Insertion of terminal alkyne into Pt-N bond of the square planar [PtI2(Me2phen)] complex.

PubMed

Benedetti, Michele; De Castro, Federica; Lamacchia, Vincenza; Pacifico, Concetta; Natile, Giovanni; Fanizzi, Francesco P

2017-11-21

The reactivity of [PtX 2 (Me 2 phen)] complexes (X = Cl, Br, I; Me 2 phen = 2,9-dimethyl-1,10-phenanthroline) with terminal alkynes has been investigated. Although the dichlorido species [PtCl 2 (Me 2 phen)] exhibits negligible reactivity, the bromido and iodido derivatives lead in short time to the formation of five-coordinate Pt(ii) complexes of the type [PtX 2 (Me 2 phen)(η 2 -CH[triple bond, length as m-dash]CR)] (X = Br, I; R = Ph, n-Bu), in equilibrium with the starting reagents. Similar to analogous complexes with simple acetylene, the five coordinate species can also undergo dissociation of an halido ligand and formation of the transient square-planar cationic species [PtX(Me 2 phen)(η 2 -CH[triple bond, length as m-dash]CR)] + . This latter can further evolve to give an unusual, sparingly soluble square planar product where the former terminal alkyne is converted into a :C[double bond, length as m-dash]C(H)(R) moiety with the α-carbon bridging the Pt(ii) core with one of the two N-donors of coordinated Me 2 phen. The final product [PtX 2 {κ 2 -N,C-(Z)-N[combining low line]1-N10-C[combining low line][double bond, length as m-dash]C(H)(R)}] (N1-N10 = 2,9-dimethyl-1,10-phenanthroline; X = Br, I) contains a Pt-N-C-C-N-C six-membered chelate ring in a square planar Pt(ii) coordination environment.

Synthesis and structural characterisation of alkali metal complexes of heteroatom-stabilised 1,4- and 1,6-dicarbanions.

PubMed

Izod, Keith; Bowman, Lyndsey J; Wills, Corinne; Clegg, William; Harrington, Ross W

2009-05-07

A straightforward Peterson olefination reaction between either [{(Me(2)PhSi)(3)C}Li(THF)] or in situ-generated [(Me(3)Si)(2){Ph(2)P(BH(3))}CLi(THF)(n)] and paraformaldehyde gives the alkenes (Me(2)PhSi)(2)C[double bond, length as m-dash]CH(2) () and (Me(3)Si){Ph(2)P(BH(3))}C[double bond, length as m-dash]CH(2) (), respectively, in good yield. Ultrasonic treatment of with lithium in THF yields the lithium complex [{(Me(2)PhSi)(2)C(CH(2))}Li(THF)(n)](2) (), which reacts in situ with one equivalent of KOBu(t) in diethyl ether to give the potassium salt [{(Me(2)PhSi)(2)C(CH(2))}K(THF)](2) (). Similarly, ultrasonic treatment of with lithium in THF yields the lithium complex [[{Ph(2)P(BH(3))}(Me(3)Si)C(CH(2))]Li(THF)(3)](2).2THF (). The bis(phosphine-borane) [(Me(3)Si){Me(2)(H(3)B)P}CH(Me(2)Si)(CH(2))](2) () may be prepared by the reaction of [Me(2)P(BH(3))CH(SiMe(3))]Li with half an equivalent of ClSiMe(2)CH(2)CH(2)SiMe(2)Cl in refluxing THF. Metalation of with two equivalents of MeLi in refluxing THF yields the lithium complex [[{Me(2)P(BH(3))}(Me(3)Si)C{(SiMe(2))(CH(2))}]Li(THF)(3)](2) (), whereas metalation with two equivalents of MeK in cold diethyl ether yields the potassium complex [[{Me(2)P(BH(3))}(Me(3)Si)C{(SiMe(2))(CH(2))}](2)K(2)(THF)(4)](infinity) () after recrystallisation. X-Ray crystallography shows that, whereas the lithium complex crystallises as a discrete molecular species, the potassium complexes and crystallise as sheet and chain polymers, respectively.

Characterization of the HCNCO complex and its radiation-induced transformation to HNCCO in cold media: an experimental and theoretical investigation.

PubMed

Kameneva, Svetlana V; Tyurin, Daniil A; Feldman, Vladimir I

2017-09-13

The HCNCO complex and its X-ray induced transformation to HNCCO in solid noble gas (Ng) matrices (Ng = Ne, Ar, Kr, Xe) was first characterized by matrix isolation FTIR spectroscopy at 5 K. The HCNCO complex was obtained by deposition of HCN/CO/Ng gaseous mixtures. The assignment was based on extensive quantum chemical calculations at the CCSD(T) level of theory. The calculations predicted two computationally stable structures for HCNCO and three stable structures for HNCCO. However, only the most energetically favorable linear structures corresponding to the co-ordination between the H atom of HCN (HNC) and the C atom of CO have been found experimentally. The HCNCO complex demonstrates a considerable red shift of the H-C stretching vibrations (-24 to -38 cm -1 , depending on the matrix) and a blue shift of the HCN bending vibrations (+29 to +32 cm -1 ) with respect to that of the HCN monomer, while the C[double bond, length as m-dash]O stretching mode is blue-shifted by 15 to 20 cm -1 as compared to the CO monomer. The HNCCO complex reveals a strong red shift of the H-N bending (-77 to -118 cm -1 ) and a strong blue shift of the HNC bending mode (ca. +100 cm -1 ) as compared to the HNC monomer, whereas the C[double bond, length as m-dash]O stretching is blue-shifted by 24 to 29 cm -1 with respect to that of the CO monomer. The interaction energies were determined to be 1.01 and 1.87 kcal mol -1 for HCNCO and HNCCO, respectively. It was found that the formation of complexes with CO had a remarkable effect on the radiation-induced transformations of HCN. While the dissociation of HCN to H and CN is suppressed in complexes, the isomerization of HCN to HNC is strongly catalyzed by the complexation with CO. The astrochemical implications of the results are discussed.

TiO(2) doping by hydroxyurea at the nucleation stage: towards a new photocatalyst in the visible spectral range.

PubMed

Azouani, R; Tieng, S; Chhor, K; Bocquet, J-F; Eloy, P; Gaigneaux, E M; Klementiev, K; Kanaev, A V

2010-10-07

We report an original method of preparation of OCN-doped TiO(2) for photocatalysis in the visible spectral range. The preparation is achieved by a sol-gel route using titanium tetraisopropoxide precursor. Special attention was paid to fluid micromixing, which enables homogeneous reaction conditions in the reactor bulk and monodispersity of the produced clusters/nanoparticles. The dopant hydroxyurea (HyU, CH(4)N(2)O(2)) is injected into the reactive fluid at the nucleation stage, which lasts tens of milliseconds. The doping results in a strong yellow coloration of the nanocolloids due to the absorption band in the spectral range 380-550 nm and accelerates the aggregation kinetics of both nuclei at the induction stage and sub-nuclei units (clusters) at the nucleation stage. FTIR, Raman and UV-visible absorption analyses show the formation of a stable HyU-TiO(2) complex. EXAFS spectra indicate no appreciable changes of the first-shell Ti atom environment. The doping agent takes available surface sites of TiO(2) clusters/nanoparticles attaining ∼10% molar loading. The reaction kinetics then accelerates due to a longer collisional lifetime between nanoparticles induced by the formation of a weak [double bond, length as m-dash]OTi bond. The OCN-group bonding to titanium atoms produces a weakening of the C[double bond, length as m-dash]O double bond and a strengthening of the C-N and N-O bonds.

A Zn(2+)-responsive highly sensitive fluorescent probe and 1D coordination polymer based on a coumarin platform.

PubMed

Kumar, Virendra; Kumar, Ajit; Diwan, Uzra; Upadhyay, K K

2013-09-28

A coumarin-based Schiff base (receptor 1) exhibited fluorescence enhancement selectively with Zn(2+) at a nanomolar level in near-aqueous medium (EtOH-H2O; 1:1, v/v). The response was instantaneous with a detection limit of 3.26 × 10(-9) M. The sensing event is supposed to incorporate a combinational effect of intramolecular charge transfer (ICT), chelation-enhanced fluorescence (CHEF) and C[double bond, length as m-dash]N isomerization mechanisms. Various spectroscopic methods, viz. IR, UV-visible, fluorescence and NMR in association with single crystal XRD studies, were used for thorough investigation of the structure of receptor 1 as well as of the sensing event. The Zn(2+) complex of receptor 1 exhibited a very nice 1D chain coordination polymeric framework in its single crystal XRD.

First-principles study of adsorption-desorption kinetics of aqueous V2+/V3+ redox species on graphite in a vanadium redox flow battery.

PubMed

Jiang, Zhen; Klyukin, Konstantin; Alexandrov, Vitaly

2017-06-14

Vanadium redox flow batteries (VRFBs) represent a promising solution to grid-scale energy storage, and understanding the reactivity of electrode materials is crucial for improving the power density of VRFBs. However, atomistic details about the interactions between vanadium ions and electrode surfaces in aqueous electrolytes are still lacking. Here, we examine the reactivity of the basal (0001) and edge (112[combining macron]0) graphite facets with water and aqueous V 2+ /V 3+ redox species at 300 K employing Car-Parrinello molecular dynamics (CPMD) coupled with metadynamics simulations. The results suggest that the edge surface is characterized by the formation of ketonic C[double bond, length as m-dash]O functional groups due to complete water dissociation into the H/O/H configuration with surface O atoms serving as active sites for adsorption of V 2+ /V 3+ species. The formation of V-O bonds at the surface should significantly improve the kinetics of electron transfer at the edge sites, which is not the case for the basal surface, in agreement with the experimentally hypothesized mechanism.

The concept, reality and utility of single-site heterogeneous catalysts (SSHCs).

PubMed

Thomas, John Meurig

2014-05-07

Very substantial advances have recently been made in the design and construction of solid catalysts and in elucidating both their mode of operation and the factors that determine their selectivity and longevity. This Perspective explains how and why such progress has been made. One important factor, the deployment of single-site heterogeneous and enzymatic catalysts, used either alone or in conjunction with other strategies, including metabolic engineering, enables a multitude of new products (for example, environmentally clean jet fuel) to be readily manufactured. In a practical sense SSHCs enable the advantages of homogeneous and to a lesser degree enzymatic catalysts to be united with those of heterogeneous ones. With the aid of the vastly increasing families of nanoporous solids, desired catalytically active sites may be engineered in atomic detail on their inner, accessible surfaces, thereby opening up new possibilities in synthetic organic chemistry - as in the smooth formation of C-C and C[double bond, length as m-dash]N bonds in a number of intermolecular reactions - as well as in photocatalysts and in fluidized catalytic cracking of hydrocarbons.

Synthesis, structure and reactivity of rare-earth metallacarborane alkyls [η(1):η(5)-O(CH2)2C2B9H9]Ln(σ:η(1)-CH2C6H4-o-NMe2)(THF)2.

PubMed

Yang, Jingying; Xie, Zuowei

2015-04-14

Rare-earth metallacarborane alkyls can be stabilized by the incorporation of a functional sidearm into both π and σ ligands. Reaction of [Me3NH][7,8-O(CH2)2-7,8-C2B9H10] with one equiv. of Ln(CH2C6H4-o-NMe2)3 gave metallacarborane alkyls [η(1):η(5)-O(CH2)2C2B9H9]Ln(σ:η(1)-CH2C6H4-o-NMe2)(THF)2 (Ln = Y (), Gd (), Er ()) via alkane elimination. They represent the first examples of rare-earth metallacarborane alkyls. Treatment of with RN[double bond, length as m-dash]C[double bond, length as m-dash]NR (R = Cy, (i)Pr) or 2-benzoylpyridine afforded the corresponding mono-insertion products [η(1):η(5)-O(CH2)2C2B9H9]Y[η(2)-(RN)2C(CH2C6H4-o-NMe2)](DME) (R = Cy (), (i)Pr ()) or [η(1):η(5)-O(CH2)2C2B9H9]Y[C5H4NC(Ph)(CH2C6H4-o-NMe2)O](THF)2 (), respectively. Complex also reacted with ArNCO or ArNC (Ar = 2,6-diisopropylphenyl, 2,6-dimethylphenyl) to give di-insertion products [η(1):η(5)-O(CH2)2C2B9H9]Y[OC([double bond, length as m-dash]NC6H3Me2)N(C6H3Me2)C(CH2C6H4-o-NMe2)O](THF)2 () or [η(1):η(5)-O(CH2)2C2B9H9]Y[C([double bond, length as m-dash]NC6H3(i)Pr2)C([double bond, length as m-dash]NC6H3(i)Pr2)(CH2C6H4-o-NMe2)](DME) (). These results showed that the reactivity pattern of the Ln-C σ bond in rare-earth metallacarborane alkyls was dependent on the nature of the unsaturated organic molecules. New complexes were characterized by various spectroscopic techniques and elemental analysis. Some were further confirmed by single-crystal X-ray analysis.

Base free N-alkylation of anilines with ArCH2OH and transfer hydrogenation of aldehydes/ketones catalyzed by the complexes of η5-Cp*Ir(iii) with chalcogenated Schiff bases of anthracene-9-carbaldehyde.

PubMed

Dubey, Pooja; Gupta, Sonu; Singh, Ajai K

2018-03-12

The condensation of anthracene-9-carbaldehyde with 2-(phenylthio/seleno)ethylamine results in Schiff bases [PhS(CH 2 ) 2 C[double bond, length as m-dash]N-9-C 14 H 9 ](L1) and [PhSe(CH 2 ) 2 C[double bond, length as m-dash]N-9-C 14 H 9 ] (L2). On their reaction with [(η 5 -Cp*)IrCl(μ-Cl)] 2 and CH 3 COONa at 50 °C followed by treatment with NH 4 PF 6 , iridacycles, [(η 5 -Cp*)Ir(L-H)][PF 6 ] (1: L = L1; 2: L = L2), result. The same reaction in the absence of CH 3 COONa gives complexes [(η 5 -Cp*)Ir(L)Cl][PF 6 ] (3-4) in which L = L1(3)/L2(4) ligates in a bidentate mode. The ligands and complexes were authenticated with HR-MS and NMR spectra [ 1 H, 13 C{ 1 H} and 77 Se{ 1 H} (in the case of L2 and its complexes only)]. Single crystal structures of L2 and half sandwich complexes 1-4 were established with X-ray crystallography. Three coordination sites of Ir in each complex are covered with η 5 -Cp* and on the remaining three, donor atoms present are: N, S/Se and C - /Cl - , resulting in a piano-stool structure. The moisture and air insensitive 1-4 act as efficient catalysts under mild conditions for base free N-alkylation of amines with benzyl alcohols and transfer hydrogenation (TH) of aldehydes/ketones. The optimum loading of 1-4 as a catalyst is 0.1-0.5 mol% for both the activations. The best reaction temperature is 80 °C for transfer hydrogenation and 100 °C for N-alkylation. The mercury poisoning test supports a homogeneous pathway for both the reactions catalyzed by 1-4. The two catalytic processes are most efficient with 3 followed by 4 > 1 > 2. The mechanism proposed on the basis of HR-MS of the reaction mixtures of the two catalytic processes taken after 1-2 h involves the formation of an alkoxy and hydrido species. The real catalytic species proposed in the case of iridacycles results due to the loss of the Cp* ring.

Microsolvation of the acetanilide cation (AA(+)) in a nonpolar solvent: IR spectra of AA(+)-L(n) clusters (L = He, Ar, N2; n ≤ 10).

PubMed

Schmies, Matthias; Patzer, Alexander; Schütz, Markus; Miyazaki, Mitsuhiko; Fujii, Masaaki; Dopfer, Otto

2014-05-07

Infrared photodissociation (IRPD) spectra of mass-selected cluster ions of acetanilide (N-phenylacetamide), AA(+)-Ln, with the ligands L = He (n = 1-2), Ar (n = 1-7), and N2 (n = 1-10) are recorded in the hydride stretch (amide A, νNH, νCH) and fingerprint (amide I-III) ranges of AA(+) in its (2)A'' ground electronic state. Cold AA(+)-Ln clusters are generated in an electron impact ion source, which predominantly produces the most stable isomer of a given cluster ion. Systematic vibrational frequency shifts of the N-H stretch fundamentals (νNH) provide detailed information about the sequential microsolvation process of AA(+) in a nonpolar (L = He and Ar) and quadrupolar (L = N2) solvent. In the most stable AA(+)-Ln clusters, the first ligand forms a hydrogen bond (H-bond) with the N-H proton of trans-AA(+) (t-AA(+)), whereas further ligands bind weakly to the aromatic ring (π-stacking). There is no experimental evidence for complexes with the less stable cis-AA(+) isomer. Quantum chemical calculations at the M06-2X/aug-cc-pVTZ level confirm the cluster growth sequence derived from the IR spectra. The calculated binding energies of De(H) = 720 and 1227 cm(-1) for H-bonded and De(π) = 585 and 715 cm(-1) for π-bonded Ar and N2 ligands in t-AA(+)-L are consistent with the observed photofragmentation branching ratios of AA(+)-Ln. Comparison between charged and neutral AA((+))-L dimers indicates that ionization switches the preferred ion-ligand binding motif from π-stacking to H-bonding. Electron removal from the HOMO of AA(+) delocalized over both the aromatic ring and the amide group significantly strengthens the C[double bond, length as m-dash]O bond and weakens the N-H bond of the amide group.

Assessment of the amide-I local modes in gamma- and beta-turns of peptides.

PubMed

Wang, Jianping

2009-07-14

The amide-I local modes, mainly the C[double bond, length as m-dash]O stretching vibrations, form the structural basis of femtosecond 2D IR spectroscopy in characterizing backbone structures and dynamics of peptides and proteins. In this work, a density functional theory (DFT) level of computational assessment of the amide-I local modes in oligomers mostly in the turn conformations was carried out. It is shown that local mode properties, including transition frequencies and transition dipole magnitudes and orientations, are slightly conformational dependent. However, the distributions of these properties in the peptide oligomers are narrow and have mean values almost identical to those from an isolated peptide monomer, justifying the prevalent use of a uniform local mode in modeling the 1D and 2D IR spectra. In addition, it is shown that the transition dipole magnitude and orientation of the peptide monomer predicted by the DFT calculations can be well approximated by electrostatic potential-based transition charge schemes, e.g. Merz-Singh-Kollman, CHELP, as well as CHELPG.

New ruthenium carboxylate complexes having a 1-5-. eta. sup 5 -cyclooctadienyl ligand

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

Osakada, Kohtaro; Grohmann, A.; Yamamoto, Akio

1990-07-01

Reaction of 3-butenoic acid with Ru(cod)(cot) (cod) = 1-2-{eta}{sup 2}:5-6-{eta}{sup 2}-cyclooctadiene; cot = 1-6-{eta}{sup 6}-cyclooctatriene in the presence of PMe{sub 3} gives a new ruthenium(II) complex formulated as Ru(1-5-{eta}{sup 5}-C{sub 8}H{sub 11}){eta}{sup 1}(O),{eta}{sup 2}(C,C{prime}-OCOCH{sub 2}CH{double bond}CH{sub 2})(PMe{sub 3}) (1). X-ray crystallography revealed its structure as having a piano-stool coordination around the ruthenium center. Crystals of 1 are tetragonal, space group P4{sub 3}2{sub 1}2, with a = 12.559 (3) {angstrom}, c = 20.455 (4) {angstrom}, and Z = 8. {sup 1}H and {sup 13}C({sup 1}H) NMR spectra of 1 agree well for the structure with the allyl entity of the carboxylatemore » {pi}-bonded through the C{double bond}C double bond to ruthenium.« less

Influences of the molecular fuel structure on combustion reactions towards soot precursors in selected alkane and alkene flames.

PubMed

Ruwe, Lena; Moshammer, Kai; Hansen, Nils; Kohse-Höinghaus, Katharina

2018-04-25

In this study, we experimentally investigate the high-temperature oxidation kinetics of n-pentane, 1-pentene and 2-methyl-2-butene (2M2B) in a combustion environment using flame-sampling molecular beam mass spectrometry. The selected C5 fuels are prototypes for linear and branched, saturated and unsaturated fuel components, featuring different C-C and C-H bond structures. It is shown that the formation tendency of species, such as polycyclic aromatic hydrocarbons (PAHs), yielded through mass growth reactions increases drastically in the sequence n-pentane < 1-pentene < 2M2B. This comparative study enables valuable insights into fuel-dependent reaction sequences of the gas-phase combustion mechanism that provide explanations for the observed difference in the PAH formation tendency. First, we investigate the fuel-structure-dependent formation of small hydrocarbon species that are yielded as intermediate species during the fuel decomposition, because these species are at the origin of the subsequent mass growth reaction pathways. Second, we review typical PAH formation reactions inspecting repetitive growth sequences in dependence of the molecular fuel structure. Third, we discuss how differences in the intermediate species pool influence the formation reactions of key aromatic ring species that are important for the PAH growth process underlying soot formation. As a main result it was found that for the fuels featuring a C[double bond, length as m-dash]C double bond, the chemistry of their allylic fuel radicals and their decomposition products strongly influences the combination reactions to the initially formed aromatic ring species and as a consequence, the PAH formation tendency.

A review of high temperature co-electrolysis of H2O and CO2 to produce sustainable fuels using solid oxide electrolysis cells (SOECs): advanced materials and technology.

PubMed

Zheng, Yun; Wang, Jianchen; Yu, Bo; Zhang, Wenqiang; Chen, Jing; Qiao, Jinli; Zhang, Jiujun

2017-03-06

High-temperature solid oxide electrolysis cells (SOECs) are advanced electrochemical energy storage and conversion devices with high conversion/energy efficiencies. They offer attractive high-temperature co-electrolysis routes that reduce extra CO 2 emissions, enable large-scale energy storage/conversion and facilitate the integration of renewable energies into the electric grid. Exciting new research has focused on CO 2 electrochemical activation/conversion through a co-electrolysis process based on the assumption that difficult C[double bond, length as m-dash]O double bonds can be activated effectively through this electrochemical method. Based on existing investigations, this paper puts forth a comprehensive overview of recent and past developments in co-electrolysis with SOECs for CO 2 conversion and utilization. Here, we discuss in detail the approaches of CO 2 conversion, the developmental history, the basic principles, the economic feasibility of CO 2 /H 2 O co-electrolysis, and the diverse range of fuel electrodes as well as oxygen electrode materials. SOEC performance measurements, characterization and simulations are classified and presented in this paper. SOEC cell and stack designs, fabrications and scale-ups are also summarized and described. In particular, insights into CO 2 electrochemical conversions, solid oxide cell material behaviors and degradation mechanisms are highlighted to obtain a better understanding of the high temperature electrolysis process in SOECs. Proposed research directions are also outlined to provide guidelines for future research.

Redox properties of undoped 5 nm diamond nanoparticles.

PubMed

Holt, Katherine B; Ziegler, Christoph; Caruana, Daren J; Zang, Jianbing; Millán-Barrios, Enrique J; Hu, Jingping; Foord, John S

2008-01-14

This paper demonstrates the promoting effects of 5 nm undoped detonation diamond nanoparticles on redox reactions in solution. An enhancement in faradaic current for the redox couples Ru(NH(3))(6)(3+/2+) and Fe(CN)(6)(4-/3-) was observed for a gold electrode modified with a drop-coated layer of nanodiamond (ND), in comparison to the bare gold electrode. The ND layer was also found to promote oxygen reduction. Surface modification of the ND powders by heating in air or in a hydrogen flow resulted in oxygenated and hydrogenated forms of the ND, respectively. Oxygenated ND was found to exhibit the greatest electrochemical activity and hydrogenated ND the least. Differential pulse voltammetry of electrode-immobilised ND layers in the absence of solution redox species revealed oxidation and reduction peaks that could be attributed to direct electron transfer (ET) reactions of the ND particles themselves. It is hypothesised that ND consists of an insulating sp(3) diamond core with a surface that has significant delocalised pi character due to unsatisfied surface atoms and C[double bond, length as m-dash]O bond formation. At the nanoscale surface properties of the particles dominate over those of the bulk, allowing ET to occur between these essentially insulating particles and a redox species in solution or an underlying electrode. We speculate that reversible reduction of the ND may occur via electron injection into available surface states at well-defined reduction potentials and allow the ND particles to act as a source and sink of electrons for the promotion of solution redox reactions.

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

PubMed

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

2016-03-07

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

Tuning the nature and stability of self-assemblies formed by ester benzene 1,3,5-tricarboxamides: the crucial role played by the substituents.

