorial plane to which the Cu—N bonds to the INA ligands are almost perpendicular, the Cu—N vectors subtending angles of 2.4 (1) and 2.3 (1)° to the normal to the plane. The metal coordination geometry can be described as a slightly distorted trigonal bipyramid if the extremely weak Cu—O bond is disregarded, or as a highly distorted square bipyramid if it is not. The double acetate bridge between the copper ions is not coplanar with the CuO4 equatorial planes, the dihedral angle between the (O—C—O)2 and O—Cu—O groups being 34.3 (1)°, resulting in a sofa-like conformation for the 8-member bridging loop. In the crystal, N—H⋯O hydrogen bonds occur, some of which generate a head-to tail-linkage between INA units, giving raise to chains along [101]; the remaining ones make inter-chain contacts, defining a three-dimensional network. There are in addition a number of C—H⋯O bonds involving aromatic H atoms. Probably due to steric hindrance, the aromatic rings are not involved in significant π⋯π inter­actions. PMID:21580223

Crystal structures of 5-amino-N-phenyl-3H-1,2,4-di-thia-zol-3-iminium chloride and 5-amino-N-(4-chloro-phen-yl)-3H-1,2,4-di-thia-zol-3-iminium chloride monohydrate.

PubMed

Yeo, Chien Ing; Tan, Yee Seng; Tiekink, Edward R T

2015-10-01

The crystal and mol-ecular structures of the title salt, C8H8N3S2 (+)·Cl(-), (I), and salt hydrate, C8H7ClN3S2 (+)·Cl(-)·H2O, (II), are described. The heterocyclic ring in (I) is statistically planar and forms a dihedral angle of 9.05 (12)° with the pendant phenyl ring. The comparable angle in (II) is 15.60 (12)°, indicating a greater twist in this cation. An evaluation of the bond lengths in the H2N-C-N-C-N sequence of each cation indicates significant delocalization of π-electron density over these atoms. The common feature of the crystal packing in (I) and (II) is the formation of charge-assisted amino-N-H⋯Cl(-) hydrogen bonds, leading to helical chains in (I) and zigzag chains in (II). In (I), these are linked by chains mediated by charge-assisted iminium-N(+)-H⋯Cl(-) hydrogen bonds into a three-dimensional architecture. In (II), the chains are linked into a layer by charge-assisted water-O-H⋯Cl(-) and water-O-H⋯O(water) hydrogen bonds with charge-assisted iminium-N(+)-H⋯O(water) hydrogen bonds providing the connections between the layers to generate the three-dimensional packing. In (II), the chloride anion and water mol-ecules are resolved into two proximate sites with the major component being present with a site occupancy factor of 0.9327 (18).

Scalable bonding of nanofibrous polytetrafluoroethylene (PTFE) membranes on microstructures

NASA Astrophysics Data System (ADS)

Mortazavi, Mehdi; Fazeli, Abdolreza; Moghaddam, Saeed

2018-01-01

Expanded polytetrafluoroethylene (ePTFE) nanofibrous membranes exhibit high porosity (80%-90%), high gas permeability, chemical inertness, and superhydrophobicity, which makes them a suitable choice in many demanding fields including industrial filtration, medical implants, bio-/nano- sensors/actuators and microanalysis (i.e. lab-on-a-chip). However, one of the major challenges that inhibit implementation of such membranes is their inability to bond to other materials due to their intrinsic low surface energy and chemical inertness. Prior attempts to improve adhesion of ePTFE membranes to other surfaces involved surface chemical treatments which have not been successful due to degradation of the mechanical integrity and the breakthrough pressure of the membrane. Here, we report a simple and scalable method of bonding ePTFE membranes to different surfaces via the introduction of an intermediate adhesive layer. While a variety of adhesives can be used with this technique, the highest bonding performance is obtained for adhesives that have moderate contact angles with the substrate and low contact angles with the membrane. A thin layer of an adhesive can be uniformly applied onto micro-patterned substrates with feature sizes down to 5 µm using a roll-coating process. Membrane-based microchannel and micropillar devices with burst pressures of up to 200 kPa have been successfully fabricated and tested. A thin layer of the membrane remains attached to the substrate after debonding, suggesting that mechanical interlocking through nanofiber engagement is the main mechanism of adhesion.

Calculations of molecular multipole electric moments of a series of exo-insaturated four-membered heterocycles, Y = CCH2CH2X

NASA Astrophysics Data System (ADS)

Romero, Angel H.

2017-10-01

The influence of ring puckering angle on the multipole moments of sixteen four-membered heterocycles (1-16) was theoretically estimated using MP2 and different DFTs in combination with the 6-31+G(d,p) basis set. To obtain an accurate evaluation, CCSD/cc-pVDZ level and, the MP2 and PBE1PBE methods in combination with the aug-cc-pVDZ and aug-cc-pVTZ basis sets were performed on the planar geometries of 1-16. In general, the DFT and MP2 approaches provided an identical dependence of the electrical properties with the puckering angle for 1-16. Quantitatively, the quality of the level of theory and basis sets affects significant the predictions of the multipole moments, in particular for the heterocycles containing C=O and C=S bonds. Convergence basis sets within the MP2 and PBE1PBE approximations are reached in the dipole moment calculations when the aug-cc-pVTZ basis set is used, while the quadrupole and octupole moment computations require a larger basis set than aug-cc-pVTZ. On the other hand, the multipole moments showed a strong dependence with the molecular geometry and the nature of the carbon-heteroatom bonds. Specifically, the C-X bond determines the behavior of the μ(ϕ), θ(ϕ) and Ώ(ϕ) functions, while the C=Y bond plays an important role in the magnitude of the studied properties.

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.

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

Daily, Michael D.; Olsen, Brett N.; Schlesinger, Paul H.

In mammalian cells cholesterol is essential for membrane function, but in excess can be cytototoxic. The cellular response to acute cholesterol loading involves biophysical-based mechanisms that regulate cholesterol levels, through modulation of the “activity” or accessibility of cholesterol to extra-membrane acceptors. Experiments and united atom (UA) simulations show that at high concentrations of cholesterol, lipid bilayers thin significantly and cholesterol availability to external acceptors increases substantially. Such cholesterol activation is critical to its trafficking within cells. Here we aim to reduce the computational cost to enable simulation of large and complex systems involved in cholesterol regulation, such as those includingmore » oxysterols and cholesterol-sensing proteins. To accomplish this, we have modified the published MARTINI coarse-grained force field to improve its predictions of cholesterol-induced changes in both macroscopic and microscopic properties of membranes. Most notably, MARTINI fails to capture both the (macroscopic) area condensation and membrane thickening seen at less than 30% cholesterol and the thinning seen above 40% cholesterol. The thinning at high concentration is critical to cholesterol activation. Microscopic properties of interest include cholesterol-cholesterol radial distribution functions (RDFs), tilt angle, and accessible surface area. First, we develop an “angle-corrected” model wherein we modify the coarse-grained bond angle potentials based on atomistic simulations. This modification significantly improves prediction of macroscopic properties, most notably the thickening/thinning behavior, and also slightly improves microscopic property prediction relative to MARTINI. Second, we add to the angle correction a “volume correction” by also adjusting phospholipid bond lengths to achieve a more accurate volume per molecule. The angle + volume correction substantially further improves the quantitative agreement of the macroscopic properties (area per molecule and thickness) with united atom simulations. However, this improvement also reduces the accuracy of microscopic predictions like radial distribution functions and cholesterol tilt below that of either MARTINI or the angle-corrected model. Thus, while both of our forcefield corrections improve MARTINI, the combined angle and volume correction should be used for problems involving sterol effects on the overall structure of the membrane, while our angle-corrected model should be used in cases where the properties of individual lipid and sterol models are critically important.« less

Surface properties and bond strength measurements of N-vinylcaprolactam (NVC)-containing glass-ionomer cements.

PubMed

Moshaverinia, Alireza; Chee, Winston W; Brantley, William A; Schricker, Scott R

2011-03-01

N-vinylcaprolactam (NVC)-containing glass ionomers are promising dental restorative materials with improved mechanical properties; however, little information is available on other physical characteristics of these types of modified glass ionomers, especially their surface properties. Understanding the surface characteristics and behavior of glass ionomers is important for understanding their clinical behavior and predictability as dental restorative materials. The purpose of this study was to investigate the effect of NVC-containing terpolymers on the surface properties and bond strength to dentin of GIC (glass-ionomer cement), and to evaluate the effect of NVC-containing terpolymer as a dentin conditioner. The terpolymer of acrylic acid (AA)-itaconic acid (IA)-N-vinylcaprolactam (NVC) with a molar ratio of 8:1:1 (AA:IA:NVC) was synthesized by free radical polymerization and characterized using nuclear magnetic resonance ((1)H-NMR) and Fourier transform infrared spectroscopy (FTIR). The synthesized terpolymer was used in glass-ionomer cement formulations (Fuji IX GP). Ten disc-shaped specimens (12 × 1 mm) were mixed and fabricated at room temperature. Surface properties (wettability) of modified cements were studied by contact angle measurements as a function of time. Work of adhesion values of different surfaces were also determined. The effect of NVC-modified polyacid on the bond strength of glass-ionomer cement to dentin was investigated. The mean data obtained from contact angle and bonding strength measurements were subjected to t test and 2-way ANOVA (α=.05). NVC-modified glass-ionomer cements showed significantly (P<.05) lower contact angles (46 degrees) and higher work of adhesion (W(A)=60.33 erg/cm(2)) in comparison to commercially available Fuji IX GP (57 degrees and W(A)=53.01 erg/cm(2)). The wettability of dentin surfaces conditioned with NVC-containing terpolymer was significantly higher (P<.05) (22 degrees, WA=73.77 erg/cm(2)) than dentin conditioned with GC dentin conditioner (29 degrees, W(A)=70.52 erg/cm(2)). The experimental cement also showed significantly higher values for shear bond strength to dentin (8.7 ±0.15 MPa after 1 month) when compared to the control group (8.4 ±0.13 MPa after 1 month). NVC-containing terpolymers may enhance the surface properties of GICs and increase their bond strength to the dentin. Furthermore, NVC-containing polyelectrolytes are better dentin conditioners than a commercially available dentin conditioner (GC dentin conditioner). Copyright © 2011 The Editorial Council of the Journal of Prosthetic Dentistry. Published by Mosby, Inc. All rights reserved.

Picosecond Pulsed Laser Ablation for the Surface Preparation of Epoxy Composites

NASA Technical Reports Server (NTRS)

Palmieri, Frank; Ledesma, Rodolfo; Fulton, Tayler; Arthur, Alexandria; Eldridge, Keishara; Thibeault, Sheila; Lin, Yi; Wohl, Chris; Connell, John

2017-01-01

As part of a technical challenge under the Advanced Composites Program, methods for improving pre-bond process control for aerospace composite surface treatments and inspections, in conjunction with Federal Aviation Administration guidelines, are under investigation. The overall goal is to demonstrate high fidelity, rapid and reproducible surface treatment and surface characterization methods to reduce uncertainty associated with the bonding process. The desired outcomes are reliable bonded airframe structure, and reduced timeline to certification. In this work, laser ablation was conducted using a q-switched Nd:YVO4 laser capable of nominal pulse durations of 8 picoseconds (ps). Aerospace structural carbon fiber reinforced composites with an epoxy resin matrix were laser treated, characterized, processed into bonded assemblies and mechanically tested. The characterization of ablated surfaces were conducted using scanning electron microscopy (SEM), water contact angle (WCA) goniometry, micro laser induced breakdown spectroscopy (uLIBS), and electron spin resonance (ESR). The bond performance was assessed using a double cantilever beam (DCB) test with an epoxy adhesive. The surface characteristics and bond performance obtained from picosecond ablated carbon fiber reinforced plastics (CFRPs) are presented herein.

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.

Identifying Floppy and Rigid Regions in Proteins

NASA Astrophysics Data System (ADS)

Jacobs, D. J.; Thorpe, M. F.; Kuhn, L. A.

1998-03-01

In proteins it is possible to separate hard covalent forces involving bond lengths and bond angles from other weak forces. We model the microstructure of the protein as a generic bar-joint truss framework, where the hard covalent forces and strong hydrogen bonds are regarded as rigid bar constraints. We study the mechanical stability of proteins using FIRST (Floppy Inclusions and Rigid Substructure Topography) based on a recently developed combinatorial constraint counting algorithm (the 3D Pebble Game), which is a generalization of the 2D pebble game (D. J. Jacobs and M. F. Thorpe, ``Generic Rigidity: The Pebble Game'', Phys. Rev. Lett.) 75, 4051-4054 (1995) for the special class of bond-bending networks (D. J. Jacobs, "Generic Rigidity in Three Dimensional Bond-bending Networks", Preprint Aug (1997)). This approach is useful in identifying rigid motifs and flexible linkages in proteins, and thereby determines the essential degrees of freedom. We will show some preliminary results from the FIRST analysis on the myohemerythrin and lyozyme proteins.

UV Resonance Raman Elucidation of the Terminal and Internal Peptide Bond Conformations of Crystalline and Solution Oligoglycines.

PubMed

Bykov, Sergei V; Asher, Sanford A

2010-11-30

Spectroscopic investigations of macromolecules generally attempt to interpret the measured spectra in terms of the summed contributions of the different molecular fragments. This is the basis of the local mode approximation in vibrational spectroscopy. In the case of resonance Raman spectroscopy independent contributions of molecular fragments require both a local mode-like behavior and the uncoupled electronic transitions. Here we show that the deep UV resonance Raman spectra of aqueous solution phase oligoglycines show independent peptide bond molecular fragment contributions indicating that peptide bonds electronic transitions and vibrational modes are uncoupled. We utilize this result to separately determine the conformational distributions of the internal and penultimate peptide bonds of oligoglycines. Our data indicate that in aqueous solution the oligoglycine terminal residues populate conformations similar to those found in crystals (3(1)-helices and β-strands), but with a broader distribution, while the internal peptide bond conformations are centered around the 3(1)-helix Ramachandran angles.

C sbnd H…F hydrogen bonds as the organising force in F-substituted α-phenyl cinnamic acid aggregates studied by the combination of FTIR spectroscopy and computations

NASA Astrophysics Data System (ADS)

Tolnai, B.; Kiss, J. T.; Felföldi, K.; Pálinkó, I.

2009-04-01

Various F-substituted E-2,3-diphenyl propenoic acid molecules were synthesised and their aggregation behaviour was studied by experimental (FT-IR spectroscopy) and computational (semiempirical and DFT) methods. Experimental approach embraced the identification of potential hydrogen bonding sites through finding the relevant IR bands and monitoring their shifts upon increasing the acid concentration and on going to the solid state. It was found that fluorine engaged in C sbnd H…F hydrogen bonding easily, where the carbon atom could be of any kind available in the molecule (aromatic, aliphatic or olefinic). Shifts were found even in moderately concentrated solutions and in the solid state too. Hydrogen bonding sites could be assigned and relevant aggregate models could be built. Molecular modelling allowed obtaining good estimates for hydrogen bond lengths and angles and visualisation of the geometric arrangements even of extended networks also became feasible.

Realistic sampling of amino acid geometries for a multipolar polarizable force field

PubMed Central

Hughes, Timothy J.; Cardamone, Salvatore

2015-01-01

The Quantum Chemical Topological Force Field (QCTFF) uses the machine learning method kriging to map atomic multipole moments to the coordinates of all atoms in the molecular system. It is important that kriging operates on relevant and realistic training sets of molecular geometries. Therefore, we sampled single amino acid geometries directly from protein crystal structures stored in the Protein Databank (PDB). This sampling enhances the conformational realism (in terms of dihedral angles) of the training geometries. However, these geometries can be fraught with inaccurate bond lengths and valence angles due to artefacts of the refinement process of the X‐ray diffraction patterns, combined with experimentally invisible hydrogen atoms. This is why we developed a hybrid PDB/nonstationary normal modes (NM) sampling approach called PDB/NM. This method is superior over standard NM sampling, which captures only geometries optimized from the stationary points of single amino acids in the gas phase. Indeed, PDB/NM combines the sampling of relevant dihedral angles with chemically correct local geometries. Geometries sampled using PDB/NM were used to build kriging models for alanine and lysine, and their prediction accuracy was compared to models built from geometries sampled from three other sampling approaches. Bond length variation, as opposed to variation in dihedral angles, puts pressure on prediction accuracy, potentially lowering it. Hence, the larger coverage of dihedral angles of the PDB/NM method does not deteriorate the predictive accuracy of kriging models, compared to the NM sampling around local energetic minima used so far in the development of QCTFF. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:26235784

1H-Indole-3-carbaldehyde.

PubMed

Dileep, C S; Abdoh, M M M; Chakravarthy, M P; Mohana, K N; Sridhar, M A

2012-11-01

In the title compound, C(9)H(7)NO, the benzene ring forms a dihedral angle of 3.98 (12)° with the pyrrole ring. In the crystal, N-H⋯O hydrogen bonds links the mol-ecules into chains which run parallel to [02-1].

4-[(E)-(2,4-Difluoro­phen­yl)(hydroxy­imino)meth­yl]piperidinium picrate

PubMed Central

Jasinski, Jerry P.; Butcher, Ray J.; Yathirajan, H. S.; Mallesha, L.; Mohana, K. N.

2009-01-01

The title compound, C12H15F2N2O+·C6H2N3O7 −, a picrate salt of 4-[(E)-(2,4-difluoro­phen­yl)(hydroxy­imino)meth­yl]piper­idine, crystallizes with two independent mol­ecules in a cation–anion pair in the asymmetric unit. In the cation, a methyl group is tris­ubstituted by hydroxy­imino, piperidin-4-yl and 2,4-difluoro­phenyl groups, the latter of which contains an F atom disordered over two positions in the ring [occupancy ratio 0.631 (4):0.369 (4)]. The mean plane of the hydr­oxy group is in a synclinical conformation nearly orthogonal [N—C—C—C = 72.44 (19)°] to the mean plane of the piperidine ring, which adopts a slightly distorted chair conformation. The dihedral angle between the mean plane of the 2,4-difluoro­phenyl and piperidin-4-yl groups is 60.2 (3)°. In the picrate anion, the mean planes of the two o-NO2 and single p-NO2 groups adopt twist angles of 5.7 (2), 25.3 (7) and 8.3 (6)°, respectively, with the attached planar benzene ring. The dihedral angle between the mean planes of the benzene ring in the picrate anion and those in the hydroxy­imino, piperidin-4-yl and 2,4-difluoro­phenyl groups in the cation are 84.9 (7), 78.9 (4) and 65.1 (1)°, respectively. Extensive hydrogen-bond inter­actions occur between the cation–anion pair, which help to establish the crystal packing in the unit cell. This includes dual three-center hydrogen bonds with the piperidin-4-yl group, the phenolate and o-NO2 O atoms of the picrate anion at different positions in the unit cell, which form separate N—H⋯(O,O) bifurcated inter­molecular hydrogen-bond inter­actions. Also, the hydr­oxy group forms a separate hydrogen bond with a nearby piperidin-4-yl N atom, thus providing two groups of hydrogen bonds, which form an infinite two-dimensional network along (011). PMID:21577832

Crystal chemistry and structure refinement of five hydrated calcium borates

USGS Publications Warehouse

Clark, J.R.; Appleman, D.E.; Christ, C.L.

1964-01-01

The crystal structures of the five known members of the series Ca2B6O11??xH2O (x = 1, 5, 5, 7, 9, and 13) have been refined by full-matrix least-squares techniques, yielding bond distances and angles with standard errors of less than 0??01 A?? and 0??5??, respectively. The results illustrate the crystal chemical principles that govern the structures of hydrated borate compounds. The importance of hydrogen bonding in the ferroelectric transition of colemanite is confirmed by more accurate proton assignments. ?? 1964.

N-(2-Allyl-4-eth-oxy-2H-indazol-5-yl)-4-methyl-benzene-sulfonamide.

PubMed

Chicha, Hakima; Rakib, El Mostapha; Bouissane, Latifa; Viale, Maurizio; Saadi, Mohamed; El Ammari, Lahcen

2014-05-01

The indazole ring system of the title compound, C19H21N3O3S, is almost planar (r.m.s. deviation = 0.0192 Å) and forms dihedral angles of 77.99 (15) and 83.9 (3)° with the benzene ring and allyl group, respectively. In the crystal, centrosymmetrically related mol-ecules are connected by pairs of N-H⋯O hydrogen bonds into dimers, which are further linked by C-H⋯O hydrogen bonds, forming columns parallel to the b axis.

Structure identification methods for atomistic simulations of crystalline materials

DOE PAGES

Stukowski, Alexander

2012-05-28

Here, we discuss existing and new computational analysis techniques to classify local atomic arrangements in large-scale atomistic computer simulations of crystalline solids. This article includes a performance comparison of typical analysis algorithms such as common neighbor analysis (CNA), centrosymmetry analysis, bond angle analysis, bond order analysis and Voronoi analysis. In addition we propose a simple extension to the CNA method that makes it suitable for multi-phase systems. Finally, we introduce a new structure identification algorithm, the neighbor distance analysis, which is designed to identify atomic structure units in grain boundaries.

(Z)-3-(1-Chloro-prop-1-en-yl)-2-methyl-1-phenyl-sulfonyl-1H-indole.

PubMed

Umadevi, M; Saravanan, V; Yamuna, R; Mohanakrishnan, A K; Chakkaravarthi, G

2013-11-16

In the title compound, C18H16ClNO2S, the indole ring system forms a dihedral angle of 75.07 (8)° with the phenyl ring. The mol-ecular structure is stabilized by a weak intra-molecular C-H⋯O hydrogen bond. In the crystal, mol-ecules are linked by weak C-H⋯O hydrogen bonds, forming a chain along [10-1]. C-H⋯π inter-actions are also observed, leading to a three-dimensional network.

Ab initio study of the electrostatic multipole nature of torsional potentials in CH3SSCH3, CH3SSH, and HOOH

NASA Technical Reports Server (NTRS)

Sokalski, W. A.; Lai, J.; Luo, N.; Sun, S.; Shibata, M.; Ornstein, R.; Rein, R.

1991-01-01

The origin of torsional potentials in H3CSSCH3, H3CSSH, and HOOH and the anisotropy of the local charge distribution has been analyzed in terms of atomic multipoles calculated from the ab initio LCAO-MO-SCF wave function in the 6-31G* basis set. The results indicate that for longer -S-S-bonds the major contribution to these torsional barriers are electrostatic interactions of the atomic multipoles located on two atoms forming the rotated bond. This finding demonstrates the important role of electrostatic 1-2 interatomic interactions, usually neglected in conformational studies. It also opens the possibility to derive directly from accurate ab initio wave functions a simple nonempirical torsional potential involving atomic multipoles of two bonded atoms defining the torsional angle. For shorter -O-O- bonds, use of more precise models and inclusion of 1-3 interactions seems to be necessary.

N-(Diphenyl­carbamo­yl)-N,N′,N′,N′′,N′′-penta­methyl­guanidinium tetra­phenyl­borate

PubMed Central

Tiritiris, Ioannis

2013-01-01

In the title salt, C19H25N4O+·C24H20B−, the C=N and C—N bond lengths in the CN3 unit are 1.3327 (8)/1.3364 (9) and 1.3802 (9) Å, indicating double- and single-bond character, respectively. The N—C—N angles are 118.77 (6), 120.29 (6) and 120.81 (6)°, showing only a small deviation of the CN3 plane from an ideal trigonal-planar geometry. The bonds between the N atoms and the terminal methyl C atoms all have values close to a typical single bond [1.4636 (9)–1.4772 (9) Å]. The crystal packing is caused by electrostatic inter­actions between cations and anions. PMID:23476477

Metal-ligand bond directionality in the M2-NH3 complexes (M = Cu, Ag and Au)

NASA Astrophysics Data System (ADS)

Eskandari, K.; Ebadinejad, F.

2018-05-01

The metal-ligand bonds in the M2-NH3 complexes (M = Au, Ag and Cu) are directional and the M-M-N angles tend to be linear. Natural energy decomposition analysis (NEDA) and localised molecular orbital energy decomposition analysis (LMOEDA) approaches indicate that the metal-ligand bonds in these complexes are mainly electrostatic in nature, however, the electrostatic is not the cause of the linearity of M-M-N arrangements. Instead, NEDA shows that the charge transfer and core repulsion are mainly responsible for the directionality of these bonds. In the LMOEDA point of view, the repulsion term is the main reason for the linearity of these complexes. Interacting quantum atoms (IQA) analysis shows that inter-atomic and inter-fragment interactions favour the nonlinear arrangements; however, these terms are compensated by the atomic self-energies, which stabilise the linear structure.

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.

Structural Characterization of β-Agostic Bonds in Pd-Catalyzed Polymerization

DOE PAGES

Xu, Hongwei; Hu, Chunhua Tony; Wang, Xiaoping; ...

2017-10-23

β-agostic Pd complexes are critical intermediates in catalytic reactions, such as olefin polymerization and Heck reactions. Pd β-agostic complexes, however, have eluded structural characterization, due to the fact that these highly unstable molecules are difficult to isolate. In this paper, we report the single-crystal X-ray and neutron diffraction characterization of β-agostic (α-diimine)Pd–ethyl intermediates in polymerization. Short C α–C β distances and acute Pd–C α–C β bond angles combined serve as unambiguous evidence for the β-agostic interaction. Finally, characterization of the agostic structure and the kinetic barrier for β-H elimination offer important insight into the fundamental understanding of agostic bonds andmore » the mechanism of polymerization.« less

Structural Characterization of β-Agostic Bonds in Pd-Catalyzed Polymerization

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

Xu, Hongwei; Hu, Chunhua Tony; Wang, Xiaoping

β-agostic Pd complexes are critical intermediates in catalytic reactions, such as olefin polymerization and Heck reactions. Pd β-agostic complexes, however, have eluded structural characterization, due to the fact that these highly unstable molecules are difficult to isolate. In this paper, we report the single-crystal X-ray and neutron diffraction characterization of β-agostic (α-diimine)Pd–ethyl intermediates in polymerization. Short C α–C β distances and acute Pd–C α–C β bond angles combined serve as unambiguous evidence for the β-agostic interaction. Finally, characterization of the agostic structure and the kinetic barrier for β-H elimination offer important insight into the fundamental understanding of agostic bonds andmore » the mechanism of polymerization.« less

Transformations of organic compounds under the action of mechanical stress

NASA Astrophysics Data System (ADS)

Dubinskaya, Aleksandra M.

1999-08-01

Transformations of organic compounds (monomeric and polymeric) under the action of mechanical stress are considered. Two types of processes occur under these conditions. The first type involves disordering and amorphisation of crystal structure and conformational transformations as a result of rupture of intermolecular bonds. The second type includes mechanochemical reactions activated by deformation of valence bonds and angles under mechanical stress, namely, the rupture of bonds, oxidation and hydrolysis. Data on the organic mechanochemical synthesis of new compounds or molecular complexes are systematised and generalised. It is demonstrated that mechanical treatment ensures mass transfer and the contact of reacting species in these reactions. Proteins are especially sensitive to mechanical stress and undergo denaturation; enzymes are inactivated. The bibliography includes 115 references.

Characterization, photophysical and DFT calculation study on 2-(2,4-difluorophenyl)-1-(4-methoxyphenyl)-1H-imidazo[4,5-f][1,10]phenanthroline ligand.

PubMed

Jayabharathi, Jayaraman; Thanikachalam, Venugopal; Venkatesh Perumal, Marimuthu

2012-09-01

The synthesized imidazole derivative 2-(2,4-difluorophenyl)-1-(4-methoxyphenyl)-1H-imidazo[4,5-f][1,10] phenanthroline (dfpmpip) has been characterized using IR, mass, (1)H, (13)C NMR and elemental analysis. The photophysical properties of dfpmpip have been studied using UV-visible and fluorescence spectroscopy in different solvents. The solvent effect on the absorption and fluorescence bands has been analyzed by a multi-component linear regression. Theoretically calculated bond lengths, bond angles and dihedral angles are found to be slightly higher than that of X-ray Diffraction (XRD) values of its parent compound. The charge distribution has been calculated from the atomic charges by non-linear optical (NLO) and natural bond orbital (NBO) analysis. Since the synthesized imidazole derivative has the largest μ(g)β(0) value, the reported imidazole can be used as potential NLO material. The energies of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) levels and the molecular electrostatic potential (MEP) energy surface studies evidenced the existence of intramolecular charge transfer (ICT) within the molecule. Theoretical calculations regarding the chemical potential (μ), hardness (η) and electrophilicity index (ω) have also been calculated. Copyright © 2012 Elsevier B.V. All rights reserved.

The structure of 3'-O-anthraniloyladenosine, an analogue of the 3'-end of aminoacyl-tRNA.