PubMed

Desmarchelier, Alaric; Alvarenga, Bruno Giordano; Caumes, Xavier; Dubreucq, Ludovic; Troufflard, Claire; Tessier, Martine; Vanthuyne, Nicolas; Idé, Julien; Maistriaux, Thomas; Beljonne, David; Brocorens, Patrick; Lazzaroni, Roberto; Raynal, Matthieu; Bouteiller, Laurent

2016-09-20

As the benzene 1,3,5-tricarboxamide (BTA) moiety is commonly used as the central assembling unit for the construction of functionalized supramolecular architectures, strategies to tailor the nature and stability of BTA assemblies are needed. The assembly properties of a library of structurally simple BTAs derived from amino dodecyl esters (ester BTAs, 13 members) have been studied, either in the bulk or in cyclohexane solutions, by means of a series of analytical methods (NMR, DSC, POM, FT-IR, UV-Vis, CD, ITC, high-sensitivity DSC, SANS). Two types of hydrogen-bonded species have been identified and characterized: the expected amide-bonded helical rods (or stacks) that are structurally similar to those formed by BTAs with simple alkyl side chains (alkyl BTAs), and ester-bonded dimers in which the BTAs are connected by means of hydrogen bonds linking the amide N-H and the ester C[double bond, length as m-dash]O. MM/MD calculations coupled with simulations of CD spectra allow for the precise determination of the molecular arrangement and of the hydrogen bond pattern of these dimers. Our study points out the crucial influence of the substituent attached on the amino-ester α-carbon on the relative stability of the rod-like versus dimeric assemblies. By varying this substituent, one can precisely tune the nature of the dominant hydrogen-bonded species (stacks or dimers) in the neat compounds and in cyclohexane over a wide range of temperatures and concentrations. In the neat BTAs, stacks are stable up to 213 °C and dimers above 180 °C whilst in cyclohexane stacks form at c* > 3 × 10 -5 M at 20 °C and dimers are stable up to 80 °C at 7 × 10 -6 M. Ester BTAs that assemble into stacks form a liquid-crystalline phase and yield gels or viscous solutions in cyclohexane, demonstrating the importance of controlling the structure of these assemblies. Our systematic study of these structurally similar ester BTAs also allows for a better understanding of how a single atom or moiety can impact the nature and stability of BTA aggregates, which is of importance for the future development of functionalized BTA supramolecular polymers.

Prediction of apatite lattice constants from their constituent elemental radii and artificial intelligence methods.

PubMed

Wu, P; Zeng, Y Z; Wang, C M

2004-03-01

Lattice constants (LCs) of all possible 96 apatite compounds, A(5)(BO(4))(3)C, constituted by A[double bond]Ba(2+), Ca(2+), Cd(2+), Pb(2+), Sr(2+), Mn(2+); B[double bond]As(5+), Cr(5+), P(5+), V(5+); and C[double bond]F(1-), Cl(1-), Br(1-), OH(1-), are predicted from their elemental ionic radii, using pattern recognition (PR) and artificial neural networks (ANN) techniques. In particular, by a PR study it is demonstrated that ionic radii predominantly govern the LCs of apatites. Furthermore, by using ANN techniques, prediction models of LCs a and c are developed, which reproduce well the measured LCs (R(2)=0.98). All the literature reported on 30 pure and 22 mixed apatite compounds are collected and used in the present work. LCs of all possible 66 new apatites (assuming they exist) are estimated by the developed ANN models. These proposed new apatites may be of interest to biomedical research especially in the design of new apatite biomaterials for bone remodeling. Similarly these techniques may also be applied in the study of interface growth behaviors involving other biomaterials.

Controlling factors of oligomerization at the water surface: why is isoprene such a unique VOC?

PubMed

Ishizuka, Shinnosuke; Fujii, Tomihide; Matsugi, Akira; Sakamoto, Yosuke; Hama, Tetsuya; Enami, Shinichi

2018-06-06

Recent studies have shown that atmospheric particles are sufficiently acidic to enhance the uptake of unsaturated volatile organic compounds (VOCs) by triggering acid-catalyzed oligomerization. Controlling factors of oligomerization at the aqueous surfaces, however, remain to be elucidated. Herein, isoprene (2-methyl-1,3-butadiene, ISO), 1,3-butadiene (1,3-b), 1,4-pentadiene (1,4-p), 1-pentene (1-p), and 2-pentene (2-p) vapors are exposed to an acidic water microjet (1 ≤ pH ≤ 5), where cationic products are generated on its surface within ∼10 μs and directly detected using surface-sensitive mass spectrometry. We found that carbocations form at the air-water interface in all the cases, whereas the extent of oligomerization largely depends on the structure in the following order: ISO ≫ 1,3-b > 1,4-p ≫ 1-p ≈ 2-p. Importantly, the cationic oligomerization of ISO yields a protonated decamer ((ISO)10H+, a C50 species of m/z 681.6), while the pentenes 1-p/2-p remain as protonated monomers. We suggest that ISO oligomerization is uniquely facilitated by (1) the resonance stabilization of (ISO)H+ through the formation of a tertiary carbocation with a conjugated C[double bond, length as m-dash]C bond pair, and (2) π-electron enrichment induced by the neighboring methyl group. Experiments in D2O and D2O : H2O mixtures revealed that ISO oligomerization on the acidic water surface proceeds via two competitive mechanisms: chain-propagation and proton-exchange reactions. Furthermore, we found that ISO carbocations undergo addition to relatively inert 1-p, generating hitherto uncharacterized co-oligomers.

Structural and electrochemical studies of TiO2 complexes with (4,4'-((1E,1'E)-(2,5-bis(octyloxy)-1,4-phenylene)bis(ethene-2,1-diyl))bis-(E)-N-(2,5-bis(octyloxy)benzylidene)) imine derivative bases towards organic devices.

PubMed

Rozycka, Anna; Iwan, Agnieszka; Bogdanowicz, Krzysztof Artur; Filapek, Michal; Górska, Natalia; Hreniak, Agnieszka; Marzec, Monika

2018-06-12

Three (4,4'-((1E,1'E)-(2,5-bis(octyloxy)-1,4-phenylene)bis(ethene-2,1-diyl))bis-(E)-N-(2,5-bis(octyloxy)benzylidene)) imine derivatives were synthesized via a condensation reaction with p-toluenesulfonic acid as a catalyst. The effects of the end groups and vinylene (-HC[double bond, length as m-dash]CH-) moieties on the structural, thermal, optical, electrochemical and photovoltaic properties of imines were investigated to check the influence of TiO2 on the imine properties. The thermal behavior of imines and their complexes with TiO2 was widely investigated using FT-IR, XRD, DSC and POM methods in order to determine the order type in the imine structure. All imines present the highest occupied molecular orbital (HOMO) levels of about -5.39 eV (SAI1 and SAI2) and -5.27 eV (SAI3) and the lowest unoccupied molecular orbital (LUMO) levels at about -3.17 eV. The difference of the end groups in the imines in each case did not affect redox properties. Generally, both oxidation and reduction are easier after TiO2 addition and it also changes the HOMO-LUMO levels of imines. Moreover, changes in the characteristic bands for imines in the region 1500-1700 cm-1 observed as a drastic decrease of intensity or even disappearance of bands in the imine : TiO2 mixture suggest the formation of a complex (C[double bond, length as m-dash]N)-TiO2. Organic devices with the configuration of ITO/TiO2/SAIx (or SAIx : TiO2)/Au were fabricated and investigated in the presence and absence of visible light irradiation with an intensity of 93 mW cm-2. In all imines and complexes with TiO2, the generation of the photocurrent indicates their use as photodiodes and the best result was observed for SAI3 : TiO2 complexes.

Organic Compounds Produced by Photolysis of Realistic Interstellar and Cometary Ice Analogs Containing Methanol

NASA Technical Reports Server (NTRS)

Bernstein, Max P.; Sandford, Scott A.; Allamandola, Louis J.; Chang, Sherwood; Scharberg, Maureen A.

1995-01-01

The InfraRed (IR) spectra of UltraViolet (UV) and thermally processed, methanol-containing interstellar / cometary ice analogs at temperatures from 12 to 300 K are presented. Infrared spectroscopy, H-1 and C-13 Nuclear Magnetic Resonance (NMR) spectroscopy, and gas chromatography-mass spectrometry indicate that CO (carbon monoxide), CO2 (carbon dioxide), CH4 (methane), HCO (the formyl radical), H2CO (formaldehyde), CH3CH2OH (ethanol), HC([double bond]O)NH2 (formamide), CH3C([double bond]O)NH2 (acetamide), and R[single bond]C[triple bond]N (nitriles) are formed. In addition, the organic materials remaining after photolyzed ice analogs have been warmed to room temperature contain (in rough order of decreasing abundance), (1) hexamethylenetetramine (HMT, C6H12N4), (2) ethers, alcohols, and compounds related to PolyOxyMethylene (POM, ([single bond]CH2O[single bond](sub n)), and (3) ketones (R[single bond]C([double bond]O)[single bond]R') and amides (H2NC([double bond]O)[single bond]R). Most of the carbon in these residues is thought to come from the methanol in the original ice. Deuterium and C-13 isotopic labeling demonstrates that methanol is definitely the source of carbon in HMT. High concentrations of HMT in interstellar and cometary ices could have important astrophysical consequences. The ultraviolet photolysis of HMT frozen in H2O ice readily produces the 'XCN' band observed in the spectra of protostellar objects and laboratory ices, as well as other nitriles. Thus, HMT may be a precursor of XCN and a source of CN in comets and the interstellar medium. Also, HMT is known to hydrolyze under acidic conditions to yield ammonia, formaldehyde, and amino acids. Thus, HMT may be a significant source of prebiogenic compounds on asteroidal parent bodies. A potential mechanism for the radiative formation of HMT in cosmic ices is outlined.

Hydrogen atom transfer reactions in thiophenol: photogeneration of two new thione isomers.

PubMed

Reva, Igor; Nowak, Maciej J; Lapinski, Leszek; Fausto, Rui

2015-02-21

Photoisomerization reactions of monomeric thiophenol have been investigated for the compound isolated in low-temperature argon matrices. The initial thiophenol population consists exclusively of the thermodynamically most stable thiol form. Phototransformations were induced by irradiation of the matrices with narrowband tunable UV light. Irradiation at λ > 290 nm did not induce any changes in isolated thiophenol molecules. Upon irradiation at 290-285 nm, the initial thiol form of thiophenol converted into its thione isomer, cyclohexa-2,4-diene-1-thione. This conversion occurs by transfer of an H atom from the SH group to a carbon atom at the ortho position of the ring. Subsequent irradiation at longer wavelengths (300-427 nm) demonstrated that this UV-induced hydrogen-atom transfer is photoreversible. Moreover, upon irradiation at 400-425 nm, the cyclohexa-2,4-diene-1-thione product converts, by transfer of a hydrogen atom from the ortho to para position, into another thione isomer, cyclohexa-2,5-diene-1-thione. The latter thione isomer is also photoreactive and is consumed if irradiated at λ < 332 nm. The obtained results clearly show that H-atom-transfer isomerization reactions dominate the unimolecular photochemistry of thiophenol confined in a solid argon matrix. A set of low-intensity infrared bands, observed in the spectra of UV irradiated thiophenol, indicates the presence of a phenylthiyl radical with an H- atom detached from the SH group. Alongside the H-atom-transfer and H-atom-detachment processes, the ring-opening photoreaction occurred in cyclohexa-2,4-diene-1-thione by the cleavage of the C-C bond at the alpha position with respect to the thiocarbonyl C[double bond, length as m-dash]S group. The resulting open-ring conjugated thioketene adopts several isomeric forms, differing by orientations around single and double bonds. The species photogenerated upon UV irradiation of thiophenol were identified by comparison of their experimental infrared spectra with the spectra theoretically calculated for the candidate structures at the B3LYP/aug-cc-pVTZ level.

Phototransformation of anthraquinone-2-sulphonate in aqueous solution.

PubMed

Bedini, Andrea; De Laurentiis, Elisa; Sur, Babita; Maurino, Valter; Minero, Claudio; Brigante, Marcello; Mailhot, Gilles; Vione, Davide

2012-09-01

Anthraquinone-2-sulphonate (AQ2S) is a triplet sensitiser that has recently been used to model the photoreactivity of chromophoric dissolved organic matter (CDOM). We show that the photolysis quantum yield of AQ2S under UVA irradiation varies from (3.4 ± 0.2) × 10(-3) at μM AQ2S levels to (1.8 ± 0.1) × 10(-2) at 3 mM AQ2S (μ±σ). This trend is consistent with a combination of direct phototransformation and transformation sensitised by a photogenerated reactive species. In both cases a transient water adduct of AQ2S would be involved. Depending on the initial quinone concentration, the adduct could undergo transformation, give back ground-state AQ2S or react with it. The prevalence of the latter process at high AQ2S concentration would account for the increased values of the photolysis quantum yield. When using AQ2S as a triplet sensitiser, one should not exceed an initial concentration of 0.1 mM. Under the latter conditions the sensitised process is negligible compared to the direct photolysis, providing a simpler system to be studied, and the photolysis quantum yield is independent of the initial AQ2S concentration. This paper also shows, by adoption of density functional theory calculations, that the triplet state of AQ2S has most of the spin density localised on C[double bond, length as m-dash]O, analogous to other photoactive quinones, which accounts for the oxidising character of the triplet state that tends to be reduced to a semiquinone radical.

Mean bond-length variations in crystals for ions bonded to oxygen

PubMed Central

2017-01-01

Variations in mean bond length are examined in oxide and oxysalt crystals for 55 cation configurations bonded to O2−. Stepwise multiple regression analysis shows that mean bond length is correlated to bond-length distortion in 42 ion configurations at the 95% confidence level, with a mean coefficient of determination (〈R 2〉) of 0.35. Previously published correlations between mean bond length and mean coordination number of the bonded anions are found not to be of general applicability to inorganic oxide and oxysalt structures. For two of 11 ions tested for the 95% confidence level, mean bond lengths predicted using a fixed radius for O2− are significantly more accurate as those predicted using an O2− radius dependent on coordination number, and are statistically identical otherwise. As a result, the currently accepted ionic radii for O2− in different coordinations are not justified by experimental data. Previously reported correlation between mean bond length and the mean electronegativity of the cations bonded to the oxygen atoms of the coordination polyhedron is shown to be statistically insignificant; similar results are obtained with regard to ionization energy. It is shown that a priori bond lengths calculated for many ion configurations in a single structure-type leads to a high correlation between a priori and observed mean bond lengths, but a priori bond lengths calculated for a single ion configuration in many different structure-types leads to negligible correlation between a priori and observed mean bond lengths. This indicates that structure type has a major effect on mean bond length, the magnitude of which goes beyond that of the other variables analyzed here.

Design of a catalyst through Fe doping of the boron cage B10H14 for CO2 hydrogenation and investigation of the catalytic character of iron hydride (Fe-H).

PubMed

Qian, Lei; Ma, Kai-Yang; Zhou, Zhong-Jun; Ma, Fang

2017-12-13

The innovative catalyst Fe@B 10 H 14 is designed through Fe doping of the boron cage B 10 H 14 and is employed to catalyze CO 2 hydrogenation using a quantum mechanical method. First, the structure of the Fe@B 10 H 14 complex is characterized through calculated 11 B NMR chemical shifts and Raman spectra, and the interactions between Fe and the four H atoms of the opening in the cage are analyzed, which show that various iron hydride (Fe-H) characteristics exist. Subsequently, the potential of Fe@B 10 H 14 as a catalyst for the hydrogenative reduction of CO 2 in the gas phase is computationally evaluated. We find that an equivalent of Fe@B 10 H 14 can consecutively reduce double CO 2 to obtain the double product HCOOH through a two-step reduction, and Fe@B 10 H 12 and Fe@B 10 H 10 are successively obtained. The Fe presents single-atom character in the reduction of CO 2 , which is different from the common iron(ii) catalyzed CO 2 reduction. The calculated total free energy barrier of the first CO 2 reduction is only 8.79 kcal mol -1 , and that of the second CO 2 reduction is 25.71 kcal mol -1 . Every reduction reaction undergoes two key transition states TSC-H and TSO-H. Moreover, the transition state of the C-H bond formation TSC-H is the rate-determining step, where the interaction between π C[double bond, length as m-dash]O * and the weak σ Fe-H bond plays an important role. Furthermore, the hydrogenations of Fe@B 10 H 12 and Fe@B 10 H 10 are investigated, which aim at determining the ability of Fe-H circulation in the Fe doped decaborane complex. We find that the hydrogenation of Fe@B 10 H 10 undergoes a one-step H 2 -adsorbed transition state TSH-adsorb with an energy barrier of 6.42 kcal mol -1 from Fe@B 10 H 12 . Comparing with the hydrogenation of Fe@B 10 H 10 , it is slightly more difficult for the hydrogenation of Fe@B 10 H 12 , where the rate-determining step is the H 2 -cleaved transition state TS2H-H with an energy barrier of 17.38 kcal mol -1 .

Electronegativity effects and single covalent bond lengths of molecules in the gas phase.

PubMed

Lang, Peter F; Smith, Barry C

2014-06-07

This paper discusses in detail the calculation of internuclear distances of heteronuclear single bond covalent molecules in the gaseous state. It reviews briefly the effect of electronegativity in covalent bond length. A set of single bond covalent radii and electronegativity values are proposed. Covalent bond lengths calculated by an adapted form of a simple expression (which calculated internuclear separation of different Group 1 and Group 2 crystalline salts to a remarkable degree of accuracy) show very good agreement with observed values. A small number of bond lengths with double bonds as well as bond lengths in the crystalline state are calculated using the same expression and when compared with observed values also give good agreement. This work shows that covalent radii are not additive and that radii in the crystalline state are different from those in the gaseous state. The results also show that electronegativity is a major influence on covalent bond lengths and the set of electronegativity scale and covalent radii proposed in this work can be used to calculate covalent bond lengths in different environments that have not yet been experimentally measured.

Electronic communication in phosphine substituted bridged dirhenium complexes - clarifying ambiguities raised by the redox non-innocence of the C4H2- and C4-bridges.

PubMed

Li, Yan; Blacque, Olivier; Fox, Thomas; Luber, Sandra; Polit, Walther; Winter, Rainer F; Venkatesan, Koushik; Berke, Heinz

2016-04-07

The mononuclear rhenium carbyne complex trans-[Re(C[triple bond, length as m-dash]CSiMe3)([triple bond, length as m-dash]C-Me)(PMe3)4][PF6] (2) was prepared in 90% yield by heating a mixture of the dinitrogen complex trans-[ReCl(N2)(PMe3)4] (1), TlPF6, and an excess of HC[triple bond, length as m-dash]CSiMe3. 2 could be deprotonated with KOtBu to the vinylidene complex trans-[Re(C[triple bond, length as m-dash]CSiMe3)([double bond, length as m-dash]C[double bond, length as m-dash]CH2)(PMe3)4] (3) in 98% yield. Oxidation of 3 with 1.2 equiv. of [Cp2Fe][PF6] at -78 °C gave the Cβ-C'β coupled dinuclear rhenium biscarbyne complex trans-[(Me3SiC[triple bond, length as m-dash]C)(PMe3)4Re[triple bond, length as m-dash]C-CH2-CH2-C[triple bond, length as m-dash]Re(PMe3)4(C[triple bond, length as m-dash]CSiMe3)][PF6]2 (5) in 92% yield. Deprotonation of 5 with an excess of KOtBu in THF produced the diamagnetic trans-[(Me3SiC[triple bond, length as m-dash]C)(PMe3)4Re[double bond, length as m-dash]C[double bond, length as m-dash]CH-CH[double bond, length as m-dash]C[double bond, length as m-dash]Re(PMe3)4(C[triple bond, length as m-dash]CSiMe3)] complex (E-6(S)) in 87% yield with an E-butadienediylidene bridge. Density functional theory (DFT) calculations of E-6(S) confirmed its singlet ground state. The Z-form of 6 (Z-6(S)) could not be observed, which is in accord with its DFT calculated 17.8 kJ mol(-1) higher energy. Oxidation of E-6 with 2 equiv. of [Cp2Fe][PF6] resulted in the stable diamagnetic dicationic trans-[(Me3SiC[triple bond, length as m-dash]C)(PMe3)4Re[triple bond, length as m-dash]C-CH[double bond, length as m-dash]CH-C[triple bond, length as m-dash]Re(PMe3)4(C[triple bond, length as m-dash]CSiMe3)][PF6]2 complex (E-6[PF6]2) with an ethylenylidene dicarbyne structure of the bridge. The paramagnetic mixed-valence (MV) complex E-6[PF6] was obtained by comproportionation of E-6(S) and E-6[PF6]2 or by oxidation of E-6(S) with 1 equiv. of [Cp2Fe][PF6]. The dicationic trans-[(Me3SiC[triple bond, length as m-dash]C)(PMe3)4Re[triple bond, length as m-dash]C-C[triple bond, length as m-dash]C-C[triple bond, length as m-dash]Re(PMe3)4(C[triple bond, length as m-dash]CSiMe3)][PF6]2 (7[PF6]2) complex, attributed a butynedi(triyl) bridge structure, was obtained by deprotonation of E-6[PF6]2 with KOtBu followed by oxidation with 2 equiv. of [Cp2Fe][PF6]. The neutral complex 7 could be accessed best by reduction of 7[PF6]2 with KH in the presence of 18-crown-6. According to DFT calculations 7 possesses two equilibrating electronic states: diamagnetic 7(S) and triplet 7(F) with ferromagnetically coupled spins. The latter is calculated to be 5.2 kcal mol(-1) lower in energy than 7(S). There is experimental evidence that 7(S) prevails in solution. 7 could not be isolated in the crystalline state and is unstable transforming mainly by H-abstraction to give E-6(S). UV-Vis-NIR spectroscopy for the dinuclear rhenium complexes E-6(S), E-6[PF6] and E-6[PF6]2, as well as EPR spectroscopic and variable-temperature magnetization measurements for the MV complex E-6[PF6] were also conducted. Spectro-electrochemical reduction studies on 7[PF6]2 allowed the characterization of the mono- and direduced forms of 7(+) and 7 by means of IR- and UV-Vis-NIR-spectroscopy and revealed the chemical fate of the higher reduced form.

Metal-metal bond lengths in complexes of transition metals.

PubMed

Pauling, L

1976-12-01

In complexes of the transition metals containing clusters of metal atoms the cobalt-cobalt bond lengths are almost always within 1 pm of the single-bond value 246 pm given by the enneacovalent radius of cobalt, whereas most of the observed iron-iron bond lengths are significantly larger than the single-bond value 248 pm, the mean being 264 pm, which corresponds to a half-bond. A simple discussion of the structures of these complexes based on spd hybrid orbitals, the electroneutrality principle, and the partial ionic character of bonds between unlike atoms leads to the conclusion that resonance between single bonds and no-bonds would occur for iron and its congeners but not for cobalt and its congeners, explaining the difference in the bond lengths.

On the correlation between bond-length change and vibrational frequency shift in halogen-bonded complexes

NASA Astrophysics Data System (ADS)

Wang, Weizhou; Zhang, Yu; Ji, Baoming; Tian, Anmin

2011-06-01

The C-Hal (Hal = Cl, Br, or I) bond-length change and the corresponding vibrational frequency shift of the C-Hal stretch upon the C-Hal ⋯Y (Y is the electron donor) halogen bond formation have been determined by using density functional theory computations. Plots of the C-Hal bond-length change versus the corresponding vibrational frequency shift of the C-Hal stretch all give straight lines. The coefficients of determination range from 0.94366 to 0.99219, showing that the correlation between the C-Hal bond-length change and the corresponding frequency shift is very good in the halogen-bonded complexes. The possible effects of vibrational coupling, computational method, and anharmonicity on the bond-length change-frequency shift correlation are discussed in detail.

A P-H functionalized Al/P-based frustrated Lewis pair - hydrophosphination of nitriles, ring opening with cyclopropenones and evidence of P[double bond, length as m-dash]C double bond formation.

PubMed

Keweloh, Lukas; Aders, Niklas; Hepp, Alexander; Pleschka, Damian; Würthwein, Ernst-Ulrich; Uhl, Werner

2018-06-12

Hydroalumination of R-P(H)-C[triple bond, length as m-dash]C-tBu with bulky H-Al[CH(SiMe3)2]2 afforded the new P-H functionalized Al/P-based frustrated Lewis pair R-P(H)-C[[double bond, length as m-dash]C(H)-tBu]-AlR2 [R = CH(SiMe3)2; FLP 7]. A weak adduct of 7 with benzonitrile (8) was detected by NMR spectroscopy, but could not be isolated. tert-Butyl isocyanide afforded a similar, but isolable adduct (9), in which the isocyanide C atom was coordinated to aluminium. The unique reactivity of 7 became evident from its reactions with the heteroatom substituted nitriles PhO-C[triple bond, length as m-dash]N, PhCH2S-C[triple bond, length as m-dash]N and H8C4N-C[triple bond, length as m-dash]N. Hydrophosphination of the C[triple bond, length as m-dash]N triple bonds afforded imines at room temperature which were coordinated to the FLP by Al-N and P-C bonds to yield AlCPCN heterocycles (10 to 12). These processes depend on substrate activation by the FLP. Diphenylcyclopropenone and its sulphur derivative reacted with 7 by addition of the P-H bond to a C-C bond of the strained C3 ring and ring opening to afford the fragment (Z)-Ph-C(H)[double bond, length as m-dash]C(Ph)-C-X-Al (X = O, S). The C-O or C-S groups were coordinated to the FLP to yield AlCPCX heterocycles (13 and 14). The thiocarbonyl derived compound 14 contains an internally stabilized phosphenium cation with a localized P[double bond, length as m-dash]C bond, a trigonal planar coordinated P atom and a short P[double bond, length as m-dash]C distance (168.9 pm). Insight into formation mechanisms, the structural and energetic properties of FLP 7 and compounds 13 and 14 was gained by quantum chemical DFT calculations.

Metal-metal bond lengths in complexes of transition metals*

PubMed Central

Pauling, Linus

1976-01-01

In complexes of the transition metals containing clusters of metal atoms the cobalt-cobalt bond lengths are almost always within 1 pm of the single-bond value 246 pm given by the enneacovalent radius of cobalt, whereas most of the observed iron-iron bond lengths are significantly larger than the single-bond value 248 pm, the mean being 264 pm, which corresponds to a half-bond. A simple discussion of the structures of these complexes based on spd hybrid orbitals, the electroneutrality principle, and the partial ionic character of bonds between unlike atoms leads to the conclusion that resonance between single bonds and no-bonds would occur for iron and its congeners but not for cobalt and its congeners, explaining the difference in the bond lengths. PMID:16592368

Bent Bonds and Multiple Bonds.

ERIC Educational Resources Information Center

Robinson, Edward A.; Gillespie, Ronald J.

1980-01-01

Considers carbon-carbon multiple bonds in terms of Pauling's bent bond model, which allows direct calculation of double and triple bonds from the length of a CC single bond. Lengths of these multiple bonds are estimated from direct measurements on "bent-bond" models constructed of plastic tubing and standard kits. (CS)

Some transition metal complexes derived from mono- and di-ethynyl perfluorobenzenes.

PubMed

Armitt, David J; Bruce, Michael I; Gaudio, Maryka; Zaitseva, Natasha N; Skelton, Brian W; White, Allan H; Le Guennic, Boris; Halet, Jean-François; Fox, Mark A; Roberts, Rachel L; Hartl, Frantisek; Low, Paul J

2008-12-21

Transition metal alkynyl complexes containing perfluoroaryl groups have been prepared directly from trimethylsilyl-protected mono- and di-ethynyl perfluoroarenes by simple desilylation/metallation reaction sequences. Reactions between Me(3)SiC[triple bond, length as m-dash]CC(6)F(5) and RuCl(dppe)Cp' [Cp' = Cp, Cp*] in the presence of KF in MeOH give the monoruthenium complexes Ru(C[triple bond, length as m-dash]CC(6)F(5))(dppe)Cp' [Cp' = Cp (); Cp* ()], which are related to the known compound Ru(C[triple bond, length as m-dash]CC(6)F(5))(PPh(3))(2)Cp (). Treatment of Me(3)SiC[triple bond, length as m-dash]CC(6)F(5) with Pt(2)(mu-dppm)(2)Cl(2) in the presence of NaOMe in MeOH gave the bis(alkynyl) complex Pt(2)(mu-dppm)(2)(C[triple bond, length as m-dash]CC(6)F(5))(2) (). The Pd(0)/Cu(i)-catalysed reactions between Au(C[triple bond, length as m-dash]CC(6)F(5))(PPh(3)) and Mo( identical withCBr)(CO)(2)Tp* [Tp* = hydridotris(3.5-dimethylpyrazoyl)borate], Co(3)(mu(3)-CBr)(mu-dppm)(CO)(7) or IC[triple bond, length as m-dash]CFc [Fc = (eta(5)-C(5)H(4))FeCp] afford Mo( identical withCC[triple bond, length as m-dash]CC(6)F(5))(CO)(2)Tp* (), Co(3)(mu(3)-CC[triple bond, length as m-dash]CC(6)F(5))(mu-dppm)(CO)(7) () and FcC[triple bond, length as m-dash]CC[triple bond, length as m-dash]CC(6)F(5) (), respectively. The diruthenium complexes 1,4-{Cp'(PP)RuC[triple bond, length as m-dash]C}(2)C(6)F(4) [(PP)Cp' = (PPh(3))(2)Cp (); (dppe)Cp (); (dppe)Cp* ()] are prepared from 1,4-(Me(3)SiC[triple bond, length as m-dash]C)(2)C(6)F(4) in a manner similar to that described for the monoruthenium complexes -. The non-fluorinated complexes 1,4-{Cp'(PP)RuC[triple bond, length as m-dash]C}(2)C(6)H(4) [(PP)Cp' = (PPh(3))(2)Cp (); (dppe)Cp (); (dppe)Cp* ()], prepared for comparison, are obtained from 1,4-(Me(3)SiC[triple bond, length as m-dash]C)(2)C(6)H(4). Spectro-electrochemical studies of the ruthenium aryl and arylene alkynyl complexes - and -, together with DFT-based computational studies on suitable model systems, indicate that perfluorination of the aromatic ring has little effect on the electronic structures of these compounds, and that the frontier orbitals have appreciable diethynylphenylene character. Molecular structure determinations are reported for the fluoroaromatic complexes , , , and .

Sulfide bonded atomic radii

NASA Astrophysics Data System (ADS)

Gibbs, G. V.; Ross, N. L.; Cox, D. F.

2017-09-01

The bonded radius, r b(S), of the S atom, calculated for first- and second-row non-transition metal sulfide crystals and third-row transition metal sulfide molecules and crystals indicates that the radius of the sulfur atom is not fixed as traditionally assumed, but that it decreases systematically along the bond paths of the bonded atoms with decreasing bond length as observed in an earlier study of the bonded radius of the oxygen atom. When bonded to non-transition metal atoms, r b(S) decreases systematically with decreasing bond length from 1.68 Å when the S atom is bonded to the electropositive VINa atom to 1.25 Å when bonded to the more electronegative IVP atom. In the case of transition metal atoms, rb(S) likewise decreases with decreasing bond length from 1.82 Å when bonded to Cu and to 1.12 Å when bonded to Fe. As r b(S) is not fixed at a given value but varies substantially depending on the bond length and the field strength of the bonded atoms, it is apparent that sets of crystal and atomic sulfide atomic radii based on an assumed fixed radius for the sulfur atom are satisfactory in that they reproduce bond lengths, on the one hand, whereas on the other, they are unsatisfactory in that they fail to define the actual sizes of the bonded atoms determined in terms of the minima in the electron density between the atoms. As such, we urge that the crystal chemistry and the properties of sulfides be studied in terms of the bond lengths determined by adding the radii of either the atomic and crystal radii of the atoms but not in terms of existing sets of crystal and atomic radii. After all, the bond lengths were used to determine the radii that were experimentally determined, whereas the individual radii were determined on the basis of an assumed radius for the sulfur atom.

Origin of the X-Hal (Hal = Cl, Br) bond-length change in the halogen-bonded complexes.

PubMed

Wang, Weizhou; Hobza, Pavel

2008-05-01

The origin of the X-Hal bond-length change in the halogen bond of the X-Hal...Y type has been investigated at the MP2(full)/6-311++G(d,p) level of theory using a natural bond orbital analysis, atoms in molecules procedure, and electrostatic potential fitting methods. Our results have clearly shown that various theories explaining the nature of the hydrogen bond cannot be applied to explain the origin of the X-Hal bond-length change in the halogen bond. We provide a new explanation for this change. The elongation of the X-Hal bond length is caused by the electron-density transfer to the X-Hal sigma* antibonding orbital. For the blue-shifting halogen bond, the electron-density transfer to the X-Hal sigma* antibonding orbital is only of minor importance; it is the electrostatic attractive interaction that causes the X-Hal bond contraction.

Pi Bond Orders and Bond Lengths

ERIC Educational Resources Information Center

Herndon, William C.; Parkanyi, Cyril

1976-01-01

Discusses three methods of correlating bond orders and bond lengths in unsaturated hydrocarbons: the Pauling theory, the Huckel molecular orbital technique, and self-consistent-field techniques. (MLH)

Bond-length distributions for ions bonded to oxygen: alkali and alkaline-earth metals.

PubMed

Gagné, Olivier Charles; Hawthorne, Frank Christopher

2016-08-01

Bond-length distributions have been examined for 55 configurations of alkali-metal ions and 29 configurations of alkaline-earth-metal ions bonded to oxygen, for 4859 coordination polyhedra and 38 594 bond distances (alkali metals), and for 3038 coordination polyhedra and 24 487 bond distances (alkaline-earth metals). Bond lengths generally show a positively skewed Gaussian distribution that originates from the variation in Born repulsion and Coulomb attraction as a function of interatomic distance. The skewness and kurtosis of these distributions generally decrease with increasing coordination number of the central cation, a result of decreasing Born repulsion with increasing coordination number. We confirm the following minimum coordination numbers: ([3])Li(+), ([3])Na(+), ([4])K(+), ([4])Rb(+), ([6])Cs(+), ([3])Be(2+), ([4])Mg(2+), ([6])Ca(2+), ([6])Sr(2+) and ([6])Ba(2+), but note that some reported examples are the result of extensive dynamic and/or positional short-range disorder and are not ordered arrangements. Some distributions of bond lengths are distinctly multi-modal. This is commonly due to the occurrence of large numbers of structure refinements of a particular structure type in which a particular cation is always present, leading to an over-representation of a specific range of bond lengths. Outliers in the distributions of mean bond lengths are often associated with anomalous values of atomic displacement of the constituent cations and/or anions. For a sample of ([6])Na(+), the ratio Ueq(Na)/Ueq(bonded anions) is partially correlated with 〈([6])Na(+)-O(2-)〉 (R(2) = 0.57), suggesting that the mean bond length is correlated with vibrational/displacement characteristics of the constituent ions for a fixed coordination number. Mean bond lengths also show a weak correlation with bond-length distortion from the mean value in general, although some coordination numbers show the widest variation in mean bond length for zero distortion, e.g. Li(+) in [4]- and [6]-coordination, Na(+) in [4]- and [6]-coordination. For alkali-metal and alkaline-earth-metal ions, there is a positive correlation between cation coordination number and the grand mean incident bond-valence sum at the central cation, the values varying from 0.84 v.u. for ([5])K(+) to 1.06 v.u. for ([8])Li(+), and from 1.76 v.u. for ([7])Ba(2+) to 2.10 v.u. for ([12])Sr(2+). Bond-valence arguments suggest coordination numbers higher than [12] for K(+), Rb(+), Cs(+) and Ba(2+).

Correlation of the bond-length change and vibrational frequency shift in model hydrogen-bonded complexes of pyrrole

NASA Astrophysics Data System (ADS)

McDowell, Sean A. C.

2017-04-01

An MP2 computational study of model hydrogen-bonded pyrrole⋯YZ (YZ = NH3, NCH, BF, CO, N2, OC, FB) complexes was undertaken in order to examine the variation of the Nsbnd H bond length change and its associated vibrational frequency shift. The chemical hardness of Y, as well as the YZ dipole moment, were found to be important parameters in modifying the bond length change/frequency shift. The basis set effect on the computed properties was also assessed. A perturbative model, which accurately reproduced the ab initio Nsbnd H bond length changes and frequency shifts, was useful in rationalizing the observed trends.

Bond Strength of Composite CFRP Reinforcing Bars in Timber

PubMed Central

Corradi, Marco; Righetti, Luca; Borri, Antonio

2015-01-01

The use of near-surface mounted (NSM) fibre-reinforced polymer (FRP) bars is an interesting method for increasing the shear and flexural strength of existing timber members. This article examines the behaviour of carbon FRP (CFRP) bars in timber under direct pull-out conditions. The objective of this experimental program is to investigate the bond strength between composite bars and timber: bars were epoxied into small notches made into chestnut and fir wood members using a commercially-available epoxy system. Bonded lengths varied from 150 to 300 mm. Failure modes, stress and strain distributions and the bond strength of CFRP bars have been evaluated and discussed. The pull-out capacity in NSM CFRP bars at the onset of debonding increased with bonded length up to a length of 250 mm. While CFRP bar’s pull-out was achieved only for specimens with bonded lengths of 150 and 200 mm, bar tensile failure was mainly recorded for bonded lengths of 250 and 300 mm. PMID:28793423

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

PubMed

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

2016-10-07

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

The series of carbon-chain complexes {Ru(dppe)Cp*}₂{μ-(C≡C )x} (x = 4–8, 11): Synthesis, structures, properties and some reactions

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

Bruce, Michael I.; Cole, Marcus L.; Ellis, Benjamin G.

The construction of a series of compounds {Ru(dppe)Cp*} 2(μ-C 2x) (Ru*-C2x-Ru*, x = 4–8, 11)) is described. A direct reaction between RuCl(dppe)Cp* and Me 3Si(Ctriple bond; length of mdashC) 4SiMe 3 afforded Ru*-C8-Ru* in 89% yield. The Pd(0)/Cu(I)-catalysed coupling of Ru{Ctriple bond; length of mdashCCtriple bond; length of mdashCAu(PPh 3)}(dppe)Cp*Ru*-C4-Au (2 equiv.) with diiodoethyne gave Ru*-C10-Ru* (64%), or of 1 equiv. with I(Ctriple bond; length of mdashC) 3I gave Ru*-C14-Ru* (36%); similarly, Ru{(Ctriple bond; length of mdashC) 4Au(PPh 3)}(dppe)Cp*Ru*-C8-Au and I(Ctriple bond; length of mdashC) 3I gave Ru*-C22-Ru* (12%). Desilylation (TBAF) of Ru{(Ctriple bond; length of mdashC)xSiMe 3}(dppe)Cp*Ru*-C2x-Si (x =more » 3, 4) followed by oxidative coupling [Cu(OAc) 2/py] gave Ru*-C12-Ru* (82%) and Ru*-C16-Ru* (58%), respectively. Similar oxidative coupling of Ru(Ctriple bond; length of mdashCCtriple bond; length of mdashCH)(dppe)Cp* was a second route to Ru*-C8-Ru* (82%). Appropriate precursors are already known, or obtained by coupling of Ru*-C2x-Si (x = 2, 4) with AuCl(PPh 3)/NaOMe [Ru*-C4-Au, 95%; Ru*-C8-Au, 74%] or from Pd(0)/Cu(I) catalysed coupling of Ru*-C2x-Au (x = 2, 3) with I(Ctriple bond; length of mdashC) 2SiMe 3 (Ru*-C8-Si, 64%; Ru*-C10-Si, 2%). Reactions between Ru*-C2x-Ru* (x = 3, 4) and Fe 2(CO) 9 gave {Fe 3(CO) 9}{μ 3-CCtriple bond; length of mdashC[Ru(dppe)Cp*]} 2Fe(C 3-Ru*) 2 and {Fe 3(CO) 9}{μ 3-CCtriple bond; length of mdashC[Ru(dppe)Cp*]}{μ 3-C(Ctriple bond; length of mdashC) 2[Ru(dppe)Cp*]} Fe(C 3-Ru*)(C 5-Ru*), respectively. The redox properties of the series of complexes with 2x = 2–16 were measured and showed a diminution of the separation of the first two oxidation potentials, ΔE = E 2 - E 1, with increasing carbon chain length. The X-ray-determined molecular structures of Ru*-C8-Si, Ru*-C8-Ru*, Ru*-C14-Ru* (two C 6H 6 solvates), {Ru(PPh 3) 2Cp} 2{μ-(Ctriple bond; length of mdashC) 4}·4CHCl 3Ru-C 8-Ru·4CHCl 3 and of Fe(C 3-Ru*) 2 and Fe(C 3-Ru*)(C 5-Ru*) are reported.« less

Analysis of North Atlantic Aircraft Data on Oxygenated Intermediate Species Using an Adapted Regional Chemistry-Transport Model

NASA Technical Reports Server (NTRS)

Chatfield, Robert; Mathur, Rohit; Alapaty, Kiran; Hanna, Adel; Binkowski, Frank; Guan, Hong; Esswein, Robert

2004-01-01

Our study is on the interaction of nitrogen oxides with organics as they are exported from their complex sources in Eastern North America. Both urban and specific industrial emissions contribute the nitrogen of the C-H-O-N compounds that affect the global atmosphere, helping determine both ozone and the self-cleaning radical chemistry of the troposphere mediated by the OH radical. Different industrial sources, urban, and natural emissions contribute the organic C. Peroxyacetyl nitrate, CH3C(double bonds O)OONO2 is the most interesting compound for which we can measure the outflow to the full depth of the Atlantic troposphere. As we adapt the 3-d chemical model to describe outflow for specific periods with sufficient accuracy, we are analyzing some valuable information in the NARE-97 complete airborne dataset. (NARE: North Atlantic Regional Experiment). Ames researchers find that there are substantial puzzles in the ratios of PAN/NO2. Peroxy acetyl nitrate provides one of the major long-distance export pathways for active nitrogen from Eastern North America. It should be closely linked with NO, (defined as the sum NO + NO2) by simple thermal association and decomposition reactions, at least when the ambient temperature is substantially above 5 C.

Sensitivity of hydrogen bonds of DNA and RNA to hydration, as gauged by 1JNH measurements in ethanol-water mixtures.

PubMed

Manalo, Marlon N; Kong, Xiangming; LiWang, Andy

2007-04-01

Hydrogen-bond lengths of nucleic acids are (1) longer in DNA than in RNA, and (2) sequence dependent. The physicochemical basis for these variations in hydrogen-bond lengths is unknown, however. Here, the notion that hydration plays a significant role in nucleic acid hydrogen-bond lengths is tested. Watson-Crick N1...N3 hydrogen-bond lengths of several DNA and RNA duplexes are gauged using imino 1J(NH) measurements, and ethanol is used as a cosolvent to lower water activity. We find that 1J(NH) values of DNA and RNA become less negative with added ethanol, which suggests that mild dehydration reduces hydrogen-bond lengths even as the overall thermal stabilities of these duplexes decrease. The 1J(NH) of DNA are increased in 8 mol% ethanol to those of RNA in water, which suggests that the greater hydration of DNA plays a significant role in its longer hydrogen bonds. The data also suggest that ethanol-induced dehydration is greater for the more hydrated G:C base pairs and thereby results in greater hydrogen-bond shortening than for the less hydrated A:T/U base pairs of DNA and RNA.

Sacrificial bonds and hidden length in biomaterials -- a kinetic description of strength and toughness in bone

NASA Astrophysics Data System (ADS)

Lieou, Charles K. C.; Elbanna, Ahmed E.; Carlson, Jean M.

2013-03-01

Sacrificial bonds and hidden length in structural molecules account for the greatly increased fracture toughness of biological materials compared to synthetic materials without such structural features, by providing a molecular-scale mechanism of energy dissipation. One example of occurrence of sacrificial bonds and hidden length is in the polymeric glue connection between collagen fibrils in animal bone. In this talk, we propose a simple kinetic model that describes the breakage of sacrificial bonds and the revelation of hidden length, based on Bell's theory. We postulate a master equation governing the rates of bond breakage and formation, at the mean-field level, allowing for the number of bonds and hidden lengths to take up non-integer values between successive, discrete bond-breakage events. This enables us to predict the mechanical behavior of a quasi-one-dimensional ensemble of polymers at different stretching rates. We find that both the rupture peak heights and maximum stretching distance increase with the stretching rate. In addition, our theory naturally permits the possibility of self-healing in such biological structures.

The effect of redox-active cyanomanganese(I) ligands on intramolecular electron transfer to, and alkyne alignment in, M(CO)(RC[triple bond, length as m-dash]CR)Tp' (M = Mo or W) units.

PubMed

Adams, Christopher J; Connelly, Neil G; Onganusorn, Sriwipha

2009-04-28

The complexes [(eta-C(5)Me(5))(ON)LMn(micro-CN)M(CO)(RC[triple bond, length as m-dash]CR)Tp'](+) (L = CNXyl, M = Mo; L = CNBu(t), M = Mo or W, R = Ph or Me) and trans- or cis-[(dppm){(EtO)(3)P}(OC)(2)Mn(micro-CN)M(CO)(PhC[triple bond, length as m-dash]CPh)Tp'](+), and their linkage isomers [(eta-C(5)Me(5))(ON)LMn(micro-NC)M(CO)(PhC[triple bond, length as m-dash]CPh)Tp'](+) and trans- or cis-[(dppm){(EtO)(3)P}(OC)(2)Mn(micro-NC)M(CO)(PhC[triple bond, length as m-dash]CPh)Tp'](+), undergo two one-electron oxidations. The complexes [(eta-C(5)Me(5))(ON)LMn(micro-XY)M(CO)(RC[triple bond, length as m-dash]CR)Tp'](+) (XY = CN or NC) are oxidised first at the N-bound metal centre and then at the C-bound centre. For [(dppm){(EtO)(3)P}(OC)(2)Mn(micro-XY)M(CO)(PhC[triple bond, length as m-dash]CPh)Tp'](+), the trans isomers are first oxidised at manganese whereas the cis isomers are first oxidised at M. Thus, the order of one-electron oxidation of the two series of binuclear monocations is influenced by linkage isomerisation of the cyanide bridge and cis-trans isomerisation of the Mn(CO)(2) group. IR spectroscopic changes on reaction of Ag(+) with [(eta-C(5)Me(5))(ON)(Bu(t)NC)Mn(micro-CN)W(CO)(MeC[triple bond, length as m-dash]CMe)Tp'](+) are consistent with one-electron at the N-bound tungsten centre. Likewise, trans-[(dppm){(EtO)(3)P}(OC)(2)Mn(micro-NC)M(CO)(PhC[triple bond, length as m-dash]CPh)Tp'](+) (M = Mo or W) give the stable dications [(dppm){(EtO)(3)P}(OC)(2)Mn(micro-NC)M(CO)(PhC[triple bond, length as m-dash]CPh)Tp'](2+). Significantly longer Mn-P bond distances in trans-[(dppm){(EtO)(3)P}(OC)(2)Mn(micro-NC)Mo(CO)(PhC[triple bond, length as m-dash]CPh)Tp'](2+) than in trans-[(dppm){(EtO)(3)P}(OC)(2)Mn(micro-NC)Mo(CO)(PhC[triple bond, length as m-dash]CPh)Tp'](+) are consistent with one-electron oxidation first at Mn(I); the alignment of the (CN)Mn(CO)(2){P(OEt)(3)}(dppm) fragment relative to the alkyne in trans-[(dppm){(EtO)(3)P}(OC)(2)Mn(micro-NC)Mo(CO)(PhC[triple bond, length as m-dash]CPh)Tp'](+) suggests it acts as a pi-acceptor, in contrast to related species such as trans-(NC)Mn(CO)(2){P(OEt)(3)}(dppm) and (NC)Mn(NO){P(OPh)(3)}(pi-C(5)H(4)Me) which behave as simple N-donors.

Bond length variation in Zn substituted NiO studied from extended X-ray absorption fine structure

NASA Astrophysics Data System (ADS)

Singh, S. D.; Poswal, A. K.; Kamal, C.; Rajput, Parasmani; Chakrabarti, Aparna; Jha, S. N.; Ganguli, Tapas

2017-06-01

Bond length behavior for Zn substituted NiO is determined through extended x-ray absorption fine structure (EXAFS) measurements performed at ambient conditions. We report bond length value of 2.11±0.01 Å for Zn-O of rock salt (RS) symmetry, when Zn is doped in RS NiO. Bond length for Zn substituted NiO RS ternary solid solutions shows relaxed behavior for Zn-O bond, while it shows un-relaxed behavior for Ni-O bond. These observations are further supported by first-principles calculations. It is also inferred that Zn sublattice remains nearly unchanged with increase in lattice parameter. On the other hand, Ni sublattice dilates for Zn compositions up to 20% to accommodate increase in the lattice parameter. However, for Zn compositions more than 20%, it does not further dilate. It has been attributed to the large disorder that is incorporated in the system at and beyond 20% of Zn incorporation in the cubic RS lattice of ternary solid solutions. For these large percentages of Zn incorporation, the Ni and the Zn atoms re-arrange themselves microscopically about the same nominal bond length rather than systematically increase in magnitude to minimize the energy of the system. This results in an increase in the Debye-Waller factor with increase in the Zn concentration rather than a systematic increase in the bond lengths.