PubMed Central

Nawrot, B; Milius, W; Ejchart, A; Limmer, S; Sprinzl, M

1997-01-01

3'-O-Anthraniloyladenosine, an analogue of the 3'- terminal aminoacyladenosine residue in aminoacyl-tRNAs, was prepared by chemical synthesis, and its crystal structure was determined. The sugar pucker of 3'-O-anthraniloyladenosine is 2'-endo resulting in a 3'-axial position of the anthraniloyl residue. The nucleoside is insynconformation, which is stabilized by alternating stacking of adenine and benzoyl residues of the neighboring molecules in the crystal lattice. The conformation of the 5'-hydroxymethylene in 3'-O- anthraniloyladenosine is gauche-gauche. There are two intramolecular and two intermolecular hydrogen bonds and several H-bridges with surrounding water molecules. The predominant structure of 3'-O-anthraniloyladenosine in solution, as determined by NMR spectroscopy, is 2'-endo,gauche-gauche and anti for the sugar ring pucker, the torsion angle around the C4'-C5'bond and the torsion angle around the C1'-N9 bond, respectively. The 2'-endo conformation of the ribose in 2'(3')-O-aminoacyladenosine, which places the adenine and aminoacyl residues in equatorial and axial positions, respectively, could serve as a structural element that is recognized by enzymes that interact with aminoacyl-tRNA or by ribosomes to differentiate between aminoacylated and non-aminoacylated tRNA. PMID:9023103

Crystal structure of 3-{[4-(2-meth-oxy-phen-yl)piperazin-1-yl]meth-yl}-5-(thio-phen-2-yl)-1,3,4-oxa-diazole-2(3H)-thione.

PubMed

Al-Alshaikh, Monirah A; Abuelizz, Hatem A; El-Emam, Ali A; Abdelbaky, Mohammed S M; Garcia-Granda, Santiago

2016-02-01

The title compound, C18H20N4O2S2, is a new 1,3,4-oxa-diazole and a key pharmacophore of several biologically active agents. It is composed of a meth-yl(thio-phen-2-yl)-1,3,4-oxa-diazole-2(3H)-thione moiety linked to a 2-meth-oxy-phenyl unit via a piperazine ring that has a chair conformation. The thio-phene ring mean plane lies almost in the plane of the oxa-diazole ring, with a dihedral angle of 4.35 (9)°. The 2-meth-oxy-phenyl ring is almost normal to the oxa-diazole ring, with a dihedral angle of 84.17 (10)°. In the crystal, mol-ecules are linked by weak C-H⋯S hydrogen bonds and C-H⋯π inter-actions, forming layers parallel to the bc plane. The layers are linked via weak C-H⋯O hydrogen bonds and slipped parallel π-π inter-actions [inter-centroid distance = 3.6729 (10) Å], forming a three-dimensional structure. The thio-phene ring has an approximate 180° rotational disorder about the bridging C-C bond.

Ab initio conformational analysis of N-formyl ?-alanine amide including electron correlation

NASA Astrophysics Data System (ADS)

Yu, Ching-Hsing; Norman, Mya A.; Schäfer, Lothar; Ramek, Michael; Peeters, Anik; van Alsenoy, Christian

2001-06-01

The conformational properties of N-formyl L-alanine amide (ALA) were investigated using RMP2/6-311G∗∗ ab initio gradient geometry optimization. One hundred forty four structures of ALA were optimized at 30° grid points in its φ(N-C(α)), ψ(C(α)-C‧) conformational space. Using cubic spline functions, the grid structures were then used to construct analytical representations of complete surfaces, in φ,ψ-space, of bond lengths, bond angles, torsional sensitivity and electrostatic atomic charges. Analyses show that, in agreement with previous studies, the right-handed helical conformation, αR, is not a local energy minimum of the potential energy surface of ALA. Comparisons with protein crystallographic data show that the characteristic differences between geometrical trends in dipeptides and proteins, previously found for ab initio dipeptide structures obtained without electron correlation, are also found in the electron-correlated geometries. In contrast to generally accepted features of force fields used in empirical molecular modeling, partial atomic charges obtained by the CHELPG method are found to be not constant, but to vary significantly throughout the φ,ψ-space. By comparing RHF and MP2 structures, the effects of dispersion forces on ALA were studied, revealing molecular contractions for those conformations, in which small adjustments of torsional angles entail large changes in non-bonded distances.

Mechanism for Ring-Opening of Aromatic Polymers by Remote Atmospheric Pressure Plasma

NASA Astrophysics Data System (ADS)

Gonzalez, Eleazar; Barankin, Michael; Guschl, Peter; Hicks, Robert

2009-10-01

A low-temperature, atmospheric pressure oxygen and helium plasma was used to treat the surfaces of polyetheretherketone, polyphenylsulfone, polyethersulfone, and polysulfone. These aromatic polymers were exposed to the afterglow of the plasma, which contained oxygen atoms, and to a lesser extent metastable oxygen (^1δg O2) and ozone. After less than 2.5 seconds treatment, the polymers were converted from a hydrophobic state with a water contact angle of 85±5 to a hydrophilic state with a water contact angle of 13±5 . It was found that plasma activation increased the bond strength to adhesives by as much as 4 times. X-ray photoelectron spectroscopy revealed that between 7% and 27% of the aromatic carbon atoms on the polymer surfaces was oxidized and converted into aldehyde and carboxylic acid groups. Analysis of polyethersulfone by internal reflection infrared spectroscopy showed that a fraction of the aromatic carbon atoms were transformed into C=C double bonds, ketones, and carboxylic acids after plasma exposure. It was concluded that the oxygen atoms generated by the atmospheric pressure plasma insert into the double bonds on the aromatic rings, forming a 3-member epoxy ring, which subsequently undergoes ring opening and oxidation to yield an aldehyde and a carboxylic acid group.

High-Resolution Infrared and Electron-Diffraction Studies of Trimethylenecyclopropane ([3]-Radialene)

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

Wright, Corey; Holmes, Joshua; Nibler, Joseph W.

2013-05-16

Combined high-resolution spectroscopic, electron-diffraction, and quantum theoretical methods are particularly advantageous for small molecules of high symmetry and can yield accurate structures that reveal subtle effects of electron delocalization on molecular bonds. The smallest of the radialene compounds, trimethylenecyclopropane, [3]-radialene, has been synthesized and examined in the gas phase by these methods. The first high-resolution infrared spectra have been obtained for this molecule of D3h symmetry, leading to an accurate B0 rotational constant value of 0.1378629(8) cm-1, within 0.5% of the value obtained from electronic structure calculations (density functional theory (DFT) B3LYP/cc-pVTZ). This result is employed in an analysis ofmore » electron-diffraction data to obtain the rz bond lengths (in Å): C-H = 1.072 (17), C-C = 1.437 (4), and C=C = 1.330 (4). The analysis does not lead to an accurate value of the HCH angle; however, from comparisons of theoretical and experimental angles for similar compounds, the theoretical prediction of 117.5° is believed to be reliable to within 2°. The effect of electron delocalization in radialene is to reduce the single C-C bond length by 0.07 Å compared to that in cyclopropane.« less

Two-Photon Absorption Properties of Gold Fluorescent Protein: A Combined Molecular Dynamics and Quantum Chemistry Study.

PubMed

Şimşek, Yusuf; Brown, Alex

2018-06-07

Molecular dynamics (MD) simulations were carried out to obtain the conformational changes of the chromophore in the gold fluorescent protein (PDB ID: 1OXF ). To obtain two-photon absorption (TPA) cross-sections, time dependent density functional theory (TD-DFT) computations were performed for chromophore geometries sampled along the trajectory. The TD-DFT computations used the CAM-B3LYP functional and 6-31+G(d) basis set. Results showed that two dihedral angles change remarkably over the simulation time. TPA cross-sections were found to average 13.82 GM for the excitation to S 1 computed from the equilibrium geometries; however, extending the structures with a water molecule and GLU residue, which make H bonds with the chromophore molecule, increased excitation energies and TPA cross-sections significantly. Besides the effects of the surrounding residues and the dihedrals on the spectroscopic properties, some bond lengths affected the excitation energies and the TPA cross-sections significantly (up to ±25-30%), while the effects of the bond angles were smaller (±5%). Overall the present results provide insight into the effects of the conformational flexibility on TPA (with gold fluorescent protein as a specific example) and suggest that further experimental measurements of TPA for the gold fluorescent protein should be undertaken.

Embarras de richesses - It is not good to be too anomalous: Accurate structure of selenourea, a chiral crystal of planar molecules.

PubMed

Luo, Zhipu; Dauter, Zbigniew

2017-01-01

Selenourea, SeC(NH2)2, recently found an application as a derivatization reagent providing a significant anomalous diffraction signal used for phasing macromolecular crystal structures. The crystal structure of selenourea itself was solved about 50 years ago, from data recorded on films and evaluated by eye and refined to R = 0.15 with errors of bond lengths and angles about 0.1 Å and 6°. In the current work this structure is re-evaluated on the basis of synchrotron data and refined to R1 = 0.021 with bond and angle errors about 0.007 Å and 0.5°. The nine planar molecules of selenourea pack either in the P31 or in the P32 unit cell. All unique molecules are connected by a complex network of Se•••H-N hydrogen bonds and Se•••Se contacts. The packing of selenourea molecules is highly pseudosymmetric, approximating either of the P31(2)12, R3, and R32 space groups. Because the overwhelming majority of diffracted X-ray intensity originates form the anomalously scattering selenium atoms, the measurable anomalous Bijvoet differences are diminished and it was not possible to solve this crystal structure based on the anomalous signal alone.

(E)-1,2-Bis(4-fluoro­phen­yl)ethane-1,2-dione

PubMed Central

Fun, Hoong-Kun; Kia, Reza

2008-01-01

The title compound, C14H8F2O2, is a substituted benzil with an s-trans conformation of the dicarbonyl unit. This conformation is also shown by the O—C—C—O torsion angle of −110.65 (12)°. An unusual feature of the structure is the length, 1.536 (2) Å, of the central C—C bond connecting the carbonyl units, which is significantly longer than a normal Csp 2—Csp 2 single bond. This is probably the result of decreasing the unfavourable vicinal dipole–dipole inter­actions by increasing the distance between the two electronegative O atoms [O⋯O = 3.1867 (12) Å] and allowing orbital overlap of the dione with the π system of the benzene rings. The dihedral angle between the aromatic rings is 64.74 (5)°. In the crystal structure, neighbouring mol­ecules are linked together by weak inter­molecular C—H⋯O (× 2) hydrogen bonds. In addition, the crystal structure is further stabilized by inter­molecular π–π inter­actions with centroid–centroid distances in the range 3.6416 (6)–3.7150 (7) Å. PMID:21203308

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

Laminate behavior for SiC fiber-reinforced reaction-bonded silicon nitride matrix composites

NASA Technical Reports Server (NTRS)

Rhatt, R. T.; Phillips, R. E.

1988-01-01

The room temperature mechanical properties of SiC fiber reinforced reaction-bonded silicon nitride matrix composite laminates (SiC/RBSN) have been measured. The laminates contained approx 30 volume fraction of aligned 142-micron diameter SiC fiber in a porous RBSN matrix. Three types of laminate studied were unidirectional: (1) (0) sub 8, (2) (10) sub 8, and (3) (45) sub 8, and (90) sub 8; cross plied laminates (0 sub 2/90 sub 2); and angle plied laminates: (+45 sub 2/-45 sub 2). Each laminate contained eight fiber plies. Results of the unidirectionally reinforced composites tested at various angles to the reinforcement direction indicate large anisotropy in in-plane properties. In addition, strength properties of these composites along the fiber direction were independent of specimen gage length and were unaffected by notches normal to the fiber direction. Splitting parallel to the fiber at the notch tip appears to be the dominant crack blunting mechanism responsible for notch insensitive behavior of these composites. In-plane properties of the composites can be improved by 2-D laminate construction. Mechanical property results for (0 sub 2/90 sub 2)sub s and (+45/-45 sub 2) sub s laminates showed that their matrix failure strains were similar to that for (0) sub 8 laminates, but their primary elastic moduli, matrix cracking strengths, and ultimate composite strengths were lower. The elastic properties of unidirectional, cross-ply, and angle-ply composites can be predicted from modified constitutive equations and laminate theory. Further improvements in laminate properties may be achieved by reducing the matrix porosity and by optimizing the bond strength between the SiC fiber and RBSN matrix.

Laminate behavior for SiC fiber-reinforced reaction-bonded silicon nitride matrix composites

NASA Technical Reports Server (NTRS)

Bhatt, Ramakrishna T.; Phillips, Ronald E.

1990-01-01

The room temperature mechanical properties of SiC fiber reinforced reaction-bonded silicon nitride matrix composite laminates (SiC/RBSN) have been measured. The laminates contained approx 30 volume fraction of aligned 142-micron diameter SiC fiber in a porous RBSN matrix. Three types of laminate studied were unidirectional: (1) (0) sub 8, (2) (10) sub 8, and (3) (45) sub 8, and (90) sub 8; cross plied laminates (0 sub 2/90 sub 2); and angle plied laminates: (+45 sub 2/-45 sub 2). Each laminate contained eight fiber plies. Results of the unidirectionally reinforced composites tested at various angles to the reinforcement direction indicate large anisotropy in in-plane properties. In addition, strength properties of these composites along the fiber direction were independent of specimen gage length and were unaffected by notches normal to the fiber direction. Splitting parallel to the fiber at the notch tip appears to be the dominant crack blunting mechanism responsible for notch insensitive behavior of these composites. In-plane properties of the composites can be improved by 2-D laminate construction. Mechanical property results for (0 sub 2/90 sub 2) sub s and (+45/-45 sub 2) sub s laminates showed that their matrix failure strains were similar to that for (0) sub 8 laminates, but their primary elastic moduli, matrix cracking strengths, and ultimate composite strengths were lower. The elastic properties of unidirectional, cross-ply, and angle-ply composites can be predicted from modified constitutive equations and laminate theory. Further improvements in laminate properties may be achieved by reducing the matrix porosity and by optimizing the bond strength between the SiC fiber and RBSN matrix.

The effect of temperature, matrix alloying and substrate coatings on wettability and shear strength of Al/Al2O3 couples

NASA Astrophysics Data System (ADS)

Sobczak, N.; Ksiazek, M.; Radziwill, W.; Asthana, R.; Mikulowski, B.

2004-03-01

A fresh approach has been advanced to examine in the Al/Al2O3 system the effects of temperature, alloying of Al with Ti or Sn, and Ti and Sn coatings on the substrate, on contact angles measured using a sessile-drop test, and on interface strength measured using a modified push-off test that allows shearing of solidified droplets with less than 90 deg contact angle. In the modified test, the solidified sessile-drop samples are bisected perpendicular to the drop/Al2O3 interface at the midplane of the contact circle to obtain samples that permit bond strength measurement by stress application to the flat surface of the bisected couple. The test results show that interface strength is strongly influenced by the wetting properties; low contact angles correspond to high interface strength, which also exhibits a strong temperature dependence. An increase in the wettability test temperature led to an increase in the interface strength in the low-temperature range where contact angles were large and wettability was poor. The room-temperature shear tests conducted on thermally cycled sessile-drop test specimens revealed the effect of chemically formed interfacial oxides; a weakening of the thermally cycled Al/Al2O3 interface was caused under the following conditions: (1) slow contact heating and short contact times in the wettability test, and (2) fast contact heating and longer contact times. The addition of 6 wt pct Ti or 7 wt pct Sn to Al only marginally influenced the contact angle and interfacial shear strength. However, Al2O3 substrates having thin (<1 µm) Ti coatings yielded relatively low contact angles and high bond strength, which appears to be related to the dissolution of the coating in Al and formation of a favorable interface structure.

Impact of different rectangular wires on torsional expression of different sizes of buccal tube.

PubMed

Ajami, Shabnam; Boroujeni, Afshar-Rasti

2018-01-01

Torsions in rectangular wires are the essential part of corrections in the finishing stage of treatment. Moreover the greatest amounts of torques are applied in the molar areas. a clinically effective moment is between 5 and 20 Nmm. In this study we have decided to evaluate the impact of different tube sizes and different dimensions of wires with different modulus of elasticities on the amount torsional bond strength of molar tubes. 60 human impacted molar teeth were collected. A buccal tube was bonded on the buccal surface of all the samples by using light cured adhesive resin. After that, the teeth were mounted in a hard acrylic block. According to the size of buccal tube and the rectangular wires to be tested 4 groups will be designed. Torsional force was applied by instron machine. The torque angle at 5Nmm and at 20Nmm point will be calculated: which means, how many degrees of torque is required to reach the maximum 20Nmm moment from the minimum 5Nmm.One-way ANOVA was used to compare torque angle in all of the groups. The least amount of clinically significant angle was 2.2 ᵒ in the 0.017×0.025 SS and the largest amount of it was 23.7 ᵒ in the 0.017×0.025 TMA in 0.018×0.025 slot molar tube. But, this angle was 19.9 ᵒand 13.6 ᵒ in 0.019×0.025 SS and 0.019×0.025 TMA archwire in 0.022×0.028 molar tube. The 0.017×0.025 SS archwire in 0.018×0.025 molar tube had the lowest clinically significant angle. The largest amount was seen in group 0.017×0.025 TMA in 0.018×0.025 slot molar tube. Key words: Torsional efficacy, rectangular wires, buccal tubes, torque angle.

Impact of different rectangular wires on torsional expression of different sizes of buccal tube

PubMed Central

Boroujeni, Afshar-Rasti

2018-01-01

Background Torsions in rectangular wires are the essential part of corrections in the finishing stage of treatment. Moreover the greatest amounts of torques are applied in the molar areas. a clinically effective moment is between 5 and 20 Nmm. In this study we have decided to evaluate the impact of different tube sizes and different dimensions of wires with different modulus of elasticities on the amount torsional bond strength of molar tubes. Material and Methods 60 human impacted molar teeth were collected. A buccal tube was bonded on the buccal surface of all the samples by using light cured adhesive resin. After that, the teeth were mounted in a hard acrylic block. According to the size of buccal tube and the rectangular wires to be tested 4 groups will be designed. Torsional force was applied by instron machine. The torque angle at 5Nmm and at 20Nmm point will be calculated: which means, how many degrees of torque is required to reach the maximum 20Nmm moment from the minimum 5Nmm.One-way ANOVA was used to compare torque angle in all of the groups. Results The least amount of clinically significant angle was 2.2 ᵒ in the 0.017×0.025 SS and the largest amount of it was 23.7 ᵒ in the 0.017×0.025 TMA in 0.018×0.025 slot molar tube. But, this angle was 19.9 ᵒand 13.6 ᵒ in 0.019×0.025 SS and 0.019×0.025 TMA archwire in 0.022×0.028 molar tube. Conclusions The 0.017×0.025 SS archwire in 0.018×0.025 molar tube had the lowest clinically significant angle. The largest amount was seen in group 0.017×0.025 TMA in 0.018×0.025 slot molar tube. Key words: Torsional efficacy, rectangular wires, buccal tubes, torque angle. PMID:29670712

(2E)-3-(6-Meth­oxy­naphthalen-2-yl)-1-[4-(methyl­sulfan­yl)phen­yl]prop-2-en-1-one

PubMed Central

Fun, Hoong-Kun; Chia, Tze Shyang; Padaki, Mahesh; Isloor, Arun M.; Ismail, A. F.

2012-01-01

The asymmetric unit of the title compound, C21H18O2S, consists of two crystallographically independent mol­ecules (A and B). The mol­ecules exist in a trans conformation with respect to the central C=C bond. The naphthalene ring system makes dihedral angles of 51.62 (12) (mol­ecule A) and 52.69 (12)° (mol­ecule B) with the benzene ring. In mol­ecule A, the prop-2-en-1-one group forms dihedral angles of 22.84 (15) and 29.02 (12)° with the adjacent naphthalene ring system and benzene ring, respectively, whereas the corresponding angles are 30.04 (12) and 23.33 (12)° in mol­ecule B. In the crystal, mol­ecules are linked by inter­molecular C—H⋯O hydrogen bonds into head-to-tail chains along the a axis. The crystal packing also features C—H⋯π inter­actions. The crystal studied was a pseudo-merohedral twin with twin law (100 0-10 00-1) and a refined component ratio of 0.6103 (16):0.3897 (16). PMID:22798922

The Significance of Interfacial Water Structure in Soluble Salt Flotation Systems.

PubMed

Hancer, M.; Celik, M. S.; Miller, J. D.

2001-03-01

Flotation of soluble salts with dodecyl amine hydrochloride (DAH) and sodium dodecyl sulfate (SDS) collectors has demonstrated that the interfacial water structure and hydration states of soluble salt surfaces together with the precipitation tendency of the corresponding collector salts are of considerable importance in explaining their flotation behavior. In particular, the high concentration of ions in these soluble salt brines and their hydration appear to modify the bulk and interfacial structure of water as revealed by contact angle measurements and this effect is shown to be an important feature in the flotation chemistry of soluble salt minerals including alkali halide and alkali oxyanion salts. Depending on characteristic chemical features (salt type), the salt can serve either as a structure maker, in which intermolecular hydrogen bonding between water molecules is facilitated, or as a structure breaker, in which intermolecular hydrogen bonding between water molecules is disrupted. For structure making salts the brine completely wets the salt surface and no contact angle can be measured. For structure breaking salts the brine does not completely wet the salt surface and a finite contact angle is measured. In this regard it has been found that soluble salt flotation either with the cationic DAH or anionic SDS collector is possible only if the salt is a structure breaker. Copyright 2001 Academic Press.

Evaluation of the orientation of 90* and 180* reinforcing bar hooks.

DOT National Transportation Integrated Search

2012-01-01

This report describes test results of a study initiated to evaluate the potential influence of hook tilt angle of standard reinforcing hooks : on the bond strength of concrete. The topic of the evaluation of the orientation of 90 and 180 degree reinf...

One-step solvothermal deposition of ZnO nanorod arrays on a wood surface for robust superamphiphobic performance and superior ultraviolet resistance

PubMed Central

Yao, Qiufang; Wang, Chao; Fan, Bitao; Wang, Hanwei; Sun, Qingfeng; Jin, Chunde; Zhang, Hong

2016-01-01

In the present paper, uniformly large-scale wurtzite-structured ZnO nanorod arrays (ZNAs) were deposited onto a wood surface through a one-step solvothermal method. The as-prepared samples were characterized by X-ray diffraction (XRD), field-emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), thermogravimetry (TG), and differential thermal analysis (DTA). ZNAs with a diameter of approximately 85 nm and a length of approximately 1.5 μm were chemically bonded onto the wood surface through hydrogen bonds. The superamphiphobic performance and ultraviolet resistance were measured and evaluated by water or oil contact angles (WCA or OCA) and roll-off angles, sand abrasion tests and an artificially accelerated ageing test. The results show that the ZNA-treated wood demonstrates a robust superamphiphobic performance under mechanical impact, corrosive liquids, intermittent and transpositional temperatures, and water spray. Additionally, the as-prepared wood sample shows superior ultraviolet resistance. PMID:27775091

Crystal structure of N′-[(E)-(1S,3R)-(3-isopropyl-1-methyl-2-oxo­cyclo­pent­yl)methyl­idene]-4-methyl­benzene­sulfono­hydrazide

PubMed Central

Tymann, David; Dragon, Dina Christina; Golz, Christopher; Preut, Hans; Strohmann, Carsten; Hiersemann, Martin

2015-01-01

The title compound, C17H24N2O3S, was synthesized in order to determine the relative configuration of the corresponding β-keto aldehyde. In the U-shaped mol­ecule, the five-membered ring approximates an envelope, with the methyl­ene C atom adjacent to the quaternary C atom being the flap, and the methyl and isopropyl substituents lying to the same side of the ring. The dihedral angles between the four nearly coplanar atoms of the five-membered ring and the flap and the aromatic ring are 35.74 (15) and 55.72 (9)°, respectively. The bond angles around the S atom are in the range from 103.26 (12) to 120.65 (14)°. In the crystal, mol­ecules are linked via N—H⋯O hydrogen bonds, forming a chain along the a axis. PMID:26870519

N-(2-{[5-Bromo-2-(morpholin-4-yl)pyrimidin-4-yl]sulfan­yl}-4-meth­oxy­phen­yl)-4-chloro­benzene­sulfonamide

PubMed Central

Kumar, Mohan; Mallesha, L.; Sridhar, M. A.; Kapoor, Kamini; Gupta, Vivek K.; Kant, Rajni

2012-01-01

In the title compound, C21H20BrClN4O4S2, the benzene rings bridged by the sulfonamide group are tilted relative to each other by a dihedral angle of 70.2 (1)° and the dihedral angle between the sulfur-bridged pyrimidine and benzene rings is 69.5 (1)°. The mol­ecular conformation is stabilized by a weak intra­molecular π–π stacking inter­action between the pyrimidine and the 4-chloro­benzene rings [centroid–centroid distance = 3.978 (2) Å]. The morpholine ring adopts a chair conformation. In the crystal, mol­ecules are linked into inversion dimers by pairs of C—H⋯N hydrogen bonds and these dimers are further connected by N—H⋯O hydrogen bonds, forming a tape along the a axis. PMID:22969673

Ab initio studies of 1,3,5,7-tetranitro-1,3,5,7-tetrazocine/1,3-dimethyl-2-imidazolidinone cocrystal under high pressure using dispersion corrected density functional theory

NASA Astrophysics Data System (ADS)

Gu, Bang-Ming; Lin, He; Zhu, Shun-Guan

2014-04-01

A detailed study of structural, electronic, and thermodynamic properties of 1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX)/1,3-dimethyl-2-imidazolidinone (DMI) cocrystal under the hydrostatic pressure of 0-100 GPa was performed by using dispersion-corrected density functional theory (DFT-D) method. The calculated crystal structure is in reasonable agreement with the experimental data at the ambient pressure. Based on the analysis of lattice constants, bond lengths, bond angles, and dihedral angles under compression, it is found that HMX molecules in HMX/DMI cocrystal are seriously distorted. In addition, as the pressure increases, the band gap decreases gradually, which suggests that HMX/DMI cocrystal is becoming more metallic. Some important intermolecular interactions between HMX and DMI are also observed in the density of states spectrum. Finally, its thermodynamic properties were characterized, and the results show that HMX/DMI cocrystal is more easily formed in the low pressure.

(E)-4-Meth­oxy-N′-[(6-methyl-4-oxo-4H-chromen-3-yl)methyl­idene]benzo­hydrazide monohydrate

PubMed Central

Ishikawa, Yoshinobu; Watanabe, Kohzoh

2014-01-01

In the title hydrate, C19H16N2O4·H2O, the 4H-chromen-4-one segment is slightly twisted, with a dihedral angle between the two six-membered rings of 3.30 (5)°. The dihedral angles between the plane of the pyran­one ring and the hydrazide plane and between the planes of the pyran­one ring and the benzene ring of the p-meth­oxy­benzene unit are 26.69 (4) and 2.23 (3)°, respectively. The mol­ecule is connected to the solvent water mol­ecule by an N—H⋯O hydrogen bond. In the crystal, there are π–π stacking inter­actions between centrosymmetrically related pyran­one rings [centroid–centroid distance = 3.5394 (9) Å], as well as bridges formed by the water mol­ecules via O—H⋯O hydrogen bonds. PMID:25161570

(E)-4-Meth-oxy-N'-(2,4,5-tri-meth-oxy-benzyl-idene)benzohydrazide hemihydrate.

PubMed

Chantrapromma, Suchada; Boonnak, Nawong; Horkaew, Jirapa; Quah, Ching Kheng; Fun, Hoong-Kun

2014-02-01

The title compound crystallizes as a hemihydrate, C18H20N2O5·0.5H2O. The mol-ecule exists in an E conformation with respect to the C=N imine bond. The 4-meth-oxy-phenyl unit is disordered over two sets of sites with a refined occupancy ratio of 0.54 (2):0.46 (2). The dihedral angles between the benzene rings are 29.20 (9) and 26.59 (9)°, respectively, for the major and minor components of the 4-meth-oxy-substituted ring. All meth-oxy substituents lie close to the plane of the attached benzene rings [the Cmeth-yl-O-C-C torsion angles range from -4.0 (12) to 3.9 (2)°]. In the crystal, the components are linked into chains propagating along [001] via N-H⋯O and O-H⋯O hydrogen bonds and weak C-H⋯O inter-actions.

One-step solvothermal deposition of ZnO nanorod arrays on a wood surface for robust superamphiphobic performance and superior ultraviolet resistance

NASA Astrophysics Data System (ADS)

Yao, Qiufang; Wang, Chao; Fan, Bitao; Wang, Hanwei; Sun, Qingfeng; Jin, Chunde; Zhang, Hong

2016-10-01

In the present paper, uniformly large-scale wurtzite-structured ZnO nanorod arrays (ZNAs) were deposited onto a wood surface through a one-step solvothermal method. The as-prepared samples were characterized by X-ray diffraction (XRD), field-emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), thermogravimetry (TG), and differential thermal analysis (DTA). ZNAs with a diameter of approximately 85 nm and a length of approximately 1.5 μm were chemically bonded onto the wood surface through hydrogen bonds. The superamphiphobic performance and ultraviolet resistance were measured and evaluated by water or oil contact angles (WCA or OCA) and roll-off angles, sand abrasion tests and an artificially accelerated ageing test. The results show that the ZNA-treated wood demonstrates a robust superamphiphobic performance under mechanical impact, corrosive liquids, intermittent and transpositional temperatures, and water spray. Additionally, the as-prepared wood sample shows superior ultraviolet resistance.