A vector-based representation of the chemical bond for the substituted torsion of biphenyl

NASA Astrophysics Data System (ADS)

Li, Jiahui; Huang, Weijie; Xu, Tianlv; Kirk, Steven R.; Jenkins, Samantha

2018-06-01

We use a new interpretation of the chemical bond within QTAIM, the bond-path framework set B = {p, q, r} with associated linkages with lengths H∗, H and the familiar bond-path length is used to describe a torsion θ, 0.0° ≤ θ < 22.0° of para-substituted biphenyl, C12H9-x, x = N(CH3)2, NH2, CH3, CHO, CN, NO2. We include consideration of the H--H bonding interactions and find that the lengths H > H∗ that we explain in terms of the most and least preferred directions of charge density accumulation. We also consider the fractional eigenvector-following path with lengths Hf and Hfθmin.

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.

Extreme oxatriquinanes and a record C-O bond length

NASA Astrophysics Data System (ADS)

Gunbas, Gorkem; Hafezi, Nema; Sheppard, William L.; Olmstead, Marilyn M.; Stoyanova, Irini V.; Tham, Fook S.; Meyer, Matthew P.; Mascal, Mark

2012-12-01

Oxatriquinanes are fused, tricyclic oxonium ions that are known to have exceptional stability compared to simple alkyl oxonium salts. C-O bonds in ethers are generally ˜1.43 Å in length, but oxatriquinane has been found to have C-O bond lengths of 1.54 Å. A search of the Cambridge Structural Database turned up no bona fide C-O bond length exceeding this value. Computational modelling of oxatriquinane alongside other alkyl oxonium ions indicated that the electronic consequences of molecular strain were primarily responsible for the observed bond elongation. We also show that substitution of the oxatriquinane ring system with alkyl groups of increasing steric demand pushes the C-O bond to unheard of distances, culminating in a tert-butyl derivative at a predicted 1.60 Å. Chemical synthesis and an X-ray crystallographic study of these compounds validated the results of the modelling work and, finally, an extraordinary 1.622 Å C-O bond was observed in 1,4,7-tri-tert-butyloxatriquinane.

1 mil gold bond wire study.

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

Huff, Johnathon; McLean, Michael B.; Jenkins, Mark W.

2013-05-01

In microcircuit fabrication, the diameter and length of a bond wire have been shown to both affect the current versus fusing time ratio of a bond wire as well as the gap length of the fused wire. This study investigated the impact of current level on the time-to-open and gap length of 1 mil by 60 mil gold bond wires. During the experiments, constant current was provided for a control set of bond wires for 250ms, 410ms and until the wire fused; non-destructively pull-tested wires for 250ms; and notched wires. The key findings were that as the current increases, themore » gap length increases and 73% of the bond wires will fuse at 1.8A, and 100% of the wires fuse at 1.9A within 60ms. Due to the limited scope of experiments and limited data analyzed, further investigation is encouraged to confirm these observations.« less

Vibrational overtone spectra of metallocenes: effect of the coordinating metal on the CH bond lengths

NASA Astrophysics Data System (ADS)

Billinghurst, Brant E.; Gough, Kathleen M.

2003-03-01

The first through third overtone spectra of ferrocene, ruthenocene, nickelocene, cobaltocene, dicyclopentadienyl magnesium and sodium cyclopentadienyl are examined with particular attention to the CH stretching of the cyclopentadienyl. Using semi-empirical correlations between CH bond length and CH stretching frequencies in each overtone region, we have determined that the type of metal atom within a metallocene complex has little effect on the CH bond length in the cyclopentadienyl. The only exception is cobaltocene where there is evidence that the Jahn-Teller effect results in several different CH bond lengths. Evidence that bis(cyclopentadienyl) magnesium is not ionic has been observed.

Influence of metal bonding layer on strain transfer performance of FBG

NASA Astrophysics Data System (ADS)

Liu, Hao; Chen, Weimin; Zhang, Peng; Liu, Li; Shu, Yuejie; Wu, Jun

2013-01-01

Metal bonding layer seriously affects the strain transfer performance of Fiber Bragg Grating (FBG). Based on the mode of FBG strain transfer, the influence of the length, the thickness, Poisson's ratio, elasticity modulus of metal bonding layer on the strain transfer coefficient of FBG is analyzed by numerical simulation. FBG is packaged to steel wire using metal bonding technology of FBG. The tensile tests of different bonding lengths and elasticity modulus are carried out. The result shows the strain transfer coefficient of FBGs are 0.9848,0.962 and their average strain sensitivities are 1.076 pm/μɛ,1.099 pm/μɛ when the metal bonding layer is zinc, whose lengths are 15mm, 20mm, respectively. The strain transfer coefficient of FBG packaged by metal bonding layer raises 8.9 percent compared to epoxy glue package. The preliminary experimental results show that the strain transfer coefficient increases with the length of metal bonding layer, decreases with the thickness of metal bonding layer and the influence of Poisson's ratio can be ignored. The experiment result is general agreement with the analysis and provides guidance for metal package of FBG.

Bond-Slip Relationship for CFRP Sheets Externally Bonded to Concrete under Cyclic Loading.

PubMed

Li, Ke; Cao, Shuangyin; Yang, Yue; Zhu, Juntao

2018-02-26

The objective of this paper was to explore the bond-slip relationship between carbon fiber-reinforced polymer (CFRP) sheets and concrete under cyclic loading through experimental and analytical approaches. Modified beam tests were performed in order to gain insight into the bond-slip relationship under static and cyclic loading. The test variables are the CFRP-to-concrete width ratio, and the bond length of the CFRP sheets. An analysis of the test results in this paper and existing test results indicated that the slope of the ascending segment of the bond-slip curve decreased with an increase in the number of load cycles, but the slip corresponding to the maximum shear stress was almost invariable as the number of load cycles increased. In addition, the rate of reduction in the slope of the ascending range of the bond-slip curve during cyclic loading decreased as the concrete strength increased, and increased as the load level or CFRP-to-concrete width ratio enhanced. However, these were not affected by variations in bond length if the residual bond length was longer than the effective bond length. A bilinear bond-slip model for CFRP sheets that are externally bonded to concrete under cyclic loading, which considered the effects of the cyclic load level, concrete strength, and CFRP-to-concrete ratio, was developed based on the existing static bond-slip model. The accuracy of this proposed model was verified by a comparison between this proposed model and test results.

Can HN[double bond, length as m-dash]NH, FN[double bond, length as m-dash]NH, or HN[double bond, length as m-dash]CHOH bridge the σ-hole and the lone pair at P in binary complexes with H2XP, for X = F, Cl, NC, OH, CN, CCH, CH3, and H?

PubMed

Del Bene, Janet E; Alkorta, Ibon; Elguero, José

2015-11-11

Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to investigate the properties of complexes formed between H2XP, for X = F, Cl, NC, OH, CN, CCH, CH3, and H, and the possible bridging molecules HN[double bond, length as m-dash]NH, FN[double bond, length as m-dash]NH, and HN[double bond, length as m-dash]CHOH. H2XP:HNNH and H2XP:FNNH complexes are stabilized by PN pnicogen bonds, except for H2(CH3)P:FNNH and H3P:FNNH which are stabilized by N-HP hydrogen bonds. H2XP:HNCHOH complexes are stabilized by PN pnicogen bonds and nonlinear O-HP hydrogen bonds. For a fixed H2XP molecule, binding energies decrease in the order HNCHOH > HNNH > FNNH, except for the binding energies of H2(CH3)P and H3P with HNNH and FNNH. Binding energies of complexes with HNCHOH and HNNH increase as the P-N1 distance decreases, but binding energies of complexes with FNNH show little dependence on this distance. The large binding energies of H2XP:HNCHOH complexes arise from a cooperative effect involving electron-pair acceptance by P to form a pnicogen bond, and electron-pair donation by P to form a hydrogen bond. The dominant charge-transfer interaction in these complexes involves electron-pair donation by N across the pnicogen bond, except for complexes in which X is one of the more electropositive substituents, CCH, CH3, and H. For these, lone-pair donation by P across the hydrogen bond dominates. AIM and NBO data for these complexes are consistent with their bonding characteristics, showing molecular graphs with bond critical points and charge-transfer interactions associated with hydrogen and pnicogen bonds. EOM-CCSD spin-spin coupling constants (1p)J(P-N) across the pnicogen bond for each series of complexes correlate with the P-N distance. In contrast, (2h)J(O-P) values for complexes H2XP:HNCHOH do not correlate with the O-P distance, a consequence of the nonlinearity of these hydrogen bonds.

A Computational Study on the Ground and Excited States of Nickel Silicide.

PubMed

Schoendorff, George; Morris, Alexis R; Hu, Emily D; Wilson, Angela K

2015-09-17

Nickel silicide has been studied with a range of computational methods to determine the nature of the Ni-Si bond. Additionally, the physical effects that need to be addressed within calculations to predict the equilibrium bond length and bond dissociation energy within experimental error have been determined. The ground state is predicted to be a (1)Σ(+) state with a bond order of 2.41 corresponding to a triple bond with weak π bonds. It is shown that calculation of the ground state equilibrium geometry requires a polarized basis set and treatment of dynamic correlation including up to triple excitations with CR-CCSD(T)L resulting in an equilibrium bond length of only 0.012 Å shorter than the experimental bond length. Previous calculations of the bond dissociation energy resulted in energies that were only 34.8% to 76.5% of the experimental bond dissociation energy. It is shown here that use of polarized basis sets, treatment of triple excitations, correlation of the valence and subvalence electrons, and a Λ coupled cluster approach is required to obtain a bond dissociation energy that deviates as little as 1% from experiment.

Pauling bond strength, bond length and electron density distribution

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

Gibbs, Gerald V.; Ross, Nancy L.; Cox, David F.

2014-01-18

A power law regression equation, = 1.46(/r)-0.19, connecting the average experimental bond lengths, , with the average accumulation of the electron density at the bond critical point, , between bonded metal M and oxygen atoms, determined at ambient conditions for oxide crystals, where r is the row number of the M atom, is similar to the regression equation R(M-O) = 1.39(ρ(rc)/r)-0.21 determined for three perovskite crystals for pressures as high as 80 GPa. The two equations are also comparable with those, = 1.43( /r)-0.21, determined for a large number of oxide crystals at ambient conditions and = 1.39(/r)-0.22, determined formore » geometry optimized hydroxyacid molecules, that connect the bond lengths to the average Pauling electrostatic bond strength, , for the M-O bonded interactions. On the basis of the correspondence between the two sets of equations connecting ρ(rc) and the Pauling bond strength s with bond length, it appears that Pauling’s simple definition of bond strength closely mimics the accumulation of the electron density between bonded pairs of atoms. The similarity of the expressions for the crystals and molecules is compelling evidence that the M-O bonded interactions for the crystals and molecules 2 containing the same bonded interactions are comparable. Similar expressions, connecting bond lengths and bond strength, have also been found to hold for fluoride, nitride and sulfide molecules and crystals. The Brown-Shannon bond valence, σ, power law expression σ = [R1/(R(M-O)]N that has found wide use in crystal chemistry, is shown to be connected to a more universal expression determined for oxides and the perovskites, = r[(1.41)/]4.76, demonstrating that the bond valence for a bonded interaction is likewise closely connected to the accumulation of the electron density between the bonded atoms. Unlike the Brown-Shannon expression, it is universal in that it holds for the M-O bonded interactions for a relatively wide range of M atoms of the periodic table. The power law equation determined for the oxide crystals at ambient conditions is similar to the power law expression = r[1.46/]5.26 determined for the perovskites at pressures as high as 80 GPa, indicating that the intrinsic connection between R(M-O) and ρ(rc) that holds at ambient conditions also holds, to a first approximation, at high pressures.« less

Analisis parametrico de las variables que influyen en el comportamiento adherente de las armaduras pretesas en el hormigon

NASA Astrophysics Data System (ADS)

Arbelaez Jaramillo, Cesar Augusto

Prestressed concrete technique through the use of prestressed reinforcement is extended in the precast concrete industry. This technique consists on casting a concrete element over a previously prestressed reinforcement, proceeding to release once the concrete has reached a determined strength so the prestressed stress introduced to the reinforcement be transmitted, by bond, to concrete. The bond behaviour of prestressed reinforcement includes two phenomena: prestress transmission from the reinforcement to concrete and anchorage of the reinforcement. This bond behaviour is characterized by mean of two lengths: transmission length and anchorage length. The good design of these lengths is a basic and fundamental aspect in the project of precast prestressed concrete elements to guaranty the appropriate transmission of prestress and to allow the anchorage of the reinforcement along the structural element service life. The influence of the parameters related to the concrete dosage on the transmission and anchorage lengths of prestressing strands have been analyzed. The ECADA test method has been applied. With this method the operations of transmission of prestress and anchorage of the reinforcement are sequentially done. The transmission and anchorage lengths are determined from the force control supported by the reinforcement testing series of specimens with different embedment lengths. The differentiation of the concepts of anchorage length without slips and with slips has been proposed. The relationship of the parameters of dosage with the bond stress and the registered slips during the processes of transmission and anchorage has been studied. Expressions to value the slips distribution of the reinforcement in the transmission zone and in the anchorage zone have been proposed. A study on the determination of the transmission length from the free reinforcement slip end has been done and the viability to experimentally determine the transmission length from the slips sequence in the pull-out end as a function of the embedment length has been verified. The experimental results have been compared with results and predictions from other authors and standards, and an expression to calculate the transmission length have been proposed. Finally, the bond behaviour of self-compacting concretes has been compared with the bond behaviour of traditional concretes.

How Is the Enamel Affected by Different Orthodontic Bonding Agents and Polishing Techniques?

PubMed

Heravi, Farzin; Shafaee, Hooman; Abdollahi, Mojtaba; Rashed, Roozbeh

2015-03-01

The objective of this study was to assess the effect of new bonding techniques on enamel surface. Sixty upper central incisors were randomly divided into two equal groups. In the first group, metal brackets were bonded using TransbondXT and, in the second group, the same brackets were bonded with Maxcem Elite. The shear bond strength (SBS) of both agents to enamel was measured and the number and length of enamel cracks before bonding, after debonding and after polishing were compared. The number of visible cracks and the adhesive remnant index (ARI) scores in each group were also measured. There were significantly more enamel cracks in the Transbond XT group after debonding and polishing compared to the Maxcem Elite group. There was no significant difference in the length of enamel cracks between the two groups; but, in each group, a significant increase in the length of enamel cracks was noticeable after debonding. Polishing did not cause any statistically significant change in crack length. The SBS of Maxcem Elite was significantly lower than that of Transbond XT (95% confidence interval). Maxcem Elite offers clinically acceptable bond strength and can thus be used as a routine adhesive for orthodontic purposes since it is less likely to damage the enamel.

Utilisation of an eta(3)-allyl hydride complex, formed by UV irradiation, as a controlled source of 16-electron (eta(5)-C(5)Me(5))Rh(CH(2)[double bond, length as m-dash]CHMe).

PubMed

Sexton, Catherine J; López-Serrano, Joaquín; Lledós, Agustí; Duckett, Simon B

2008-10-21

Low temperature UV irradiation of solutions of (eta(5)-C(5)Me(5))Rh(CH(2)[double bond, length as m-dash]CHMe)(2) yields (eta(5)-C(5)Me(5))Rh(eta(3)-CH(2)CHCH(2))(H), which provides controlled access to the 16-electron fragment (eta(5)-C(5)Me(5))Rh(CH(2)[double bond, length as m-dash]CHMe).

Capture of SO3 isomers in the oxidation of sulfur monoxide with molecular oxygen.

PubMed

Wu, Zhuang; Lu, Bo; Feng, Ruijuan; Xu, Jian; Lu, Yan; Wan, Huabin; Eckhardt, André K; Schreiner, Peter R; Xie, Changjian; Guo, Hua; Zeng, Xiaoqing

2018-02-13

When mixing SO with O 2 in N 2 , Ne, or Ar, an end-on complex OS-OO forms in the gas phase and can subsequently be trapped at cryogenic temperatures (2.8-15.0 K). Upon infrared light irradiation, OS-OO converts to SO 3 and SO 2 + O with the concomitant formation of a rare 1,2,3-dioxathiirane 2-oxide, i.e., cyclic OS([double bond, length as m-dash]O)O. Unexpectedly, the ring-closure of 16 OS- 18 O 18 O yields a ca. 2 : 1 mixture of cyclic 18 OS([double bond, length as m-dash] 16 O) 18 O and 16 OS([double bond, length as m-dash] 18 O) 18 O. The characterization of OS-OO and OS([double bond, length as m-dash]O)O with IR and UV/Vis spectroscopy is supported by high-level ab initio computations.

A revised set of values of single-bond radii derived from the observed interatomic distances in metals by correction for bond number and resonance energy

PubMed Central

Pauling, Linus; Kamb, Barclay

1986-01-01

An earlier discussion [Pauling, L. (1947) J. Am. Chem. Soc. 69, 542] of observed bond lengths in elemental metals with correction for bond number and resonance energy led to a set of single-bond metallic radii with values usually somewhat less than the corresponding values obtained from molecules and complex ions. A theory of resonating covalent bonds has now been developed that permits calculation of the number of resonance structures per atom and of the effective resonance energy per bond. With this refined method of correcting the observed bond lengths for the effect of resonance energy, a new set of single-bond covalent radii, in better agreement with values from molecules and complex ions, has been constructed. PMID:16593698

The Changing Nature of the Chemical Bond

NASA Astrophysics Data System (ADS)

Angel, R. J.; Ross, N. L.; Zhao, J.

2006-12-01

It is commonly assumed that the relationship between bond strength and bond length for a particular pair of atoms is a simple and single-valued one for a given coordination environment; longer bonds are weaker. This is the basis of the concept of bond valence, for example. Indeed, in strongly-bonded oxide minerals, the range of bond lengths found for a given cation-anion polyhedron is so small that it was long thought that the polyhedral bulk moduli were essentially independent of structure type and thus the environment of the polyhedron. This view is incompatible with the discovery that the response of the perovskite structure to high pressures is controlled by the equipartition of bond-valence strain between the A and B cation sites within the structure [1]. The same appears to be true, within experimental uncertainties, for all framework structures with rigid-unit modes. In perovskites, this explicitly implies that the octahedral compressibility depends not only upon the octahedral cation, but also upon the compressibility of the cation-oxygen bonds of the extra-framework (nominally dodecahedral) site. Thus the octahedral compressibility of a B cation site must change as the A- site cation is changed, whether or not the B-O bond lengths change as a result of the substitution on the A site. The strength of bonds is thus dependent upon the crystal environment and not solely upon the bond length. The observation of a plateau effect in the variation of octahedral compressibilities in perovskite solid solutions suggests that the bond-valence matching principle is followed not just globally, but on a local scale as well. Such observations should allow the change with pressure of the excess thermodynamic properties of solid solutions to be directly related to the microscopic (atomic scale) evolution of the structure. [1] Zhao, Ross, & Angel (2004). Acta Cryst. B60:263

Bond-length relaxation in crystalline Si1-xGex alloys: An extended x-ray-absorption fine-structure study

NASA Astrophysics Data System (ADS)

Kajiyama, Hiroshi; Muramatsu, Shin-Ichi; Shimada, Toshikazu; Nishino, Yoichi

1992-06-01

Extended x-ray-absorption fine-structure spectra for crystalline Si1-xGex alloys, measured at the K edge of Ge at room temperature, are analyzed with a curve-fitting method based on the spherical-wave approximation. The Ge-Ge and Ge-Si bond lengths, coordination numbers of Ge and Si atoms around a Ge atom, and Debye-Waller factors of Ge and Si atoms are obtained. It is shown that Ge-Ge and Ge-Si bonds relax completely, for all Ge concentrations of their study, while the lattice constant varies monotonically, following Vegard's law. As noted by Bragg and later by Pauling and Huggins, the Ge-Ge and Ge-Si bond lengths are close to the sum of their constituent-element atomic radii: nearly 2.45 Å for Ge-Ge bonds and 2.40 Å for Ge-Si bonds. A study on the coordination around a Ge atom in the alloys revealed that Ge and Si atoms mix randomly throughout the compositional range studied.

Hydridosilylamido complexes of Ta and Mo isolobal with Berry's zirconocenes: syntheses, β-Si-H agostic interactions, catalytic hydrosilylation, and insight into mechanism.

PubMed

McLeod, Nicolas A; Kuzmina, Lyudmila G; Korobkov, Ilia; Howard, Judith A K; Nikonov, Georgii I

2016-02-14

The syntheses of novel Group 5 and Group 6 hydrosilylamido complexes of the type R(ArN[double bond, length as m-dash])M{N((t)Bu)SiMe2-H}X (M = Ta, R = Cp; M = Mo, R = ArN; X = Cl, H, OBn, Me) are described. The various substituents in the X position seem to play the key role in determining the extent of β-agostic interaction with the Si-H bond. The Mo agostic hydrido complex (ArN[double bond, length as m-dash])2Mo{η(3)-N((t)Bu)SiMe2-H}H is a pre-catalyst for the hydrosilylation of carbonyls. The stoichiometric reaction between benzaldehyde and (ArN[double bond, length as m-dash])2Mo{η(3)-N((t)Bu)SiMe2-H}H gives the benzoxy complex (ArN[double bond, length as m-dash])2Mo{N((t)Bu)SiMe2-H}(OBn), which showed a similar catalytic reactivity compared to the parent hydride. Mechanistic studies suggest that a non-hydride mechanism is operative.

Short Carboxylic Acid–Carboxylate Hydrogen Bonds Can Have Fully Localized Protons

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

Lin, Jiusheng; Pozharski, Edwin; Wilson, Mark A.

Short hydrogen bonds (H-bonds) have been proposed to play key functional roles in several proteins. The location of the proton in short H-bonds is of central importance, as proton delocalization is a defining feature of low-barrier hydrogen bonds (LBHBs). Experimentally determining proton location in H-bonds is challenging. Here, bond length analysis of atomic (1.15–0.98 Å) resolution X-ray crystal structures of the human protein DJ-1 and its bacterial homologue, YajL, was used to determine the protonation states of H-bonded carboxylic acids. DJ-1 contains a buried, dimer-spanning 2.49 Å H-bond between Glu15 and Asp24 that satisfies standard donor–acceptor distance criteria for amore » LBHB. Bond length analysis indicates that the proton is localized on Asp24, excluding a LBHB at this location. However, similar analysis of the Escherichia coli homologue YajL shows both residues may be protonated at the H-bonded oxygen atoms, potentially consistent with a LBHB. A Protein Data Bank-wide screen identifies candidate carboxylic acid H-bonds in approximately 14% of proteins, which are typically short [O–O> = 2.542(2) Å]. Chemically similar H-bonds between hydroxylated residues (Ser/Thr/Tyr) and carboxylates show a trend of lengthening O–O distance with increasing H-bond donor pK a. This trend suggests that conventional electronic effects provide an adequate explanation for short, charge-assisted carboxylic acid–carboxylate H-bonds in proteins, without the need to invoke LBHBs in general. This study demonstrates that bond length analysis of atomic resolution X-ray crystal structures provides a useful experimental test of certain candidate LBHBs.« less

Evaluation of enamel damages following orthodontic bracket debonding in fluorosed teeth bonded with adhesion promoter.

PubMed

Baherimoghadam, Tahreh; Akbarian, Sahar; Rasouli, Reza; Naseri, Navid

2016-01-01

To evaluate shear bond strength (SBS) of the orthodontic brackets bonded to fluorosed and nonfluorosed teeth using Light Bond with and without adhesion promoters and compare their enamel damages following debonding. In this study, 30 fluorosed (Thylstrup and Fejerskov Index = 4-5) and 30 nonfluorosed teeth were randomly distributed between two subgroups according to the bonding materials: Group 1, fluorosed teeth bonded with Light Bond; Group 2, fluorosed teeth bonded with adhesion promoters and Light Bond; Group 3, nonfluorosed teeth bonded with Light Bond; Group 4, nonfluorosed bonded with adhesion promoters and Light Bond. After bonding, the SBS of the brackets was tested with a universal testing machine. Stereomicroscopic evaluation was performed by unbiased stereology in all teeth to determine the amount of adhesive remnants and the number and length of enamel cracks before bonding and after debonding. The data were analyzed using two-way analysis of variance, Kruskal-Wallis, Wilcoxon Signed Rank, and Mann-Whitney test. While fluorosis reduced the SBS of orthodontic bracket (P = 0.017), Enhance Locus Ceruleus LC significantly increased the SBS of the orthodontic bracket in fluorosed and nonfluorosed teeth (P = 0.039). Significant increasing in the number and length of enamel crack after debonding was found in all four groups. There were no significant differences in the length of enamel crack increased after debonding among four groups (P = 0.768) while increasing in the number of enamel cracks after debonding was significantly different among the four groups (P = 0.023). Teeth in Group 2 showed the highest enamel damages among four groups following debonding. Adhesion promoters could improve the bond strength of orthodontic brackets, but conservative debonding methods for decreasing enamel damages would be necessary.