1-(4,4''-Difluoro-5'-meth-oxy-1,1':3',1''-terphenyl-4'-yl)ethanone.

PubMed

Fun, Hoong-Kun; Hemamalini, Madhukar; Samshuddin, S; Narayana, B; Sarojini, B K

2012-01-01

In the title compound, C(21)H(16)F(2)O(2), the central benzene ring is inclined at dihedral angles of 30.91 (8) and 46.88 (7)° to the two terminal fluoro-substituted rings. The dihedral angle between the two terminal fluoro-subsituted rings is 68.34 (8)°. An intra-molecular C-H⋯O hydrogen bond generates an S(6) ring motif. The crystal structure is stabilized by weak C-H⋯π inter-actions.

N-(3-Chloro-1H-indazol-5-yl)-4-meth­oxy­benzene­sulfonamide

PubMed Central

Chicha, Hakima; Rakib, El Mostapha; Bouissane, Latifa; Saadi, Mohamed; El Ammari, Lahcen

2013-01-01

In the title compound, C14H12ClN3O3S, the fused five- and six-membered rings are folded slightly along the common edge, forming a dihedral angle of 3.2 (1)°. The mean plane through the indazole system makes a dihedral angle of 30.75 (7)° with the distant benzene ring. In the crystal, N—H⋯O hydrogen bonds link the mol­ecules, forming a two-dimensional network parallel to (001). PMID:24454078

Imidazolium 3-nitro­benzoate

PubMed Central

Hou, Guang-Yang; Zhou, Li-Na; Yin, Qiu-Xiang; Su, Wei-Yi; Mao, Hui-Lin

2009-01-01

In the title compound, C3H5N2 +·C7H4NO4 −, the benzene ring forms a dihedral angle of 40.60 (5)° with the imidizolium ring. The nitro­benzoate anion is approximately planar: the benzene ring makes dihedral angles of 3.8 (3) and 3.2 (1)° with the nitro and carboxyl­ate groups, respectively. In the crystal structure, the cations and anions are linked by inter­molecular N—H⋯O hydrogen bonds, forming a zigzag chain along the b axis. PMID:21583857

Structures and anti-inflammatory properties of 4-halogenated -mofebutazones

NASA Astrophysics Data System (ADS)

Reichelt, Hendrik; Paradies, Henrich H.

2018-02-01

The crystal structures of the 4-halogenated (hal: F, Cl, Br)-4-butyl-1-phenyl-1,3-pyrolidine-dione (mofebutazone) are determined, and compared with their solution structures. The racemic 4-halogenated mofebutazone approximants crystallize in a monoclinic space group with four molecules in the unit cell. The 4-hal-mofebutazone molecules reveal strong hydrogen bonding between the hydrogen atom located at the N-2 nitrogen atom and a carbonyl oxygen atom of an adjacent 4-hal-mofebutazone molecule. The hydrogen bond angle for 4-Br-mifebutazone N (2)sbnd H (1)⋯O (1) is 173(3) °, so that the hydrogen bond is essentially linear indicating an infinite chain hydrogen bond network. The 3d and 2d structures are stabilized by π-π and σ-π interactions, short intermolecular distances, and apolar forces between adjacently stacked phenyl rings. Small-angle-X-ray scattering (SAXS) experiments and osmometric measurements reveal the presence of dimers for the 4-hal-mofebutazone molecules. Molecular simulations indicate similar solution structure factors for the 4-hal-mofebutazones solutions, S(Q), and in the solid state. There is a strong indication that the [1,1,0], [1,0,0], and [1,0,0] periodicities of the 4-Brsbnd , 4-Clsbnd and 4-F-mofebutazone in the crystalline solid state were also present in the solution phase. The biochemical and cellular activities of the different 4-hal-mofebutazones were monitored by the magnitude of their inhibition of the PGE2 biosynthesis through the cyclo-oxygenase (COX-1) in macrophages, and on the inhibition of LTD4 (5-lipoxygenase) in polymorphonuclear leukocytes.

Conformational stability of the propylene oxide-water adduct: direct spectroscopic detection of O-H...O hydrogen bonded conformers.

PubMed

Su, Zheng; Wen, Qing; Xu, Yunjie

2006-05-24

The 1:1 molecular adduct of propylene oxide and water (PO-H(2)O) was studied using Fourier transform microwave spectroscopy and high level ab initio methods. Two distinct structural conformers with the water molecule acting as a proton donor were detected experimentally: one with the water on the same side as the methyl group with respect to the ether ring, i.e., syn-PO-H(2)O, the other with the water molecule binding to the O-atom from the opposite side of the methyl group, i.e., anti-PO-H(2)O. The nonbonded hydrogen is entgegen to the ether ring in both conformers. Rotational spectra of four isotopic species, namely PO-H(2)O, PO-DOH, PO-HOD, and PO-D(2)O, were recorded for the two conformers. The hydrogen bond parameters: r(O(epoxy)...H), angle(ring-O(epoxy)...H), and angle(O(epoxy)...H-O) are 1.908 A, 112 degrees, and 177 degrees for syn-PO-H(2)O, and 1.885 A, 104.3 degrees, and 161.7 degrees for anti-PO-H(2)O, respectively. The experimental results suggest that the hydrogen bond in syn-PO-H(2)O is stronger and the monomer subunits are more rigidly locked in their positions than in the ethylene oxide-water adduct. The stabilizing effect of the methyl group to the intermolecular hydrogen bond is discussed in terms of the experimentally estimated binding energies, the structural parameters, and the ab initio calculations.

X-ray structure determination, Hirshfeld surface analysis, spectroscopic (FT-IR, NMR, UV-Vis, fluorescence), non-linear optical properties, Fukui function and chemical activity of 4‧-(2,4-dimethoxyphenyl)-2,2‧:6‧,2″-terpyridine

NASA Astrophysics Data System (ADS)

Demircioğlu, Zeynep; Yeşil, Ahmet Emin; Altun, Mehmet; Bal-Demirci, Tülay; Özdemir, Namık

2018-06-01

The compound 4‧-(2,4-dimethoxyphenyl)-2,2‧:6‧,2″-terpyridine (Mtpyr) was synthesized and investigated using X-ray single crystal structure determination, combined with Hirshfeld topology analysis of the molecular packing. In addition, Mtpyr was characterized by experimental and theoretical FT-IR, UV-Vis, 1H NMR, 13C NMR and fluorescence emission spectra. The optimized molecular geometry (bond length, bond angle, torsion angle), the complete vibrational frequency and all other theoretical computations were calculated by using density functional theory (DFT) B3LYP method with the help of 6-311++G(d,p) basis set. From the recorded UV-Vis spectrum, the electronic properties such as excitation energies, wavelength and oscillator strength are evaluated by TD-DFT in chloroform solution. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the gauge-independent atomic orbital (GIAO) method and compared with experimental results. The calculated HOMO-LUMO band gap energies confirmed that charge transfer and chemical stability within the molecule. The hyperconjugative interaction energy E(2) and electron densities of donor (i) and acceptor (j) bonds were calculated using natural bond orbital (NBO) analysis. Besides Mulliken and natural population charges (NPA), non-linear optic properties (NLO), Fukui Function analysis, molecular electrostatic potential (MEP) were also computed which helps to identifying the electrophilic/nucleophilic nature.

Comparative Evaluation of Impact Strength of Fragment Bonded Teeth and Intact Teeth: An In Vitro Study

PubMed Central

Venugopal, L; Lakshmi, M Narasimha; Babu, Devatha Ashok; Kiran, V Ravi

2014-01-01

Background: To test and compare the impact strength of fragment bonded teeth with that of intact teeth by using impact testing machine (pendulum type) as a mode of load. Materials and Methods: Forty extracted, maxillary, central incisors selected for this study (20 control group and 20 experimental group). In experimental group, teeth crowns were fractured with a microtome at 2.5 mm from mesioincisal angle cervically, fractured portion is attached to original crown portion with 3 M single bond dentin bonding agent and 3 M Z ‘100’, composite resin. Impact strength of fragment bonded teeth and intact teeth tested with impact testing machine and compared. Results: Mean impact strength of fragment bonded teeth (30.76 KJ/M2 ) is not statistically significant deferent from mean impact strength of intact teeth (31.11 KJ/M2 ). Conclusion: Mean impact strength of fragment bonded teeth is not statistically different with that of intact teeth. Hence, after fracture of teeth if it is restored with fragment reattachment by using 3 M single bond dentin bonding agent and 3 M Z ‘100’ composite resin is having impact strength like that of intact teeth. How to cite the article: Venugopal L, Lakshmi MN, Babu DA, Kiran VR. Comparative evaluation of impact strength of fragment bonded teeth and intact teeth: An in vitro study. J Int Oral Health 2014;6(3):73-6. PMID:25083037

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.

Multicanonical molecular dynamics simulations combined with Metadynamics for the free energy landscape of a biomolecular system with high energy barriers

NASA Astrophysics Data System (ADS)

Yonezawa, Yasushige; Shimoyama, Hiromitsu; Nakamura, Haruki

2011-01-01

Multicanonical molecular-dynamics (McMD) simulation and Metadynamics (MetaD) are useful for obtaining the free-energies, and can be mutually complementary. We combined McMD with MetaD, and applied it to the conformational free energy calculations of a proline dipeptide. First, MetaD was performed along the dihedral angle at the prolyl bond and we obtained a coarse biasing potential. After adding the biasing potential to the dihedral angle potential energy, we conducted McMD with the modified potential energy. Enhanced sampling was achieved for all degrees-of-freedom, and the sampling of the dihedral angle space was facilitated. After reweighting, we obtained an accurate free energy landscape.

1H-Indole-3-carbaldehyde

PubMed Central

Dileep, C. S.; Abdoh, M. M. M.; Chakravarthy, M. P.; Mohana, K. N.; Sridhar, M. A.

2012-01-01

In the title compound, C9H7NO, the benzene ring forms a dihedral angle of 3.98 (12)° with the pyrrole ring. In the crystal, N–H⋯O hydrogen bonds links the mol­ecules into chains which run parallel to [02-1]. PMID:23284457

The Significance of the Bond Angle in Sulfur Dioxide.

ERIC Educational Resources Information Center

Purser, Gordon H.

1989-01-01

Examined are the illustrations and descriptions of the molecular structure of sulfur dioxide found in selected chemistry textbooks. Inconsistencies and incorrect information are indicated. It is suggested that molecules other than sulfur dioxide be used as examples of molecules for which resonance is important. (CW)

Generalized Brewster effect in dielectric metasurfaces

PubMed Central

Paniagua-Domínguez, Ramón; Yu, Ye Feng; Miroshnichenko, Andrey E.; Krivitsky, Leonid A.; Fu, Yuan Hsing; Valuckas, Vytautas; Gonzaga, Leonard; Toh, Yeow Teck; Kay, Anthony Yew Seng; Luk'yanchuk, Boris; Kuznetsov, Arseniy I.

2016-01-01

Polarization is a key property defining the state of light. It was discovered by Brewster, while studying light reflected from materials at different angles. This led to the first polarizers, based on Brewster's effect. Now, one of the trends in photonics is the study of miniaturized devices exhibiting similar, or improved, functionalities compared with bulk optical elements. In this work, it is theoretically predicted that a properly designed all-dielectric metasurface exhibits a generalized Brewster's effect potentially for any angle, wavelength and polarization of choice. The effect is experimentally demonstrated for an array of silicon nanodisks at visible wavelengths. The underlying physics is related to the suppressed scattering at certain angles due to the interference between the electric and magnetic dipole resonances excited in the nanoparticles. These findings open doors for Brewster phenomenon to new applications in photonics, which are not bonded to a specific polarization or angle of incidence. PMID:26783075

Biomolecular Chemistry of Isopropyl Fibrates

PubMed Central

Rath, Niharika; Kotheimer, Amenda; Miller, Chad; Zeller, Matthias; Rath, Nigam P.

2012-01-01

Isopropyl 2-[4-(4-chlorobenzoyl)-phenoxy]-2-methylpropanoic acid and isopropyl 2-(4-chlorophenoxy)-2-methylpropanoate, also known as fenofibrate and isopropyl clofibrate, are hypolipidemic agents of the fibrate family. In a previously reported triclinic structure of fenofibrate (polymorph I) the methyl groups of the isopropyl moiety (iPr) are located symmetrically about the carboxylate group. We report a new monoclinic form (polymorph II) of fenofibrate and a first structural description of isopropyl clofibrate, and in these the methyl groups are placed asymmetrically about the carboxylate group. In particular the dihedral (torsion) angle between the hydrogen atom on the secondary C and the C atom of the carboxyl group makes a 2.74° angle about the ester O-C bond in the symmetric fenofibrate structure of polymorph I, whereas the same dihedral angle is 45.94° in polymorph II and -30.9° in the crystal structure of isopropyl clofibrate. Gas phase DFT geometry minimizations of fenofibrate and isopropyl clofibrate result in lowest energy conformations for both molecules with a value of about ± 30° for this same angle between the O=C-O-C plane and the C-H bond of the iPr group. A survey of crystal structures containing an iPr ester group reveals that the asymmetric conformation is predominant. Although the hydrogen atom on the secondary C atom of the isopropyl group is located at a comparable distance from the carbonyl oxygen in the symmetric and asymmetric fenofibrate (2.52 and 2.28 Å) and the isopropyl clofibrate (2.36 Å) structures, this hydrogen atom participates in a puckered five membered ring arrangement in the latter two that is unlike the planar arrangement found in symmetric fenofibrate (polymorph I). Polar molecular surface area (PSA) values indicate fenofibrate and isopropyl clofibrate are less able to act as acceptors of hydrogen bonds than their corresponding acid derivatives. Surface area calculations show dynamic polar molecular surface area (PSAd) values of the iPr esters of the fibrates are lower than those of their acids, implying that the fibrates have better membrane permeability and a higher absorbability and hence are better prodrugs when these agents need to be orally administered. PMID:22246648

(E)-2-[2-(3-Nitro­phen­yl)ethen­yl]quinolin-8-ol

PubMed Central

Schulze, Mathias; Seichter, Wilhelm; Weber, Edwin

2013-01-01

In the title compound, C17H12N2O3, the mean planes of the benzene ring and the quinoline moiety are inclined to one another by 11.0 (1)°. The nitro substituent is twisted at an angle of 7.9 (2)° with respect to the attached benzene ring. Intra­molecular O—H⋯N and C—H⋯N hydrogen bonds occur. The crystal is constructed of mol­ecular stacks without involvement of π-stacking inter­actions, but showing inter­stack association via O—H⋯O and C—H⋯O hydrogen bonding. Thus, the supramolecular architecture of the crystal results from stacked molecules stabilized by hydrogen bonding between the stacks. PMID:24454092

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.

Conformational studies of bacterial peptidoglycan: structure and stereochemistry of N-acetyl-β- D-glucosamine and N-acetyl-β- D-muramic acid

NASA Astrophysics Data System (ADS)

Yadav, P. N. S.; Rai, D. K.; Yadav, J. S.

1989-03-01

The energies of various conformations of N-acetyl-β- D-glucosamine (NAG) and its 3-O- D-lactic acid derivative N-acetyl-β- D-muramic acid (NAM) have been calculated by geometry optimization using the molecular mechanics program MM2. The geometries of these systems have been analyzed in the light of ring torsion, bond lengths, bond angles and conformational states of side groups of the pyranosyl ring and compared with available experimental data of similar pyranose derivatives. The present study indicates the presence of hydrogen bonds to stabilize the side group conformations. Discrepancies with experimental data that are seen in a few cases are ascribed to the nature of the side groups and their geometry.

4-Amino-N-(3-meth­oxy­pyrazin-2-yl)benzene­sulfonamide

PubMed Central

Bruni, Bruno; Coran, Silvia A.; Bartolucci, Gianluca; Di Vaira, Massimo

2010-01-01

The overall mol­ecular geometry of the title compound, C11H12N4O3S, is bent, with a dihedral angle of 89.24 (5)° between the best planes through the two aromatic rings. Each mol­ecule behaves as a hydrogen-bond donor toward three different mol­ecules, through its amidic and the two aminic H atoms, and it behaves as a hydrogen-bond acceptor from two other mol­ecules via one of its sulfonamidic O atoms. In the crystal, mol­ecules linked by N—H⋯N and N—H⋯O hydrogen bonds form kinked layers parallel to (001), adjacent layers being connected by van der Waals inter­actions. PMID:21587634

5-Methylpyrazine-2-carboxamide

DOE PAGES

Rillema, D. Paul; Senaratne, Nilmini K.; Moore, Curtis; ...

2017-07-28

The title compound, C 6H 7N 3O, is nearly planar, with a dihedral angle of 2.14 (11)° between the pyrazine ring and the mean plane of the carboxamide group [C—C(=O)—N]. In the crystal, molecules are linked via pairs of N—H...O hydrogen bonds forming inversion dimers with an R 2 2 (8) ring motif. These dimers are further linked by a pair of N—H...N hydrogen bonds, enclosing an R 2 2 (10) ring motif, and C—H...O hydrogen bonds, forming ribbons lying parallel to the ab plane. The ribbons are linked by offset π–π interactions [intercentroid distance = 3.759(1)Å], forming two setsmore » of mutually perpendicular slabs parallel to planes (110) and (1-10).« less

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}

Magnetic exchange in {Gd(III)-radical} complexes: method assessment, mechanism of coupling and magneto-structural correlations.

PubMed

Gupta, Tulika; Rajeshkumar, Thayalan; Rajaraman, Gopalan

2014-07-28

Density functional studies have been performed on ten different {Gd(III)-radical} complexes exhibiting both ferro and antiferromagnetic exchange interaction with an aim to assess a suitable exchange-correlation functional within DFT formalism. This study has also been extended to probe the mechanism of magnetic coupling and to develop suitable magneto-structural correlations for this pair. Our method assessments reveal the following order of increasing accuracy for the evaluation of J values compared to experimental coupling constants: B(40HF)LYP < BHandHLYP < TPSSH < PW91 < PBE < BP86 < OLYP < BLYP < PBE0 < X3LYP < B3LYP < B2PLYP. Grimme's double-hybrid functional is found to be superior compared to other functionals tested and this is followed very closely by the conventional hybrid B3LYP functional. At the basis set front, our calculations reveal that the incorporation of relativistic effect is important in these calculations and the relativistically corrected effective core potential (ECP) basis set is found to yield better Js compared to other methods. The supposedly empty 5d/6s/6p orbitals of Gd(III) are found to play an important role in the mechanism of magnetic coupling and different contributions to the exchange terms are probed using Molecular Orbital (MO) and Natural Bond Orbital (NBO) analysis. Magneto-structural correlations for Gd-O distances, Gd-O-N angles and Gd-O-N-C dihedral angles are developed where the bond angles as well as dihedral angle parameters are found to dictate the sign and strength of the magnetic coupling in this series.

Design, fabrication and test of graphite/polyimide composite joints and attachments for advanced aerospace vehicles

NASA Technical Reports Server (NTRS)

Barclay, D. L.

1980-01-01

Results of an experimental program to develop several types of graphite/polyimide (GR/PI) bonded and bolted joints for lightly loaded flight components for advanced space transportation systems and high speed aircraft are presented. Tasks accomplished include: a literature survey; design of static discriminator specimens; design allowables testing; fabrication of test panels and specimens; small specimen testing; and standard joint testing. Detail designs of static discriminator specimens for each of the four major attachment types are presented. Test results are given for the following: (1) transverse tension of Celion 3000/PMR-15 laminate; (2) net tension of a laminate for both a loaded and unloaded bolt hole; (3) comparative testing of bonded and co-cured doublers along with pull-off tests of single and double bonded angles; (4) single lap shear tests, transverse tension and coefficient of thermal expansion tests of A7F (LARC-13 amide-imide modified) adhesive; and (5) tension tests of standard single lap, double lap, and symmetric step lap bonded joints. Also, included are results of a finite element analysis of a single lap bonded composite joint.

Effects of surface treatments and bonding types on the interfacial behavior of fiber metal laminate based on magnesium alloy

NASA Astrophysics Data System (ADS)

Zhang, Xi; Ma, Quanyang; Dai, Yu; Hu, Faping; Liu, Gang; Xu, Zouyuan; Wei, Guobing; Xu, Tiancai; Zeng, Qingwen; Xie, Weidong

2018-01-01

Fiber metal laminates based on magnesium alloys (MgFML) with different surface treatments and different bonding types were tested and analyzed. By using dynamic contact angle measurement and scanning electron microscopy (SEM), it was found that phosphating treatment can significantly improve the surface energy and wettability of magnesium alloy, and the surface energy of phosphated magnesium alloy was approximately 50% higher than that of abraded-only magnesium alloy. The single cantilever beam (SCB) test showed that the interfacial fracture energies of directly bonded MgFMLs based on abraded-only magnesium and abraded + phosphated magnesium were 650 J/m2 and 1030 J/m2, respectively, whereas the interfacial fracture energies of indirectly bonded MgFMLs were 1650 J/m2 and 2260 J/m2, respectively. Phosphating treatment and modified polypropylene interleaf were observed to improve the tensile strength and interfacial fracture toughness of MgFML. In addition, the rougher surface was more conducive to enhance the bonding strength and interfacial fracture toughness of MgFML.

Non-classical adhesive-bonded joints in practical aerospace construction

NASA Technical Reports Server (NTRS)

Hart-Smith, L. J.

1973-01-01

Solutions are derived for adhesive-bonded joints of non-classical geometries. Particular attention is given to bonded doublers and to selective reinforcement by unidirectional composites. Non-dimensionalized charts are presented for the efficiency limit imposed on the skin as the result of the eccentricity in the load path through the doubler. It is desirable to employ a relativly large doubler to minimize the effective eccentricity in the load path. The transfer stresses associated with selective reinforcement of metal structures by advanced composites are analyzed. Reinforcement of bolt holes in composites by bonded metal doublers is covered quantitatively. Also included is the adhesive joint analysis for shear flow in a multi-cell torque box, in which the bond on one angle becomes more critical sooner than those on the others, thereby restricting the strength to less than the total of each maximum strength when acting alone. Adhesive plasticity and adherend stiffness and thermal imbalances are included. A simple analysis/design technique of solution in terms of upper and lower bounds on an all-plastic adhesive analysis is introduced.

Detection and structural characterization of nitrosamide H2NNO: A central intermediate in deNOx processes.

PubMed

McCarthy, Michael C; Lee, Kin Long Kelvin; Stanton, John F

2017-10-07

The structure and bonding of H 2 NNO, the simplest N-nitrosamine, and a key intermediate in deNO x processes, have been precisely characterized using a combination of rotational spectroscopy of its more abundant isotopic species and high-level quantum chemical calculations. Isotopic spectroscopy provides compelling evidence that this species is formed promptly in our discharge expansion via the NH 2 + NO reaction and is collisionally cooled prior to subsequent unimolecular rearrangement. H 2 NNO is found to possess an essentially planar geometry, an NNO angle of 113.67(5)°, and a N-N bond length of 1.342(3) Å; in combination with the derived nitrogen quadrupole coupling constants, its bonding is best described as an admixture of uncharged dipolar (H 2 N-N=O, single bond) and zwitterion (H 2 N + =N-O - , double bond) structures. At the CCSD(T) level, and extrapolating to the complete basis set limit, the planar geometry appears to represent the minimum of the potential surface, although the torsional potential of this molecule is extremely flat.

Detection and structural characterization of nitrosamide H2NNO: A central intermediate in deNOx processes

NASA Astrophysics Data System (ADS)

McCarthy, Michael C.; Lee, Kin Long Kelvin; Stanton, John F.

2017-10-01

The structure and bonding of H2NNO, the simplest N-nitrosamine, and a key intermediate in deNOx processes, have been precisely characterized using a combination of rotational spectroscopy of its more abundant isotopic species and high-level quantum chemical calculations. Isotopic spectroscopy provides compelling evidence that this species is formed promptly in our discharge expansion via the NH2 + NO reaction and is collisionally cooled prior to subsequent unimolecular rearrangement. H2NNO is found to possess an essentially planar geometry, an NNO angle of 113.67(5)°, and a N-N bond length of 1.342(3) Å; in combination with the derived nitrogen quadrupole coupling constants, its bonding is best described as an admixture of uncharged dipolar (H2N-N=O, single bond) and zwitterion (H2N+=N-O-, double bond) structures. At the CCSD(T) level, and extrapolating to the complete basis set limit, the planar geometry appears to represent the minimum of the potential surface, although the torsional potential of this molecule is extremely flat.

Polar Cation Ordering: A Route to Introducing >10% Bond Strain Into Layered Oxide Films

DOE PAGES

Nelson-Cheeseman, Brittany B.; Zhou, Hua; Balachandran, Prasanna V.; ...

2014-09-05

The 3d transition metal (M) perovskite oxides exhibit a remarkable array of properties, including novel forms of superconductivity, magnetism and multiferroicity. Strain can have a profound effect on many of these properties. This is due to the localized nature of the M 3d orbitals, where even small changes in the M–O bond lengths and M–O–M bond angles produced by strain can be used to tune the 3d– O 2p hybridization, creating large changes in electronic structure. We present a new route to strain the M–O bonds in epitaxial two-dimensional perovskite films by tailoring local electrostatic dipolar interactions within every formulamore » unit via atomic layer-by-layer synthesis. The response of the O anions to the resulting dipole electric fields distorts the M–O bonds by more than 10%, without changing substrate strain or chemical composition. We found that this distortion is largest for the apical oxygen atoms (O ap), and alters the transition metal valence state via self-doping without chemical substitution.« less

A Comparison of Fabrication Techniques for Hollow Retroreflectors

NASA Technical Reports Server (NTRS)

Preston, Alix; Merkowitz, Stephen

2014-01-01

Despite the wide usage of hollow retroreflectors, there is limited literature involving their fabrication techniques and only two documented construction methods could be found. One consists of an adjustable fixture that allows for the independent alignment of each mirror, while the other consists of a modified solid retroreflector that is used as a mandrel. Although both methods were shown to produce hollow retroreflectors with arcsecond dihedral angle errors, a comparison and analysis of each method could not be found which makes it difficult to ascertain which method would be better suited to use for precision-aligned retroreflectors. Although epoxy bonding is generally the preferred method to adhere the three mirrors, a relatively new method known as hydroxide-catalysis bonding (HCB) presents several potential advantages over epoxy bonding. HCB has been used to bond several optical components for space-based missions, but has never been applied for construction of hollow retroreflectors. In this paper we examine the benefits and limitations of each bonding fixture as well as present results and analysis of hollow retroreflectors made using both epoxy and HCB techniques.

Novel poly(dimethylsiloxane) bonding strategy via room temperature "chemical gluing".

PubMed

Lee, Nae Yoon; Chung, Bong Hyun

2009-04-09

Here we propose a new scheme for bonding poly(dimethylsiloxane) (PDMS), namely, a "chemical gluing", at room temperature by anchoring chemical functionalities on the surfaces of PDMS. Aminosilane and epoxysilane are anchored separately on the surfaces of two PDMS substrates, the reaction of which are well-known to form a strong amine-epoxy bond, therefore acting as a chemical glue. The bonding is performed for 1 h at room temperature without employing heat. We characterize the surface properties and composition by contact angle measurement, X-ray photoelectron spectroscopy analysis, and fluorescence measurement to confirm the formation of surface functionalities and investigate the adhesion strength by means of pulling, tearing, and leakage tests. As confirmed by the above-mentioned analyses and tests, PDMS surfaces were successfully modified with amine and epoxy functionalities, and a bonding based on the amine-epoxy chemical gluing was successfully realized within 1 h at room temperature. The bonding was sufficiently robust to tolerate intense introduction of liquid whose per minute injection volume was almost 2000 times larger than the total internal volume of the microchannel used. In addition to the bonding of PDMS-PDMS homogeneous assembly, the bonding of the PDMS-poly(ethylene terephthalate) heterogeneous assembly was also examined. We also investigate the potential use of the multifunctionalized walls inside the microchannel, generated as a consequence of the chemical gluing, as a platform for the targeted immobilization.

Compressibility behaviour of conducting ceramic TiB2

NASA Astrophysics Data System (ADS)

Arpita Aparajita, A. N.; Kumar, N. R. Sanjay; Shekar, N. V. Chandra; Kalavathi, S.

2017-09-01

To address the large spread in the bulk modulus value of TiB2 reported in literature, high pressure compressibility study of a phase pure polycrystalline sample has been carried out using in situ high pressure x-ray diffraction technique (HPXRD) in angle dispersive mode. The study has been done up to 23 GPa at ambient temperature with methanol-ethanol-water (MEW) as pressure transmitting medium. The hexagonal lattice has been found to be stable in the pressure range studied. The isothermal bulk modulus is estimated to be 333(6) GPa by employing 3rd order Birch-Murnaghan equation of state. The obtained high value of bulk modulus is understood in terms of band filling effect, and the nature of bonding between B-B and Ti-B in TiB2. Compressibility along ‘a’ and ‘c’ axis is found to be anisotropic with compressibility values of 0.93(2) TPa-1 and 1.14(2) TPa-1 respectively. From the estimated bond lengths for Ti-B and B-B it is found that B-B bonds are less compressible compared to Ti-B bonds which is in accordance with the respective nature of Ti-B and B-B bonds. A change in the rate of bond contraction was seen around 12 GPa which is due to the bond hardening for both Ti-B and B-B bonds with pressure.

Stress intensity factors in bonded half planes containing inclined cracks and subjected to antiplane shear loading

NASA Technical Reports Server (NTRS)

Bassani, J. L.; Erdogan, F.

1979-01-01

The antiplane shear problem for two bonded dissimilar half planes containing a semi-infinite crack or two arbitrarily located collinear cracks is considered. For the semi-infinite crack the problem is solved for a concentrated wedge load and the stress intensity factor and the angular distribution of stresses are calculated. For finite cracks the problem is reduced to a pair of integral equations. Numerical results are obtained for cracks fully imbedded in a homogeneous medium, one crack tip touching the interface, and a crack crossing the interface for various crack angles.

3-(4-Carb­oxy-5-carboxyl­ato-1H-imidazol-2-yl)pyridin-1-ium monohydrate

PubMed Central

Liu, Guang-Jun; Zhao, Guang-Wang; Li, Li; Gao, Hong-Tao

2011-01-01

In the zwitterionic mol­ecule of the title compound, C10H7N3O4·H2O, one carboxyl group is deprotonated and the pyridine N atom is protonated. The pyridinium and imidazole rings form a dihedral angle of 5.23 (1)°. An intramolecular O—H⋯O hydrogen bond occurs. In the crystal, inter­molecular N—H⋯O, O—H⋯N and O—H⋯O hydrogen bonds link the zwitterions and water mol­ecules into sheets parallel to (102). PMID:21523144

1,4-Bis(4H-1,2,4-triazol-4-yl)benzene dihydrate

PubMed Central

Wang, Xiu-Guang; Li, Jian-Hui; Ding, Bin; Du, Gui-Xiang

2012-01-01

The asymmetric unit of the title compound, C10H8N6·2H2O, comprises half the organic species, the mol­ecule being completed by inversion symmetry, and one water mol­ecule. The dihedral angle between the 1,2,4-triazole ring and the central benzene ring is 32.2 (2)°. The water mol­ecules form O—H⋯N hydrogen bonds with N-atom acceptors of the triazole rings. C—H⋯N hydrogen bonds are also observed, giving a three-dimensional framework. PMID:22904851

N-[4-Cyano-3-(trifluoro­meth­yl)phen­yl]-2-eth­oxy­benzamide

PubMed Central

Naveen, S.; Basappa; Manjunath, H. R.; Sridhar, M. A.; Shashidhara Prasad, J.; Rangappa, K. S.

2010-01-01

In the title compound, C17H13F3N2O2, the two aromatic rings are essentially coplanar, forming a dihedral angle of 2.78 (12)°. The non-H atoms of the eth­oxy group are coplanar with the attached ring [maximum deviation = 0.271 (3) Å]. An intra­molecular N—H⋯O hydrogen bond occurs. In the crystal structure, mol­ecules are linked by inter­molecular C—H⋯N and C—H⋯F hydrogen bonds. PMID:21587782

4-[(3-Hy­droxy­anil­ino)­(phenyl)­methyl­idene]-3-methyl-1-phenyl-1H-pyrazol-5(4H)-one

PubMed Central

Saida, Keraghel; Fatiha, Benghanem; Ouarda, Dehbi; Ali, Ourari; Kamel, Ouari; Brelot, Lydia

2012-01-01

In the title compound, C23H19N3O2, the dihedral angles formed by the pyrazolone ring with the three benzene rings are 30.91 (6), 60.96 (4) and 57.01 (4)°. The ligand is in the enamine–keto form and its structure is stabilized by an intra­molecular N—H⋯O hydrogen bond. In the crystal, O—H⋯N hydrogen bonds link mol­ecules into chains parallel to [01-1]. PMID:22719664

Stress intensity factors in bonded half planes containing inclined cracks and subjected to antiplane shear loading

NASA Technical Reports Server (NTRS)

Bassani, J. L.; Erdogan, F.

1978-01-01

The antiplane shear problem for two bonded dissimilar half planes containing a semi-infinite crack or two arbitrarily located collinear cracks was considered. For the semi-infinite crack the problem was solved for a concentrated wedge load and the stress intensity factor and the angular distribution of stresses were calculated. For finite cracks the problem was reduced to a pair of integral equations. Numerical results were obtained for cracks fully imbedded in a homogeneous medium, one crack tip touching the interface, and a crack crossing the interface for various crack angles.

N-(2-Allyl-4-eth­oxy-2H-indazol-5-yl)-4-methyl­benzene­sulfonamide

PubMed Central

Chicha, Hakima; Rakib, El Mostapha; Bouissane, Latifa; Viale, Maurizio; Saadi, Mohamed; El Ammari, Lahcen

2014-01-01

The indazole ring system of the title compound, C19H21N3O3S, is almost planar (r.m.s. deviation = 0.0192 Å) and forms dihedral angles of 77.99 (15) and 83.9 (3)° with the benzene ring and allyl group, respectively. In the crystal, centrosymmetrically related mol­ecules are connected by pairs of N—H⋯O hydrogen bonds into dimers, which are further linked by C—H⋯O hydrogen bonds, forming columns parallel to the b axis. PMID:24860413

5-Chloro-2-nitro-phenol.

PubMed

Ren, Dong-Mei

2012-05-01

The asymmetric unit of the title compound, C(6)H(4)ClNO(3), contains two independent mol-ecules in which the dihedral angles between the benzene ring and the nitro groups are 2.5 (1) and 8.5 (1)°. Intra-molecular O-H⋯O hydrogen bonds involving the hy-droxy and nitro substituents result in the formation of S(6) six-membered rings. In the crystal, O-H⋯O, O-H⋯Cl and C-H⋯O hydrogen bonds together with Cl⋯O contacts [3.238 (3) and 3.207 (3) Å] generate a three-dimensional network.

Phthalazin-1(2H)-one–picric acid (1/1)

PubMed Central

Yathirajan, H. S.; Narayana, B.; Swamy, M. T.; Sarojini, B. K.; Bolte, Michael

2008-01-01

The geometric parameters of the title compound, C8H6N2O·C6H3N3O7, are in the usual ranges. The three nitro groups are almost coplanar with the aromatic picrate ring [dihedral angles 10.2 (2)°, 7.62 (16) and 8.08 (17)°]. The mol­ecular conformation of the picric acid is stabilized by an intra­molecular O—H⋯O hydrogen bond. The phthalazin-1(2H)-one mol­ecules are connected via N—H⋯O hydrogen bonds, forming centrosymmetric dimers. PMID:21200682

Topological Qubits from Valence Bond Solids

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Hydroxyl orientations in cellobiose and other polyhydroxy compounds – modeling versus experiment

USDA-ARS?s Scientific Manuscript database

Theoretical and experimental gas-phase studies of carbohydrates show that their hydroxyl groups are located in homodromic partial rings that resemble cooperative hydrogen bonds, albeit with long H…O distances and small O-H…O angles. On the other hand, anecdotal experience with disaccharide crystal ...

1,5-Bis(1-phenyl-ethyl-idene)thio-carbono-hydrazide.

PubMed

Feng, Lei; Ji, Haiwei; Wang, Renliang; Ge, Haiyan; Li, Li

2011-06-01

The title mol-ecule, C(17)H(18)N(4)S, is not planar, as indicated by the dihedral angle of 27.24 (9)° between the two benzene rings. In the crystal, inter-molecular N-H⋯S hydrogen bonds link pairs of mol-ecules into inversion dimers.

A Reference-Free and Non-Contact Method for Detecting and Imaging Damage in Adhesive-Bonded Structures Using Air-Coupled Ultrasonic Transducers.

PubMed

Yonathan Sunarsa, Timotius; Aryan, Pouria; Jeon, Ikgeun; Park, Byeongjin; Liu, Peipei; Sohn, Hoon

2017-12-08

Adhesive bonded structures have been widely used in aerospace, automobile, and marine industries. Due to the complex nature of the failure mechanisms of bonded structures, cost-effective and reliable damage detection is crucial for these industries. Most of the common damage detection methods are not adequately sensitive to the presence of weakened bonding. This paper presents an experimental and analytical method for the in-situ detection of damage in adhesive-bonded structures. The method is fully non-contact, using air-coupled ultrasonic transducers (ACT) for ultrasonic wave generation and sensing. The uniqueness of the proposed method relies on accurate detection and localization of weakened bonding in complex adhesive bonded structures. The specimens tested in this study are parts of real-world structures with critical and complex damage types, provided by Hyundai Heavy Industries ® and IKTS Fraunhofer ® . Various transmitter and receiver configurations, including through transmission, pitch-catch scanning, and probe holder angles, were attempted, and the obtained results were analyzed. The method examines the time-of-flight of the ultrasonic waves over a target inspection area, and the spatial variation of the time-of-flight information was examined to visualize and locate damage. The proposed method works without relying on reference data obtained from the pristine condition of the target specimen. Aluminum bonded plates and triplex adhesive layers with debonding and weakened bonding were used to examine the effectiveness of the method.

A Reference-Free and Non-Contact Method for Detecting and Imaging Damage in Adhesive-Bonded Structures Using Air-Coupled Ultrasonic Transducers

PubMed Central

Yonathan Sunarsa, Timotius; Aryan, Pouria; Jeon, Ikgeun; Park, Byeongjin; Liu, Peipei

2017-01-01

Adhesive bonded structures have been widely used in aerospace, automobile, and marine industries. Due to the complex nature of the failure mechanisms of bonded structures, cost-effective and reliable damage detection is crucial for these industries. Most of the common damage detection methods are not adequately sensitive to the presence of weakened bonding. This paper presents an experimental and analytical method for the in-situ detection of damage in adhesive-bonded structures. The method is fully non-contact, using air-coupled ultrasonic transducers (ACT) for ultrasonic wave generation and sensing. The uniqueness of the proposed method relies on accurate detection and localization of weakened bonding in complex adhesive bonded structures. The specimens tested in this study are parts of real-world structures with critical and complex damage types, provided by Hyundai Heavy Industries® and IKTS Fraunhofer®. Various transmitter and receiver configurations, including through transmission, pitch-catch scanning, and probe holder angles, were attempted, and the obtained results were analyzed. The method examines the time-of-flight of the ultrasonic waves over a target inspection area, and the spatial variation of the time-of-flight information was examined to visualize and locate damage. The proposed method works without relying on reference data obtained from the pristine condition of the target specimen. Aluminum bonded plates and triplex adhesive layers with debonding and weakened bonding were used to examine the effectiveness of the method. PMID:29292752

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.

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

Conduction Properties of KcsA Measured Using Brownian Dynamics with Flexible Carbonyl Groups in the Selectivity Filter

PubMed Central

Chung, Shin-Ho; Corry, Ben

2007-01-01

In the narrow segment of an ion conducting pathway, it is likely that a permeating ion influences the positions of the nearby atoms that carry partial or full electronic charges. Here we introduce a method of incorporating the motion of charged atoms lining the pore into Brownian dynamics simulations of ion conduction. The movements of the carbonyl groups in the selectivity filter of the KcsA channel are calculated explicitly, allowing their bond lengths, bond angles, and dihedral angels to change in response to the forces acting upon them. By systematically changing the coefficients of bond stretching and of angle bending, the carbon and oxygen atoms can be made to fluctuate from their fixed positions by varying mean distances. We show that incorporating carbonyl motion in this way does not alter the mechanism of ion conduction and only has a small influence on the computed current. The slope conductance of the channel increases by ∼25% when the root mean-square fluctuations of the carbonyl groups are increased from 0.01 to 0.61 Å. The energy profiles and the number of resident ions in the channel remain unchanged. The method we utilized here can be extended to allow the movement of glutamate or aspartate side chains lining the selectivity filters of other ionic channels. PMID:17434934

Conduction properties of KcsA measured using brownian dynamics with flexible carbonyl groups in the selectivity filter.

PubMed

Chung, Shin-Ho; Corry, Ben

2007-07-01

In the narrow segment of an ion conducting pathway, it is likely that a permeating ion influences the positions of the nearby atoms that carry partial or full electronic charges. Here we introduce a method of incorporating the motion of charged atoms lining the pore into Brownian dynamics simulations of ion conduction. The movements of the carbonyl groups in the selectivity filter of the KcsA channel are calculated explicitly, allowing their bond lengths, bond angles, and dihedral angels to change in response to the forces acting upon them. By systematically changing the coefficients of bond stretching and of angle bending, the carbon and oxygen atoms can be made to fluctuate from their fixed positions by varying mean distances. We show that incorporating carbonyl motion in this way does not alter the mechanism of ion conduction and only has a small influence on the computed current. The slope conductance of the channel increases by approximately 25% when the root mean-square fluctuations of the carbonyl groups are increased from 0.01 to 0.61 A. The energy profiles and the number of resident ions in the channel remain unchanged. The method we utilized here can be extended to allow the movement of glutamate or aspartate side chains lining the selectivity filters of other ionic channels.

A method to explore the quantitative interactions between metal and ceria for M/CeO2 catalysts

NASA Astrophysics Data System (ADS)

Zhu, Kong-Jie; Liu, Jie; Yang, Yan-Ju; Xu, Yu-Xing; Teng, Bo-Tao; Wen, Xiao-Dong; Fan, Maohong

2018-03-01

To explore the quantitative relationship of metal interaction with ceria plays a key role in the theoretical design of M/CeO2 catalysts, especially for the new hot topic of atomically dispersed catalysts. A method to quantitatively explore the interactions between metal and ceria is proposed in the present work on the basis of the qualitative analysis of the effects of different factors on metal adsorption at different ceria surfaces by using Ag/CeO2 as a case. Two parameters are firstly presented, Ep which converts the total adsorption energy into the interaction energy per Agsbnd O bond, and θdiff which measures the deviation of Agsbnd Osbnd Ce bond angle from the angle of the sp3 orbital hybridization of O atom. Using the two parameters, the quantitative relationship of the interaction energy between Ag and ceria is established. There is a linear correlation between Ep and dAgsbndO with θdiff. The higher θdiff, the weaker Ep, and the longer Agsbnd O bond. This method is also suitable for other metals (Cu, Ni, Pd, and Rh, etc.) on ceria. It is the first time to establish the quantitative relationship for the interaction between metal and ceria, and sheds light into the theoretical design of M/CeO2 catalysts.

Ionic ASi{sub 2}N{sub 3} (A=Li, Na, K and Rb) stabilized by the covalent Si–N bonding: First-principles calculations

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

Zhang, Huijun; Ren, Jiadong, E-mail: jdren@ysu.edu.cn; Wu, Lailei

The structural, elastic and electronic properties of LiSi{sub 2}N{sub 3} and its substitutions by Na, K and Rb were investigated through first-principles computations. The expansion of lattice parameters of ASi{sub 2}N{sub 3} from Li, Na, K to Rb is found to be determined by the bond angle of Si–N1–Si, which suggests a possible way to improve the lithium ionic conductivity by substitutions. ASi{sub 2}N{sub 3} (A=Li, Na, K and Rb) shows the similar elastic behaviors, while the electronic band gap gradually decreases from 5.1 to 3.4 eV from LiSi{sub 2}N{sub 3} to RbSi{sub 2}N{sub 3}. Interestingly, the analysis of electronicmore » structure, crystal orbital Hamiltonian populations and Bader charges shows that the covalence of Si–N bonding is critical for the stability of ASi{sub 2}N{sub 3} phase. Among ASi{sub 2}N{sub 3} phases, there is a relatively high ionicity in NaSi{sub 2}N{sub 3}; the Si–N bond strength in [Si{sub 2}N{sub 3}]{sup −} net for KSi{sub 2}N{sub 3} and RbSi{sub 2}N{sub 3} is comparable to LiSi{sub 2}N{sub 3}, but stronger than NaSi{sub 2}N{sub 3}. - Graphic abstract: Universal trend of structural and electronic properties in alkaline metal silicon nitrides, ASi{sub 2}N{sub 3}, A=Li, Na, K and Rb. - Highlights: • Trend in structure, electronic and mechanical properties of ASi{sub 2}N{sub 3} (A=Li-Rb) were predicted. • Lattice expansion of ASi{sub 2}N{sub 3} induced by the bond angle of Si–N1–Si was found. • Calculated band gap decreases from 5.1 to 3.4 eV from LiSi{sub 2}N{sub 3} to RbSi{sub 2}N{sub 3}. • Covalent Si–N bonding is critical for the stability of ASi{sub 2}N{sub 3}.« less

pi-Turns: types, systematics and the context of their occurrence in protein structures

PubMed Central

Dasgupta, Bhaskar; Chakrabarti, Pinak

2008-01-01

Background For a proper understanding of protein structure and folding it is important to know if a polypeptide segment adopts a conformation inherent in the sequence or it depends on the context of its flanking secondary structures. Turns of various lengths have been studied and characterized starting from three-residue γ-turn to six-residue π-turn. The Schellman motif occurring at the C-terminal end of α-helices is a classical example of hydrogen bonded π-turn involving residues at (i) and (i+5) positions. Hydrogen bonded and non-hydrogen bonded β- and α-turns have been identified previously; likewise, a systematic characterization of π-turns would provide valuable insight into turn structures. Results An analysis of protein structures indicates that at least 20% of π-turns occur independent of the Schellman motif. The two categories of π-turns, designated as π-HB and SCH, have been further classified on the basis of backbone conformation and both have AAAa as the major class. They differ in the residue usage at position (i+1), the former having a large preference for Pro that is absent in the latter. As in the case of shorter length β- and α-turns, π-turns have also been identified not only on the basis of the existence of hydrogen bond, but also using the distance between terminal Cα-atoms, and this resulted in a comparable number of non-hydrogen-bonded π-turns (π-NHB). The presence of shorter β- and α-turns within all categories of π-turns, the subtle variations in backbone torsion angles along the turn residues, the location of the turns in the context of tertiary structures have been studied. Conclusion π-turns have been characterized, first using hydrogen bond and the distance between Cα atoms of the terminal residues, and then using backbone torsion angles. While the Schellman motif has a structural role in helix termination, many of the π-HB turns, being located on surface cavities, have functional role and there is also sequence conservation. PMID:18808671

pi-Turns: types, systematics and the context of their occurrence in protein structures.

PubMed

Dasgupta, Bhaskar; Chakrabarti, Pinak

2008-09-22

For a proper understanding of protein structure and folding it is important to know if a polypeptide segment adopts a conformation inherent in the sequence or it depends on the context of its flanking secondary structures. Turns of various lengths have been studied and characterized starting from three-residue gamma-turn to six-residue pi-turn. The Schellman motif occurring at the C-terminal end of alpha-helices is a classical example of hydrogen bonded pi-turn involving residues at (i) and (i+5) positions. Hydrogen bonded and non-hydrogen bonded beta- and alpha-turns have been identified previously; likewise, a systematic characterization of pi-turns would provide valuable insight into turn structures. An analysis of protein structures indicates that at least 20% of pi-turns occur independent of the Schellman motif. The two categories of pi-turns, designated as pi-HB and SCH, have been further classified on the basis of backbone conformation and both have AAAa as the major class. They differ in the residue usage at position (i+1), the former having a large preference for Pro that is absent in the latter. As in the case of shorter length beta- and alpha-turns, pi-turns have also been identified not only on the basis of the existence of hydrogen bond, but also using the distance between terminal C alpha-atoms, and this resulted in a comparable number of non-hydrogen-bonded pi-turns (pi-NHB). The presence of shorter beta- and alpha-turns within all categories of pi-turns, the subtle variations in backbone torsion angles along the turn residues, the location of the turns in the context of tertiary structures have been studied. pi-turns have been characterized, first using hydrogen bond and the distance between C alpha atoms of the terminal residues, and then using backbone torsion angles. While the Schellman motif has a structural role in helix termination, many of the pi-HB turns, being located on surface cavities, have functional role and there is also sequence conservation.

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

Mikhlina, Ya. A., E-mail: altik@inbox.ru; Bolotin, B. M.; Kuz'mina, L. G., E-mail: kuzmina@igic.ras.ru

Two crystal modifications (1o and 1y) of N-butyl-2-cyano-3-[4-(dimethylamino)phenyl]-2-propenamide, which differ in the color of crystals and the color of luminescence, have been studied by X-ray diffraction and spectral-luminescence methods. The corresponding bond lengths and bond angles in the molecules of two crystal modifications are virtually identical. In both crystal structures, there are two systems of weak intermolecular interactions: {pi}-stacking interactions and -CN Horizontal-Ellipsis H-N hydrogen bonds involving nitrile and NH groups. In the crystal structures, two hydrogen bonds connect pairs of molecules into centrosymmetric dimers. The N Horizontal-Ellipsis H distances are 2.21 and 2.41 A in 1o and 1y, respectively.more » The interplanar distances in the {pi}-stacked systems of 1o and 1y are 3.33 and 3.41 A, respectively. Both types of weak interactions are stronger in 1o than in 1y, which accounts for a larger shift of absorption and luminescence bands for the former compound.« less

A non-collinear mixing technique to measure the acoustic nonlinearity parameter of adhesive bond

NASA Astrophysics Data System (ADS)

Ju, Taeho; Achenbach, Jan. D.; Jacobs, Laurence J.; Qu, Jianmin

2018-04-01

In this work, we employed a wave mixing technique with an incident longitudinal wave and a shear wave to measure the Acoustic Nonlinearity Parameter (ANLP) of adhesive bonds. An adhesive transfer tape (F-9473PC) was used as an adhesive material: two aluminum plates are bonded together by the tape. To achieve a high signal to noise ratio, the optimal interaction angle and frequency ratio between the two incident waves were carefully selected so resonance occurs primarily in the adhesive layer, which somewhat suppressed the resonance in the aluminum plates. One of the most significant features of this method is that the measurements need only one-side access to the sample being measured. To demonstrate the effectiveness of the proposed technique, the adhesively bonded aluminum sample was placed in a temperature-controlled chamber for thermal aging. The ANLP of the thermally aged sample was compared with that of a freshly made adhesive sample. The results show that the ANLP increases with aging time and temperature.

Enhancing protein stability with extended disulfide bonds

DOE PAGES

Liu, Tao; Wang, Yan; Luo, Xiaozhou; ...

2016-05-09

Disulfide bonds play an important role in protein folding and stability. However, the cross-linking of sites within proteins by cysteine disulfides has significant distance and dihedral angle constraints. In this paper, we report the genetic encoding of noncanonical amino acids containing long side-chain thiols that are readily incorporated into both bacterial and mammalian proteins in good yields and with excellent fidelity. These amino acids can pair with cysteines to afford extended disulfide bonds and allow cross-linking of more distant sites and distinct domains of proteins. To demonstrate this notion, we preformed growth-based selection experiments at nonpermissive temperatures using a librarymore » of random β-lactamase mutants containing these noncanonical amino acids. A mutant enzyme that is cross-linked by one such extended disulfide bond and is stabilized by ~9 °C was identified. Finally, this result indicates that an expanded set of building blocks beyond the canonical 20 amino acids can lead to proteins with improved properties by unique mechanisms, distinct from those possible through conventional mutagenesis schemes.« less

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.

Crystal structure of 6-chloro-5-iso-propyl-pyrimidine-2,4(1H,3H)-dione.

PubMed

Haress, Nadia G; Ghabbour, Hazem A; El-Emam, Ali A; Chidan Kumar, C S; Fun, Hoong-Kun

2014-11-01

In the mol-ecule of the title compound, C7H9ClN2O2, the conformation is determined by intra-molecular C-H⋯O and C-H⋯Cl hydrogen bonds, which generate S(6) and S(5) ring motifs. The isopropyl group is almost perpendicular to the pyrimidine ring with torsion angles of -70.8 (3) and 56.0 (3)°. In the crystal, two inversion-related mol-ecules are linked via a pair of N-H⋯O hydrogen bonds into R 2 (2)(8) dimers; these dimers are connected into chains extending along the bc plane via an additional N-H⋯O hydrogen bond and weaker C-H⋯O hydrogen bonds. The crystal structure is further stabilized by a weak π-π inter-action [3.6465 (10) Å] between adjacent pyrimidine-dione rings arranged in a head-to-tail fashion, producing a three-dimensional network.

Adhesive Bonding Experiments for Titanium 6 Aluminum 4 Vanadium (Ti6Al4V). Part I. Anodization Treatments.

DTIC Science & Technology

1979-12-01

Identification of Surface Treat- 4 ments of Ti 6-4 II Effect of Increasing Oxide Porosity on H20 Contact Angle on Titanium 6 Aluminum 4 Vanadium 26 viii SECTIONI...and a high SIMS yield. The lithium does not appear in the oxide formed on titanium by this mixture. Similarly porosity may be induced by anodization at...Porous Oxide (B). 25 TABLE II EFFECT OF INCREASING OXIDE POROSITY ON H2 0 CONTACT ANGLE ON TITANIUM 6 ALUMINUM 4 VANADIUM - I H 2 0Sample Electrolyte

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

Angle-Resolved Photoemission of Solvated Electrons in Sodium-Doped Clusters.

PubMed

West, Adam H C; Yoder, Bruce L; Luckhaus, David; Saak, Clara-Magdalena; Doppelbauer, Maximilian; Signorell, Ruth

2015-04-16

Angle-resolved photoelectron spectroscopy of the unpaired electron in sodium-doped water, methanol, ammonia, and dimethyl ether clusters is presented. The experimental observations and the complementary calculations are consistent with surface electrons for the cluster size range studied. Evidence against internally solvated electrons is provided by the photoelectron angular distribution. The trends in the ionization energies seem to be mainly determined by the degree of hydrogen bonding in the solvent and the solvation of the ion core. The onset ionization energies of water and methanol clusters do not level off at small cluster sizes but decrease slightly with increasing cluster size.

Theoretical predictions of vibration-rotation-tunneling dynamics of the weakly bound trimer (H 2O) 2HCl

NASA Astrophysics Data System (ADS)

Struniewicz, Cezary; Korona, Tatiana; Moszynski, Robert; Milet, Anne

2001-08-01

In this Letter we report a theoretical study of the vibration-rotation-tunneling (VRT) states of the (H 2O) 2HCl trimer. Five degrees of freedom are considered: two angles corresponding to the torsional (flipping) motions of the free, non-hydrogen-bonded, hydrogen atoms in the complex, and three angles describing the overall rotation of the trimer in the space. A two-dimensional potential energy surface is generated ab initio by symmetry-adapted perturbation theory (SAPT). Tunneling splittings, frequencies of the intermolecular vibrations, and vibrational line strengths of spectroscopic transitions are predicted.

Influence of aramid fiber moisture regain during atmospheric plasma treatment on aging of treatment effects on surface wettability and bonding strength to epoxy

NASA Astrophysics Data System (ADS)

Ren, Yu; Wang, Chunxia; Qiu, Yiping

2007-09-01

One of the main differences between a low-pressure plasma treatment and an atmospheric pressure plasma treatment is that in atmosphere, the substrate material may absorb significant amount of water which may potentially influence the plasma treatment effects. This paper investigates how the moisture absorbed by aramid fibers during the atmospheric pressure plasma treatment influences the aging behavior of the modified surfaces. Kevlar 49 fibers with different moisture regains (MR) (0.5, 3.5 and 5.5%, respectively) are treated with atmospheric pressure plasma jet (APPJ) with helium as the carrier gas and oxygen as the treatment gas. Surface wettability and chemical compositions, and interfacial shear strengths (IFSS) to epoxy for the aramid fibers in all groups are determined using water contact angle measurements, X-ray photoelectron spectroscopy (XPS), and micro-bond pull out tests, respectively. Immediately after the plasma treatment, the treated fibers have substantially lower water contact angles, higher surface oxygen and nitrogen contents, and larger IFSS to epoxy than those of the control group. At the end of 30 day aging period, the fibers treated with 5.5% moisture regain had a lower water contact angle and more polar groups on the fiber surface, leading to 75% improvement of IFSS over the control fibers, while those for the 0.5 and 3.5% moisture regain groups were only 30%.