Short Carboxylic Acid-Carboxylate Hydrogen Bonds Can Have Fully Localized Protons.

PubMed

Lin, Jiusheng; Pozharski, Edwin; Wilson, Mark A

2017-01-17

Short hydrogen bonds (H-bonds) have been proposed to play key functional roles in several proteins. The location of the proton in short H-bonds is of central importance, as proton delocalization is a defining feature of low-barrier hydrogen bonds (LBHBs). Experimentally determining proton location in H-bonds is challenging. Here, bond length analysis of atomic (1.15-0.98 Å) resolution X-ray crystal structures of the human protein DJ-1 and its bacterial homologue, YajL, was used to determine the protonation states of H-bonded carboxylic acids. DJ-1 contains a buried, dimer-spanning 2.49 Å H-bond between Glu15 and Asp24 that satisfies standard donor-acceptor distance criteria for a LBHB. Bond length analysis indicates that the proton is localized on Asp24, excluding a LBHB at this location. However, similar analysis of the Escherichia coli homologue YajL shows both residues may be protonated at the H-bonded oxygen atoms, potentially consistent with a LBHB. A Protein Data Bank-wide screen identifies candidate carboxylic acid H-bonds in approximately 14% of proteins, which are typically short [⟨d O-O ⟩ = 2.542(2) Å]. Chemically similar H-bonds between hydroxylated residues (Ser/Thr/Tyr) and carboxylates show a trend of lengthening O-O distance with increasing H-bond donor pK a . This trend suggests that conventional electronic effects provide an adequate explanation for short, charge-assisted carboxylic acid-carboxylate H-bonds in proteins, without the need to invoke LBHBs in general. This study demonstrates that bond length analysis of atomic resolution X-ray crystal structures provides a useful experimental test of certain candidate LBHBs.

Negative hyperconjugation and red-, blue- or zero-shift in X-Z∙∙∙Y complexes.

PubMed

Joy, Jyothish; Jemmis, Eluvathingal D; Vidya, Kaipanchery

2015-01-01

A generalized explanation is provided for the existence of the red- and blue-shifting nature of X-Z bonds (Z=H, halogens, chalcogens, pnicogens, etc.) in X-Z∙∙∙Y complexes based on computational studies on a selected set of weakly bonded complexes and analysis of existing literature data. The additional electrons and orbitals available on Z in comparison to H make for dramatic differences between the H-bond and the rest of the Z-bonds. The nature of the X-group and its influence on the X-Z bond length in the parent X-Z molecule largely controls the change in the X-Z bond length on X-Z∙∙∙Y bond formation; the Y-group usually influences only the magnitude of the effects controlled by X. The major factors which control the X-Z bond length change are: (a) negative hyperconjugative donation of electron density from X-group to X-Z σ* antibonding molecular orbital (ABMO) in the parent X-Z, (b) induced negative hyperconjugation from the lone pair of electrons on Z to the antibonding orbitals of the X-group, and (c) charge transfer (CT) from the Y-group to the X-Z σ* orbital. The exchange repulsion from the Y-group that shifts partial electron density at the X-Z σ* ABMO back to X leads to blue-shifting and the CT from the Y-group to the σ* ABMO of X-Z leads to red-shifting. The balance between these two opposing forces decides red-, zero- or blue-shifting. A continuum of behaviour of X-Z bond length variation is inevitable in X-Z∙∙∙Y complexes.

Bond between smooth prestressing wires and concrete : finite element model and transfer length analysis for pretensioned concrete crossties.

DOT National Transportation Integrated Search

2014-04-03

Pretensioned concrete ties are increasingly employed in railroad high speed : and heavy haul applications. The bond between prestressing wires or strands and : concrete plays an important role in determining the transfer length of pretensioned : conc...

Continuum in the X-Z---Y weak bonds: Z= main group elements.

PubMed

Joy, Jyothish; Jose, Anex; Jemmis, Eluvathingal D

2016-01-15

The Continuum in the variation of the X-Z bond length change from blue-shifting to red-shifting through zero- shifting in the X-Z---Y complex is inevitable. This has been analyzed by ab-initio molecular orbital calculations using Z= Hydrogen, Halogens, Chalcogens, and Pnicogens as prototypical examples. Our analysis revealed that, the competition between negative hyperconjugation within the donor (X-Z) molecule and Charge Transfer (CT) from the acceptor (Y) molecule is the primary reason for the X-Z bond length change. Here, we report that, the proper tuning of X- and Y-group for a particular Z- can change the blue-shifting nature of X-Z bond to zero-shifting and further to red-shifting. This observation led to the proposal of a continuum in the variation of the X-Z bond length during the formation of X-Z---Y complex. The varying number of orbitals and electrons available around the Z-atom differentiates various classes of weak interactions and leads to interactions dramatically different from the H-Bond. Our explanations based on the model of anti-bonding orbitals can be transferred from one class of weak interactions to another. We further take the idea of continuum to the nature of chemical bonding in general. © 2015 Wiley Periodicals, Inc.

Crystal structure of (eth­oxy­ethyl­idene)di­methyl­aza­nium ethyl sulfate

PubMed Central

Tiritiris, Ioannis; Saur, Stefan; Kantlehner, Willi

2015-01-01

In the title salt, C6H14NO+·C2H5SO4 −, the C—N bond lengths in the cation are 1.2981 (14), 1.4658 (14) and 1.4707 (15) Å, indicating double- and single-bond character, respectively. The C—O bond length of 1.3157 (13) Å shows double-bond character, indicating charge delocalization within the NCO plane of the iminium ion. In the crystal, C—H⋯O hydrogen bonds between H atoms of the cations and O atoms of neighbouring ethyl sulfate anions are present, generating a three-dimensional network. PMID:26870525

The Effect of Limited Diffusion and Wet-Dry Cycling on Reversible Polymerization Reactions: Implications for Prebiotic Synthesis of Nucleic Acids.

PubMed

Higgs, Paul G

2016-06-08

A long-standing problem for the origins of life is that polymerization of many biopolymers, including nucleic acids and peptides, is thermodynamically unfavourable in aqueous solution. If bond making and breaking is reversible, monomers and very short oligomers predominate. Recent experiments have shown that wetting and drying cycles can overcome this problem and drive the formation of longer polymers. In the dry phase, bond formation is favourable, but diffusion is restricted, and bonds only form between monomers that are initially close together. In the wet phase, some of the bonds are hydrolyzed. However, repositioning of the molecules allows new bonds to form in the next dry phase, leading to an increase in mean polymer length. Here, we consider a simple theoretical model that explains the effect of cycling. There is an equilibrium length distribution with a high mean length that could be achieved if diffusion occurred freely in the dry phase. This equilibrium is inaccessible without diffusion. A single dry cycle without diffusion leads to mean lengths much shorter than this. Repeated cycling leads to a significant increase in polymerization relative to a single cycle. In the most favourable case, cycling leads to the same equilibrium length distribution as would be achieved if free diffusion were possible in the dry phase. These results support the RNA World scenario by explaining a potential route to synthesis of long RNAs; however, they also imply that cycling would be beneficial to the synthesis of other kinds of polymers, including peptides, where bond formation involves a condensation reaction.

The Effect of Limited Diffusion and Wet–Dry Cycling on Reversible Polymerization Reactions: Implications for Prebiotic Synthesis of Nucleic Acids

PubMed Central

Higgs, Paul G.

2016-01-01

A long-standing problem for the origins of life is that polymerization of many biopolymers, including nucleic acids and peptides, is thermodynamically unfavourable in aqueous solution. If bond making and breaking is reversible, monomers and very short oligomers predominate. Recent experiments have shown that wetting and drying cycles can overcome this problem and drive the formation of longer polymers. In the dry phase, bond formation is favourable, but diffusion is restricted, and bonds only form between monomers that are initially close together. In the wet phase, some of the bonds are hydrolyzed. However, repositioning of the molecules allows new bonds to form in the next dry phase, leading to an increase in mean polymer length. Here, we consider a simple theoretical model that explains the effect of cycling. There is an equilibrium length distribution with a high mean length that could be achieved if diffusion occurred freely in the dry phase. This equilibrium is inaccessible without diffusion. A single dry cycle without diffusion leads to mean lengths much shorter than this. Repeated cycling leads to a significant increase in polymerization relative to a single cycle. In the most favourable case, cycling leads to the same equilibrium length distribution as would be achieved if free diffusion were possible in the dry phase. These results support the RNA World scenario by explaining a potential route to synthesis of long RNAs; however, they also imply that cycling would be beneficial to the synthesis of other kinds of polymers, including peptides, where bond formation involves a condensation reaction. PMID:27338479

Theoretical electrical conductivity of hydrogen-bonded benzamide-derived molecules and single DNA bases.

PubMed

Chen, Xiang

2013-09-01

A benzamide molecule is used as a "reader" molecule to form hydrogen bonds with five single DNA bases, i.e., four normal single DNA bases A,T,C,G and one for 5methylC. The whole molecule is then attached to the gold surface so that a meta-molecule junction is formed. We calculate the transmission function and conductance for the five metal-molecule systems, with the implementation of density functional theory-based non-equilibrium Green function method. Our results show that each DNA base exhibits a unique conductance and most of them are on the pS level. The distinguishable conductance of each DNA base provides a way for the fast sequencing of DNA. We also investigate the dependence of conductivity of such a metal-molecule system on the hydrogen bond length between the "reader" molecule and DNA base, which shows that conductance follows an exponential decay as the hydrogen bond length increases, i.e., the conductivity is highly sensitive to the change in hydrogen bond length.

Symmetry and novelty in the electronic and geometric structure of nanoalloys:. the case of Ag27Cu7

NASA Astrophysics Data System (ADS)

Ortigoza, M. Alcántara; Rahman, T. S.

2008-04-01

Nanoparticles of bimetallic alloys have been shown to possess composition dependent characteristics which distinguish themselves from the corresponding bulk alloys. Taking the 34-atom nanoalloy of Ag and Cu (Ag27Cu7), we show using first principles electronic structure calculations that this core-shell alloy indeed has perfect D5h symmetry and consists of only 6 non-equivalent (2 Cu and 4 Ag) atoms. Analysis of the interatomic bond lengths and detailed electronic structure further reveal that the Cu atoms play a major role in controlling the characteristics of the nanoalloy. The higher cohesive energy, together with shorter bond length for Cu, compared to Ag, conspire to produce a hierarchy in the relative strengths of the Ag - Cu, Ag - Ag, and Cu - Cu bonds and corresponding interatomic bond lengths, point to the uniqueness in the characteristics of this nanoalloy. Charge density plots of Ag27Cu7 provide further insights into the relative strengths of the various interatomic bonds.

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.

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.

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.

Observation of pendular butterfly Rydberg molecules

PubMed Central

Niederprüm, Thomas; Thomas, Oliver; Eichert, Tanita; Lippe, Carsten; Pérez-Ríos, Jesús; Greene, Chris H.; Ott, Herwig

2016-01-01

Engineering molecules with a tunable bond length and defined quantum states lies at the heart of quantum chemistry. The unconventional binding mechanism of Rydberg molecules makes them a promising candidate to implement such tunable molecules. A very peculiar type of Rydberg molecules are the so-called butterfly molecules, which are bound by a shape resonance in the electron–perturber scattering. Here we report the observation of these exotic molecules and employ their exceptional properties to engineer their bond length, vibrational state, angular momentum and orientation in a small electric field. Combining the variable bond length with their giant dipole moment of several hundred Debye, we observe counter-intuitive molecules which locate the average electron position beyond the internuclear distance. PMID:27703143

Sacrificial bonds and hidden length in biomaterials: A kinetic constitutive description of strength and toughness in bone

NASA Astrophysics Data System (ADS)

Lieou, Charles K. C.; Elbanna, Ahmed E.; Carlson, Jean M.

2013-07-01

Sacrificial bonds and hidden length in structural molecules account for the greatly increased fracture toughness of biological materials compared to synthetic materials without such structural features by providing a molecular-scale mechanism for energy dissipation. One example is in the polymeric glue connection between collagen fibrils in animal bone. In this paper we propose a simple kinetic model that describes the breakage of sacrificial bonds and the release of hidden length, based on Bell's theory. We postulate a master equation governing the rates of bond breakage and formation. This enables us to predict the mechanical behavior of a quasi-one-dimensional ensemble of polymers at different stretching rates. We find that both the rupture peak heights and maximum stretching distance increase with the stretching rate. In addition, our theory naturally permits the possibility of self-healing in such biological structures.

Studies of EXAFSSpectra using Copper (II) Schiff Base complexes and Determination of Bond lengths Using Synchrotron Radiation

NASA Astrophysics Data System (ADS)

Mishra, A.; Vibhute, V.; Ninama, S.; Parsai, N.; Jha, S. N.; Sharma, P.

2016-10-01

X-ray absorption fine structure (XAFS) at the K-edge of copper has been studied in some copper (II) complexes with substituted anilines like (2Cl, 4Br, 2NO2, 4NO2 and pure aniline) with o-PDA (orthophenylenediamine) as ligand. The X-ray absorption measurements have been performed at the recently developed BL-8 dispersive EXAFS beam line at 2.5 GeV Indus-2 Synchrotron Source at RRCAT, Indore, India. The data obtained has been processed using EXAFS data analysis program Athena.The graphical method gives the useful information about bond length and also the environment of the absorbing atom. The theoretical bond lengths of the complexes were calculated by using interactive fitting of EXAFS using fast Fourier inverse transformation (IFEFFIT) method. This method is also called as Fourier transform method. The Lytle, Sayers and Stern method and Levy's method have been used for determination of bond lengths experimentally of the studied complexes. The results of both methods have been compared with theoretical IFEFFIT method.

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

Theoretical verification and extension of the McKean relationship between bond lengths and stretching frequencies

NASA Astrophysics Data System (ADS)

Larsson, J. A.; Cremer, D.

1999-08-01

Vibrational spectra contain explicit information on the electronic structure and the bonding situation of a molecule, which can be obtained by transforming the vibrational normal modes of a molecule into appropriate internal coordinate modes, which are localized in a fragment of the molecule and which are associated to that internal coordinate that describes the molecular fragment in question. It is shown that the adiabatic internal modes derived recently (Int. J. Quant. Chem., 67 (1998) 1) are the theoretical counterparts of McKean's isolated CH stretching modes (Chem. Soc. Rev., 7 (1978) 399). Adiabatic CH stretching frequencies obtained from experimental vibrational spectra can be used to determine CH bond lengths with high accuracy. Contrary to the concept of isolated stretching frequencies a generalization to any bond of a molecule is possible as is demonstrated for the CC stretching frequencies. While normal mode frequencies do not provide a basis to determine CC bond lengths and CC bond strengths, this is possible with the help of the adiabatic CC stretching frequencies. Measured vibrational spectra are used to describe different types of CC bonds in a quantitative way. For CH bonds, it is also shown that adiabatic stretching frequency leads to the definition of an ideal dissociation energy, which contrary to the experimentally determined dissociation energy is a direct measure of the bond strength. The difference between measured and ideal dissociation energies gives information on stabilization or destabilization of the radicals formed in a dissociation process.

Raman spectroscopic determination of the length, strength, compressibility, Debye temperature, elasticity, and force constant of the C-C bond in graphene.

PubMed

Yang, X X; Li, J W; Zhou, Z F; Wang, Y; Yang, L W; Zheng, W T; Sun, Chang Q

2012-01-21

From the perspective of bond relaxation and bond vibration, we have formulated the Raman phonon relaxation of graphene, under the stimuli of the number-of-layers, the uni-axial strain, the pressure, and the temperature, in terms of the response of the length and strength of the representative bond of the entire specimen to the applied stimuli. Theoretical unification of the measurements clarifies that: (i) the opposite trends of the Raman shifts, which are due to the number-of-layers reduction, of the G-peak shift and arises from the vibration of a pair of atoms, while the D- and the 2D-peak shifts involve the z-neighbor of a specific atom; (ii) the tensile strain-induced phonon softening and phonon-band splitting arise from the asymmetric response of the C(3v) bond geometry to the C(2v) uni-axial bond elongation; (iii) the thermal softening of the phonons originates from bond expansion and weakening; and (iv) the pressure stiffening of the phonons results from bond compression and work hardening. Reproduction of the measurements has led to quantitative information about the referential frequencies from which the Raman frequencies shift as well as the length, energy, force constant, Debye temperature, compressibility and elastic modulus of the C-C bond in graphene, which is of instrumental importance in the understanding of the unusual behavior of graphene.

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.

X-ray absorption spectral studies of copper (II) mixed ligand complexes

NASA Astrophysics Data System (ADS)

Soni, B.; Dar, Davood Ah; Shrivastava, B. D.; Prasad, J.; Srivastava, K.

2014-09-01

X-ray absorption spectra at the K-edge of copper have been studied in two copper mixed ligand complexes, one having tetramethyethylenediamine (tmen) and the other having tetraethyethylenediamine (teen) as one of the ligands. The spectra have been recorded at BL-8 dispersive extended X-ray absorption fine structure (EXAFS) beamline at the 2.5 GeV INDUS- 2 synchrotron, RRCAT, Indore, India. The data obtained has been processed using the data analysis program Athena. The energy of the K-absorption edge, chemical shift, edge-width and shift of the principal absorption maximum in the complexes have been determined and discussed. The values of these parameters have been found to be approximately the same in both the complexes indicating that the two complexes possess similar chemical environment around the copper metal atom. The chemical shift has been utilized to estimate effective nuclear charge on the absorbing atom. The normalized EXAFS spectra have been Fourier transformed. The position of the first peak in the Fourier transform gives the value of first shell bond length, which is shorter than the actual bond length because of energy dependence of the phase factors in the sine function of the EXAFS equation. This distance is thus the phase- uncorrected bond length. Bond length has also been determined by Levy's, Lytle's and Lytle, Sayers and Stern's (LSS) methods. The results obtained from LSS and the Fourier transformation methods are comparable with each other, since both are phase uncorrected bond lengths.

Finite Element Bond Modeling for Indented Wires in Pretensioned Concrete Crossties

DOT National Transportation Integrated Search

2016-04-12

Indented wires have been increasingly employed by : concrete crosstie manufacturers to improve the bond between : prestressing steel reinforcements and concrete, as bond can : affect several critical performance measures, including transfer : length,...

Bond–Slip Relationship for CFRP Sheets Externally Bonded to Concrete under Cyclic Loading

PubMed Central

Li, Ke; Cao, Shuangyin; Yang, Yue; Zhu, Juntao

2018-01-01

The objective of this paper was to explore the bond–slip relationship between carbon fiber-reinforced polymer (CFRP) sheets and concrete under cyclic loading through experimental and analytical approaches. Modified beam tests were performed in order to gain insight into the bond–slip relationship under static and cyclic loading. The test variables are the CFRP-to-concrete width ratio, and the bond length of the CFRP sheets. An analysis of the test results in this paper and existing test results indicated that the slope of the ascending segment of the bond–slip curve decreased with an increase in the number of load cycles, but the slip corresponding to the maximum shear stress was almost invariable as the number of load cycles increased. In addition, the rate of reduction in the slope of the ascending range of the bond–slip curve during cyclic loading decreased as the concrete strength increased, and increased as the load level or CFRP-to-concrete width ratio enhanced. However, these were not affected by variations in bond length if the residual bond length was longer than the effective bond length. A bilinear bond–slip model for CFRP sheets that are externally bonded to concrete under cyclic loading, which considered the effects of the cyclic load level, concrete strength, and CFRP-to-concrete ratio, was developed based on the existing static bond–slip model. The accuracy of this proposed model was verified by a comparison between this proposed model and test results. PMID:29495383

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

PubMed Central

Reichelt, Martin; Reuter, Hans

2014-01-01

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

Compositional effects on Si–OH bond length in hydrous silicates with implications for trends in the SiOH acidity

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

Zarubin, Dmitri P., E-mail: dmitri.zarubin@mtu-net.ru

2014-04-01

Theoretical calculations of the structure and Brønsted acidity of SiOH groups in silica clusters have never addressed the question if these vary with the degree of SiOH deprotonation. In this connection, a statistical analysis is presented of Si–OH bond lengths in crystalline hydrogen silicates with well-determined structures with a special emphasis placed on effects of the silicate composition. It is found that among hydrogen silicates of large cations with low charges the Si–OH bonds are always longer than terminal Si–O bonds in the same anion and correlate in length with the anionic charge per tetrahedron. The findings are explained bymore » steric limitations on charge balancing at oxygen atoms by hydrogen bonds and/or cations. It is suggested that similar limitations and imbalances may underlie the well-known trends in the Brønsted acidity of silicic acids and silicas in aqueous media: decreased acidity with increased SiOH deprotonation and increased acidity with increased tetrahedra connectivity. - Graphical abstract: Si–OH bonds in crystalline silicates lengthen with the anionic charge per tetrahedron, which is in parallel with the well-known trend of decreased acidity of silicic acids and silicas in solution with increased degree of deprotonation. - Highlights: • Si–OH bonds in alkali hydrogen silicates are always longer than terminal Si–O bonds. • Si–OH bonds in silicates lengthen with the anionic charge per tetrahedron. • The Si–OH bond elongation results from inherent underbonding of terminal O atoms. • The longer the Si–OH bond, the less acidic the OH group is.« less

Variations in enamel damage after debonding of two different bracket base designs: An in vitro study.

PubMed

Ahangar Atashi, Mohammad Hossein; Sadr Haghighi, Amir Hooman; Nastarin, Parastou; Ahangar Atashi, Sina

2018-01-01

Background. Bracket base design is a factor influencing shear bond strength. High shear bond strength leads to enamel crack formation during debonding. The aim of this study was to compare enamel damage variations, including the number and length of enamel cracks after debonding of two different base designs. Methods. Eighty-eight extracted human premolars were randomly divided into2 groups (n=44). The teeth in each group were bonded by two types of brackets with different base designs: 80-gauge mesh design versus anchor pylon design with pylons for adhesive retention. The number and length of enamel cracks before bonding and after debonding were evaluated under an optical stereomicroscope ×40 in both groups. Mann-Whitney U test was used to compare the number of cracks between the two groups. ANCOVA was used for comparison of crack lengths after and before debonding in each group and between the two groups. Results. There was a significant increase in enamel crack length and numbers in each group after debonding. There was no significant difference in enamel crack numbers after debonding between the two groups, whereas the length of enamel cracks was significantly greater in anchor pylon base design after debonding. Conclusion. Bracket bases with pylon design for adhesive retention caused more iatrogenic debonding damage to enamel surface.

Shock response of 1,3,5-trinitroperhydro-1,3,5-triazine (RDX): The C-N bond scission studied by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Yuan, Jiao-Nan; Wei, Yong-Kai; Zhang, Xiu-Qing; Chen, Xiang-Rong; Ji, Guang-Fu; Kotni, Meena Kumari; Wei, Dong-Qing

2017-10-01

The shock response has a great influence on the design, synthesis, and application of energetic materials in both industrial and military areas. Therefore, the initial decomposition mechanism of bond scission at the atomistic level of condensed-phase α-RDX under shock loading has been studied based on quantum molecular dynamics simulations in combination with a multi-scale shock technique. First, based on the frontier molecular orbital theory, our calculated result shows that the N-NO2 bond is the weakest bond in the α-RDX molecule in the ground state, which may be the initial bond for pyrolysis. Second, the changes of bonds under shock loading are investigated by the changes of structures, kinetic bond lengths, and Laplacian bond orders during the simulation. Also, the variation of thermodynamic properties with time in shocked α-RDX at 10 km/s along the lattice vector a for a timescale of up to 3.5 ps is presented. By analyzing the detailed structural changes of RDX under shock loading, we find that the shocked RDX crystal undergoes a process of compression and rotation, which leads to the C-N bond initial rupture. The time variation of dynamic bond lengths in a shocked RDX crystal is calculated, and the result indicates that the C-N bond is easier to rupture than other bonds. The Laplacian bond orders are used to predict the molecular reactivity and stability. The values of the calculated bond orders show that the C-N bonds are more sensitive than other bonds under shock loading. In a word, the C-N bond scission has been validated as the initial decomposition in a RDX crystal shocked at 10 km/s. Finally, the bond-length criterion has been used to identify individual molecules in the simulation. The distance thresholds up to which two particles are considered direct neighbors and assigned to the same cluster have been tested. The species and density numbers of the initial decomposition products are collected according to the trajectory.

Bond Length Dependence on Quantum States as Shown by Spectroscopy

ERIC Educational Resources Information Center

Lim, Kieran F.

2005-01-01

A discussion on how a spreadsheet simulation of linear-molecular spectra could be used to explore the dependence of rotational band spacing and contours on average bond lengths in the initial and final quantum states is presented. The simulation of hydrogen chloride IR, iodine UV-vis, and nitrogen UV-vis spectra clearly show whether the average…

Complex transition metal hydrides: linear correlation of countercation electronegativity versus T-D bond lengths.