Crystal and mol­ecular structure of (2Z,5Z)-3-(2-meth­oxy­phen­yl)-2-[(2-meth­oxy­phen­yl)imino]-5-(4-nitro­benzyl­idene)thia­zolidin-4-one

PubMed Central

Djafri, Ahmed; Daran, Jean-Claude; Djafri, Ayada

2017-01-01

In the title compound, C24H19N3O5S, the thia­zole ring (r.m.s. deviation = 0.012 Å) displays a planar geometry and is surrounded by three fragments, two meth­oxy­phenyl and one nitro­phenyl. The thia­zole ring is almost in the same plane as the nitro­phenyl ring, making a dihedral angle of 20.92 (6)°. The two meth­oxy­phenyl groups are perpendicular to the thia­zole ring [dihedral angles of 79.29 (6) and 71.31 (7)° and make a dihedral angle of 68.59 (7)°. The mol­ecule exists in an Z,Z conformation with respect to the C=N imine bond. In the crystal, a series of C—H⋯N, C—H⋯O and C—H⋯S hydrogen bonds, augmented by several π–π(ring) inter­actions, produce a three-dimensional architecture of mol­ecules stacked along the b-axis direction. The experimentally derived structure is compered with that calculated theoretically using DFT(B3YLP) methods. PMID:28435709

Structural colored liquid membrane without angle dependence.

PubMed

Takeoka, Yukikazu; Honda, Masaki; Seki, Takahiro; Ishii, Masahiko; Nakamura, Hiroshi

2009-05-01

We have demonstrated for the first time that condensed gel particle suspensions in amorphous-like states display structural color with low angle dependence. This finding is in contrast to the common understanding that a periodic dielectric structure is fundamental to photonic band gap (PBG) production, and it validates the theory that a "tight bonding model" that is applicable to semiconductor systems can also be applied to photonic systems. More practically, this structural colored suspension represents a promising new material for the manufacture of reflective full-color displays with a wide viewing angle and nonfading color materials. This liquid system shows promise as a display material because electronic equipment used for display systems can easily be filled with the liquid in the same way that liquid crystals are currently used.

Surface Nanobubbles in Nonaqueous Media: Looking for Nanobubbles in DMSO, Formamide, Propylene Carbonate, Ethylammonium Nitrate, and Propylammonium Nitrate.

PubMed

An, Hongjie; Liu, Guangming; Atkin, Rob; Craig, Vincent S J

2015-07-28

Surface nanobubbles produced by supersaturation during the exchange of ethanol for water are routinely observed on hydrophobic surfaces, are stable for days, and have contact angles that are very much greater than observed macroscopically. Here, we test the hypothesis that nanobubbles can also be observed in nonaqueous solvents in order to ascertain if their anomalous lifetimes and contact angles are related to properties of the solvent. Nanobubbles were seen in the protic solvents formamide, ethylammonium nitrate, and propylammonium nitrate, but not in propylene carbonate or dimethyl sulfoxide. Solvents in which nanobubbles were observed exhibit a three-dimensional hydrogen-bonding network. Like in aqueous systems, the nanobubbles were stable for days and exhibited high contact angles (∼165°).

Structural and electronic properties of double-walled boron nitride nanocones

NASA Astrophysics Data System (ADS)

Brito, E.; Silva, T. S.; Guerra, T.; Leite, L.; Azevedo, S.; Freitas, A.; Kaschny, J. R.

2018-01-01

First principles calculations were applied to study the structural and electronic properties of different configurations of double-walled boron nitride nanocones with a disclination angle of 60°. The analysis includes different rotation angles, distance between apexes, as well as distinct types of antiphase boundaries. The calculations indicate that the non-rotated configuration of double-walled nanocone with a defective line composed by C and N atoms, forming C-N bonds, is the most stable configuration. It was found that the yam angle, apexes distance and defective line composition present significant influence on the electronic properties of such structures. Moreover, analyzing the spin charge density, for the electronic states near the Fermi level, it was also found that the configuration with a defective line containing C atoms presents a net magnetic moment.

Expanded turn conformations: characterization and sequence-structure correspondence in alpha-turns with implications in helix folding.

PubMed

Dasgupta, Bhaskar; Pal, Lipika; Basu, Gautam; Chakrabarti, Pinak

2004-05-01

Like the beta-turns, which are characterized by a limiting distance between residues two positions apart (i, i+3), a distance criterion (involving residues at positions i and i+4) is used here to identify alpha-turns from a database of known protein structures. At least 15 classes of alpha-turns have been enumerated based on the location in the phi,psi space of the three central residues (i+1 to i+3)-one of the major being the class AAA, where the residues occupy the conventional helical backbone torsion angles. However, moving towards the C-terminal end of the turn, there is a shift in the phi,psi angles towards more negative phi, such that the electrostatic repulsion between two consecutive carbonyl oxygen atoms is reduced. Except for the last position (i+4), there is not much similarity in residue composition at different positions of hydrogen and non-hydrogen bonded AAA turns. The presence or absence of Pro at i+1 position of alpha- and beta-turns has a bearing on whether the turn is hydrogen-bonded or without a hydrogen bond. In the tertiary structure, alpha-turns are more likely to be found in beta-hairpin loops. The residue composition at the beginning of the hydrogen bonded AAA alpha-turn has similarity with type I beta-turn and N-terminal positions of helices, but the last position matches with the C-terminal capping position of helices, suggesting that the existence of a "helix cap signal" at i+4 position prevents alpha-turns from growing into helices. Our results also provide new insights into alpha-helix nucleation and folding. Copyright 2004 Wiley-Liss, Inc.

Validation and extraction of molecular-geometry information from small-molecule databases.

PubMed

Long, Fei; Nicholls, Robert A; Emsley, Paul; Graǽulis, Saulius; Merkys, Andrius; Vaitkus, Antanas; Murshudov, Garib N

2017-02-01

A freely available small-molecule structure database, the Crystallography Open Database (COD), is used for the extraction of molecular-geometry information on small-molecule compounds. The results are used for the generation of new ligand descriptions, which are subsequently used by macromolecular model-building and structure-refinement software. To increase the reliability of the derived data, and therefore the new ligand descriptions, the entries from this database were subjected to very strict validation. The selection criteria made sure that the crystal structures used to derive atom types, bond and angle classes are of sufficiently high quality. Any suspicious entries at a crystal or molecular level were removed from further consideration. The selection criteria included (i) the resolution of the data used for refinement (entries solved at 0.84 Å resolution or higher) and (ii) the structure-solution method (structures must be from a single-crystal experiment and all atoms of generated molecules must have full occupancies), as well as basic sanity checks such as (iii) consistency between the valences and the number of connections between atoms, (iv) acceptable bond-length deviations from the expected values and (v) detection of atomic collisions. The derived atom types and bond classes were then validated using high-order moment-based statistical techniques. The results of the statistical analyses were fed back to fine-tune the atom typing. The developed procedure was repeated four times, resulting in fine-grained atom typing, bond and angle classes. The procedure will be repeated in the future as and when new entries are deposited in the COD. The whole procedure can also be applied to any source of small-molecule structures, including the Cambridge Structural Database and the ZINC database.

Crystal structure of a mononuclear Ru(II) complex with a back-to-back terpyridine ligand: [RuCl(bpy)(tpy-tpy)](.).

PubMed

Rein, Francisca N; Chen, Weizhong; Scott, Brian L; Rocha, Reginaldo C

2015-09-01

We report the structural characterization of [6',6''-bis-(pyridin-2-yl)-2,2':4',4'':2'',2'''-quaterpyridine](2,2'-bi-pyridine)-chlorido-ruthenium(II) hexa-fluorido-phosphate, [RuCl(C10H8N2)(C30H20N6)]PF6, which contains the bidentate ligand 2,2'-bi-pyridine (bpy) and the tridendate ligand 6',6''-bis-(pyridin-2-yl)-2,2':4',4'':2'',2'''-quaterpyridine (tpy-tpy). The [RuCl(bpy)(tpy-tpy)](+) monocation has a distorted octa-hedral geometry at the central Ru(II) ion due to the restricted bite angle [159.32 (16)°] of the tridendate ligand. The Ru-bound tpy and bpy moieties are nearly planar and essentially perpendicular to each other with a dihedral angle of 89.78 (11)° between the least-squares planes. The lengths of the two Ru-N bonds for bpy are 2.028 (4) and 2.075 (4) Å, with the shorter bond being opposite to Ru-Cl. For tpy-tpy, the mean Ru-N distance involving the outer N atoms trans to each other is 2.053 (8) Å, whereas the length of the much shorter bond involving the central N atom is 1.936 (4) Å. The Ru-Cl distance is 2.3982 (16) Å. The free uncoordinated moiety of tpy-tpy adopts a trans,trans conformation about the inter-annular C-C bonds, with adjacent pyridyl rings being only approximately coplanar. The crystal packing shows significant π-π stacking inter-actions based on tpy-tpy. The crystal structure reported here is the first for a tpy-tpy complex of ruthenium.

Spectroscopic characterization of 1-[3-(1H-imidazol-1-yl)propyl]-3-phenylthiourea and assessment of reactive and optoelectronic properties employing DFT calculations and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

War, Javeed Ahmad; Jalaja, K.; Mary, Y. Sheena; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Srivastava, Santosh Kumar; Van Alsenoy, C.

2017-02-01

IR and Raman spectra of 1-[3-(1H-imidazol-1-yl)propyl]-3-phenylthiourea (HIPPT) have been recorded in the solid phase and the vibrational wave numbers are calculated theoretically by B3LYP/6-31G(d,p) (6D, 7F) method. All the fundamental vibrational modes have been assigned using potential energy distribution values and the molecular structure was analyzed in terms of parameters like bond length, bond angles and dihedral angles. The ring breathing mode of the phenyl ring is observed at 1016 cm-1 in the IR spectrum, 1014 cm-1 in the Raman spectrum and at 1014 cm-1 theoretically. The values of polarizability and hyperpolarizabilities were calculated and nonlinear optical properties are discussed. The HOMO-LUMO plot reveals the charge transfer possibilities in the molecule. The NBO analysis was computed and possible transitions were correlated with the electronic transitions. In the title compound, the imidazole ring and CH2 groups are tilted from each other and the thiourea group is tilted from the phenyl ring. Using MEP plot the electrophilic and nucleophilic regions are identified. Local reactivity properties were investigated by analysis of ALIE surfaces and Fukui functions. Oxidation and degradation properties were initially assessed by calculation of bond dissociation energies of all single acyclic bonds. Determination of atoms with pronounced interactions with water molecules was performed by calculation of radial distribution functions after molecular dynamics simulations. Chargehopping rates were calculated within Marcus semi-empiric approach, employing both DFT calculations and MD simulations. The molecular docking computational predictions were complemented by the in vitro antibacterial activity evaluation.

Hydrogen bond network around the semiquinone of the secondary quinone acceptor Q(B) in bacterial photosynthetic reaction centers.

PubMed

Taguchi, Alexander T; O'Malley, Patrick J; Wraight, Colin A; Dikanov, Sergei A

2015-05-07

By utilizing a combined pulsed EPR and DFT approach, the high-resolution structure of the QB site semiquinone (SQB) was determined. The development of such a technique is crucial toward an understanding of protein-bound semiquinones on the structural level, as (i) membrane protein crystallography typically results in low resolution structures, and (ii) obtaining protein crystals in the semiquinone form is rarely feasible. The SQB hydrogen bond network was investigated with Q- (∼34 GHz) and X-band (∼9.7 GHz) pulsed EPR spectroscopy on fully deuterated reactions centers from Rhodobacter sphaeroides. Simulations in the SQB g-tensor reference frame provided the principal values and directions of the H-bond proton hyperfine tensors. Three protons were detected, one with an anisotropic tensor component, T = 4.6 MHz, assigned to the histidine NδH of His-L190, and two others with similar anisotropic constants T = 3.2 and 3.0 MHz assigned to the peptide NpH of Gly-L225 and Ile-L224, respectively. Despite the strong similarity in the peptide couplings, all hyperfine tensors were resolved in the Q-band ENDOR spectra. The Euler angles describing the series of rotations that bring the hyperfine tensors into the SQB g-tensor reference frame were obtained by least-squares fitting of the spectral simulations to the ENDOR data. These Euler angles show the locations of the hydrogen bonded protons with respect to the semiquinone. Our geometry optimized model of SQB used in previous DFT work is in strong agreement with the angular constraints from the spectral simulations, providing the foundation for future joint pulsed EPR and DFT semiquinone structural determinations in other proteins.

Theoretical studies of structure-property relations in graphene-based carbon nanostructures

NASA Astrophysics Data System (ADS)

Maroudas, Dimitrios

2014-03-01

This presentation focuses on establishing relations between atomic structure, electronic structure, and properties in graphene-based carbon nanostructures through first-principles density functional theory calculations and molecular-dynamics simulations. We have analyzed carbon nanostructure formation from twisted bilayer graphene, upon creation of interlayer covalent C-C bonds due to patterned hydrogenation or fluorination. For small twist angles and twist angles near 30 degrees, interlayer covalent bonding generates superlattices of diamond-like nanocrystals and of fullerene-like configurations, respectively, embedded within the graphene layers. The electronic band gaps of these superlattices can be tuned through selective chemical functionalization and creation of interlayer bonds, and range from a few meV to over 1.2 eV. The mechanical properties of these superstructures also can be precisely tuned by controlling the extent of chemical functionalization. Importantly, the shear modulus is shown to increase monotonically with the fraction of sp3-hybridized C-C bonds. We have also studied collective interactions of multiple defects such as random distributions of vacancies in single-layer graphene (SLG). We find that a crystalline-to-amorphous structural transition occurs at vacancy concentrations of 5-10% over a broad temperature range. The structure of our defect-induced amorphized graphene is in excellent agreement with experimental observations of SLG exposed to a high electron irradiation dose. Simulations of tensile tests on these irradiated graphene sheets identify trends for the ultimate tensile strength, failure strain, and toughness as a function of vacancy concentration. The vacancy-induced amorphization transition is accompanied by a brittle-to-ductile transition in the failure response of irradiated graphene sheets and even heavily damaged samples exhibit tensile strengths near 30 GPa, in significant excess of those typical of engineering materials.

Investigation of base pairs containing oxidized guanine using ab initio method and ABEEMσπ polarizable force field.

PubMed

Liu, Cui; Wang, Yang; Zhao, Dongxia; Gong, Lidong; Yang, Zhongzhi

2014-02-01

The integrity of the genetic information is constantly threatened by oxidizing agents. Oxidized guanines have all been linked to different types of cancers. Theoretical approaches supplement the assorted experimental techniques, and bring new sight and opportunities to investigate the underlying microscopic mechanics. Unfortunately, there is no specific force field to DNA system including oxidized guanines. Taking high level ab initio calculations as benchmark, we developed the ABEEMσπ fluctuating charge force field, which uses multiple fluctuating charges per atom. And it was applied to study the energies, structures and mutations of base pairs containing oxidized guanines. The geometries were obtained in reference to other studies or using B3LYP/6-31+G* level optimization, which is more rational and timesaving among 24 quantum mechanical methods selected and tested by this work. The energies were determined at MP2/aug-cc-pVDZ level with BSSE corrections. Results show that the constructed potential function can accurately simulate the change of H-bond and the buckled angle formed by two base planes induced by oxidized guanine, and it provides reliable information of hydrogen bonding, stacking interaction and the mutation processes. The performance of ABEEMσπ polarizable force field in predicting the bond lengths, bond angles, dipole moments etc. is generally better than those of the common force fields. And the accuracy of ABEEMσπ PFF is close to that of the MP2 method. This shows that ABEEMσπ model is a reliable choice for further research of dynamics behavior of DNA fragment including oxidized guanine. Copyright © 2013 Elsevier Inc. All rights reserved.

Crystal structure and hydrogen-bonding patterns in 5-fluoro-cytosinium picrate.

PubMed

Mohana, Marimuthu; Thomas Muthiah, Packianathan; McMillen, Colin D

2017-03-01

In the crystal structure of the title compound, 5-fluoro-cytosinium picrate, C 4 H 5 FN 3 O + ·C 6 H 2 N 3 O 7 - , one N heteroatom of the 5-fluoro-cytosine (5FC) ring is protonated. The 5FC ring forms a dihedral angle of 19.97 (11)° with the ring of the picrate (PA - ) anion. In the crystal, the 5FC + cation inter-acts with the PA - anion through three-centre N-H⋯O hydrogen bonds, forming two conjoined rings having R 2 1 (6) and R 1 2 (6) motifs, and is extended by N-H⋯O hydrogen bonds and C-H⋯O inter-actions into a two-dimensional sheet structure lying parallel to (001). Also present in the crystal structure are weak C-F⋯π inter-actions.

Geometric structure of thin SiO xN y films on Si(100)

NASA Astrophysics Data System (ADS)

Behrens, K.-M.; Klinkenberg, E.-D.; Finster, J.; Meiwes-Broer, K.-H.

1998-05-01

Thin films of amorphous stoichometric SiO xN y are deposited on radiation-heated Si(100) by rapid thermal low-pressure chemical vapour deposition. We studied the whole range of possible compositions. In order to determine the geometric structure, we used EXAFS and photoelectron spectroscopy. Tetrahedrons constitute the short-range units with a central Si atom connected to N and O. The distribution of the possible tetrahedrons can be described by a mixture of the Random Bonding Model and the Random Mixture Model. For low oxygen contents x/( x+ y)≤0.3, the geometric structure of the film is almost the structure of a-Si 3N 4, with the oxygen preferably on top of Si-N 3 triangles. Higher oxygen contents induce changes in the bond lengths, bond angles and coordination numbers.

catena-Poly[[(benzil bis{[(pyridin-2-yl)methylidene]hydrazone}-κ⁴N,N',N'',N''')mercury(II)]-μ-chlorido-[dichloridomercury(II)]-μ-chlorido].

PubMed

Akkurt, Mehmet; Khandar, Ali Akbar; Tahir, Muhammad Nawaz; Hosseini-Yazdi, Seyed Abolfazl; Mahmoudi, Ghodrat

2012-07-01

In the title coordination polymer, [Hg₄Cl₄(C₂₆H₂₀N₆)](n), one Hg(II) ion is coordinated by four N atoms from the benzylbis((pyridin-2-yl)methyl-idenehydrazone) ligand and two Cl⁻ ions in a very distorted cis-HgCl₂N₄ octa-hedral geometry. The other Hg(II) ion is coordinated in a distorted tetra-hedral geometry by four Cl⁻ ions. Bridging chloride ions link the Hg(II) ions into a chain propagating in [010]: the Hg-Cl bridging bonds are significantly longer than the terminal bonds. The dihedral angle between the central benzene rings of the ligand is 83.3 (2)°. The packing is consolidated by weak C-H⋯Cl hydrogen bonds and C-H⋯π inter-actions.

Influence of Hydrogen Bond on Thermal and Phase Transitions of Binary Complex Liquid Crystals

NASA Astrophysics Data System (ADS)

Vijayakumar, V. N.; Rajasekaran, T. R.; Baskar, K.

2017-12-01

A novel supramolecular liquid crystal (LC) is synthesized from the binary complex of 4-decyloxy benzoic acid and cholesteryl acetate. Fourier transform infrared (FTIR) spectroscopic study confirms the formation of intermolecular hydrogen bond between the mesogens. Various mesophases and corresponding textural changes in the complex are observed by comparing with its constituents through polarizing optical microscopic (POM) studies. The thermal stability factor of smectic phase for present complex is calculated. An interesting observation of present work is that investigation of extended thermal span of mesomorphic phases, decreased enthalpy, a nematic phase with a high clearing point and a low melting point. This is due to an arrangement of molecular reorientations and the development of new associations by hydrogen bonding. Optical tilt angle for smectic C phase is determined and the same is fitted to a power law.

Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network.

PubMed

Lyons, James; Dehzangi, Abdollah; Heffernan, Rhys; Sharma, Alok; Paliwal, Kuldip; Sattar, Abdul; Zhou, Yaoqi; Yang, Yuedong

2014-10-30

Because a nearly constant distance between two neighbouring Cα atoms, local backbone structure of proteins can be represented accurately by the angle between C(αi-1)-C(αi)-C(αi+1) (θ) and a dihedral angle rotated about the C(αi)-C(αi+1) bond (τ). θ and τ angles, as the representative of structural properties of three to four amino-acid residues, offer a description of backbone conformations that is complementary to φ and ψ angles (single residue) and secondary structures (>3 residues). Here, we report the first machine-learning technique for sequence-based prediction of θ and τ angles. Predicted angles based on an independent test have a mean absolute error of 9° for θ and 34° for τ with a distribution on the θ-τ plane close to that of native values. The average root-mean-square distance of 10-residue fragment structures constructed from predicted θ and τ angles is only 1.9Å from their corresponding native structures. Predicted θ and τ angles are expected to be complementary to predicted ϕ and ψ angles and secondary structures for using in model validation and template-based as well as template-free structure prediction. The deep neural network learning technique is available as an on-line server called Structural Property prediction with Integrated DEep neuRal network (SPIDER) at http://sparks-lab.org. Copyright © 2014 Wiley Periodicals, Inc.

3-Benzyl­sulfanyl-1H-1,2,4-triazol-5-amine

PubMed Central

Zhang, Shuai; Liu, Pei-Jiang; Ma, Dong-Sheng; Hou, Guang-Feng

2012-01-01

In the title mol­ecule, C9H10N4S, the dihedral angle between the benzene and triazole rings is 81.05 (5)°. In the crystal, N—H⋯N hydrogen bonds link the mol­ecules into infinite zigzag chains along [010]. PMID:22259582

(E)-N-[(6-Bromo­pyridin-2-yl)methyl­idene]-4-methyl­aniline

PubMed Central

Cai, Mingjian; Ma, Penggao; Wang, Xiuge; Sun, Tao

2011-01-01

The title compound, C13H11BrN2, a Schiff base obtained from 6-bromo­picolinaldehyde and p-toluidine, has an E configuration about the C=N bond. The dihedral angle between the benzene and pyridine rings is 30.4 (1)°. PMID:22058956

1-(4-Chloro­benzyl­ideneamino)pyridinum iodide

PubMed Central

Cui, Yong-Tao; Wang, Jian-Qiang; Ji, Chun-Xiang; Wang, Hai-Bo; Cheng, Guo

2009-01-01

In the title compound, C12H10ClN2 +·I−, the aromatic rings are oriented at a dihedral angle of 54.55 (3)°. In the crystal structure, inter­molecular C—H⋯I and C—H⋯Cl hydrogen bonds link the mol­ecules. PMID:21581845

4-[(3-Chloro-2-methyl-phen-yl)imino-meth-yl]phenol.

PubMed

Manjunath, B C; Abdoh, M M M; Mallesha, L; Mohana, K N; Lokanath, N K

2012-11-01

In the title compound, C(14)H(12)ClNO, the dihedral angle between the aromatic rings is 39.84 (7)°. In th crystal, mol-ecules are connected by O-H⋯N hydrogen bonds into chains parallel to [001]. In addition, a C-H⋯π contact occurs.

Theoretical discovery of stable structures of group III-V monolayers: The materials for semiconductor devices

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

Suzuki, Tatsuo, E-mail: dr.tatsuosuzuki@gmail.com

Group III-V compounds are very important as the materials of semiconductor devices. Stable structures of the monolayers of group III-V binary compounds have been discovered by using first-principles calculations. The primitive unit cell of the discovered structures is a rectangle, which includes four group-III atoms and four group-V atoms. A group-III atom and its three nearest-neighbor group-V atoms are placed on the same plane; however, these connections are not the sp{sup 2} hybridization. The bond angles around the group-V atoms are less than the bond angle of sp{sup 3} hybridization. The discovered structure of GaP is an indirect transition semiconductor,more » while the discovered structures of GaAs, InP, and InAs are direct transition semiconductors. Therefore, the discovered structures of these compounds have the potential of the materials for semiconductor devices, for example, water splitting photocatalysts. The discovered structures may become the most stable structures of monolayers which consist of other materials.« less

Measurements of the microwave spectrum, Re-H bond length, and Re quadrupole coupling for HRe(CO)5

NASA Astrophysics Data System (ADS)

Kukolich, Stephen G.; Sickafoose, Shane M.

1993-11-01

Rotational transition frequencies for rhenium pentacarbonyl hydride were measured in the 4-10 GHz range using a Flygare-Balle type microwave spectrometer. The rotational constants and Re nuclear quadrupole coupling constants for the four isotopomers, (1) H187Re(CO)5, (2) H185Re(CO)5, (3) D187Re(CO)5, and (4) D185Re(CO)5, were obtained from the spectra. For the most common isotopomer, B(1)=818.5464(2) MHz and eq Q(187Re)=-900.13(3) MHz. The Re-H bond length (r0) determined by fitting the rotational constants is 1.80(1) Å. Although the Re atom is located at a site of near-octahedral symmetry, the quadrupole coupling is large due to the large Re nuclear moments. A 2.7% increase in Re quadrupole coupling was observed for D-substituted isotopomers, giving a rather large isotope effect on the quadrupole coupling. The Cax-Re-Ceq angle is 96(1)°, when all Re-C-O angles are constrained to 180°.

The introduction of hydrogen bond and hydrophobicity effects into the rotational isomeric states model for conformational analysis of unfolded peptides.

PubMed

Engin, Ozge; Sayar, Mehmet; Erman, Burak

2009-01-13

Relative contributions of local and non-local interactions to the unfolded conformations of peptides are examined by using the rotational isomeric states model which is a Markov model based on pairwise interactions of torsion angles. The isomeric states of a residue are well described by the Ramachandran map of backbone torsion angles. The statistical weight matrices for the states are determined by molecular dynamics simulations applied to monopeptides and dipeptides. Conformational properties of tripeptides formed from combinations of alanine, valine, tyrosine and tryptophan are investigated based on the Markov model. Comparison with molecular dynamics simulation results on these tripeptides identifies the sequence-distant long-range interactions that are missing in the Markov model. These are essentially the hydrogen bond and hydrophobic interactions that are obtained between the first and the third residue of a tripeptide. A systematic correction is proposed for incorporating these long-range interactions into the rotational isomeric states model. Preliminary results suggest that the Markov assumption can be improved significantly by renormalizing the statistical weight matrices to include the effects of the long-range correlations.

Composite Yb:YAG/SiC-prism thin disk laser.

PubMed

Newburgh, G A; Michael, A; Dubinskii, M

2010-08-02

We report the first demonstration of a Yb:YAG thin disk laser wherein the gain medium is intracavity face-cooled through bonding to an optical quality SiC prism. Due to the particular design of the composite bonded Yb:YAG/SiC-prism gain element, the laser beam impinges on all refractive index interfaces inside the laser cavity at Brewster's angles. The laser beam undergoes total internal reflection (TIR) at the bottom of the Yb(10%):YAG thin disk layer in a V-bounce cavity configuration. Through the use of TIR and Brewster's angles, no optical coatings, either anti-reflective (AR) or highly reflective (HR), are required inside the laser cavity. In this first demonstration, the 936.5-nm diode pumped laser performed with approximately 38% slope efficiency at 12 W of quasi-CW (Q-CW) output power at 1030 nm with a beam quality measured at M(2) = 1.5. This demonstration opens up a viable path toward novel thin disk laser designs with efficient double-sided room-temperature heatsinking via materials with the thermal conductivity of copper on both sides of the disk.

Ab initio studies of 1,3,5,7-tetranitro-1,3,5,7-tetrazocine/1,3-dimethyl-2-imidazolidinone cocrystal under high pressure using dispersion corrected density functional theory

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

Gu, Bang-Ming; Lin, He; Zhu, Shun-Guan, E-mail: zhusguan@yahoo.com

A detailed study of structural, electronic, and thermodynamic properties of 1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX)/1,3-dimethyl-2-imidazolidinone (DMI) cocrystal under the hydrostatic pressure of 0–100 GPa was performed by using dispersion-corrected density functional theory (DFT-D) method. The calculated crystal structure is in reasonable agreement with the experimental data at the ambient pressure. Based on the analysis of lattice constants, bond lengths, bond angles, and dihedral angles under compression, it is found that HMX molecules in HMX/DMI cocrystal are seriously distorted. In addition, as the pressure increases, the band gap decreases gradually, which suggests that HMX/DMI cocrystal is becoming more metallic. Some important intermolecular interactions between HMXmore » and DMI are also observed in the density of states spectrum. Finally, its thermodynamic properties were characterized, and the results show that HMX/DMI cocrystal is more easily formed in the low pressure.« less

Structure analysis on synthetic emerald crystals

NASA Astrophysics Data System (ADS)

Lee, Pei-Lun; Lee, Jiann-Shing; Huang, Eugene; Liao, Ju-Hsiou

2013-05-01

Single crystals of emerald synthesized by means of the flux method were adopted for crystallographic analyses. Emerald crystals with a wide range of Cr3+-doping content up to 3.16 wt% Cr2O3 were examined by X-ray single crystal diffraction refinement method. The crystal structures of the emerald crystals were refined to R 1 (all data) of 0.019-0.024 and w R 2 (all data) of 0.061-0.073. When Cr3+ substitutes for Al3+, the main adjustment takes place in the Al-octahedron and Be-tetrahedron. The effect of substitution of Cr3+ for Al3+ in the beryl structure results in progressively lengthening of the Al-O distance, while the length of the other bonds remains nearly unchanged. The substitution of Cr3+ for Al3+ may have caused the expansion of a axis, while keeping the c axis unchanged in the emerald lattice. As a consequence, the Al-O-Si and Al-O-Be bonding angles are found to decrease, while the angle of Si-O-Be increases as the Al-O distance increases during the Cr replacement.

Atomic structure of unligated laccase from Cerrena maxima at 1.76 A with molecular oxygen and hydrogen peroxide

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

Zhukova, Yu. N., E-mail: amm@ns.crys.ras.ru; Lyashenko, A. V.; Lashkov, A. A.

2010-05-15

The three-dimensional structure of unligated laccase from Cerrena maxima was established by X-ray diffraction at 1.76-A resolution; R{sub work} = 18.07%, R{sub free} = 21.71%, rmsd of bond lengths, bond angles, and chiral angles are 0.008 A, 1.19{sup o}, and 0.077{sup o}, respectively. The coordinate error for the refined structure estimated from the Luzzati plot is 0.195 A. The maximum average error in the atomic coordinates is 0.047 A. A total of 99.4% of amino-acid residues of the polypeptide chain are in the most favorable, allowable, and accessible regions of the Ramachandran plot. The three-dimensional structures of the complexes ofmore » laccase from C. maxima with molecular oxygen and hydrogen peroxide were determined by the molecular simulation. These data provide insight into the structural aspect of the mechanism of the enzymatic cycle. The structure factors and the refined atomic coordinates were deposited in the Protein Data Bank (PDB-ID code is 3DIV).« less

Steric engineering of metal-halide perovskites with tunable optical band gaps

NASA Astrophysics Data System (ADS)

Filip, Marina R.; Eperon, Giles E.; Snaith, Henry J.; Giustino, Feliciano

2014-12-01

Owing to their high energy-conversion efficiency and inexpensive fabrication routes, solar cells based on metal-organic halide perovskites have rapidly gained prominence as a disruptive technology. An attractive feature of perovskite absorbers is the possibility of tailoring their properties by changing the elemental composition through the chemical precursors. In this context, rational in silico design represents a powerful tool for mapping the vast materials landscape and accelerating discovery. Here we show that the optical band gap of metal-halide perovskites, a key design parameter for solar cells, strongly correlates with a simple structural feature, the largest metal-halide-metal bond angle. Using this descriptor we suggest continuous tunability of the optical gap from the mid-infrared to the visible. Precise band gap engineering is achieved by controlling the bond angles through the steric size of the molecular cation. On the basis of these design principles we predict novel low-gap perovskites for optimum photovoltaic efficiency, and we demonstrate the concept of band gap modulation by synthesising and characterising novel mixed-cation perovskites.

The introduction of hydrogen bond and hydrophobicity effects into the rotational isomeric states model for conformational analysis of unfolded peptides

NASA Astrophysics Data System (ADS)

Engin, Ozge; Sayar, Mehmet; Erman, Burak

2009-03-01

Relative contributions of local and non-local interactions to the unfolded conformations of peptides are examined by using the rotational isomeric states model which is a Markov model based on pairwise interactions of torsion angles. The isomeric states of a residue are well described by the Ramachandran map of backbone torsion angles. The statistical weight matrices for the states are determined by molecular dynamics simulations applied to monopeptides and dipeptides. Conformational properties of tripeptides formed from combinations of alanine, valine, tyrosine and tryptophan are investigated based on the Markov model. Comparison with molecular dynamics simulation results on these tripeptides identifies the sequence-distant long-range interactions that are missing in the Markov model. These are essentially the hydrogen bond and hydrophobic interactions that are obtained between the first and the third residue of a tripeptide. A systematic correction is proposed for incorporating these long-range interactions into the rotational isomeric states model. Preliminary results suggest that the Markov assumption can be improved significantly by renormalizing the statistical weight matrices to include the effects of the long-range correlations.

Application of geometric algebra for the description of polymer conformations.

PubMed

Chys, Pieter

2008-03-14

In this paper a Clifford algebra-based method is applied to calculate polymer chain conformations. The approach enables the calculation of the position of an atom in space with the knowledge of the bond length (l), valence angle (theta), and rotation angle (phi) of each of the preceding bonds in the chain. Hence, the set of geometrical parameters {l(i),theta(i),phi(i)} yields all the position coordinates p(i) of the main chain atoms. Moreover, the method allows the calculation of side chain conformations and the computation of rotations of chain segments. With these features it is, in principle, possible to generate conformations of any type of chemical structure. This method is proposed as an alternative for the classical approach by matrix algebra. It is more straightforward and its final symbolic representation considerably simpler than that of matrix algebra. Approaches for realistic modeling by means of incorporation of energetic considerations can be combined with it. This article, however, is entirely focused at showing the suitable mathematical framework on which further developments and applications can be built.

2-Amino­benzoic acid–4-(pyridin-4-yl­disulfan­yl)pyridine (1/1)

PubMed Central

Arman, Hadi D.; Kaulgud, Trupta; Tiekink, Edward R. T.

2011-01-01

The title 1:1 co-crystal, C7H7NO2·C10H8N2S2, features a highly twisted 4-(pyridin-4-yldisulfan­yl)pyridine mol­ecule [dihedral angle between the pyridine rings = 89.06 (10)°]. A small twist is evident in the 2-amino­benzoic acid mol­ecule, with the C—C—C—O torsion angle being −7.7 (3)°. An N—H⋯O hydrogen bond occurs in the 2-amino­benzoic acid mol­ecule. In the crystal, mol­ecules are linked by O—H⋯N and N—H⋯N hydrogen bonds into a supra­molecular chain along the b axis. These are connected into layers by π–π inter­actions occurring between pyridine rings [centroid–centroid distance = 3.8489 (15) Å]. The layers are connected along the a axis by C—H⋯O contacts. The crystal studied was a racemic twin. PMID:22199855

Effect of Impact Angle on the Erosion Rate of Coherent Granular Soil, with a Chernozemic Soil as an Example

NASA Astrophysics Data System (ADS)

Larionov, G. A.; Bushueva, O. G.; Gorobets, A. V.; Dobrovol'skaya, N. G.; Kiryukhina, Z. P.; Krasnov, S. F.; Kobylchenko Kuksina, L. V.; Litvin, L. F.; Sudnitsyn, I. I.

2018-02-01

It has been shown in experiments in a hydraulic flume with a knee-shaped bend that the rate of soil erosion more than doubles at the flow impact angles to the channel side from 0° to 50°. At higher channel bends, the experiment could not be performed because of backwater. Results of erosion by water stream approaching the sample surface at angles between 2° and 90° are reported. It has been found that the maximum erosion rate is observed at flow impact angles of about 45°, and the minimum rate at 90°. The minimum soil erosion rate is five times lower than the maximum erosion rate. This is due to the difference in the rate of free water penetration into the upper soil layer, and the impact of the hydrodynamic pressure, which is maximum at the impact angle of 90°. The penetration of water into the interaggregate space results in the breaking of bonds between aggregates, which is the main condition for the capture of particles by the flow.

Sterically controlled mechanochemistry under hydrostatic pressure

NASA Astrophysics Data System (ADS)

Yan, Hao; Yang, Fan; Pan, Ding; Lin, Yu; Hohman, J. Nathan; Solis-Ibarra, Diego; Li, Fei Hua; Dahl, Jeremy E. P.; Carlson, Robert M. K.; Tkachenko, Boryslav A.; Fokin, Andrey A.; Schreiner, Peter R.; Galli, Giulia; Mao, Wendy L.; Shen, Zhi-Xun; Melosh, Nicholas A.

2018-02-01

Mechanical stimuli can modify the energy landscape of chemical reactions and enable reaction pathways, offering a synthetic strategy that complements conventional chemistry. These mechanochemical mechanisms have been studied extensively in one-dimensional polymers under tensile stress using ring-opening and reorganization, polymer unzipping and disulfide reduction as model reactions. In these systems, the pulling force stretches chemical bonds, initiating the reaction. Additionally, it has been shown that forces orthogonal to the chemical bonds can alter the rate of bond dissociation. However, these bond activation mechanisms have not been possible under isotropic, compressive stress (that is, hydrostatic pressure). Here we show that mechanochemistry through isotropic compression is possible by molecularly engineering structures that can translate macroscopic isotropic stress into molecular-level anisotropic strain. We engineer molecules with mechanically heterogeneous components—a compressible (‘soft’) mechanophore and incompressible (‘hard’) ligands. In these ‘molecular anvils’, isotropic stress leads to relative motions of the rigid ligands, anisotropically deforming the compressible mechanophore and activating bonds. Conversely, rigid ligands in steric contact impede relative motion, blocking reactivity. We combine experiments and computations to demonstrate hydrostatic-pressure-driven redox reactions in metal-organic chalcogenides that incorporate molecular elements that have heterogeneous compressibility, in which bending of bond angles or shearing of adjacent chains activates the metal-chalcogen bonds, leading to the formation of the elemental metal. These results reveal an unexplored reaction mechanism and suggest possible strategies for high-specificity mechanosynthesis.

Microfabrication of plastic-PDMS microfluidic devices using polyimide release layer and selective adhesive bonding

DOE PAGES

Wang, Shuyu; Yu, Shifeng; Lu, Ming; ...

2017-03-15

In this study, we present an improved method to bond poly(dimethylsiloxane) (PDMS) with polyimide (PI) to develop flexible substrate microfluidic devices. The PI film was separately fabricated on a silicon wafer by spin coating followed by thermal treatment to avoid surface unevenness of the flexible substrate. In this way, we could also integrate flexible substrate into standard micro-electromechanical systems (MEMS) fabrication. Meanwhile, the adhesive epoxy was selectively transferred to the PDMS microfluidic device by a stamp-and-stick method to avoid epoxy clogging the microfluidic channels. To spread out the epoxy evenly on the transferring substrate, we used superhydrophilic vanadium oxide filmmore » coated glass as the transferring substrate. After the bonding process, the flexible substrate could easily be peeled off from the rigid substrate. Contact angle measurement was used to characterize the hydrophicity of the vanadium oxide film. X-ray photoelectron spectroscopy analysis was conducted to study the surface of the epoxy. We further evaluated the bonding quality by peeling tests, which showed a maximum bonding strength of 100 kPa. By injecting with black ink, the plastic microfluidic device was confirmed to be well bonded with no leakage for a day under 1 atm. Finally, this proposed versatile method could bond the microfluidic device and plastic substrate together and be applied in the fabrication of some biosensors and lab-on-a-chip systems.« less

Enhancement in Organic Photovoltaic Efficiency through the Synergistic Interplay of Molecular Donor Hydrogen Bonding and -Stacking

DOE PAGES

Shewmon, Nathan; Watkins, Davita; Galindo, Johan; ...

2015-07-20

For organic photovoltaic (OPV) cells based on the bulk heterojunction (BHJ) structure, it remains challenging to rationally control the degree of phase separation and percolation within blends of donors and acceptors to secure optimal charge separation and transport. Reported is a bottom-up, supramolecular approach to BHJ OPVs wherein tailored hydrogen bonding (H-bonding) interactions between π-conjugated electron donor molecules encourage formation of vertically aligned donor π-stacks while simultaneously suppressing lateral aggregation; the programmed arrangement facilitates fine mixing with fullerene acceptors and efficient charge transport. The approach is illustrated using conventional linear or branched quaterthiophene donor chromophores outfitted with terminal functional groupsmore » that are either capable or incapable of self-complementary H-bonding. When applied to OPVs, the H-bond capable donors yield a twofold enhancement in power conversion efficiency relative to the comparator systems, with a maximum external quantum efficiency of 64%. H-bond promoted assembly results in redshifted absorption (in neat films and donor:C 60 blends) and enhanced charge collection efficiency despite disparate donor chromophore structure. Both features positively impact photocurrent and fill factor in OPV devices. Film structural characterization by atomic force microscopy, transmission electron microscopy, and grazing incidence wide angle X-ray scattering reveals a synergistic interplay of lateral H-bonding interactions and vertical π-stacking for directing the favorable morphology of the BHJ.« less

How many hydrogen-bonded α-turns are possible?

PubMed

Schreiber, Anette; Schramm, Peter; Hofmann, Hans-Jörg

2011-06-01

The formation of α-turns is a possibility to reverse the direction of peptide sequences via five amino acids. In this paper, a systematic conformational analysis was performed to find the possible isolated α-turns with a hydrogen bond between the first and fifth amino acid employing the methods of ab initio MO theory in vacuum (HF/6-31G*, B3LYP/6-311 + G*) and in solution (CPCM/HF/6-31G*). Only few α-turn structures with glycine and alanine backbones fulfill the geometry criteria for the i←(i + 4) hydrogen bond satisfactorily. The most stable representatives agree with structures found in the Protein Data Bank. There is a general tendency to form additional hydrogen bonds for smaller pseudocycles corresponding to β- and γ-turns with better hydrogen bond geometries. Sometimes, this competition weakens or even destroys the i←(i + 4) hydrogen bond leading to very stable double β-turn structures. This is also the reason why an "ideal" α-turn with three central amino acids having the perfect backbone angle values of an α-helix could not be localized. There are numerous hints for stable α-turns with a distance between the C(α)-atoms of the first and fifth amino acid smaller than 6-7 Å, but without an i←(i + 4) hydrogen bond.

Solid state direct bonding of polymers by vacuum ultraviolet light below 160 nm

NASA Astrophysics Data System (ADS)

Hashimoto, Yuki; Yamamoto, Takatoki

2017-10-01

This work investigated the application of vacuum ultraviolet (VUV) irradiation to the bonding of various substrates, including glass, polycarbonate (PC), cyclic olefin polymer (COP), polydimethylsiloxane (PDMS) and polymethyl methacrylate (PMMA). This method has the advantage of being able to bond various substrates without the application of heat or adhesives, and therefore may be very useful in the fabrication of micro/nanoscale structures composed of polymers. In contrast to previous applications of this technique, the present study used VUV radiation at wavelengths at and below 160 nm so as to take advantage of the higher energy in this range. Bonding was assessed based on measuring the shear stress of various test specimens subjected to VUV irradiation and then pressed together, and a number of analytical methods were also employed to examine the irradiated surfaces in order to elucidate the morphological and chemical changes following VUV treatment. These analyses included water contact angle measurements, attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), time of flight secondary ion mass spectrometry (TOF-SIMS) and atomic force microscopy (AFM). Poor bonding was identified between combinations consisting of PMMA/PC, PMMA/COP, PMMA/PMMA, PMMA/glass, and PC/COP, whereas all other combinations resulted in successful bonding with the bonding stress values such as PC/PC = 2.0 MPa, PC/glass = 10.7 MPa and COP/COP = 1.7 MPa, respectively.

Microfabrication of plastic-PDMS microfluidic devices using polyimide release layer and selective adhesive bonding

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

Wang, Shuyu; Yu, Shifeng; Lu, Ming

In this study, we present an improved method to bond poly(dimethylsiloxane) (PDMS) with polyimide (PI) to develop flexible substrate microfluidic devices. The PI film was separately fabricated on a silicon wafer by spin coating followed by thermal treatment to avoid surface unevenness of the flexible substrate. In this way, we could also integrate flexible substrate into standard micro-electromechanical systems (MEMS) fabrication. Meanwhile, the adhesive epoxy was selectively transferred to the PDMS microfluidic device by a stamp-and-stick method to avoid epoxy clogging the microfluidic channels. To spread out the epoxy evenly on the transferring substrate, we used superhydrophilic vanadium oxide filmmore » coated glass as the transferring substrate. After the bonding process, the flexible substrate could easily be peeled off from the rigid substrate. Contact angle measurement was used to characterize the hydrophicity of the vanadium oxide film. X-ray photoelectron spectroscopy analysis was conducted to study the surface of the epoxy. We further evaluated the bonding quality by peeling tests, which showed a maximum bonding strength of 100 kPa. By injecting with black ink, the plastic microfluidic device was confirmed to be well bonded with no leakage for a day under 1 atm. Finally, this proposed versatile method could bond the microfluidic device and plastic substrate together and be applied in the fabrication of some biosensors and lab-on-a-chip systems.« less

Chemical interaction mechanism of 10-MDP with zirconia

PubMed Central

Nagaoka, Noriyuki; Yoshihara, Kumiko; Feitosa, Victor Pinheiro; Tamada, Yoshiyuki; Irie, Masao; Yoshida, Yasuhiro; Van Meerbeek, Bart; Hayakawa, Satoshi

2017-01-01

Currently, the functional monomer 10-methacryloyloxy-decyl-dihydrogen-phosphate (10-MDP) was documented to chemically bond to zirconia ceramics. However, little research has been conducted to unravel the underlying mechanisms. This study aimed to assess the chemical interaction and to demonstrate the mechanisms of coordination between 10-MDP and zirconium oxide using 1H and 31P magic angle spinning (MAS) nuclear magnetic resonance (NMR) and two dimensional (2D) 1H → 31P heteronuclear correlation (HETCOR) NMR. In addition, shear bond-strength (SBS) tests were conducted to determine the effect of 10-MDP concentration on the bonding effectiveness to zirconia. These SBS tests revealed a 10-MDP concentration-dependent SBS with a minimum of 1-ppb 10-MDP needed. 31P-NMR revealed that one P-OH non-deprotonated of the PO3H2 group from 10-MDP chemically bonded strongly to zirconia. 1H-31P HETCOR NMR indicated that the 10-MDP monomer can be adsorbed onto the zirconia particles by hydrogen bonding between the P=O and Zr-OH groups or via ionic interactions between partially positive Zr and deprotonated 10-MDP (P-O−). The combination of 1H NMR and 2D 1H-31P HETCOR NMR enabled to describe the different chemical states of the 10-MDP bonds with zirconia; they not only revealed ionic but also hydrogen bonding between 10-MDP and zirconia. PMID:28358121

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.

Equilibrium and stability of axisymmetric drops on a conical substrate under gravity

NASA Astrophysics Data System (ADS)

Nurse, A. K.; Colbert-Kelly, S.; Coriell, S. R.; McFadden, G. B.

2015-08-01

Motivated by recent investigations of toroidal tissue clusters that are observed to climb conical obstacles after self-assembly [Nurse et al., "A model of force generation in a three-dimensional toroidal cluster of cells," J. Appl. Mech. 79, 051013 (2012)], we study a related problem of the determination of the equilibrium and stability of axisymmetric drops on a conical substrate in the presence of gravity. A variational principle is used to characterize equilibrium shapes that minimize surface energy and gravitational potential energy subject to a volume constraint, and the resulting Euler equation is solved numerically using an angle/arclength formulation. The resulting equilibria satisfy a Laplace-Young boundary condition that specifies the contact angle at the three-phase trijunction. The vertical position of the equilibrium drops on the cone is found to vary significantly with the dimensionless Bond number that represents the ratio of gravitational and capillary forces; a global force balance is used to examine the conditions that affect the drop positions. In particular, depending on the contact angle and the cone half-angle, we find that the vertical position of the drop can either increase ("the drop climbs the cone") or decrease due to a nominal increase in the gravitational force. Most of the equilibria correspond to upward-facing cones and are analogous to sessile drops resting on a planar surface; however, we also find equilibria that correspond to downward facing cones that are instead analogous to pendant drops suspended vertically from a planar surface. The linear stability of the drops is determined by solving the eigenvalue problem associated with the second variation of the energy functional. The drops with positive Bond number are generally found to be unstable to non-axisymmetric perturbations that promote a tilting of the drop. Additional points of marginal stability are found that correspond to limit points of the axisymmetric base state. Drops that are far from the tip are subject to azimuthal instabilities with higher mode numbers that are analogous to the Rayleigh instability of a cylindrical interface. We have also found a range of completely stable solutions that correspond to small contact angles and cone half-angles.

Cement bond evaluation method in horizontal wells using segmented bond tool

NASA Astrophysics Data System (ADS)

Song, Ruolong; He, Li

2018-06-01

Most of the existing cement evaluation technologies suffer from tool eccentralization due to gravity in highly deviated wells and horizontal wells. This paper proposes a correction method to lessen the effects of tool eccentralization on evaluation results of cement bond using segmented bond tool, which has an omnidirectional sonic transmitter and eight segmented receivers evenly arranged around the tool 2 ft from the transmitter. Using 3-D finite difference parallel numerical simulation method, we investigate the logging responses of centred and eccentred segmented bond tool in a variety of bond conditions. From the numerical results, we find that the tool eccentricity and channel azimuth can be estimated from measured sector amplitude. The average of the sector amplitude when the tool is eccentred can be corrected to the one when the tool is centred. Then the corrected amplitude will be used to calculate the channel size. The proposed method is applied to both synthetic and field data. For synthetic data, it turns out that this method can estimate the tool eccentricity with small error and the bond map is improved after correction. For field data, the tool eccentricity has a good agreement with the measured well deviation angle. Though this method still suffers from the low accuracy of calculating channel azimuth, the credibility of corrected bond map is improved especially in horizontal wells. It gives us a choice to evaluate the bond condition for horizontal wells using existing logging tool. The numerical results in this paper can provide aids for understanding measurements of segmented tool in both vertical and horizontal wells.

2-[(E)-(1,10-Phenanthrolin-5-yl)imino­meth­yl]phenol methanol monosolvate

PubMed Central

Öztürk Yíldírím, Sema; Demirhan, Nebahat; Elmalí, Fikriye; Butcher, Ray J.

2012-01-01

In the title multi-donor Schiff base compound, C19H13N3O·CH3OH, the dihedral angle between the mean planes of the phenanthroline and phenol rings is 59.3 (1)°. The Schiff base mol­ecule is linked to the solvent mol­ecule by an O—H⋯O hydrogen bond. In the crystal, the components are linked by O—H⋯N hydrogen bonds, weak O—H⋯N inter­actions and π–π stacking inter­actions [centroid–centroid distances = 3.701 (1) and 3.656 (1) Å]. PMID:22606116

Effect of polarization on the stability of a helix dimer

NASA Astrophysics Data System (ADS)

Wang, Xing Y.; Zhang, John Z. H.

2011-01-01

Molecular dynamics (MD) simulations have been carried out to study helix-helix interaction using both standard AMBER and polarized force fields. Comparison of the two simulations shows that electrostatic polarization of intra-protein hydrogen bonds plays a significant role in stabilizing the structure of helix dimer. This stabilizing effect is clearly demonstrated by examining the monomer structure, helix crossing angle and stability of backbone hydrogen bonds under AMBER and PPC. Since reliable prediction of protein-protein structure is a significant challenge, the current study should help shed light on the importance of electrostatic polarization of protein in helix-helix interaction and helix bundle structures.

3-{[(E)-(2-Hydroxynaphthalen-1-yl)methylidene]amino}pyridinium per­chlorate

PubMed Central

Damous, Maamar; Dénès, George; Bouacida, Sofiane; Hamlaoui, Meriem; Merazig, Hocine; Daran, Jean-Claude

2013-01-01

In the title Schiff base salt, C16H13N2O+·ClO4 −, the pyridine ring and the naphthalene ring system are approximately co-planar [making a dihedral angle of 6.05 (12)°] and an intra­molecular O—H⋯N hydrogen bond occurs between the hydroxyl and imino groups. In the crystal, the cations and anions are linked by N—H⋯O and weak C—H⋯O hydrogen bonds, forming the supra­molecular layers parallel to (100). The crystal studied was an inversion twin refined with minor component = 0.43 (13). PMID:24427084

6-[6-(Pyridin-2-yl)-1,2,4,5-tetra-zin-3-yl]pyridin-3-amine monohydrate.

PubMed

Broichhagen, Johannes; Klingl, Yvonne E; Trauner, Dirk; Mayer, Peter

2016-02-01

The packing of the title compound, C12H9N7·H2O, is dominated by hydrogen bonding and π-stacking. Layers parallel to [010] are established by hydrogen bonds involving all amine donor functions and one of the water donor functions, while the remaining water donor function enables the stacking of the layers along [10-1], which is accompanied by π-stacking. In the molecule, the plane of the central tetra-zine ring forms angles of 5.33 (7) and 19.84 (8)° with the adjacent 3-amine-pyridine and pyridine rings, respectively.

1-(1,3-Benzothia­zol-2-yl)-3-benzoyl­thio­urea

PubMed Central

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

2008-01-01

The title compound, C15H11N3OS2, was synthesized from benzoyl thio­cyanate and 2-amino­benzothia­zole in dry acetone. The thio­urea group is in the thio­amide form. The mol­ecules are stabilized by two inter­molecular C—H⋯S and C—H⋯O hydrogen bonds. Intra­molecular N—H⋯O hydrogen bonding results in a pseudo-S(6) planar ring with dihedral angles of 11.23 and 11.91° with the benzothiazole ring system and the phenyl ring, respectively. PMID:21200765

Shift-bonded resonance-domain diffraction gratings.

PubMed

Axelrod, Ramon; Shacham-Diamand, Yosi; Golub, Michael

2016-10-20

Resonance-domain-transmission diffractive optics with grating periods comparable to those of the illumination wavelength offers large angles of light deflection and nearly 100% Bragg diffraction efficiency. Optical design preferences for nearly normal incidence can be met by proper choice for the slant of the diffraction grooves relative to the substrate. However, straightforward fabrication of the slanted submicron high-aspect-ratio grooves is challenging. In this paper, optical performance comparable to that of the slanted grooves was achieved by an alternative solution of bonding two half-height symmetrical gratings with a lateral shift and an optional small longitudinal spacing. Results of design, nanofabrication, and optical testing are presented.

Crystal structure of 1-meth-oxy-2,2,2-tris-(pyrazol-1-yl)ethane.

PubMed

Lyubartseva, Ganna; Parkin, Sean; Coleman, Morgan D; Mallik, Uma Prasad

2014-09-01

The title compound, C12H14N6O, consists of three pyrazole rings bound via nitro-gen to the distal ethane carbon of meth-oxy ethane. The dihedral angles between the three pyrazole rings are 67.62 (14), 73.74 (14), and 78.92 (12)°. In the crystal, mol-ecules are linked by bifurcated C-H,H⋯N hydrogen bonds, forming double-stranded chains along [001]. The chains are linked via C-H⋯O hydrogen bonds, forming a three-dimensional framework structure. The crystal was refined as a perfect (0.5:0.5) inversion twin.

[(1R,3S)-2,2-Dichloro-3-(hy­droxy­meth­yl)cyclo­prop­yl]methanol

PubMed Central

Kailani, Mohammed H.

2013-01-01

The title compound, C5H8Cl2O2, represents a meso isomer crystallizing in a chiral space group with two mol­ecules per asymmetric unit. The mol­ecules form helical associates with a pitch of 6.31 Å along the a axis via O—H⋯O hydrogen bonds. The overall three-dimesional supra­molecular architecture is stabilized by C—Cl⋯O halogen bonding, with a Cl⋯O separation of 3.139 (3) Å and a C—Cl⋯O angle of 162.5 (2)°. PMID:23424506

Experimental and theoretical studies of the crystal structures of bis-isoxazole-bis-methylene dinitrate (BIDN) and bis-isoxazole tetramethylene tetranitrate (BITN) by x-ray crystallography and density functional theory

NASA Astrophysics Data System (ADS)

Taylor, Decarlos E.; Sausa, Rosario C.

2018-06-01

The determination of crystal structures plays an important role for model testing and validation, and understanding intra and intermolecular interactions that influence crystal packing. Here, we report the molecular structure of two recently synthesized energetic molecules, 3,3-bis-isoxazole-5,5‧-bis-methylene dinitrate (C8H6N4O8, BIDN) and bis-isoxazole tetramethylene tetranitrate (C10H8N6O14, BITN) determined by single crystal x-ray diffraction and solid state density functional theory (DFT). BIDN is composed of two planar alkyl nitrate groups (r.m.s deviation = 0.0004 (1) Å) bonded to two planar azole rings (r.m.s deviation = 0.001 (1) Å, whereas BITN is composed of four planar alkyl nitrate groups (average r.m.s deviation = 0.002 (1) Å) bonded to two planar azole rings (average r.m.s deviation = 0.002 (1) Å). The theoretical calculations predict very well the planarity of both the alkyl nitrate groups and rings for both compounds. Furthermore, they predict well the bond lengths and angles of both molecules with mean deviation values of 0.018 Å (BIDN) and 0.017 Å (BITN) and 0.481° (BIDN) and 0.747° (BITN). Overall, the DFT determined torsion angles agree well with those determined experimentally for both BIDN (average deviation = 1.139°) and BITN (average deviation = 0.604°). The theoretical cell constant values are in excellent agreement with those determined experimentally for both molecules, with the BIDN a cell value and β angle showing the largest deviation, 2.1% and -1.3%, respectively. Contacts between the atoms N and H dominate the intermolecular interactions of BIDN, whereas contacts involving the atoms O and H dominate the BITN intermolecular interactions. Electrostatic potential calculations at the B3LYP/6-31G* level reveal BIDN exhibits a lower sensitivity to impact compared to BITN.

Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of a biomolecule: 5-Hydroxymethyluracil

NASA Astrophysics Data System (ADS)

Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

2014-06-01

In the present work, the experimental and theoretical vibrational spectra of 5-hydroxymethyluracil were investigated. The FT-IR (4000-400 cm-1) spectrum of the molecule in the solid phase was recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared intensities of the title molecule in the ground state were calculated using density functional B3LYP and M06-2X methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data, and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 5-hydroxymethyluracil molecule was also simulated to evaluate the effect of intermolecular hydrogen bonding on its vibrational frequencies. It was observed that the Nsbnd H stretching modes shifted to lower frequencies, while its in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular Nsbnd H⋯O hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.

Probing hydrogen bonding in cocrystals and amorphous dispersions using (14)N-(1)H HMQC solid-state NMR.

PubMed

Tatton, Andrew S; Pham, Tran N; Vogt, Frederick G; Iuga, Dinu; Edwards, Andrew J; Brown, Steven P

2013-03-04

Cocrystals and amorphous solid dispersions have generated interest in the pharmaceutical industry as an alternative to more established solid delivery forms. The identification of intermolecular hydrogen bonding interactions in a nicotinamide palmitic acid cocrystal and a 50% w/w acetaminophen-polyvinylpyrrolidone solid dispersion are reported using advanced solid-state magic-angle spinning (MAS) NMR methods. The application of a novel (14)N-(1)H HMQC experiment, where coherence transfer is achieved via through-space couplings, is shown to identify specific hydrogen bonding motifs. Additionally, (1)H isotropic chemical shifts and (14)N electric field gradient (EFG) parameters, both accessible from (14)N-(1)H HMQC experiments, are shown to be sensitive to changes in hydrogen bonding geometry. Numerous indicators of molecular association are accessible from this experiment, including NH cross-peaks occurring from intermolecular hydrogen bonds and changes in proton chemical shifts or electric field gradient parameters. First-principles calculations using the GIPAW approach that yield accurate estimates of isotropic chemical shifts, and EFG parameters were used to assist in assignment. It is envisaged that (14)N-(1)H HMQC solid state NMR experiments could become a valuable screening technique of solid delivery forms in the pharmaceutical industry.

Molecular dynamics simulations of trans- and cis- N-acetyl- N'-methylamides of XaaPro dipeptides

NASA Astrophysics Data System (ADS)

Hoon Choi, Seung; Yun Yu, Jeong; Kwang Shin, Jae; Shik Jhon, Mu

1994-07-01

The occurrence of cis imide bonds in proteins is much higher than that of cis amide bonds due to the unique properties of proline. In order to examine the relationship between the high occurrence of these cis imide bonds and the residues preceding the proline, we perform molecular dynamics simulations of trans- and cis- N-acetyl- N'-methylamides of XaaPro dipeptides (AcXaaProNHMe). We investigate the conformational energies and structures of trans- and cis-AcXaa where Xaa has 12 amino acids in the vacuum state and 5 amino acids in the solution state. It is found that the occurrence of the cis imide bonds is strongly affected by the residue preceding the proline, and the dihedral angles (φ,ψ) of the backbone in AcXaaProNHMe are influenced by the configuration of the imide bond. We also find that the equilibrium properties of XaaPro in solution simulations are more similar to the statistics of X-ray crystallographic data than are those in vacuum simulations and solvation causes a remarkable change in the conformation of the pyrrolidine ring from the endo to the exo form.

Molecular structure, Normal Coordinate Analysis, harmonic vibrational frequencies, Natural Bond Orbital, TD-DFT calculations and biological activity analysis of antioxidant drug 7-hydroxycoumarin

NASA Astrophysics Data System (ADS)

Sebastian, S.; Sylvestre, S.; Jayarajan, D.; Amalanathan, M.; Oudayakumar, K.; Gnanapoongothai, T.; Jayavarthanan, T.

2013-01-01

In this work, we report harmonic vibrational frequencies, molecular structure, NBO and HOMO, LUMO analysis of Umbelliferone also known as 7-hydroxycoumarin (7HC). The optimized geometric bond lengths and bond angles obtained by computation (monomer and dimmer) shows good agreement with experimental XRD data. Harmonic frequencies of 7HC were determined and analyzed by DFT utilizing 6-311+G(d,p) as basis set. The assignments of the vibrational spectra have been carried out with the help of Normal Coordinate Analysis (NCA) following the Scaled Quantum Mechanical Force Field Methodology (SQMFF). The change in electron density (ED) in the σ* and π* antibonding orbitals and stabilization energies E(2) have been calculated by Natural Bond Orbital (NBO) analysis to give clear evidence of stabilization originating in the hyperconjugation of hydrogen-bonded interaction. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) complements with the experimental findings. The simulated spectra satisfactorily coincides with the experimental spectra. Microbial activity of studied compounds was tested against Staphylococcus aureus, Streptococcus pyogenes, Bacillus subtilis, Escherichia coli, Psuedomonas aeruginosa, Klebsiella pneumoniae, Proteus mirabilis, Shigella flexneri, Salmonella typhi and Enterococcus faecalis.

Bond-rearrangement and ionization mechanisms in the photo-double-ionization of simple hydrocarbons (C 2H 4, C 2H 3F, and 1,1-C 2H 2F 2) near and above threshold

DOE PAGES

Gaire, B.; Gatton, A. S.; Wiegandt, F.; ...

2016-09-14

We have investigated bond-rearrangement driven by photo-double-ionization (PDI) near and above the double ionization threshold in a sequence of carbon-carbon double bonded hydrocarbon molecules: ethylene, fluoroethylene, and 1,1-difluoroethylene. We employ the kinematically complete cold target recoil ion momentum spectroscopy (COLTRIMS) method to resolve all photo-double-ionization events leading to two-ionic fragments. We observe changes in the branching ratios of different dissociative ionization channels depending on the presence of none, one, or two fluorine atoms. The role of the fluorine atom in the bond-rearrangement channels is intriguing as evident by the re-ordering of the threshold energies of the PDI in the fluorinatedmore » molecules. These effects offer a compelling argument that the electronegativity of the fluorine (or the polarity of the molecule) strongly influences the potential energy surfaces of the molcules and drives bond-rearrangement during the dissociation process. The energy sharing and the relative angle between the 3D-momentum vectors of the two electrons provide clear evidence of direct and indirect PDI processes.« less

Thermally robust and biomolecule-friendly room-temperature bonding for the fabrication of elastomer-plastic hybrid microdevices.

PubMed

Nguyen, T P O; Tran, B M; Lee, N Y

2016-08-16

Here, we introduce a simple and fast method for bonding a poly(dimethylsiloxane) (PDMS) silicone elastomer to different plastics. In this technique, surface modification and subsequent bonding processes are performed at room temperature. Furthermore, only one chemical is needed, and no surface oxidation step is necessary prior to bonding. This bonding method is particularly suitable for encapsulating biomolecules that are sensitive to external stimuli, such as heat or plasma treatment, and for embedding fracturable materials prior to the bonding step. Microchannel-fabricated PDMS was first oxidized by plasma treatment and reacted with aminosilane by forming strong siloxane bonds (Si-O-Si) at room temperature. Without the surface oxidation of the amine-terminated PDMS and plastic, the two heterogeneous substrates were brought into intimate physical contact and left at room temperature. Subsequently, aminolysis occurred, leading to the generation of a permanent seal via the formation of robust urethane bonds after only 5 min of assembling. Using this method, large-area (10 × 10 cm) bonding was successfully realized. The surface was characterized by contact angle measurements and X-ray photoelectron spectroscopy (XPS) analyses, and the bonding strength was analyzed by performing peel, delamination, leak, and burst tests. The bond strength of the PDMS-polycarbonate (PC) assembly was approximately 409 ± 6.6 kPa, and the assembly withstood the injection of a tremendous amount of liquid with the per-minute injection volume exceeding 2000 times its total internal volume. The thermal stability of the bonded microdevice was confirmed by performing a chamber-type multiplex polymerase chain reaction (PCR) of two major foodborne pathogens - Escherichia coli O157:H7 and Salmonella typhimurium - and assessing the possibility for on-site direct detection of PCR amplicons. This bonding method demonstrated high potential for the stable construction of closed microfluidic systems socketed with biomolecule-immobilized surfaces such as DNA, antibody, enzyme, peptide, and protein microarrays.

Surfaces wettability and morphology modulation in a fluorene derivative self-assembly system

NASA Astrophysics Data System (ADS)

Cao, Xinhua; Gao, Aiping; Zhao, Na; Yuan, Fangyuan; Liu, Chenxi; Li, Ruru

2016-04-01

A new organogelator based on fluorene derivative (gelator 1) was designed and synthesized. Organogels could be obtained via the self-assembly of the derivative in acetone, toluene, ethyl acetate, hexane, DMSO and petroleum ether. The self-assembly process was thoroughly characterized using field-emission scanning electron microscopy (FESEM), X-ray diffraction (XRD), UV-vis, FT-IR and the contact angle. Surfaces with different morphologies and wetting properties were formed via the self-assembly of gelator 1 in the six different solvents. Interestingly, a superhydrophobic surface with a contact angle of 150° was obtained from organogel 1 in DMSO and exhibited the lotus-effect. The sliding angle necessary for a water droplet to move on the glass was only 15°. Hydrogen bonding and van der Waals forces were attributed as the main driving forces for gel formation.

Rhenium(V) Oxo Complexes of Novel N(2)S(2) Dithiourea (DTU) Chelate Ligands: Synthesis and Structural Characterization.

PubMed

Lipowska, Malgorzata; Hayes, Brittany L.; Hansen, Lory; Taylor, Andrew; Marzilli, Luigi G.

1996-07-03

The compounds RNHC(=S)NH(CH(2))(n)()NHC(=S)NHR were prepared in a search for new, relatively small N(2)S(2) ligands. These dithiourea (DTU) ligands are the first chelates containing two potentially bidentate thiourea moieties. A one-step reaction of 1,3-diaminopropane (1) with aryl or alkyl isothiocyanates or of 1,2-diaminoethane (2) with phenyl isothiocyanate afforded the target ligands in excellent yields (95-98%). The Re(V)=O complexes of RNHC(=S)NH(CH(2))(3)NHC(=S)NHR ligands were obtained through ligand exchange reactions with Re(V) precursors. The chemistry required neither protection of the sulfur atoms for ligand synthesis nor deprotection prior to metal complexation. The structure of (1-phenyl-3-(3-phenylthioureido)propyl]thioureato)oxorhenium(V) (7a), determined by X-ray diffraction methods, revealed the expected pseudo-square-pyramidal geometry with an N(2)S(2) basal and an apical oxo donor set. Both coordinated N's (N(c)) were deprotonated. One uncoordinated N (N(u)) was deprotonated, producing a neutral complex containing an unexpected new type of dianionic, four-membered N,S chelate. In the crystal, the N(u) atoms, N(3)H and N(4), of one complex each formed an H-bond with N(4) and N(3)H, respectively, of a symmetry-related complex. The N(c)-C-S bond angles (106.1(6) and 101.5(6) degrees ) were severely distorted from the 120 degrees expected for an sp(2)-hybridized C. However, these small bite angles and the large N-Re-N bond angle (86.1(3) degrees ) allowed for the formation of two four-membered chelate rings with normal Re-N and Re-S bond distances. Attempts to prepare complexes with the PhNHC(=S)NH(CH(2))(2)NHC(=S)NHPh ligand were unsuccessful. These results suggest that a central five-membered chelate ring is too small to accommodate bidentate coordination of both thiourea moieties. NMR studies in methanol established that the neutral complex with one uncoordinated N deprotonated was the favored form in neutral and basic solutions. However, under acidic conditions, a cationic form with both uncoordinated N's protonated was favored.

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

NASA Astrophysics Data System (ADS)

Ha, T.-K.; Günthard, H. H.

1989-07-01

Structural parameters like bond length, bond angles, etc. and harmonic and anharmonic potential coefficients of molecules with internal rotation, inversion or puckering modes are generally assumed to vary with the large amplitude internal coordinates in a concerted manner (relaxation). Taking the coordinate vectors of the nuclear configuration of semirigid molecules with relaxation (SRMRs) as functions of relaxing structural parameters and finite amplitude internal coordinate, the isometric group of SRMRs is discussed and the irreducible representations of the latter are shown to classify into engendered and nonengendered ones. On this basis a concept of equivalent sets of nuclei SRMRs is introduced and an analytical expression is derived which defines the most general functional form of relaxation increments of all common types of structural parameters compatible with isometric symmetry. This formula is shown to be a close analog of an analytical expression defining the transformations induced by the isometric group of infinitesimal internal coordinates associated with typical structural parameters. Furthermore analogous formulae are given for the most general form of the relaxation of harmonic potential coefficients as a function of finite internal coordinates. The general relations are illustrated by ab initio calculations for 1,2-difluoroethane at the MP4/DZP//HF/4-31G* level for twelve values of the dihedral angle including complete structure optimization. The potential to internal rotation is found to be in essential agreement with experimentally derived data. For a complete set of ab initio structural parameters the associated relaxation increments are represented as Fourier series, which are shown to confirm the form predicted by the general formula and the isometric group of 1,2-difluoroethane. Depending on type of the structural parameters (bond length, bond angles, etc.), the associated relaxation increments appear to follow some simple rules. Similarly a complete set of harmonic potential coefficients derived from the ab initio calculations will be analyzed in terms of Fourier series and shown to conform to the symmetry requirements of the symmetry group. Relaxation of potential coefficients is found to amount to up to ≈5% for some types of diagonal and nondiagonal terms and to reflect certain "topological" rules similar to regularities of harmonic potential constants of quasi-rigid molecules found in empirical determinations of valence force fields.

Novel 3-hydroxypropyl bonded phase by direct hydrosilylation of allyl alcohol on amorphous hydride silica

PubMed Central

Gómez, Jorge E.; Navarro, Fabián H.; Sandoval, Junior E.

2015-01-01

A novel 3-hydroxypropyl (propanol) bonded silica phase has been prepared by hydrosilylation of allyl alcohol on a hydride silica intermediate, in the presence of platinum (0)-divinyltetramethyldisiloxane (Karstedt's catalyst). The regio-selectivity of this synthetic approach had been correctly predicted by previous reports involving octakis(dimethylsiloxy)octasilsesquioxane (Q8M8H) and hydrogen silsesquioxane (T8H8), as molecular analogs of hydride amorphous silica. Thus, C-silylation predominated (~ 94%) over O-silylation, and high surface coverages of propanol groups (5±1 µmol/m2) were typically obtained in this work. The propanol-bonded phase was characterized by spectroscopic (IR and solid state NMR on silica microparticles), contact angle (on fused-silica wafers) and CE (on fused-silica tubes) techniques. CE studies of the migration behavior of pyridine, caffeine, tris(2,2’-bipyridine)Ru(II) chloride and lysozyme on propanol-modified capillaries were carried out. The adsorption properties of these select silanol-sensitive solutes were compared to those on the unmodified and hydride-modified tubes. It was found that hydrolysis of the SiH species underlying the immobilized propanol moieties leads mainly to strong ion-exchange based interactions with the basic solutes at pH 4, particularly with lysozyme. Interestingly, and in agreement with water contact angle and electroosmotic mobility figures, the silanol-probe interactions on the buffer-exposed (hydrolyzed) hydride surface are quite different from those of the original unmodified tube. PMID:24934906

Crystal structure of tetra­aqua­(5,5′-dimethyl-2,2′-bipyridyl-κ2 N,N′)iron(II) sulfate

PubMed Central

Belamri, Yamine; Setifi, Fatima; Francuski, Bojana M.; Novaković, Sladjana B.; Zouaoui, Setifi

2014-01-01

In the title compound, [Fe(C12H12N2)(H2O)4]SO4, the central FeII ion is coordinated by two N atoms from the 5,5′-dimethyl-2,2′-bi­pyridine ligand and four water O atoms in a distorted octa­hedral geometry. The Fe—O coordination bond lengths vary from 2.080 (3) to 2.110 (3) Å, while the two Fe—N coordination bonds have practically identical lengths [2.175 (3) and 2.177 (3) Å]. The chelating N—Fe—N angle of 75.6 (1)° shows the largest deviation from an ideal octa­hedral geometry; the other coordination angles deviate from ideal values by 0.1 (1) to 9.1 (1)°. O—H⋯O hydrogen bonding between the four aqua ligands of the cationic complex and four O-atom acceptors of the anion leads to the formation of layers parallel to the ab plane. Neighbouring layers further inter­act by means of C—H⋯O and π–π inter­actions involving the laterally positioned bi­pyridine rings. The perpen­dicular distance between π–π inter­acting rings is 3.365 (2) Å, with a centroid–centroid distance of 3.702 (3) Å. PMID:25552988

Indoor test for thermal performance evaluation of Lenox-Honeywell solar collector. [conducted using Marshall Space Flight Center Solar Simulator

NASA Technical Reports Server (NTRS)

Shih, K.

1977-01-01

The test procedures used and the test results obtained from an evaluation test program conducted on a double-covered liquid solar collector under simulated conditions are presented. The test article was a flat plate solar collector using liquid as the heat transfer medium. The absorber plate was steel with the copper tubes bonded on the upper surface. The plate was coated with black chrome with an absorptivity factor of .95 and emissivity factor of .12. A time constant test and incident angle modifier test were conducted to determine the transient effect and the incident angle effect on the collector.

The molecular structure and conformation of tetrabromoformaldazine: ab initio and DFT calculations

NASA Astrophysics Data System (ADS)

Jeong, Myongho; Kwon, Younghi

2000-06-01

Ab initio and density functional theory methods are applied to investigate the molecular structure and conformational nature of tetrabromoformaldazine. The calculations including the effects of the electron correlation at the B3LYP and MP2 levels with the basis set 6-311+G(d) can reproduce the experimental geometrical parameters at the skew conformation. The N-N bond torsional angle φ calculated at the MP2/6-311+G(d) level is found to be closest to the observed angle. The scanning of the potential energy surface suggests that the anti-conformation is at a saddle point corresponding to the transition state.

A buoyancy-based fiber Bragg grating tilt sensor

NASA Astrophysics Data System (ADS)

Maheshwari, Muneesh; Yang, Yaowen; Chaturvedi, Tanmay

2017-04-01

In this paper, a novel design of fiber Bragg grating tilt sensor is proposed. This tilt sensor exhibits high angle sensitivity and resolution. The presented tilt sensor works on the principle of the force of buoyancy in a liquid. It has certain advantages over the other designs of tilt sensors. The temperature effect can be easily compensated by using an un-bonded or free FBG. An analytical model is established which correlates the Bragg wavelength (λB) with the angle of inclination. This model is then validated by the experiment, where the experimental and analytical results are found in good agreement with each other.

N-(3-Chloro-1-methyl-1H-indazol-5-yl)-4-methylbenzene-sulfonamide.

PubMed

Chicha, Hakima; Rakib, El Mostapha; Amiri, Ouafa; Saadi, Mohamed; El Ammari, Lahcen

2014-02-01

The asymmetric unit of the title compound, C15H14ClN3O2S, contains two independent mol-ecules showing different conformations: in one mol-ecule, the indazole ring system makes a dihedral angle of 51.5 (1)° with the benzene ring whereas in the other, the indazole unit is almost perpendicular to the benzene ring [dihedral angle 77.7 (1)°]. In the crystal, the mol-ecules are linked by N-H⋯N and N-H⋯O hydrogen bonds, forming a set of four mol-ecules linked in pairs about an inversion centre.

Vibrational assignment of aluminum(III) Tris-acetylacetone

NASA Astrophysics Data System (ADS)

Tayyari, Sayyed Faramarz; Raissi, Haydar; Ahmadabadi, Zahra

2002-10-01

The geometry, frequency and intensity of the vibrational bands of aluminum(III) Tris-acetylacetone Al(AA) 3 and its 1, 3, 5- 13C derivative were obtained by the Hartree-Fock (HF) and Density Functional Theory (DFT) with the B3LYP, B1LYP, and G96LYP functionals and using the 6-31G* basis set. The calculated frequencies are compared with the solid IR and Raman spectra. All of the measured IR and Raman bands were interpreted in terms of the calculated vibrational modes. Most computed bands are predicted to be at higher wavenumbers than the experimental bands. The calculated bond lengths and bond angles are in good agreement with the experimental results. Analysis of the vibrational spectra indicates a strong coupling between the chelated ring modes. Four bands in the 500-390 cm -1 frequency range are assigned to the vibrations of metalligand bonds.

Conformational changes of a calix[8]arene derivative at the air-water interface.

PubMed

de Miguel, Gustavo; Pedrosa, José M; Martín-Romero, María T; Muñoz, Eulogia; Richardson, Tim H; Camacho, Luis

2005-03-10

The particular behavior of a p-tert-butyl calix[8]arene derivative (C8A) has been studied at the air-water interface using surface pressure-area isotherms, surface potential-area isotherms, film relaxation measurements, Brewster angle microscopy (BAM), and infrared spectroscopy for Langmuir-Blodgett films. Thus, it is observed that the properties of the film, for example, isotherms, domain formation, and FTIR spectra, recorded during the first compression cycle differ appreciably from those during the second compression and following cycles. The results obtained are interpreted on the basis of the conformational changes of the C8A molecules by surface pressure, allowing us to inquire into the inter- and intramolecular interactions (hydrogen bonds) of those molecules. Thus, the compression induces changes in the kind of hydrogen bonds from intra- and intermolecular with other C8A molecules to hydrogen bonds with water molecules.

Comprehensive DFT study on molecular structures of Lewisites in support of the Chemical Weapons Convention

NASA Astrophysics Data System (ADS)

Saeidian, Hamid; Sahandi, Morteza

2015-11-01

The structure of all of Lewisite's stereoisomers has been examined by B3LYP/6-311++G(3df,3pd) calculations. The geometry analysis for trans Lewisite L1-1 shows that the calculated bond angles, bond distances and dipole moment have a satisfactory relation compared with experimental values. HOMO-LUMO analysis of Lewisites reveals that L1-2 and L3-7 have the maximum and minimum electrophilicity index, respectively. The calculated chemical shifts were compared with experimental data, showing a very good agreement both for 1H and 13C. The vibrational and Raman frequencies of Lewisites have been precisely assigned and theoretical data were compared with the experimental vibrations. The bonding trends and Mulliken and atomic polar tensor charge distribution in Lewisites can be explained by the Bent's rule and the donor-acceptor interaction, respectively.

Distribution of short block copolymer chains in Binary Blends of Block Copolymers Having Hydrogen Bonding

NASA Astrophysics Data System (ADS)

Kwak, Jongheon; Han, Sunghyun; Kim, Jin Kon

2014-03-01

A binary mixture of two block copolymers whose blocks are capable of forming the hydrogen bonding allows one to obtain various microdomains that could not be expected for neat block copolymer. For instance, the binary blend of symmetric polystyrene-block-poly(2-vinylpyridine) copolymer (PS-b-P2VP) and polystyrene-block-polyhydroxystyrene copolymer (PS-b-PHS) blends where the hydrogen bonding occurred between P2VP and PHS showed hexagonally packed (HEX) cylindrical and body centered cubic (BCC) spherical microdomains. To know the exact location of short block copolymer chains at the interface, we synthesized deuterated polystyrene-block-polyhydroxystyrene copolymer (dPS-b-PHS) and prepared a binary mixture with PS-b-P2VP. We investigate, via small angle X-ray scattering (SAXS) and neutron reflectivity (NR), the exact location of shorter dPS block chain near the interface of the microdomains.

Crystal structure and hydrogen-bonding patterns in 5-fluoro­cytosinium picrate

PubMed Central

Mohana, Marimuthu; Thomas Muthiah, Packianathan; McMillen, Colin D.

2017-01-01

In the crystal structure of the title compound, 5-fluoro­cytosinium picrate, C4H5FN3O+·C6H2N3O7 −, one N heteroatom of the 5-fluoro­cytosine (5FC) ring is protonated. The 5FC ring forms a dihedral angle of 19.97 (11)° with the ring of the picrate (PA−) anion. In the crystal, the 5FC+ cation inter­acts with the PA− anion through three-centre N—H⋯O hydrogen bonds, forming two conjoined rings having R 2 1(6) and R 1 2(6) motifs, and is extended by N—H⋯O hydrogen bonds and C—H⋯O inter­actions into a two-dimensional sheet structure lying parallel to (001). Also present in the crystal structure are weak C—F⋯π inter­actions. PMID:28316809

Symplectic integration of closed chain rigid body dynamics with internal coordinate equations of motion

NASA Astrophysics Data System (ADS)

Mazur, Alexey K.

1999-07-01

Internal coordinate molecular dynamics (ICMD) is a recent efficient method for modeling polymer molecules which treats them as chains of rigid bodies rather than ensembles of point particles as in Cartesian MD. Unfortunately, it is readily applicable only to linear or tree topologies without closed flexible loops. Important examples violating this condition are sugar rings of nucleic acids, proline residues in proteins, and also disulfide bridges. This paper presents the first complete numerical solution of the chain closure problem within the context of ICMD. The method combines natural implicit fixation of bond lengths and bond angles by the choice of internal coordinates with explicit constraints similar to Cartesian dynamics used to maintain the chain closure. It is affordable for large molecules and makes possible 3-5 times faster dynamics simulations of molecular systems with flexible rings, including important biological objects like nucleic acids and disulfide-bonded proteins.

Mannobiose Binding Induces Changes in Hydrogen Bonding and Protonation States of Acidic Residues in Concanavalin A As Revealed by Neutron Crystallography

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

Gerlits, Oksana O.; Coates, Leighton; Woods, Robert J.

Plant lectins are carbohydrate-binding proteins with various biomedical applications. Concanavalin A (Con A) holds promise in treating cancerous tumors. To better understand the Con A carbohydrate binding specificity, we obtained a room-temperature neutron structure of this legume lectin in complex with a disaccharide Manα1–2Man, mannobiose. The neutron structure afforded direct visualization of the hydrogen bonding between the protein and ligand, showing that the ligand is able to alter both protonation states and interactions for residues located close to and distant from the binding site. An unprecedented low-barrier hydrogen bond was observed forming between the carboxylic side chains of Asp28 andmore » Glu8, with the D atom positioned equidistant from the oxygen atoms having an O···D···O angle of 101.5°.« less

AB INITIO Molecular Dynamics Simulations on Local Structure and Electronic Properties in Liquid Sb from 913 K to 1193 K

NASA Astrophysics Data System (ADS)

Hao, Qing-Hai; Li, Y. D.; Kong, Xiang-Shan; Liu, C. S.

2013-02-01

Ab initio molecular dynamics simulations on liquid Sb have been carried out at five different temperatures from 913 K to 1193 K. We have investigated the temperature dependence of structure properties including structural factor S(Q), pair correlation function g(r), bond-angle distribution function g3(θ), cluster properties and bond order parameter Q4 and Q6. A shoulder was reproduced in the high wave number side of the first peak in the S(Q) implying that the residual structure units of crystalline Sb remain in liquid Sb. There is a noticeable bend at around 1023 K in the temperature dependence of the first-peak height of S(Q), the cluster properties and bond order parameter Q4, respectively, indicating that an abnormal structural change may occur at 973-1023 K.

catena-Poly[[(benzil bis{[(pyridin-2-yl)methylidene]hydrazone}-κ4 N,N′,N′′,N′′′)mercury(II)]-μ-chlorido-[dichloridomercury(II)]-μ-chlorido

PubMed Central

Akkurt, Mehmet; Khandar, Ali Akbar; Tahir, Muhammad Nawaz; Hosseini-Yazdi, Seyed Abolfazl; Mahmoudi, Ghodrat

2012-01-01

In the title coordination polymer, [Hg2Cl4(C26H20N6)]n, one HgII ion is coordinated by four N atoms from the benzylbis((pyridin-2-yl)methyl­idenehydrazone) ligand and two Cl− ions in a very distorted cis-HgCl2N4 octa­hedral geometry. The other HgII ion is coordinated in a distorted tetra­hedral geometry by four Cl− ions. Bridging chloride ions link the HgII ions into a chain propagating in [010]: the Hg—Cl bridging bonds are significantly longer than the terminal bonds. The dihedral angle between the central benzene rings of the ligand is 83.3 (2)°. The packing is consolidated by weak C—H⋯Cl hydrogen bonds and C—H⋯π inter­actions. PMID:22807743

Orphenadrinium picrate picric acid.