PubMed

Humphries, T D; Sheppard, D A; Buckley, C E

2015-06-30

For homoleptic 18-electron complex hydrides, an inverse linear correlation has been established between the T-deuterium bond length (T = Fe, Co, Ni) and the average electronegativity of the metal countercations. This relationship can be further employed towards aiding structural solutions and predicting physical properties of novel complex transition metal hydrides.

Thinking Like a Chemist: Intuition in Thermoelectric Materials.

PubMed

Zeier, Wolfgang G; Zevalkink, Alex; Gibbs, Zachary M; Hautier, Geoffroy; Kanatzidis, Mercouri G; Snyder, G Jeffrey

2016-06-06

The coupled transport properties required to create an efficient thermoelectric material necessitates a thorough understanding of the relationship between the chemistry and physics in a solid. We approach thermoelectric material design using the chemical intuition provided by molecular orbital diagrams, tight binding theory, and a classic understanding of bond strength. Concepts such as electronegativity, band width, orbital overlap, bond energy, and bond length are used to explain trends in electronic properties such as the magnitude and temperature dependence of band gap, carrier effective mass, and band degeneracy and convergence. The lattice thermal conductivity is discussed in relation to the crystal structure and bond strength, with emphasis on the importance of bond length. We provide an overview of how symmetry and bonding strength affect electron and phonon transport in solids, and how altering these properties may be used in strategies to improve thermoelectric performance. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Pullout Performances of Grouted Rockbolt Systems with Bond Defects

NASA Astrophysics Data System (ADS)

Xu, Chang; Li, Zihan; Wang, Shanyong; Wang, Shuren; Fu, Lei; Tang, Chunan

2018-03-01

This paper presents a numerical study on the pullout behaviour of fully grouted rockbolts with bond defects. The cohesive zone model (CZM) is adopted to model the bond-slip behaviour between the rockbolt and grout material. Tensile tests were also conducted to validate the numerical model. The results indicate that the defect length can obviously influence the load and stress distributions along the rockbolt as well as the load-displacement response of the grouted system. Moreover, a plateau in the stress distribution forms due to the bond defect. The linear limit and peak load of the load-displacement response decrease as the defect length increases. A bond defect located closer to the loaded end leads to a longer nonlinear stage in the load-displacement response. However, the peak loads measured from the specimens made with various defect locations are almost approximately the same. The peak load for a specimen with the defects equally spaced along the bolt is higher than that for a specimen with defects concentrated in a certain zone, even with the same total defect length. Therefore, the dispersed pattern of bond defects would be much safer than the concentrated pattern. For the specimen with dispersed defects, the peak load increases with an increase in the defect spacing, even if the total defect length is the same. The peak load for a grouted rockbolt system with defects increases with an increases in the bolt diameter. This work leads to a better understanding of the load transfer mechanism for grouted rockbolt systems with bond defects, and paves the way towards developing a general evaluation method for damaged rockbolt grouted systems.

Ge K-Edge Extended X-Ray Absorption Fine Structure Study of the Local Structure of Amorphous GeTe and the Crystallization

NASA Astrophysics Data System (ADS)

Maeda, Yoshihito; Wakagi, Masatoshi

1991-01-01

The local structure and crystallization of amorphous GeTe (a-GeTe) were examined by means of Ge K-edge EXAFS. In a-GeTe, both Ge-Ge and Ge-Te bonds were observed to exist in nearest neighbors of Ge. The average coordination number around Ge is 3.7, which is close to the tetrahedral structure. A random covalent network (RCN) model seems to be suitable for the local Structure. After a-GeTe crystallizes at 129°C, the Ge-Ge bond disappears and the Ge-Te bond length increases considerably. As temperature rises, in a-GeTe the Debye-Waller factor of the Ge-Te bond increases greatly, while that of the Ge-Ge bond increases only slightly. At the crystallization, it is found that the fluctuation of the Ge-Te bond length plays a major role in the change of the local structure and bonding state around Ge.

Anisotropy of atomic bonds formed by p-type dopants in bulk GaN crystals

NASA Astrophysics Data System (ADS)

Lawniczak-Jablonska, K.; Suski, T.; Gorczyca, I.; Christensen, N. E.; Libera, J.; Kachniarz, J.; Lagarde, P.; Cortes, R.; Grzegory, I.

The anisotropy of atomic bonds formed by acceptor dopants with nitrogen in bulk wurtzite GaN crystals was studied by means of linearly polarized synchrotron radiation used in measurements of X-ray-absorption spectra for the K-edgeof Mg and Zn dopants. These spectra correspond to i) a single acceptor N bond along the c-axis and ii) three bonds realized with N atoms occupying the ab-plane perpendicular to the c-axis. The Zn dopant formed resonant spectra similar to that characteristic for Ga cations. In the case of the Mg dopant, similarity to Ga cations was observed for triple bonds in the ab-plane, only. Practically no resonant structure for spectra detected along the c-axis was observed. The absorption spectra were compared with ab initio calculations using the full-potential linear muffin-tin-orbital method. These calculations were also used for determination of the bond length for Mg-N and Zn-N in wurtzite GaN crystals and show that introducing dopants causes an increase of the lengths of the bonds formed by both dopants. Extended X-ray-absorption fine-structure measurements performed for bulk GaN:Zn confirmed the prediction of the theory in the case of the Zn-N bond. Finally, it is suggested that the anisotropy in the length of the Mg-N bonds, related to their larger strength in the case of bonds in the ab-plane, can explain preferential formation of a superlattice consisting of Mg-rich layers arranged in ab-planes of several bulk GaN:Mg crystals observed by transmission electron microscopy. Within the sensitivity of the method used, no parasitic metallic clusters or oxide compounds formed by the considered acceptors in GaN crystals were found.

Investigation of non-corrin cobalt(II)-containing sites in protein structures of the Protein Data Bank.

PubMed

Abriata, Luciano Andres

2013-04-01

Protein X-ray structures with non-corrin cobalt(II)-containing sites, either natural or substituting another native ion, were downloaded from the Protein Data Bank and explored to (i) describe which amino acids are involved in their first ligand shells and (ii) analyze cobalt(II)-donor bond lengths in comparison with previously reported target distances, CSD data and EXAFS data. The set of amino acids involved in Co(II) binding is similar to that observed for catalytic Zn(II) sites, i.e. with a large fraction of carboxylate O atoms from aspartate and glutamate and aromatic N atoms from histidine. The computed Co(II)-donor bond lengths were found to depend strongly on structure resolution, an artifact previously detected for other metal-donor distances. Small corrections are suggested for the target bond lengths to the aromatic N atoms of histidines and the O atoms of water and hydroxide. The available target distance for cysteine (Scys) is confirmed; those for backbone O and other donors remain uncertain and should be handled with caution in refinement and modeling protocols. Finally, a relationship between both Co(II)-O bond lengths in bidentate carboxylates is quantified.

Vector-based model of elastic bonds for simulation of granular solids.

PubMed

Kuzkin, Vitaly A; Asonov, Igor E

2012-11-01

A model (further referred to as the V model) for the simulation of granular solids, such as rocks, ceramics, concrete, nanocomposites, and agglomerates, composed of bonded particles (rigid bodies), is proposed. It is assumed that the bonds, usually representing some additional gluelike material connecting particles, cause both forces and torques acting on the particles. Vectors rigidly connected with the particles are used to describe the deformation of a single bond. The expression for potential energy of the bond and corresponding expressions for forces and torques are derived. Formulas connecting parameters of the model with longitudinal, shear, bending, and torsional stiffnesses of the bond are obtained. It is shown that the model makes it possible to describe any values of the bond stiffnesses exactly; that is, the model is applicable for the bonds with arbitrary length/thickness ratio. Two different calibration procedures depending on bond length/thickness ratio are proposed. It is shown that parameters of the model can be chosen so that under small deformations the bond is equivalent to either a Bernoulli-Euler beam or a Timoshenko beam or short cylinder connecting particles. Simple analytical expressions, relating parameters of the V model with geometrical and mechanical characteristics of the bond, are derived. Two simple examples of computer simulation of thin granular structures using the V model are given.

IR spectroscopy as a source of data on bond strengths

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Bonding properties and bond activation of ylides: recent findings and outlook.

PubMed

Urriolabeitia, Esteban P

2008-11-14

The interaction of phosphorus and nitrogen ylides with metallic precursors has been examined from different points of view. The first one is related to the bonding properties of the ylides. Ylides with a unique stabilizing group bond through different atoms (the Calpha or the heteroatoms); while ylides with two stabilizing groups never coordinate through the Calpha atom. In the second section we examine the cause of the stereoselective coordination of bisylides of phosphorus, nitrogen and arsenic, and of mixed bisylides. We describe here the very interesting conformational preferences found in these systems, which have been determined and characterized. The DFT study of these bisylides has allowed for the characterization of strong intramolecular PO and AsO interactions, as well as moderate CHO[double bond, length as m-dash]C hydrogen bonds as the source of these conformational preferences. The third topic is related to the amazing reactivity of phosphorus ylides in bond activation processes. Depending on the nature of the metallic precursors, ylides can behave as sources of carbenes, of phosphine derivatives, of other ylides or of orthometallated complexes through P[double bond, length as m-dash]C, P-C or C-H bond activation reactions.

Synergistic oxygen atom transfer by ruthenium complexes with non-redox metal ions.

PubMed

Lv, Zhanao; Zheng, Wenrui; Chen, Zhuqi; Tang, Zhiming; Mo, Wanling; Yin, Guochuan

2016-07-28

Non-redox metal ions can affect the reactivity of active redox metal ions in versatile biological and heterogeneous oxidation processes; however, the intrinsic roles of these non-redox ions still remain elusive. This work demonstrates the first example of the use of non-redox metal ions as Lewis acids to sharply improve the catalytic oxygen atom transfer efficiency of a ruthenium complex bearing the classic 2,2'-bipyridine ligand. In the absence of Lewis acid, the oxidation of ruthenium(ii) complex by PhI(OAc)2 generates the Ru(iv)[double bond, length as m-dash]O species, which is very sluggish for olefin epoxidation. When Ru(bpy)2Cl2 was tested as a catalyst alone, only 21.2% of cyclooctene was converted, and the yield of 1,2-epoxycyclooctane was only 6.7%. As evidenced by electronic absorption spectra and EPR studies, both the oxidation of Ru(ii) by PhI(OAc)2 and the reduction of Ru(iv)[double bond, length as m-dash]O by olefin are kinetically slow. However, adding non-redox metal ions such as Al(iii) can sharply improve the oxygen transfer efficiency of the catalyst to 100% conversion with 89.9% yield of epoxide under identical conditions. Through various spectroscopic characterizations, an adduct of Ru(iv)[double bond, length as m-dash]O with Al(iii), Ru(iv)[double bond, length as m-dash]O/Al(iii), was proposed to serve as the active species for epoxidation, which in turn generated a Ru(iii)-O-Ru(iii) dimer as the reduced form. In particular, both the oxygen transfer from Ru(iv)[double bond, length as m-dash]O/Al(iii) to olefin and the oxidation of Ru(iii)-O-Ru(iii) back to the active Ru(iv)[double bond, length as m-dash]O/Al(iii) species in the catalytic cycle can be remarkably accelerated by adding a non-redox metal, such as Al(iii). These results have important implications for the role played by non-redox metal ions in catalytic oxidation at redox metal centers as well as for the understanding of the redox mechanism of ruthenium catalysts in the oxygen atom transfer reaction.

Research on Anchorage Performance of Grouting Anchor Connection of Precast Concrete Structure

NASA Astrophysics Data System (ADS)

Wang, Donghui; Liu, Xudong; Wang, Sheng; Cao, Xixi

2018-03-01

The bonding of grouted anchor bars is one of the vertical connection forms of steel bars in fabricated concrete structures. The performance of grouted connection is mainly affected by the anchorage length and lap length of steel bars. The mechanisms of bond and anchorage between steel bar and concrete are analyzed, and the factors that influence the anchorage performance of steel bar are systematically summarized. Results show that the bond and anchorage performance of steel and concrete have been studied widely, but there are still shortcomings, and the connection forms need to be further improved.

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.

Investigation of field corrosion performance and bond/development length of galvanized reinforcing steel : [tech transfer summary].

DOT National Transportation Integrated Search

2014-12-01

In reinforced concrete systems, ensuring that a good bond between the : concrete and the embedded reinforcing steel is critical to long-term structural : performance. Without good bond between the two, the system simply cannot : behave as intended. :...

Investigation of field corrosion performance and bond/development length of galvanized reinforcing steel.

DOT National Transportation Integrated Search

2014-12-01

In reinforced concrete systems, ensuring that a good bond between the concrete and the embedded reinforcing steel is critical to : long-term structural performance. Without good bond between the two, the system simply cannot behave as intended. The b...

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...

Stability and electronic structure of the low- Σ grain boundaries in CdTe: a density functional study

DOE PAGES

Park, Ji-Sang; Kang, Joongoo; Yang, Ji-Hui; ...

2015-01-15

Using first-principles density functional calculations, we investigate the relative stability and electronic structure of the grain boundaries (GBs) in zinc-blende CdTe. Among the low-Σ-value symmetric tilt Σ3 (111), Σ3 (112), Σ5 (120), and Σ5 (130) GBs, we show that the Σ3 (111)GB is always the most stable due to the absence of dangling bonds and wrong bonds. The Σ5 (120) GBs, however, are shown to be more stable than the Σ3 (112) GBs, even though the former has a higher Σ value, and the latter is often used as a model system to study GB effects in zinc-blende semiconductors. Furthermore,more » we find that although containing wrong bonds, the Σ5 (120) GBs are electrically benign due to the short wrong bond lengths, and thus are not as harmful as the Σ3 (112) GBs also having wrong bonds but with longer bond lengths.« less

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

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.

CCSDT calculations of molecular equilibrium geometries

NASA Astrophysics Data System (ADS)

Halkier, Asger; Jørgensen, Poul; Gauss, Jürgen; Helgaker, Trygve

1997-08-01

CCSDT equilibrium geometries of CO, CH 2, F 2, HF, H 2O and N 2 have been calculated using the correlation-consistent cc-pVXZ basis sets. Similar calculations have been performed for SCF, CCSD and CCSD(T). In general, bond lengths decrease when improving the basis set and increase when improving the N-electron treatment. CCSD(T) provides an excellent approximation to CCSDT for bond lengths as the largest difference between CCSDT and CCSD(T) is 0.06 pm. At the CCSDT/cc-pVQZ level, basis set deficiencies, neglect of higher-order excitations, and incomplete treatment of core-correlation all give rise to errors of a few tenths of a pm, but to a large extent, these errors cancel. The CCSDT/cc-pVQZ bond lengths deviate on average only by 0.11 pm from experiment.

Dental plaque microcosm response to bonding agents containing quaternary ammonium methacrylates with different chain lengths and charge densities

PubMed Central

Zhou, Han; Li, Fang; Weir, Michael D.; Xu, Hockin H.K.

2013-01-01

Objectives Antibacterial bonding agents are promising to combat bacteria and caries at tooth-restoration margins. The objectives of this study were to incorporate new quaternary ammonium methacrylates (QAMs) to bonding agent and determine the effects of alkyl chain length (CL) and quaternary amine charge density on dental plaque microcosm bacteria response for the first time. Methods Six QAMs were synthesized with CL = 3, 6, 9, 12, 16, 18. Each QAM was incorporated into Scotchbond Multi-purpose (SBMP). To determine the charge density effect, dimethylaminododecyl methacrylate (DMAHDM, CL = 16) was mixed into SBMP at mass fraction = 0%, 2.5%, 5%, 7.5%, 10%. Charge density was measured using a fluorescein dye method. Dental plaque microcosm using saliva from ten donors was tested. Bacteria were inoculated on resins. Early-attachment was tested at 4 hours. Biofilm colony-forming units (CFU) were measured at 2 days. Results Incorporating QAMs into SBMP reduced bacteria early-attachment. Microcosm biofilm CFU for CL = 16 was 4 log lower than SBMP control. Charge density of bonding agent increased with DMAHDM content. Bacteria early-attachment decreased with increasing charge density. Biofilm CFU at 10% DMAHDM was reduced by 4 log. The killing effect was similarly-strong against total microorganisms, total streptococci, and mutans streptococci. Conclusions Increasing alkyl chain length and charge density of bonding agent was shown for the first time to decrease microcosm bacteria attachment and reduce biofilm CFU by 4 orders of magnitude. Novel antibacterial resins with tailored chain length and charge density are promising for wide applications in bonding, cements, sealants and composites to inhibit biofilms and caries. PMID:23948394

A QM/MM study of the initial excited state dynamics of green-absorbing proteorhodopsin.

PubMed

Borin, Veniamin A; Wiebeler, Christian; Schapiro, Igor

2018-04-17

The primary photochemical reaction of the green-absorbing proteorhodopsin is studied by means of a hybrid quantum mechanics/molecular mechanics (QM/MM) approach. The simulations are based on a homology model derived from the blue-absorbing proteorhodopsin crystal structure. The geometry of retinal and the surrounding sidechains in the protein binding pocket were optimized using the QM/MM method. Starting from this geometry the isomerization was studied with a relaxed scan along the C13[double bond, length as m-dash]C14 dihedral. It revealed an "aborted bicycle pedal" mechanism of isomerization that was originally proposed by Warshel for bovine rhodopsin and bacteriorhodopsin. However, the isomerization involved the concerted rotation about C13[double bond, length as m-dash]C14 and C15[double bond, length as m-dash]N, with the latter being highly twisted but not isomerized. Further, the simulation showed an increased steric interaction between the hydrogen at the C14 of the isomerizing bond and the hydroxyl group at the neighbouring tyrosine 200. In addition, we have simulated a nonadiabatic trajectory which showed the timing of the isomerization. In the first 20 fs upon excitation the order of the conjugated double and single bonds is inverted, consecutively the C13[double bond, length as m-dash]C14 rotation is activated for 200 fs until the S1-S0 transition is detected. However, the isomerization is reverted due to the specific interaction with the tyrosine as observed along the relaxed scan calculation. Our simulations indicate that the retinal - tyrosine 200 interaction plays an important role in the outcome of the photoisomerization.

Dental plaque microcosm response to bonding agents containing quaternary ammonium methacrylates with different chain lengths and charge densities.

PubMed

Zhou, Han; Li, Fang; Weir, Michael D; Xu, Hockin H K

2013-11-01

Antibacterial bonding agents are promising to combat bacteria and caries at tooth-restoration margins. The objectives of this study were to incorporate new quaternary ammonium methacrylates (QAMs) to bonding agent and determine the effects of alkyl chain length (CL) and quaternary amine charge density on dental plaque microcosm bacteria response for the first time. Six QAMs were synthesized with CL=3, 6, 9, 12, 16, 18. Each QAM was incorporated into Scotchbond multi-purpose (SBMP). To determine the charge density effect, dimethylaminododecyl methacrylate (DMAHDM, CL=16) was mixed into SBMP at mass fraction=0%, 2.5%, 5%, 7.5%, 10%. Charge density was measured using a fluorescein dye method. Dental plaque microcosm using saliva from ten donors was tested. Bacteria were inoculated on resins. Early-attachment was tested at 4h. Biofilm colony-forming units (CFU) were measured at 2 days. Incorporating QAMs into SBMP reduced bacteria early-attachment. Microcosm biofilm CFU for CL=16 was 4 log lower than SBMP control. Charge density of bonding agent increased with DMAHDM content. Bacteria early-attachment decreased with increasing charge density. Biofilm CFU at 10% DMAHDM was reduced by 4 log. The killing effect was similarly-strong against total microorganisms, total streptococci, and mutans streptococci. Increasing alkyl chain length and charge density of bonding agent was shown for the first time to decrease microcosm bacteria attachment and reduce biofilm CFU by 4 orders of magnitude. Novel antibacterial resins with tailored chain length and charge density are promising for wide applications in bonding, cements, sealants and composites to inhibit biofilms and caries. Copyright © 2013 Elsevier Ltd. All rights reserved.

A theoretical perspective of the nature of hydrogen-bond types - the atoms in molecules approach

NASA Astrophysics Data System (ADS)

Vijaya Pandiyan, B.; Kolandaivel, P.; Deepa, P.

2014-06-01

Hydrogen bonds and their strength were analysed based on their X-H proton-donor bond properties and the parameters of the H-Y distance (Y proton acceptor). Strong, moderate and weak interactions in hydrogen-bond types were verified through the proton affinities of bases (PA), deprotanation enthalpies of acids (DPE) and the chemical shift (σ). The aromaticity and anti-aromaticity were analysed by means of the NICS (0) (nucleus-independent chemical shift), NICS (1) and ΔNICS (0), ΔNICS (1) of hydrogen-bonded molecules. The strength of a hydrogen bond depends on the capacity of hydrogen atom engrossing into the electronegative acceptor atom. The correlation between the above parameters and their relations were discussed through curve fitting. Bader's theory of atoms in molecules has been applied to estimate the occurrence of hydrogen bonds through eight criteria reported by Popelier et al. The lengths and potential energy shifts have been found to have a strong negative linear correlation, whereas the lengths and Laplacian shifts have a strong positive linear correlation. This study illustrates the common factors responsible for strong, moderate and weak interactions in hydrogen-bond types.

Relativistic Corrections to the Properties of the Alkali Fluorides

NASA Technical Reports Server (NTRS)

Dyall, Kenneth G.; Partridge, Harry

1993-01-01

Relativistic corrections to the bond lengths, dissociation energies and harmonic frequencies of KF, RbF and CsF have been obtained at the self-consistent field level by dissociating to ions. The relativistic corrections to the bond lengths, harmonic frequencies and dissociation energies to the ions are very small, due to the ionic nature of these molecules and the similarity of the relativistic and nonrelativistic ionic radii.

Optoelectronic tuning of organoborylazadipyrromethenes via effective electronegativity at the metalloid center.

PubMed

Berhe, Seare A; Rodriguez, Marco T; Park, Eunsol; Nesterov, Vladimir N; Pan, Hongjun; Youngblood, W Justin

2014-03-03

Organoborylazadipyrromethenes were synthesized from free base and fluoroborylazadipyrromethenes and characterized with regard to their structural and electronic properties. B-N bond lengths, along with photophysical and redox behavior, appear dependent on the effective electronegativity at the boron atom as tuned by its substituents, with stronger electronegativity correlating to a shorter B-N bond length, red-shifted absorbance, enhanced fluorescence lifetime and yield, and positively shifted redox potentials.

Molecular mechanism of gelation upon the addition of water to a solution of poly(acrylonitrile) in dimethylsulfoxide

NASA Astrophysics Data System (ADS)

Vettegren, V. I.; Kulik, V. B.; Savitskii, A. V.; Fetisov, O. I.; Usov, V. V.

2010-05-01

The solidification of a solution of poly(acrylonitrile) (PAN) in dimethylsulfoxide (DMSO) upon introduction of water into the solution is studied by Raman spectroscopy. In the absence of water, DMSO molecules are found to produce dipole-dipole bonds with PAN molecules. Upon the introduction of water, DMSO molecules produce hydrogen bonds with it and bands at 1005 and 1015 cm-1 appear in the Raman spectrum, which are assigned to the valence vibrations of S=O bonds involved in the hydrogen bonds. Simultaneously, water molecules produce hydrogen bonds with PAN molecules: R-C≡N...H-O-H...N≡C-R, where R is the carbon skeleton of a PAN molecule. Accordingly, a band at 2250 cm-1 arises in the Raman spectrum, which is assigned to the valence vibrations of C≡N bonds producing hydrogen bonds with a water molecule. When the water content is low and the DMSO concentration is high, the length of the hydrogen bonds varies in wide limits and the band at 2250 cm-1 is wide. As the water content rises, DMSO molecules come out of PAN, the variation of the hydrogen bond length in it decreases (the band at 2250 cm-1 narrows), and a high-viscosity system (gel) arises that consists of PAN molecules bonded to water molecules via “equally strong” hydrogen bonds.