PubMed

Fun, Hoong-Kun; Hemamalini, Madhukar; Siddaraju, B P; Yathirajan, H S; Narayana, B

2010-02-24

The asymmetric unit of the title compound N,N-dimethyl-2-[(2-methyl-phen-yl)phenyl-meth-oxy]ethanaminium picrate picric acid, C(18)H(24)NO(+)·C(6)H(2)N(3)O(7) (-)·C(6)H(3)N(3)O(7), contains one orphenadrinium cation, one picrate anion and one picric acid mol-ecule. In the orphenadrine cation, the two aromatic rings form a dihedral angle of 70.30 (7)°. There is an intra-molecular O-H⋯O hydrogen bond in the picric acid mol-ecule, which generates an S(6) ring motif. In the crystal structure, the orphenadrine cations, picrate anions and picric acid mol-ecules are connected by strong inter-molecular N-H⋯O hydrogen bonds, π⋯π inter-actions between the benzene rings of cations and anions [centroid-centroid distance = 3.5603 (9) Å] and weak C-H⋯O hydrogen bonds, forming a three-dimensional network.

Ab initio investigation of the structural and electronic properties of amorphous HgTe.

PubMed

Zhao, Huxian; Chen, Xiaoshuang; Lu, Jianping; Shu, Haibo; Lu, Wei

2014-01-29

We present the structure and electronic properties of amorphous mercury telluride obtained from first-principle calculations. The initial configuration of amorphous mercury telluride is created by computation alchemy. According to different exchange–correlation functions in our calculations, we establish two 256-atom models. The topology of both models is analyzed in terms of radial and bond angle distributions. It is found that both the Te and the Hg atoms tend to be fourfold, but with a wrong bond rate of about 10%. The fraction of threefold and fivefold atoms also shows that there are a significant number of dangling and floating bonds in our models. The electronic properties are also obtained. It is indicated that there is a bandgap in amorphous HgTe, in contrast to the zero bandgap for crystalline HgTe. The structures of the band tail and defect states are also discussed.

Equilibrium shapes of drops on membranes

NASA Astrophysics Data System (ADS)

Sharma, Ishan; Nair, Vineet; Shankar, Viswanathan

2017-11-01

Equilibrium shapes for axisymmetric sessile and pendant drops placed on / attached to geometrically nonlinear elastic membranes, in horizontal as well as inclined configurations, are obtained. The effective contact angle of the drop with the membrane, its contact radius, the maximum membrane displacement, and the volume of the drop is investigated for various values of Bond Number and membrane tension.

4-Dimethyl­amino-N′-(2-meth­oxy­benzyl­idene)benzohydrazide

PubMed Central

Su, Fu; Gu, Zheng-Gui; Lin, Jun

2011-01-01

In the title mol­ecule, C17H19N3O2, the dihedral angle between the two benzene rings is 14.05 (15)°. In the crystal, mol­ecules are linked through inter­molecular N—H⋯O hydrogen bonds, forming chains along b. PMID:22090947

Atomistic Simulation of Frictional Sliding Between Cellulose Iß Nanocrystals

Treesearch

Xiawa Wu; Robert J. Moon; Ashlie Martini

2013-01-01

Sliding friction between cellulose Iß nanocrystals is studied using molecular dynamics simulation. The effects of sliding velocity, normal load, and relative angle between sliding surface are predicted, and the results analyzed in terms of the number of hydrogen bonds within and between the cellulose chains. We find that although the observed friction trends can be...

4-[(3-Chloro-2-methyl­phen­yl)imino­meth­yl]phenol

PubMed Central

Manjunath, B. C.; Abdoh, M. M. M; Mallesha, L.; Mohana, K. N.; Lokanath, N. K.

2012-01-01

In the title compound, C14H12ClNO, the dihedral angle between the aromatic rings is 39.84 (7)°. In th crystal, mol­ecules are connected by O—H⋯N hydrogen bonds into chains parallel to [001]. In addition, a C—H⋯π contact occurs. PMID:23284502

Interaction of Simple Ions with Water: Theoretical Models for the Study of Ion Hydration

ERIC Educational Resources Information Center

Gancheff, Jorge S.; Kremer, Carlos; Ventura, Oscar N.

2009-01-01

A computational experiment aimed to create and systematically analyze models of simple cation hydrates is presented. The changes in the structure (bond distances and angles) and the electronic density distribution of the solvent and the thermodynamic parameters of the hydration process are calculated and compared with the experimental data. The…

A two-angle model of dynamic wetting in microscale capillaries under low capillary numbers with experiments.

PubMed

Lei, Da; Lin, Mian; Li, Yun; Jiang, Wenbin

2018-06-15

An accurate model of the dynamic contact angle θ d is critical for the calculation of capillary force in applications like enhanced oil recovery, where the capillary number Ca ranges from 10 -10 to 10 -5 and the Bond number Bo is less than 10 -4 . The rate-dependence of the dynamic contact angle under such conditions remains blurred, and is the main target of this study. Featuring with pressure control and interface tracking, the innovative experimental system presented in this work achieves the desired ranges of Ca and Bo, and enables the direct optical measurement of dynamic contact angles in capillaries as tiny as 40 × 20 (width × height) μm and 80 × 20 μm. The advancing and receding processes of wetting and nonwetting liquids were tested. The dynamic contact angle was confirmed velocity-independent with 10 -9  < Ca < 10 -5 (contact line velocity V = 0.135-490 μm/s) and it can be described by a two-angle model with desirable accuracy. A modified two-angle model was developed and an empirical form was obtained from experiments. For different liquids contacting the same surface, the advancing angle θ adv approximately equals the static contact angle θ o . The receding angle θ rec was found to be a linear function of θ adv , in good agreement with our and other experiments from the literature. Copyright © 2018 Elsevier Inc. All rights reserved.

Development and evaluation of an automatically adjusting coarse-grained force field for a β-O-4 type lignin from atomistic simulations

NASA Astrophysics Data System (ADS)

Li, Wenzhuo; Zhao, Yingying; Huang, Shuaiyu; Zhang, Song; Zhang, Lin

2017-01-01

This goal of this work was to develop a coarse-grained (CG) model of a β-O-4 type lignin polymer, because of the time consuming process required to achieve equilibrium for its atomistic model. The automatic adjustment method was used to develop the lignin CG model, which enables easy discrimination between chemically-varied polymers. In the process of building the lignin CG model, a sum of n Gaussian functions was obtained by an approximation of the corresponding atomistic potentials derived from a simple Boltzmann inversion of the distributions of the structural parameters. This allowed the establishment of the potential functions of the CG bond stretching and angular bending. To obtain the potential function of the CG dihedral angle, an algorithm similar to a Fourier progression form was employed together with a nonlinear curve-fitting method. The numerical potentials of the nonbonded portion of the lignin CG model were obtained using a potential inversion iterative method derived from the corresponding atomistic nonbonded distributions. The study results showed that the proposed CG model of lignin agreed well with its atomistic model in terms of the distributions of bond lengths, bending angles, dihedral angles and nonbonded distances between the CG beads. The lignin CG model also reproduced the static and dynamic properties of the atomistic model. The results of the comparative evaluation of the two models suggested that the designed lignin CG model was efficient and reliable.

A study of laser surface treatment in bonded repair of composite aircraft structures.

PubMed

Li, Shaolong; Sun, Ting; Liu, Chang; Yang, Wenfeng; Tang, Qingru

2018-03-01

Surface pre-treatment is one of the key processes in bonded repair of aircraft carbon fibre reinforced polymer composites. This paper investigates the surface modification of physical and chemical properties by laser ablation and conventional polish treatment techniques. Surface morphology analysed by laser scanning confocal microscopy and scanning electron microscopy showed that a laser-treated surface displayed higher roughness than that of a polish-treated specimen. The laser-treated laminate exhibited more functional groups in the form of O 1 s/C 1 s atomic ratio of 30.89% for laser-treated and 20.14% for polish-treated as evidenced by X-ray photoelectron spectroscopy observation. Contact angle goniometry demonstrated that laser treatment can provide increased surface free energy and wettability. In the light of mechanical interlocking, molecular bonding and thermodynamics theories on adhesion, laser etching process displayed enhanced bonding performance relative to the polishing surface treatment. These properties resulted in an increased single lap shear strength and a cohesive failure mode for laser etching while an adhesive failure mode occurred in polish-treated specimen.

A study of laser surface treatment in bonded repair of composite aircraft structures

NASA Astrophysics Data System (ADS)

Li, Shaolong; Sun, Ting; Liu, Chang; Yang, Wenfeng; Tang, Qingru

2018-03-01

Surface pre-treatment is one of the key processes in bonded repair of aircraft carbon fibre reinforced polymer composites. This paper investigates the surface modification of physical and chemical properties by laser ablation and conventional polish treatment techniques. Surface morphology analysed by laser scanning confocal microscopy and scanning electron microscopy showed that a laser-treated surface displayed higher roughness than that of a polish-treated specimen. The laser-treated laminate exhibited more functional groups in the form of O 1 s/C 1 s atomic ratio of 30.89% for laser-treated and 20.14% for polish-treated as evidenced by X-ray photoelectron spectroscopy observation. Contact angle goniometry demonstrated that laser treatment can provide increased surface free energy and wettability. In the light of mechanical interlocking, molecular bonding and thermodynamics theories on adhesion, laser etching process displayed enhanced bonding performance relative to the polishing surface treatment. These properties resulted in an increased single lap shear strength and a cohesive failure mode for laser etching while an adhesive failure mode occurred in polish-treated specimen.

Characterization of Bonding Between Poly(dimethylsiloxane) and Cyclic Olefin Coplymer Using Corona Discharge Induced Grafting Polymerization

PubMed Central

Liu, Ke; Gu, Pan; Hamaker, Kiri; Fan, Z. Hugh

2011-01-01

Thermoplastics have been increasingly used for fabricating microfluidic devices because of their low cost, mechanical/biocompatible attributes, and well-established manufacturing processes. However, there is sometimes a need to integrate such a device with components made from other materials such as polydimethylsiloxane (PDMS). Bonding thermoplastics with PDMS to produce hybrid devices is not straightforward. We have reported our method to modify the surface property of a cyclic olefin copolymer (COC) substrate by using corona discharge and grafting polymerization of 3-(trimethoxysilyl)propyl methacrylate; the modified surface enabled strong bonding of COC with PDMS. In this paper, we report our studies on the surface modification mechanism using attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM) and contact angle measurement. Using this bonding method, we fabricated a three-layer (COC/PDMS/COC) hybrid device consisting of elastomer-based valve arrays. The microvalve operation was confirmed through the displacement of a dye solution in a fluidic channel when the elastomer membrane was pneumatically actuated. Valve-enabled microfluidic handling was demonstrated. PMID:21962541

A study of laser surface treatment in bonded repair of composite aircraft structures

PubMed Central

Sun, Ting; Liu, Chang; Yang, Wenfeng; Tang, Qingru

2018-01-01

Surface pre-treatment is one of the key processes in bonded repair of aircraft carbon fibre reinforced polymer composites. This paper investigates the surface modification of physical and chemical properties by laser ablation and conventional polish treatment techniques. Surface morphology analysed by laser scanning confocal microscopy and scanning electron microscopy showed that a laser-treated surface displayed higher roughness than that of a polish-treated specimen. The laser-treated laminate exhibited more functional groups in the form of O 1 s/C 1 s atomic ratio of 30.89% for laser-treated and 20.14% for polish-treated as evidenced by X-ray photoelectron spectroscopy observation. Contact angle goniometry demonstrated that laser treatment can provide increased surface free energy and wettability. In the light of mechanical interlocking, molecular bonding and thermodynamics theories on adhesion, laser etching process displayed enhanced bonding performance relative to the polishing surface treatment. These properties resulted in an increased single lap shear strength and a cohesive failure mode for laser etching while an adhesive failure mode occurred in polish-treated specimen. PMID:29657748

Temperature-dependent interface characteristic of silicon wafer bonding based on an amorphous germanium layer deposited by DC-magnetron sputtering

NASA Astrophysics Data System (ADS)

Ke, Shaoying; Lin, Shaoming; Ye, Yujie; Mao, Danfeng; Huang, Wei; Xu, Jianfang; Li, Cheng; Chen, Songyan

2018-03-01

We report a near-bubble-free low-temperature silicon (Si) wafer bonding with a thin amorphous Ge (a-Ge) intermediate layer. The DC-magnetron-sputtered a-Ge film on Si is demonstrated to be extremely flat (RMS = 0.28 nm) and hydrophilic (contact angle = 3°). The effect of the post-annealing temperature on the surface morphology and crystallinity of a-Ge film at the bonded interface is systematically identified. The relationship among the bubble density, annealing temperature, and crystallinity of a-Ge film is also clearly clarified. The crystallization of a-Ge film firstly appears at the bubble region. More interesting feature is that the crystallization starts from the center of the bubbles and sprawls to the bubble edge gradually. The H2 by-product is finally absorbed by intermediate Ge layer with crystalline phase after post annealing. Moreover, the whole a-Ge film out of the bubble totally crystallizes when the annealing time increases. This Ge integration at the bubble region leads to the decrease of the bubble density, which in turn increases the bonding strength.

Solvent-free thermoplastic-poly(dimethylsiloxane) bonding mediated by UV irradiation followed by gas-phase chemical deposition of an adhesion linker

NASA Astrophysics Data System (ADS)

Ahn, S. Y.; Lee, N. Y.

2015-07-01

Here, we introduce a solvent-free strategy for bonding various thermoplastic substrates with poly(dimethylsiloxane) (PDMS) using ultraviolet (UV) irradiation followed by the gas-phase chemical deposition of aminosilane on the UV-irradiated thermoplastic substrates. The thermoplastic substrates were first irradiated with UV for surface hydrophilic treatment and were then grafted with vacuum-evaporated aminosilane, where the alkoxysilane side reacted with the oxidized surface of the thermoplastic substrate. Next, the amine-terminated thermoplastic substrates were treated with corona discharge to oxidize the surface and were bonded with PDMS, which was also oxidized via corona discharge. The two substrates were then hermetically sealed and pressed under atmospheric pressure for 30 min at 60 °C. This process enabled the formation of a robust siloxane bond (Si-O-Si) between the thermoplastic substrate and PDMS under relatively mild conditions using an inexpensive and commercially available UV lamp and Tesla coil. Various thermoplastic substrates were examined for bonding with PDMS, including poly(methylmethacrylate) (PMMA), polycarbonate (PC), poly(ethyleneterephthalate) (PET) and polystyrene (PS). Surface characterizations were performed by measuring the contact angle and performing x-ray photoelectron spectroscopy analysis, and the bond strength was analyzed by conducting various mechanical force measurements such as pull, delamination, leak and burst tests. The average bond strengths for the PMMA-PDMS, PC-PDMS, PET-PDMS and PS-PDMS assemblies were measured at 823.6, 379.3, 291.2 and 229.0 kPa, respectively, confirming the highly reliable performance of the introduced bonding strategy.

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.

Influence of warm air-drying on enamel bond strength and surface free-energy of self-etch adhesives.

PubMed

Shiratsuchi, Koji; Tsujimoto, Akimasa; Takamizawa, Toshiki; Furuichi, Tetsuya; Tsubota, Keishi; Kurokawa, Hiroyasu; Miyazaki, Masashi

2013-08-01

We examined the effect of warm air-drying on the enamel bond strengths and the surface free-energy of three single-step self-etch adhesives. Bovine mandibular incisors were mounted in self-curing resin and then wet ground with #600 silicon carbide (SiC) paper. The adhesives were applied according to the instructions of the respective manufacturers and then dried in a stream of normal (23°C) or warm (37°C) air for 5, 10, and 20 s. After visible-light irradiation of the adhesives, resin composites were condensed into a mold and polymerized. Ten samples per test group were stored in distilled water at 37°C for 24 h and then the bond strengths were measured. The surface free-energies were determined by measuring the contact angles of three test liquids placed on the cured adhesives. The enamel bond strengths varied according to the air-drying time and ranged from 15.8 to 19.1 MPa. The trends for the bond strengths were different among the materials. The value of the γS⁺ component increased slightly when drying was performed with a stream of warm air, whereas that of the γS⁻ component decreased significantly. These data suggest that warm air-drying is essential to obtain adequate enamel bond strengths, although increasing the drying time did not significantly influence the bond strength. © 2013 Eur J Oral Sci.

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.

Bond-length distributions for ions bonded to oxygen: results for the non-metals and discussion of lone-pair stereoactivity and the polymerization of PO4

PubMed Central

Gagné, Olivier Charles

2018-01-01

Bond-length distributions are examined for three configurations of the H+ ion, 16 configurations of the group 14–16 non-metal ions and seven configurations of the group 17 ions bonded to oxygen, for 223 coordination polyhedra and 452 bond distances for the H+ ion, 5957 coordination polyhedra and 22 784 bond distances for the group 14–16 non-metal ions, and 248 coordination polyhedra and 1394 bond distances for the group 17 non-metal ions. H⋯O and O—H + H⋯O distances correlate with O⋯O distance (R 2 = 0.94 and 0.96): H⋯O = 1.273 × O⋯O – 1.717 Å; O—H + H⋯O = 1.068 × O⋯O – 0.170 Å. These equations may be used to locate the hydrogen atom more accurately in a structure refined by X-ray diffraction. For non-metal elements that occur with lone-pair electrons, the most observed state between the n versus n+2 oxidation state is that of highest oxidation state for period 3 cations, and lowest oxidation state for period 4 and 5 cations when bonded to O2−. Observed O—X—O bond angles indicate that the period 3 non-metal ions P3+, S4+, Cl3+ and Cl5+ are lone-pair seteroactive when bonded to O2−, even though they do not form secondary bonds. There is no strong correlation between the degree of lone-pair stereoactivity and coordination number when including secondary bonds. There is no correlation between lone-pair stereoactivity and bond-valence sum at the central cation. In synthetic compounds, PO4 polymerizes via one or two bridging oxygen atoms, but not by three. Partitioning our PO4 dataset shows that multi-modality in the distribution of bond lengths is caused by the different bond-valence constraints that arise for Obr = 0, 1 and 2. For strongly bonded cations, i.e. oxyanions, the most probable cause of mean bond length variation is the effect of structure type, i.e. stress induced by the inability of a structure to follow its a priori bond lengths. For ions with stereoactive lone-pair electrons, the most probable cause of variation is bond-length distortion.

Electronic structure and bonding of intergranular glassy films in polycrystalline Si3 N4 : Ab initio studies and classical molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Rulis, P.; Chen, J.; Ouyang, L.; Ching, W.-Y.; Su, X.; Garofalini, S. H.

2005-06-01

The electronic structure and bonding of a realistic model of an intergranular glassy film (IGF) was studied with multiple computational methods. The model has a Si-O-N glassy region sandwiched between crystalline basal planes of β-Si3N4 and contains a total of 798 atoms. It was constructed with periodic boundary conditions via classical molecular dynamics (MD) techniques using an accurate multibody atomic potential. The model was then further relaxed by the VASP (Vienna ab initio simulation package) program. It is shown that the VASP-relaxed structure reduces the total energy from the MD-relaxed structure by only 47.38eV , validating the accuracy of the multiatom potential used. The calculated electronic structure shows the IGF model to be an insulator with a sizable gap of almost 3eV . Quasidefectlike states can be identified near the band edges arising from the more strained Si-N and Si-O bonds at the interface. Calculation of the Mulliken effective charge and bond order values indicates that the bonds in the glassy region and at the interface can be enhanced and weakened by distortions in the bond length and bond angle. The states at the top of the valence band are derived mostly from the crystalline part of the Si-N bonding while the states at the bottom of the conduction band are dominated by the Si-O bonding in the glassy region. Calculation of the electrostatic potential across the interface shows an average band offset of about 1.5eV between the crystalline β-Si3N4 and the glassy Si-O-N region which could be related to the space charge model for IGF.

[Effect of TiO2-SiO2-SnOx film with different firing temperatures on bond strength of low-fusing dental porcelain to pure titanium].

PubMed

Zhang, Zichuan; Zhang, Pei

2015-07-01

To evaluate the influence of TiO(2)-SiO(2)-SnOx nano-coatings with different firing temperatures on the bond strength of low-fusing dental porcelain to pure titanium. The surface of pure titanium was coated uniformly with TiO(2)-SiO(2)-SnOx nano-coatings by solution-gelatin (Sol-Gel) technology and then fired at 300 °C (group A) or 750 °C (group B) for 1 h. The specimens without any coatings were the control group (group C). There were 10 specimens in each group. Dental porcelain was sintered on the surface of titanium specimens. Surface roughness and contact angle of the coatings were also detected. The titanium-porcelain bond strength was investigated according to YY 0621-2008 standards using three-point flexure bond test. The phase composition of the TiO(2)-SiO(2)-SnOx nano-coatings was characterized by X-ray diffraction(XRD). The interface of titanium-porcelain and TiO(2)-SiO(2)-SnOx nano-coatings were observed using scanning electron microscope (SEM). No rutile phase was found in these specimens of group A and group B. The surface roughness of group A, B, C was (0.97 ± 0.06), (0.99 ± 0.03), (0.96 ± 0.07) µm, respectively. No significant difference was found among the three groups. Compared with that of group C (64.37° ± 3.01°), contact angles detected in group A (52.04° ± 3.15°) and group B (85.27° ± 4.17°) were significantly different (P < 0.05). The bond strength of titanium-porcelain in group A [(35.66 ± 2.65) MPa] was significantly increased compared with those in group B [(26.18 ± 2.22) MPa] and group C [(31.66 ± 3.52) MPa]. SEM photomicrographs of titanium-porcelain interface morphology of the specimens before porcelain sintering showed that TiO(2)-SiO(2)-SnOx nano-coatings in group A were compact and homogeneous with petty cracks and those in group B was loose and arranged disorderly. TiO(2)-SiO(2)-SnOx nano-coating fired at 300 °C is significantly effective in improving the titanium-porcelain bond strength.

[Effects of different surface treatments on the zirconia-resin cement bond strength].

PubMed

Liao, Y; Liu, X Q; Chen, L; Zhou, J F; Tan, J G

2018-02-18

To evaluate the effects of different surface treatments on the shear bond strength between zirconia and resin cement. Forty zirconia discs were randomly divided into four groups (10 discs in each group) for different surface treatments: control, no surface treatment; sandblast, applied air abrasion with aluminum oxide particles; ultraviolet (UV), the zirconia sample was placed in the UV sterilizer at the bottom of the UV lamp at 10 mm, and irradiated for 48 h; cold plasma, the discs were put in the cold plasma cabinet with the cold plasma generated from the gas of He for 30 s. Specimens of all the groups were surface treated prior to cementation with Panavia F 2.0 cement. The surface morphology and contact angle of water were measured. The shear bond strengths were tested and the failure modes were examined with a stereomicroscope. Surface morphology showed no difference between the UV/cold plasma group and the control group. Sandblasted zirconia displayed an overall heterogeneous distribution of micropores. The contact angle of the control group was 64.1°±2.0°. After sandblasting, UV irradiation and cold plasma exposure, the values significantly decreased to 48.8°±2.6°, 27.1°±3.6° and 32.0°±3.3°. The values of shear bond strength of the specimens with sandblasted (14.82±2.01) MPa were higher than those with no treatment (9.41±1.07) MPa with statistically significant difference (P<0.05). The values of shear bond strength of the specimens with UV irradiation (10.02±0.64) MPa were higher than those with no treatment (9.41±1.07) MPa, but without statistically significant difference (P>0.05). The values of cold plasma group (18.34±3.05) MPa were significantly higher than those of control group (9.41±1.07) MPa, even more than those with sandblast(14.82±2.01) MPa (P<0.05). X-ray photoelectron spectroscopy (XPS) showed increase in oxygen (O) and decrease in carbon (C) elements after UV and cold plasma treatment. The surface C/O ratio also decreased after UV and cold plasma treatment. Zirconia specimens treated with UV and cold plasma could significantly improve the hydrophilicity. The surface morphology was unaffected by the UV irradiation and cold plasma treatments. The improvements of ziconia shear bond strength were slight in UV group without statistically significant difference. Cold plasma treatment significantly improved the shear bond strength between zirconia and resin cement.

Structure and water exchange of the hydrated thiosulfate ion in aqueous solution using QMCF MD simulation and large angle X-ray scattering.

PubMed

Eklund, Lars; Hofer, Tomas S; Weiss, Alexander K H; Tirler, Andreas O; Persson, Ingmar

2014-09-07

Theoretical ab initio quantum mechanical charge field molecular dynamics (QMCF MD) has been applied in conjunction with experimental large angle X-ray scattering (LAXS) to study the structure and dynamics of the hydrated thiosulfate ion, S2O3(2-), in aqueous solution. The S-O and SC-ST bond distances have been determined to be 1.479(5) and 2.020(6) Å by LAXS and to be 1.478 and 2.017 Å by QMCF MD simulations, which are slightly longer than the mean values found in the solid state, 1.467 and 2.002 Å, respectively. This is due to the hydrogen bonds formed at hydration. The water dynamics show that water molecules are exchanged at the hydrated oxygen and sulfur atoms, and that the water exchange is ca. 50% faster at the sulfur atom than at the oxygen atoms with mean residence times, τ0.5, of 2.4 and 3.6 ps, respectively. From this point of view the water exchange dynamics mechanism resembles the sulfate ion, while it is significantly different from the sulfite ion. This shows that the lone electron-pair in the sulfite ion has a much larger impact on the water exchange dynamics than a substitution of an oxygen atom for a sulfur one. The LAXS data did give mean SCOaq1 and SCOaq2 distances of 3.66(2) and 4.36(10) Å, respectively, and SC-Othio and OthioOaq1, SC-ST and STOaq2 distances of 1.479(5), 2.845(10), 2.020(6) and 3.24(5) Å, respectively, giving SC-OthioOaq1 and SC-STOaq2 angles close to 110°, strongly indicating a tetrahedral geometry around the terminal thiosulfate sulfur and the oxygens, and thereby, three water molecules are hydrogen bound to each of them. The hydrogen bonds between thiosulfate oxygens and the hydrating water molecules are stronger and with longer mean residence times than those between water molecules in the aqueous bulk, while the opposite is true for the hydrogen bonds between the terminal thiosulfate sulfur and the hydrating water molecules. The hydration of all oxo sulfur ions is discussed using the detailed observations for the sulfate, thiosulfate and sulfite ions, and the structure of the hydrated peroxodisulfate ion, S2O8(2-), in aqueous solution has been determined by means of LAXS to support the general observations. The mean S-O bond distances are 1.448(2) and 1.675(5) Å to the oxo and peroxo oxygens, respectively.

Periodontal considerations in the use of bonds or bands on molars in adolescents and adults.

PubMed

Boyd, R L; Baumrind, S

1992-01-01

This longitudinal study compared the periodontal status of bonded and banded molars in 20 adult and 40 adolescent patients before, during and after treatment with fixed orthodontic appliances. Plaque accumulation (measured by the Plaque Index), gingival inflammation (measured by the Gingival Index and the bleeding tendency), and pocket depth were assessed by one examiner at sites along the mesio-buccal line angle of the maxillary right first molar and the mandibular left first molar. Assessments were made immediately prior to the placement of fixed appliances (pretreatment), at 1, 3, 6, 9, 12 and 18 months after appliances were placed; and 3 months after appliances were removed (posttreatment). Loss of attachment between the pretreatment and posttreatment visits also was determined. At pretreatment, no significant differences were found in gingival inflammation between maxillary and mandibular banded and bonded molars. During treatment, both maxillary and mandibular banded molars showed significantly (p less than 0.05) greater gingival inflammation and plaque accumulation than did bonded molars. Three months after appliance removal, the maxillary molars that had been banded continued to show significantly more gingival inflammation and loss of attachment than did the maxillary molars that had been bonded. When all banded and bonded teeth were grouped by patient age, mean values for plaque accumulation and gingival inflammation in the maxillary molar regions were significantly greater for adolescents than for adults.

Short-range structure of barium tellurite glasses and its correlation with stress-optic response

NASA Astrophysics Data System (ADS)

Kaur, Amarjot; Khanna, Atul; Fábián, Margit

2018-06-01

The atomic parameters of metal ion-oxygen speciation such as bond-lengths and nearest neighbor distances for Ba-O, Te-O and O-O pairs, co-ordination numbers and bond angle distributions for O-Ba-O, O-Te-O and O-O-O linkages are determined by neutron diffraction and Reverse Monte Carlo simulations on the series of xBaO-(100-x)TeO2 glasses containing 10, 15 and 20 mol% BaO. The glass network depolymerizes and the average Te-O co-ordination number decreases from 3.60 ± 0.02 to 3.48 ± 0.02 with increase in BaO concentration. Te-O bond lengths are in the range: 1.97 ± 0.01–1.92 ± 0.01 Å. Ba2+ is mostly in octahedral coordination and the Ba-O bond lengths are in the range: 2.73 ± 0.01 to 2.76 ± 0.03 Å. Te-O co-ordination number is also determined by Raman spectroscopy and it shows good agreement with the neutron data. The short-range structural properties i.e. metal ion coordination number (Nc) and bond lengths (d) were correlated with the stress-optic response. The bonding characteristic, Br values were determined from the structural data of xBaO-(100-x)TeO2 glasses and were used to predict the stress-induced birefringence properties.