3-Methyl-4,5-di­hydro­oxazolium tetra­phenyl­borate

PubMed Central

Tiritiris, Ioannis; Saur, Stefan; Kantlehner, Willi

2014-01-01

In the cation of the title salt, C4H8NO+·C24H20B−, the C—N bond lengths are 1.272 (2), 1.4557 (19) and 1.4638 (19) Å, indicating double- and single-bond character, respectively. The C—O bond length of 1.3098 (19) Å shows that double-bond character and charge delocalization occurs within the NCO plane of the cation. In the crystal, a C—H⋯π inter­action is present between the methyl­ene H atom of the cation and one phenyl ring of the tetra­phenyl­borate ion. The latter forms an aromatic pocket in which the cation is embedded. PMID:24765023

Crystal structure of (1-eth­oxy­ethyl­idene)di­methyl­aza­nium tetra­phenyl­borate

PubMed Central

Tiritiris, Ioannis; Saur, Stefan; Kantlehner, Willi

2015-01-01

In the cation of the title salt, C6H14NO+·C24H20B−, the C—N bond lengths are 1.297 (2), 1.464 (2) and 1.468 (2) Å, indicating double- and single-bond character, respectively. The C—O bond length of 1.309 (2) Å shows double-bond character, pointing towards charge delocalization within the NCO plane of the iminium ion. In the crystal, C—H⋯π inter­actions between the iminium H atoms and the phenyl C atoms of the anion are present. The phenyl rings form aromatic pockets, in which the iminium ions are embedded. PMID:26870564

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

NDT evaluation of long-term bond durability of CFRP-structural systems applied to RC highway bridges

NASA Astrophysics Data System (ADS)

Crawford, Kenneth C.

2016-06-01

The long-term durability of CFRP structural systems applied to reinforced-concrete (RC) highway bridges is a function of the system bond behavior over time. The sustained structural load performance of strengthened bridges depends on the carbon fiber-reinforced polymer (CFRP) laminates remaining 100 % bonded to concrete bridge members. Periodic testing of the CFRP-concrete bond condition is necessary to sustain load performance. The objective of this paper is to present a non-destructive testing (NDT) method designed to evaluate the bond condition and long-term durability of CFRP laminate (plate) systems applied to RC highway bridges. Using the impact-echo principle, a mobile mechanical device using light impact hammers moving along the length of a bonded CFRP plate produces unique acoustic frequencies which are a function of existing CFRP plate-concrete bond conditions. The purpose of this method is to test and locate CFRP plates de-bonded from bridge structural members to identify associated deterioration in bridge load performance. Laboratory tests of this NDT device on a CFRP plate bonded to concrete with staged voids (de-laminations) produced different frequencies for bonded and de-bonded areas of the plate. The spectra (bands) of frequencies obtained in these tests show a correlation to the CFRP-concrete bond condition and identify bonded and de-bonded areas of the plate. The results of these tests indicate that this NDT impact machine, with design improvements, can potentially provide bridge engineers a means to rapidly evaluate long lengths of CFRP laminates applied to multiple highway bridges within a national transportation infrastructure.

Analytical energy gradient for the two-component normalized elimination of the small component method

NASA Astrophysics Data System (ADS)

Zou, Wenli; Filatov, Michael; Cremer, Dieter

2015-06-01

The analytical gradient for the two-component Normalized Elimination of the Small Component (2c-NESC) method is presented. The 2c-NESC is a Dirac-exact method that employs the exact two-component one-electron Hamiltonian and thus leads to exact Dirac spin-orbit (SO) splittings for one-electron atoms. For many-electron atoms and molecules, the effect of the two-electron SO interaction is modeled by a screened nucleus potential using effective nuclear charges as proposed by Boettger [Phys. Rev. B 62, 7809 (2000)]. The effect of spin-orbit coupling (SOC) on molecular geometries is analyzed utilizing the properties of the frontier orbitals and calculated SO couplings. It is shown that bond lengths can either be lengthened or shortened under the impact of SOC where in the first case the influence of low lying excited states with occupied antibonding orbitals plays a role and in the second case the jj-coupling between occupied antibonding and unoccupied bonding orbitals dominates. In general, the effect of SOC on bond lengths is relatively small (≤5% of the scalar relativistic changes in the bond length). However, large effects are found for van der Waals complexes Hg2 and Cn2, which are due to the admixture of more bonding character to the highest occupied spinors.

Influence of anatomical, physical, and mechanical properties of diffuse-porous hardwoods on moisture durability of bonded assemblies

Treesearch

Daniel J. Yelle; Ashley M. Stirgus

2016-01-01

Studying wood adhesive bond durability is challenging because wood is highly variable and heterogeneous at all length scales. In this study, three North American diffuse-porous hardwoods (hard maple, soft maple, and basswood) and their adhesively bonded as-semblies were exposed to wet and dry cyclic tests. Then, their den-sity differences were related to bond...

Bonded Radii and the Contraction of the Electron Density of the Oxygen Atom by Bonded Interactions

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

Gibbs, Gerald V.; Ross, Nancy L.; Cox, David F.

2013-02-21

The bonded radii for more than 550 bonded pairs of atoms, comprising more than 50 crystals, determined from experimental and theoretical electron density distributions, are compared with the effective ionic, ri(M), and crystal radii, rc(M), for metal atoms, M, bonded to O atoms. At odds with the fixed ionic radius of 1.40 Å, assumed for the O atom in the compilation of the ionic radii, the bonded radius for the atom, rb(O), is not fixed but displays a relatively wide range of values as the O atom is progressively polarized by the M-O bonded interactions: as such, rb(O) decreases systematicallymore » from 1.40 Å (the Pauling radius of the oxide anion) as bond lengths decrease when bonded to an electropositive atom like sodium, to 0.64 Å (Bragg’s atomic radius of the O atom) when bonded to an electronegative atom like nitrogen. Both rb(M) and rb(O) increase in tandum with the increasing coordination number of the M atom. The bonded radii of the M atoms are highly correlated with both ri(M) and rc(M), but they both depart systematically from rb(M) and become smaller as the electronegativity of the M atom increases and the M-O bond length decreases. The well-developed correlations between both sets of radii and rb(M) testifies to the relative precision of both sets of radii and the fact that both sets are highly correlated the M-O bond 1 lengths. On the other hand, the progressive departure of rb(O) from the fixed ionic radius of the O atom with the increasing electronegativity of the bonded M atom indicates that any compilation of sets of ionic radii, assuming that the radius for the oxygen atom is fixed in value, is problematical and impacts on the accuracy of the resulting sets of ionic and crystal radii thus compiled. The assumption of a fixed O atom radius not only results in a negative ionic radii for several atoms, but it also results in values of rb(M) that are much as ~ 0.6 Å larger than the ri(M) and rc(M) values, respectively, particularly for the more electronegative M atoms. On the other hand, the ionic radii are in closer agreement with rb(M) for the more electropositive atoms. Notwithstanding that ionic radii are typically smaller than bonded radii, particularly for the more electronegative atoms, they have been used with considerable success in understanding and rationalizing problems and properties in crystal chemistry primarily because both ionic and crystal radii are highly correlated on a one-to-one basis with both the bonded radii and the associated M-O bond lengths. The lack of agreement between the effective ionic and crystal radii and the bonded radii for the more shared bonded interactions is ascribed to the progressive increase in the polarization of the O atom by the bonded atoms with a concomitant decrease in its radius, a factor that was neglected in the compilation of ionic and crystal radii for fluorides, oxides, sulfides and nitrides. This accounts for ionic radii for these materials being smaller than the bonded radii for the more electronegative atoms.« less

Temperature and composition dependence of short-range order and entropy, and statistics of bond length: the semiconductor alloy (GaN)(1-x)(ZnO)(x).

PubMed

Liu, Jian; Pedroza, Luana S; Misch, Carissa; Fernández-Serra, Maria V; Allen, Philip B

2014-07-09

We present total energy and force calculations for the (GaN)1-x(ZnO)x alloy. Site-occupancy configurations are generated from Monte Carlo (MC) simulations, on the basis of a cluster expansion model proposed in a previous study. Local atomic coordinate relaxations of surprisingly large magnitude are found via density-functional calculations using a 432-atom periodic supercell, for three representative configurations at x = 0.5. These are used to generate bond-length distributions. The configurationally averaged composition- and temperature-dependent short-range order (SRO) parameters of the alloys are discussed. The entropy is approximated in terms of pair distribution statistics and thus related to SRO parameters. This approximate entropy is compared with accurate numerical values from MC simulations. An empirical model for the dependence of the bond length on the local chemical environments is proposed.

Quantitative structure activity relationships from optimised ab initio bond lengths: steroid binding affinity and antibacterial activity of nitrofuran derivatives

NASA Astrophysics Data System (ADS)

Smith, P. J.; Popelier, P. L. A.

2004-02-01

The present day abundance of cheap computing power enables the use of quantum chemical ab initio data in Quantitative Structure-Activity Relationships (QSARs). Optimised bond lengths are a new such class of descriptors, which we have successfully used previously in representing electronic effects in medicinal and ecological QSARs (enzyme inhibitory activity, hydrolysis rate constants and pKas). Here we use AM1 and HF/3-21G* bond lengths in conjunction with Partial Least Squares (PLS) and a Genetic Algorithm (GA) to predict the Corticosteroid-Binding Globulin (CBG) binding activity of the classic steroid data set, and the antibacterial activity of nitrofuran derivatives. The current procedure, which does not require molecular alignment, produces good r2 and q2 values. Moreover, it highlights regions in the common steroid skeleton deemed relevant to the active regions of the steroids and nitrofuran derivatives.

Investigation of heat transfer and material flow of P-FSSW: Experimental and numerical study

NASA Astrophysics Data System (ADS)

Rezazadeh, Niki; Mosavizadeh, Seyed Mostafa; Azizi, Hamed

2018-02-01

Friction stir spot welding (FSSW) is the joining process which utilizes a rotating tool consisting of a shoulder and/or a probe. In this study, the novel method of FSSW, which is called protrusion friction stir spot welding (P-FSSW), has been presented and effect of shoulder diameter parameter has been studied numerically and experimentally on the weld quality including temperature field, velocity contour, material flow, bonding length, and the depth of the stirred area. The results show that the numerical findings are in good agreement with experimental measurements. The present model could well predict the temperature distribution, velocity contour, depth of the stirred area, and the bonding length. As the shoulder diameter increases, the amount of temperature rises which leads to a rise in stirred area depth, bonding length and temperatures and velocities. Therefore, a weld of higher quality will be performed.

Reductive transformation of V(iii) precursors into vanadium(ii) oxide nanowires.

PubMed

Ojelere, Olusola; Graf, David; Ludwig, Tim; Vogt, Nicholas; Klein, Axel; Mathur, Sanjay

2018-05-15

Vanadium(ii) oxide nanostructures are promising materials for supercapacitors and electrocatalysis because of their excellent electrochemical properties and high surface area. In this study, new homoleptic vanadium(iii) complexes with bi-dentate O,N-chelating heteroarylalkenol ligands (DmoxCH[double bond, length as m-dash]COCF3, PyCH[double bond, length as m-dash]COCF3 and PyN[double bond, length as m-dash]COCF3) were synthesized and successfully transformed by reductive conversion into VO nanowires. The chemical identity of V(iii) complexes and their redox behaviour were unambiguously established by single crystal X-ray diffraction studies, cyclic voltammetry, spectrometric studies and DFT calculations. Transformation into the metastable VO phase was verified by powder X-ray diffraction and thermo-gravimetry. Transmission electron microscopy and X-ray photoelectron spectroscopy data confirmed the morphology and chemical composition of VO nanostructures, respectively.

Linear free-energy relationships between a single gas-phase ab initio equilibrium bond length and experimental pKa values in aqueous solution.

PubMed

Alkorta, Ibon; Popelier, Paul L A

2015-02-02

Remarkably simple yet effective linear free energy relationships were discovered between a single ab initio computed bond length in the gas phase and experimental pKa values in aqueous solution. The formation of these relationships is driven by chemical features such as functional groups, meta/para substitution and tautomerism. The high structural content of the ab initio bond length makes a given data set essentially divide itself into high correlation subsets (HCSs). Surprisingly, all molecules in a given high correlation subset share the same conformation in the gas phase. Here we show that accurate pKa values can be predicted from such HCSs. This is achieved within an accuracy of 0.2 pKa units for 5 drug molecules. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Vibrational studies of phosphoryl transfer enzymes: ras- p21(*)magnesium-GTP and Myosin S1(*)magnesium-ADP- vanadate

NASA Astrophysics Data System (ADS)

Wang, Jianghua

1999-07-01

We have measured the Raman spectra of monophosphate compounds in aqueous solution. The measured frequencies were correlated with P••O valence bond order by using a modification of the Hardcastle- Wachs procedure. The P••O bond order and bond length in phosphates can be determined from vibrational spectra by using the derived bond order/stretching frequency correlation and the bond length/bond order correlation of Brown and Wu. The Raman and infrared spectra of guanosine 5'-diphosphate (GDP) and guanosine 5'-triphosphate (GTP) in aqueous solution were also examined. Frequency shifts were observed as Mg2+ complexes with GDP and GTP in aqueous solution. These results suggested that Mg2+ binds to GDP in a bidentate manner to the α,β P••O bonds and in a tridentate manner to the α,β and γ P••O bonds of Mg•GTP . We have analyzed the previously obtained isotope edited Raman difference spectra of 1:1 complexes of Mg•GDP and Mg•GTP in ras-p21. Frequency changes of the phosphate groups were observed when Mg•GDP , Mg•GTP bind to the protein. Employing both the previous empirical relationships between bond orders/lengths and frequencies as well as vibrational analysis from ab initio calculations, the spectral changes can be explained by the change of the Mg2+ binding sites and hydrogen-bonding. Implications of these structural results for the reaction mechanism of GTP hydrolysis catalyzed by the GTPase are discussed. We have analyzed previously obtained isotope edited Raman difference spectra of the non-bridging V••O bonds of vanadates, both in solution, and when bound to the myosin S1•MgADP complex. By use of ab initio calculations on a model of the vanadate binding site in myosin, the angles between the non-bridging V••O bonds and between these bonds and the apical bonds in the myosin S1•MgADP -Vi complex were determined. The summed bond order of the two apical bonds between the attacking and leaving group oxygens with the central vanadium ion in the S1•MgADP -Vi complex was found to increase only slightly compared with the bond order of the ester V-O bond of a monoester vanadate model compound in solution, suggesting an SN2 like mechanism for the phosphoryl transfer reaction catalyzed by myosin.

Bonding thermoplastic polymers

DOEpatents

Wallow, Thomas I [Fremont, CA; Hunter, Marion C [Livermore, CA; Krafcik, Karen Lee [Livermore, CA; Morales, Alfredo M [Livermore, CA; Simmons, Blake A [San Francisco, CA; Domeier, Linda A [Danville, CA

2008-06-24

We demonstrate a new method for joining patterned thermoplastic parts into layered structures. The method takes advantage of case-II permeant diffusion to generate dimensionally controlled, activated bonding layers at the surfaces being joined. It is capable of producing bonds characterized by cohesive failure while preserving the fidelity of patterned features in the bonding surfaces. This approach is uniquely suited to production of microfluidic multilayer structures, as it allows the bond-forming interface between plastic parts to be precisely manipulated at micrometer length scales. The bond enhancing procedure is easily integrated in standard process flows and requires no specialized equipment.

Quadratic elongation: A quantitative measure of distortion in coordination polyhedra

USGS Publications Warehouse

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

1971-01-01

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

Vibrational states and optical transitions in hydrogen bonds

NASA Astrophysics Data System (ADS)

Johannsen, P. G.

1998-03-01

Proton energies in hydrogen bonds are mostly calculated using a double Morse potential (the DMP model). This form, however, does not reproduce the experimentally observed correlation between the proton stretching frequency and the bond length in an extended bond-length region sufficiently well. An alternative potential is proposed in the present paper. The quantum states of this non-symmetric double-well potential are calculated numerically using the Numerov (Fox-Goodwin) algorithm. It is shown that the optical spectra of hydrogen bonds in various substances can be well approximated on the basis of the transition frequencies and intensities predicted by the present model. For weakly interacting OH impurities in 0953-8984/10/10/008/img1, the overtone spectrum and line intensities are well reproduced, whereas the line broadenings and the decrease of the fundamental stretching frequencies in intermediate and strong hydrogen bonds are traced back to the influence of the reduced height of the central barrier. The model is also extrapolated to the range of symmetric hydrogen bonds, and the calculated transition frequencies are discussed with respect to most recent infra-red experiments on ice under strong compression. A possible artificial infra-red signal from strained diamond anvils is thereby noted.

pKa prediction from an ab initio bond length: part 3--benzoic acids and anilines.

PubMed

Harding, A P; Popelier, P L A

2011-06-21

The prediction of pK(a) from a single ab initio bond length has been extended to provide equations for benzoic acids and anilines. The HF/6-31G(d) level of theory is used for all geometry optimisations. Similarly to phenols (Part 2 of this series of publications), the meta-/para-substituted benzoic acids can be predicted from a single model constructed from one bond length. This model had an impressive RMSEP of 0.13 pK(a) units. The prediction of ortho-substituted benzoic acids required the identification of high-correlation subsets, where the compounds in the same subset have at least one of the same (e.g. halogens, hydroxy) ortho substituent. Two pK(a) equations are provided for o-halogen benzoic acids and o-hydroxybenzoic acids, where the RMSEP values are 0.19 and 0.15 pK(a) units, respectively. Interestingly, the bond length that provided the best model differed between these two high-correlation subsets. This demonstrates the importance of investigating the most predictive bond length, which is not necessarily the bond involving the acid hydrogen. Three high-correlation subsets were identified for the ortho-substituted anilines. These were o-halogen, o-nitro and o-alkyl-substituted aniline high-correlation subsets, where the RMSEP ranged from 0.23 to 0.44 pK(a) units. The RMSEP for the meta-/para-substituted aniline model was 0.54 pK(a) units. This value exceeded our threshold of 0.50 pK(a) units and was higher than both the m-/p-benzoic acids in this work and the m-/p-phenols (RMSEP = 0.43) of Part 2. Constructing two separate models for the meta- and para- substituted anilines, where RMSEP values of 0.63 and 0.33 pK(a) units were obtained respectively, revealed it was the meta-substituted anilines that caused the large RMSEP value. For unknown reasons the RMSEP value increased with the addition of a further twenty meta-substituted anilines to this model. The C-N bond always produced the best correlations with pK(a) for all the high-correlation subsets. A higher level of theory and an ammonia probe improved the statistics only marginally for the hydroxybenzoic acid high-correlation subsets.

Computations and estimates of rate coefficients for hydrocarbon reactions of interest to the atmospheres of outer solar system

NASA Technical Reports Server (NTRS)

Laufer, A. H.; Gardner, E. P.; Kwok, T. L.; Yung, Y. L.

1983-01-01

The rate coefficients, including Arrhenius parameters, have been computed for a number of chemical reactions involving hydrocarbon species for which experimental data are not available and which are important in planetary atmospheric models. The techniques used to calculate the kinetic parameters include the Troe and semiempirical bond energy-bond order (BEBO) or bond strength-bond length (BSBL) methods.

Correlation of bond strength with surface roughness using a new roughness measurement technique.

PubMed

Winkler, M M; Moore, B K

1994-07-01

The correlation between shear bond strength and surface roughness was investigated using new surface measurement methods. Bonding agents and associated resin composites were applied to set amalgam after mechanically roughening its surface. Surface treatments were noe (as set against glass), 80 grit, and 600 grit abrasive paper. Surface roughness (R(a) as measured parallel and perpendicular (+) to the direction of the polishing scratches and true profile length were measured. A knife-edge was applied (rate = 2.54 mm/min) at the bonding agent/amalgam interface of each sample until failure. Coefficients of determination for mean bond strength vs either roughness (R(a), of profile length were significantly higher for measurements in parallel directions than for those measurements in (+) directions. The shear bond strength to set amalgam for a PENTA-containing adhesives system (L.D. Caulk Division) was not significantly different from that of a PENTA-free adhesive (3M Dental Products Division), even though PENTA has been reported to increase bond strength to nonprecious metals. The shear bond strength of resin composite to amalgam is correlated to surface roughness when it is measured parallel to the polishing scratches. This correlation is significantly lower when surface roughness is measured in the typical manner, perpendicular to the polishing scratches.

Bond breaking in epoxy systems: A combined QM/MM approach

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

Barr, Stephen A.; Ecker, Allison M.; Berry, Rajiv J., E-mail: Rajiv.Berry@us.af.mil

2016-06-28

A novel method to combine quantum mechanics (QM) and molecular mechanics has been developed to accurately and efficiently account for covalent bond breaking in polymer systems under high strain without the use of predetermined break locations. Use of this method will provide a better fundamental understanding of the mechano-chemical origins of fracture in thermosets. Since classical force fields cannot accurately account for bond breaking, and QM is too demanding to simulate large systems, a hybrid approach is required. In the method presented here, strain is applied to the system using a classical force field, and all bond lengths are monitored.more » When a bond is stretched past a threshold value, a zone surrounding the bond is used in a QM energy minimization to determine which, if any, bonds break. The QM results are then used to reconstitute the system to continue the classical simulation at progressively larger strain until another QM calculation is triggered. In this way, a QM calculation is only computed when and where needed, allowing for efficient simulations. A robust QM method for energy minimization has been determined, as well as appropriate values for the QM zone size and the threshold bond length. Compute times do not differ dramatically from classical molecular mechanical simulations.« less

Zn Coordination Chemistry:  Development of Benchmark Suites for Geometries, Dipole Moments, and Bond Dissociation Energies and Their Use To Test and Validate Density Functionals and Molecular Orbital Theory.

PubMed

Amin, Elizabeth A; Truhlar, Donald G

2008-01-01

We present nonrelativistic and relativistic benchmark databases (obtained by coupled cluster calculations) of 10 Zn-ligand bond distances, 8 dipole moments, and 12 bond dissociation energies in Zn coordination compounds with O, S, NH3, H2O, OH, SCH3, and H ligands. These are used to test the predictions of 39 density functionals, Hartree-Fock theory, and seven more approximate molecular orbital theories. In the nonrelativisitic case, the M05-2X, B97-2, and mPW1PW functionals emerge as the most accurate ones for this test data, with unitless balanced mean unsigned errors (BMUEs) of 0.33, 0.38, and 0.43, respectively. The best local functionals (i.e., functionals with no Hartree-Fock exchange) are M06-L and τ-HCTH with BMUEs of 0.54 and 0.60, respectively. The popular B3LYP functional has a BMUE of 0.51, only slightly better than the value of 0.54 for the best local functional, which is less expensive. Hartree-Fock theory itself has a BMUE of 1.22. The M05-2X functional has a mean unsigned error of 0.008 Å for bond lengths, 0.19 D for dipole moments, and 4.30 kcal/mol for bond energies. The X3LYP functional has a smaller mean unsigned error (0.007 Å) for bond lengths but has mean unsigned errors of 0.43 D for dipole moments and 5.6 kcal/mol for bond energies. The M06-2X functional has a smaller mean unsigned error (3.3 kcal/mol) for bond energies but has mean unsigned errors of 0.017 Å for bond lengths and 0.37 D for dipole moments. The best of the semiempirical molecular orbital theories are PM3 and PM6, with BMUEs of 1.96 and 2.02, respectively. The ten most accurate functionals from the nonrelativistic benchmark analysis are then tested in relativistic calculations against new benchmarks obtained with coupled-cluster calculations and a relativistic effective core potential, resulting in M05-2X (BMUE = 0.895), PW6B95 (BMUE = 0.90), and B97-2 (BMUE = 0.93) as the top three functionals. We find significant relativistic effects (∼0.01 Å in bond lengths, ∼0.2 D in dipole moments, and ∼4 kcal/mol in Zn-ligand bond energies) that cannot be neglected for accurate modeling, but the same density functionals that do well in all-electron nonrelativistic calculations do well with relativistic effective core potentials. Although most tests are carried out with augmented polarized triple-ζ basis sets, we also carried out some tests with an augmented polarized double-ζ basis set, and we found, on average, that with the smaller basis set DFT has no loss in accuracy for dipole moments and only ∼10% less accurate bond lengths.

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.

Differential segregation in a cell-cell contact interface: the dynamics of the immunological synapse.

PubMed Central

Burroughs, Nigel John; Wülfing, Christoph

2002-01-01

Receptor-ligand couples in the cell-cell contact interface between a T cell and an antigen-presenting cell form distinct geometric patterns and undergo spatial rearrangement within the contact interface. Spatial segregation of the antigen and adhesion receptors occurs within seconds of contact, central aggregation of the antigen receptor then occurring over 1-5 min. This structure, called the immunological synapse, is becoming a paradigm for localized signaling. However, the mechanisms driving its formation, in particular spatial segregation, are currently not understood. With a reaction diffusion model incorporating thermodynamics, elasticity, and reaction kinetics, we examine the hypothesis that differing bond lengths (extracellular domain size) is the driving force behind molecular segregation. We derive two key conditions necessary for segregation: a thermodynamic criterion on the effective bond elasticity and a requirement for the seeding/nucleation of domains. Domains have a minimum length scale and will only spontaneously coalesce/aggregate if the contact area is small or the membrane relaxation distance large. Otherwise, differential attachment of receptors to the cytoskeleton is required for central aggregation. Our analysis indicates that differential bond lengths have a significant effect on synapse dynamics, i.e., there is a significant contribution to the free energy of the interaction, suggesting that segregation by differential bond length is important in cell-cell contact interfaces and the immunological synapse. PMID:12324401

Pressure-induced emission band separation of the hybridized local and charge transfer excited state in a TPE-based crystal.

PubMed

Liu, Xuedan; Li, Aisen; Xu, Weiqing; Ma, Zhiyong; Jia, Xinru

2018-05-08

We herein report a newly synthesized simple molecule, named TPE[double bond, length as m-dash]C4, with twisted D-A structure. TPE[double bond, length as m-dash]C4 showed two intrinsic emission bands ascribed to the locally excited (LE) state and the intramolecular charge transfer (ICT) state, respectively. In the crystal state, the LE emission band is usually observed. However, by applying hydrostatic pressure to the powder sample and the single crystal sample of TPE[double bond, length as m-dash]C4, dual-fluorescence (445 nm and 532 nm) was emerged under high pressure, owing to the pressure-induced emission band separation of the hybridized local and charge transfer excited state (HLCT). It is found that the emission of TPE[double bond, length as m-dash]C4 is generally determined by the ratio of the LE state to the ICT state. The ICT emission band is much more sensitive to the external pressure than the LE emission band. The HLCT state leads to a sample with different responsiveness to grinding and hydrostatic pressure. This study is of significance in the molecular design of such D-A type molecules and in the control of photoluminescence features by molecular structure. Such results are expected to pave a new way to further understand the relationship between the D-A molecular structure and stimuli-responsive properties.

Lattice effects on ferromagnetism in perovskite ruthenates

PubMed Central

Cheng, J.-G.; Zhou, J.-S.; Goodenough, John B.

2013-01-01

Ferromagnetism and its evolution in the orthorhombic perovskite system Sr1–xCaxRuO3 have been widely believed to correlate with structural distortion. The recent development of high-pressure synthesis of the Ba-substituted Sr1–yBayRuO3 makes it possible to study ferromagnetism over a broader phase diagram, which includes the orthorhombic Imma and the cubic phases. However, the chemical substitutions introduce the A-site disorder effect on Tc, which complicates determination of the relationship between ferromagnetism and structural distortion. By clarifying the site disorder effect on Tc in several unique series of ruthenates in which the average bond length 〈A–O〉 remains the same but the bond-length variance varies, we are able to demonstrate a parabolic curve of Tc versus mean bond length 〈A–O〉. A much higher Tc ∼ 177 K than that found in orthorhombic SrRuO3 can be obtained from the curve at a bond length 〈A–O〉, which makes the geometric factor t = 〈A–O〉/(√2〈Ru–O〉) ∼ 1. This result reveals not only that the ferromagnetism in the ruthenates is extremely sensitive to the lattice strain, but also that it has an important implication for exploring the structure–property relationship in a broad range of oxides with perovskite or a perovskite-related structure. PMID:23904477

(Meth­oxy­methyl­idene)di­methyl­aza­nium tetra­phenyl­borate aceto­nitrile monosolvate

PubMed Central

Tiritiris, Ioannis; Saur, Stefan; Kantlehner, Willi

2014-01-01

In the cation of the title salt, C4H10NO+·C24H20B−·C2H3N, the C—N bond lengths are 1.2864 (16), 1.4651 (17) and 1.4686 (16) Å, indicating double- and single-bond character, respectively. The C—O bond length of 1.2978 (15) Å shows double-bond character, pointing towards charge delocalization within the NCO plane of the iminium ion. C—H⋯π inter­actions are present between the methine H atom and two of the phenyl rings of the tetra­phenyl­borate ion. The latter forms an aromatic pocket in which the cation is embedded. The iminium ion is further connected through a C—H⋯N hydrogen bond to the aceto­nitrile mol­ecule. This leads to the formation of a two-dimensional supramolecular pattern along the bc plane. PMID:24765028

Measurement accuracy of FBG used as a surface-bonded strain sensor installed by adhesive.

PubMed

Xue, Guangzhe; Fang, Xinqiu; Hu, Xiukun; Gong, Libin

2018-04-10

Material and dimensional properties of surface-bonded fiber Bragg gratings (FBGs) can distort strain measurement, thereby lowering the measurement accuracy. To accurately assess measurement precision and correct obtained strain, a new model, considering reinforcement effects on adhesive and measured object, is proposed in this study, which is verified to be accurate enough by the numerical method. Meanwhile, a theoretical strain correction factor is obtained, which is demonstrated to be significantly sensitive to recoating material and bonding length, as suggested by numerical and experimental results. It is also concluded that a short grating length as well as a thin but large-area (preferably covering the whole FBG) adhesive can enhance the correction precision.

Infrared Spectroscopic Investigation on CH Bond Acidity in Cationic Alkanes

NASA Astrophysics Data System (ADS)

Matsuda, Yoshiyuki; Xie, Min; Fujii, Asuka

2016-06-01

We have demonstrated large enhancements of CH bond acidities in alcohol, ether, and amine cations through infrared predissociation spectroscopy based on the vacuum ultraviolet photoionization detection. In this study, we investigate for the cationic alkanes (pentane, hexane, and heptane) with different alkyl chain lengths. The σ electrons are ejected in the ionization of alkanes, while nonbonding electrons are ejected in ionization of alcohols, ethers, and amines. Nevertheless, the acidity enhancements of CH in these cationic alkanes have also been demonstrated by infrared spectroscopy. The correlations of their CH bond acidities with the alkyl chain lengths as well as the mechanisms of their acidity enhancements will be discussed by comparison of infrared spectra and theoretical calculations.

The effect of the length of macro synthetic fibres on their performance in concrete

NASA Astrophysics Data System (ADS)

Juhász, K. P.; Kis, V.

2017-09-01

Nowadays macro synthetic fibres are able to compete with steel fibres despite their low Youngs Modulus. This is due to their different pull-out mechanism and a larger number of individual fibres per kilo compared to steel fibres. Macro synthetic fibres bond to the concrete along their full length, usually with an embossed surface, while steel fibres are mostly anchored by their hooked ends. If the bond is defined by the length of the embossed surface, logically the longer the synthetic fibre the higher post-crack capacity. In this paper the same type of macro synthetic fibre was researched with different lengths but at the same dosage. The consistency of the fresh concrete together with the quality of the distribution of the fibres have been analysed and compared with the residual strength. After analysing these data the optimum fibre length was able to be determined.

Anisotropy of the monomer random walk in a polymer melt: local-order and connectivity effects

NASA Astrophysics Data System (ADS)

Bernini, S.; Leporini, D.

2016-05-01

The random walk of a bonded monomer in a polymer melt is anisotropic due to local order and bond connectivity. We investigate both effects by molecular-dynamics simulations on melts of fully-flexible linear chains ranging from dimers (M  =  2) up to entangled polymers (M  =  200). The corresponding atomic liquid is also considered a reference system. To disentangle the influence of the local geometry and the bond arrangements, and to reveal their interplay, we define suitable measures of the anisotropy emphasising either the former or the latter aspect. Connectivity anisotropy, as measured by the correlation between the initial bond orientation and the direction of the subsequent monomer displacement, shows a slight enhancement due to the local order at times shorter than the structural relaxation time. At intermediate times—when the monomer displacement is comparable to the bond length—a pronounced peak and then decays slowly as t -1/2, becoming negligible when the displacement is as large as about five bond lengths, i.e. about four monomer diameters or three Kuhn lengths. Local-geometry anisotropy, as measured by the correlation between the initial orientation of a characteristic axis of the Voronoi cell and the subsequent monomer dynamics, is affected at shorter times than the structural relaxation time by the cage shape with antagonistic disturbance by the connectivity. Differently, at longer times, the connectivity favours the persistence of the local-geometry anisotropy, which vanishes when the monomer displacement exceeds the bond length. Our results strongly suggest that the sole consideration of the local order is not enough to understand the microscopic origin of the rattling amplitude of the trapped monomer in the cage of the neighbours.

77 FR 5728 - Airworthiness Directives; Airbus Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-06

... between bonding lead and the harness, due to over length of the bonding lead. As the affected wire is not... chafing of the wires, and corrective actions, if necessary. We are proposing this AD to detect and correct contact or chafing of wires and bonding leads which, if not detected could be a source of sparks in the...

Analytical energy gradient for the two-component normalized elimination of the small component method

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

Zou, Wenli; Filatov, Michael; Cremer, Dieter, E-mail: dcremer@smu.edu

2015-06-07

The analytical gradient for the two-component Normalized Elimination of the Small Component (2c-NESC) method is presented. The 2c-NESC is a Dirac-exact method that employs the exact two-component one-electron Hamiltonian and thus leads to exact Dirac spin-orbit (SO) splittings for one-electron atoms. For many-electron atoms and molecules, the effect of the two-electron SO interaction is modeled by a screened nucleus potential using effective nuclear charges as proposed by Boettger [Phys. Rev. B 62, 7809 (2000)]. The effect of spin-orbit coupling (SOC) on molecular geometries is analyzed utilizing the properties of the frontier orbitals and calculated SO couplings. It is shown thatmore » bond lengths can either be lengthened or shortened under the impact of SOC where in the first case the influence of low lying excited states with occupied antibonding orbitals plays a role and in the second case the jj-coupling between occupied antibonding and unoccupied bonding orbitals dominates. In general, the effect of SOC on bond lengths is relatively small (≤5% of the scalar relativistic changes in the bond length). However, large effects are found for van der Waals complexes Hg{sub 2} and Cn{sub 2}, which are due to the admixture of more bonding character to the highest occupied spinors.« less

Synthesis and SMM behaviour of trinuclear versus dinuclear 3d-5f uranyl(v)-cobalt(ii) cation-cation complexes.

PubMed

Chatelain, Lucile; Tuna, Floriana; Pécaut, Jacques; Mazzanti, Marinella

2017-05-02

Trinuclear versus dinuclear heterodimetallic U V O 2 + Co 2+ complexes were selectively assembled via a cation-cation interaction by tuning the ligand. The trimeric complex 2, with a linear [Co-O[double bond, length as m-dash]U[double bond, length as m-dash]O-Co] core, exhibits magnetic exchange and slow relaxation with a reversal barrier of 30.5 ± 0.9 K providing the first example of a U-Co exchange-coupled SMM.

Magnesium isotope fractionation between brucite [Mg(OH)2] and Mg aqueous species: Implications for silicate weathering and biogeochemical processes

NASA Astrophysics Data System (ADS)

Li, Weiqiang; Beard, Brian L.; Li, Chengxiang; Johnson, Clark M.

2014-05-01

Brucite, with its octahedral structure, has a lattice configuration that is similar to the Mg-bearing octahedral layers in phyllosilicates. Understanding stable Mg isotope fractionation between brucite and aqueous solution therefore bears on interpretation of Mg isotope data in natural weathering systems. In this study, we experimentally determined Mg isotope fractionation between brucite and two Mg aqueous species, the free Mg aquo ion ([Mg(OH2)6]2+) and EDTA-bonded Mg (Mg-EDTA2-). Results from recrystallization and brucite synthesis experiments suggest mild preferential partitioning of light Mg isotopes into brucite compared to Mg aquo ions at low temperatures, where measured ΔMgbrucite-Mg26 fractionation increased from ca. -0.3‰ at 7 °C, to ca. -0.2‰ at 22 °C, to ca. 0‰ at 40 °C. MgO hydrolysis experiments in EDTA-bearing solutions suggest that the ΔMgbrucite-Mg-EDTA26 fractionation is ⩾+2.0‰ at 22 °C, indicating that light Mg isotopes strongly partition into Mg-EDTA complex relative to brucite, as well as relative to Mg aquo ions. Magnesium atoms in brucite, Mg aquo ions, and Mg-EDTA complexes are all octahedrally coordinated, and the measured Mg isotope fractionations correlate with average bond lengths for Mg. Aqueous Mg ions have the shortest bond length among the three phases, and enrich heavy Mg isotopes relative to brucite and Mg-EDTA. In contrast, Mg-EDTA has the longest average bond length for Mg, and enriches light Mg isotopes relative to Mg aquo ions and brucite; the relatively long Mg-EDTA bond suggests that organically bound Mg may commonly have low 26Mg/24Mg ratios, which may explain proposed "vital" effects for stable Mg isotopes. Such relations between bond length and Mg isotope fractionation could be extended to other phyllosilicates such as serpentine- and clay-group minerals where Mg is also octahedrally coordinated.

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.

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

PubMed Central

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

2017-01-01

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

Ligand-to-ligand charge-transfer transitions of platinum(II) complexes with arylacetylide ligands with different chain lengths: spectroscopic characterization, effect of molecular conformations, and density functional theory calculations.

PubMed

Tong, Glenna So Ming; Law, Yuen-Chi; Kui, Steven C F; Zhu, Nianyong; Leung, King Hong; Phillips, David Lee; Che, Chi-Ming

2010-06-11

The complexes [Pt(tBu(3)tpy){C[triple bond]C(C(6)H(4)C[triple bond]C)(n-1)R}](+) (n = 1: R = alkyl and aryl (Ar); n = 1-3: R = phenyl (Ph) or Ph-N(CH(3))(2)-4; n = 1 and 2, R = Ph-NH(2)-4; tBu(3)tpy = 4,4',4''-tri-tert-butyl-2,2':6',2''-terpyridine) and [Pt(Cl(3)tpy)(C[triple bond]CR)](+) (R = tert-butyl (tBu), Ph, 9,9'-dibutylfluorene, 9,9'-dibutyl-7-dimethyl-amine-fluorene; Cl(3)tpy = 4,4',4''-trichloro-2,2':6',2''-terpyridine) were prepared. The effects of substituent(s) on the terpyridine (tpy) and acetylide ligands and chain length of arylacetylide ligands on the absorption and emission spectra were examined. Resonance Raman (RR) spectra of [Pt(tBu(3)tpy)(C[triple bond]CR)](+) (R = n-butyl, Ph, and C(6)H(4)-OCH(3)-4) obtained in acetonitrile at 298 K reveal that the structural distortion of the C[triple bond]C bond in the electronic excited state obtained by 502.9 nm excitation is substantially larger than that obtained by 416 nm excitation. Density functional theory (DFT) and time-dependent DFT (TDDFT) calculations on [Pt(H(3)tpy)(C[triple bond]CR)](+) (R = n-propyl (nPr), 2-pyridyl (Py)), [Pt(H(3)tpy){C[triple bond]C(C(6)H(4)C[triple bond]C)(n-1)Ph}](+) (n = 1-3), and [Pt(H(3)tpy){C[triple bond]C(C(6)H(4)C[triple bond]C)(n-1)C(6)H(4)-N(CH(3))(2)-4}](+)/+H(+) (n = 1-3; H(3)tpy = nonsubstituted terpyridine) at two different conformations were performed, namely, with the phenyl rings of the arylacetylide ligands coplanar ("cop") with and perpendicular ("per") to the H(3)tpy ligand. Combining the experimental data and calculated results, the two lowest energy absorption peak maxima, lambda(1) and lambda(2), of [Pt(Y(3)tpy)(C[triple bond]CR)](+) (Y = tBu or Cl, R = aryl) are attributed to (1)[pi(C[triple bond]CR)-->pi*(Y(3)tpy)] in the "cop" conformation and mixed (1)[d(pi)(Pt)-->pi*(Y(3)tpy)]/(1)[pi(C[triple bond]CR)-->pi*(Y(3)tpy)] transitions in the "per" conformation. The lowest energy absorption peak lambda(1) for [Pt(tBu(3)tpy){C[triple bond]C(C(6)H(4)C[triple bond]C)(n-1)C(6)H(4)-H-4}](+) (n = 1-3) shows a redshift with increasing chain length. However, for [Pt(tBu(3)tpy){C[triple bond]C(C6H4C[triple bond]C)(n-1)C(6)H(4)-N(CH(3))(2)-4}](+) (n = 1-3), lambda(1) shows a blueshift with increasing chain length n, but shows a redshift after the addition of acid. The emissions of [Pt(Y(3)tpy)(C[triple bond]CR)](+) (Y = tBu or Cl) at 524-642 nm measured in dichloromethane at 298 K are assigned to the (3)[pi(C[triple bond]CAr)-->pi*(Y(3)tpy)] excited states and mixed (3)[d(pi)(Pt)-->pi*(Y(3)tpy)]/(3)[pi(C[triple bond]C)-->pi*(Y(3)tpy)] excited states for R = aryl and alkyl groups, respectively. [Pt(tBu(3)tpy){C[triple bond]C(C(6)H(4)C[triple bond]C)(n-1)C(6)H(4)-N(CH(3))(2)-4}](+) (n = 1 and 2) are nonemissive, and this is attributed to the small energy gap between the singlet ground state (S(0)) and the lowest triplet excited state (T(1)).

Molecular dynamics simulations of AP/HMX composite with a modified force field.

PubMed

Zhu, Wei; Wang, Xijun; Xiao, Jijun; Zhu, Weihua; Sun, Huai; Xiao, Heming

2009-08-15

An all-atom force field for ammonium perchlorate (AP) is developed with the framework of pcff force field. The structural parameters of AP obtained with the modified force field are in good agreement with experimental values. Molecular dynamics (MD) simulations have been performed to investigate AP/HMX (1,3,5,7-tetranitro-1,3,5,7-tetrazocane) composite at different temperatures. The binding energies, thermal expansion coefficient, and the trigger bond lengths of HMX in the AP/HMX composite have been obtained. The binding energies of the system increase slightly with temperature increasing, peak at 245K, and then gradually decrease. The volume thermal expansion coefficient of the AP/HMX composite has been derived from the volume variation with temperature. As the temperature rises, the maximal lengths of the trigger bond N-NO(2) of HMX increase gradually. The simulated results indicate that the maximal length of trigger bond can be used as a criterion for judging the sensitivity of energetic composite.

Repeated bonding of fixed retainer increases the risk of enamel fracture.

PubMed

Chinvipas, Netrporn; Hasegawa, Yuh; Terada, Kazuto

2014-01-01

The aim of this study was to investigate the influences of repeated bonding, using 2 different orthodontic adhesive systems, on the shear bond strength (SBS) and the enamel surface morphology. Sixty premolars were divided into 2 groups (n = 30), and either Transbond XT (T group) or Fuji Ortho LC (F group) adhesives were used. SBS was measured 24 h after bonding, using a universal testing machine. Then, the enamel surfaces were investigated and the mode of failure was described using adhesive remnant index (ARI) scores. After each debonding, 10 teeth from each group were examined by scanning electron microscopy to determine the penetration of adhesives, the length of resin tags, and the state of the enamel surface. The other teeth were subjected to two more bonding/debonding procedures. In T group, the second debonding sequences had significantly higher bond strengths than the other sequences. The length of resin tags was greatest in the second debonding sequence, although there was no significant difference. In F group, the SBS increased with further rebonding and the failure mode tended towards cohesive failure. In both groups, the ARI scores increased with rebonding. Enamel loss could have occurred with both adhesives, although the surfaces appeared unchanged to the naked eye. From this study, we suggest that enamel damage caused by repeated bonding is of concern. To prevent bond failure, we should pay attention to the adhesion method used for bondable retainers.

Quantitative assessment of intermolecular interactions by atomic force microscopy imaging using copper oxide tips

NASA Astrophysics Data System (ADS)

Mönig, Harry; Amirjalayer, Saeed; Timmer, Alexander; Hu, Zhixin; Liu, Lacheng; Díaz Arado, Oscar; Cnudde, Marvin; Strassert, Cristian Alejandro; Ji, Wei; Rohlfing, Michael; Fuchs, Harald

2018-05-01

Atomic force microscopy is an impressive tool with which to directly resolve the bonding structure of organic compounds1-5. The methodology usually involves chemical passivation of the probe-tip termination by attaching single molecules or atoms such as CO or Xe (refs 1,6-9). However, these probe particles are only weakly connected to the metallic apex, which results in considerable dynamic deflection. This probe particle deflection leads to pronounced image distortions, systematic overestimation of bond lengths, and in some cases even spurious bond-like contrast features, thus inhibiting reliable data interpretation8-12. Recently, an alternative approach to tip passivation has been used in which slightly indenting a tip into oxidized copper substrates and subsequent contrast analysis allows for the verification of an oxygen-terminated Cu tip13-15. Here we show that, due to the covalently bound configuration of the terminal oxygen atom, this copper oxide tip (CuOx tip) has a high structural stability, allowing not only a quantitative determination of individual bond lengths and access to bond order effects, but also reliable intermolecular bond characterization. In particular, by removing the previous limitations of flexible probe particles, we are able to provide conclusive experimental evidence for an unusual intermolecular N-Au-N three-centre bond. Furthermore, we demonstrate that CuOx tips allow the characterization of the strength and configuration of individual hydrogen bonds within a molecular assembly.

Length-dependence of intramolecular electron transfer in σ-bonded rigid molecular rods: an ab initio molecular orbital study

NASA Astrophysics Data System (ADS)

Pati, Ranjit; Karna, Shashi P.

2002-01-01

The dependence of electron transfer (ET) coupling element, VAB, on the length of rigid-rod-like systems consisting of bicyclo[1.1.1]pentane (BCP), cubane (CUB), and bicyclo[2.2.2]octane (BCO) monomers, has been investigated with the use of ab initio Hartree-Fock (HF) method employing Marcus-Hush two-state (TS) model. The value of VAB decreases exponentially with increase in the number of the cage units of the σ-bonded molecules. The calculated decay constant, β, shows good agreement with previously reported data. For molecular length⩾15 Å, the value of VAB becomes negligibly small, suggesting complete suppression of the through bond direct tunneling contribution to ET process.

Dimensional Stability of Hexoloy SA® Silicon Carbide and Zerodur™ Materials for the LISA Mission

NASA Astrophysics Data System (ADS)

Preston, Alix; Cruz, Rachel J.; Thorpe, J. Ira; Mueller, Guido; Boothe, G. Trask; Delgadillo, Rodrigo; Guntaka, Sridhar R.

2006-11-01

In the LISA mission, incoming gravitational waves will modulate the distance between proof masses while laser beams monitor the optical path length changes with 20 pm/√Hz accuracy. Optical path length changes between bench components or the relative motion between the primary and secondary mirrors of the telescope need to be well below this level to result in a successful operation of LISA. The reference cavity for frequency stabilization must have a dimensional stability of a few fm/√Hz. While the effects of temperature fluctuations are well characterized in most materials at the macroscopic level (i.e. coefficients of thermal expansion), microscopic material internal processes and long term processes in the bonds between different components can dominate the dimensional stability at the pm or fm levels. Zerodur and ULE have been well studied, but the ultimate stabilities of other materials like silicon carbide or CFRP are virtually unknown. Chemical bonding techniques, like hydroxide bonding, provide significantly stronger bonds than the standard optical contacts. However, the noise levels of these bonds are also unknown. In this paper we present our latest results on the stability of silicon carbide and hydroxide bonds on Zerodur.

Crystal structure of cis-aqua­chlorido­bis­(1,10-phenanthroline-κ2 N,N′)chromium(III) tetra­chlorido­zincate monohydrate from synchrotron data

PubMed Central

Moon, Dohyun; Choi, Jong-Ha

2015-01-01

The structure of the title compound, [CrCl(C12H8N2)2(H2O)][ZnCl4]·H2O, has been determined from synchrotron data. The CrIII ion is bonded to four N atoms from two 1,10-phenanthroline (phen) ligands, one water mol­ecule and a Cl atom in a cis arrangement, displaying an overall distorted octa­hedral coordination environment. The Cr—N(phen) bond lengths are in the range of 2.0495 (18) to 2.0831 (18) Å, while the Cr—Cl and Cr—(OH2) bond lengths are 2.2734 (7) and 1.9986 (17) Å, respectively. The tetra­hedral [ZnCl4]2− anion is slightly distorted owing to its involvement in O—H⋯Cl hydrogen bonding with coordinating and non-coordinating water mol­ecules. The two types of water mol­ecules also inter­act through O—H⋯O hydrogen bonds. The observed hydrogen-bonding pattern leads to the formation of a three-dimensional network structure. PMID:25844190

A novel disulfide bond in the SH2 Domain of the C-terminal Src kinase controls catalytic activity.

PubMed

Mills, Jamie E; Whitford, Paul C; Shaffer, Jennifer; Onuchic, Jose N; Adams, Joseph A; Jennings, Patricia A

2007-02-02

The SH2 domain of the C-terminal Src kinase [Csk] contains a unique disulfide bond that is not present in other known SH2 domains. To investigate whether this unusual disulfide bond serves a novel function, the effects of disulfide bond formation on catalytic activity of the full-length protein and on the structure of the SH2 domain were investigated. The kinase activity of full-length Csk decreases by an order of magnitude upon formation of the disulfide bond in the distal SH2 domain. NMR spectra of the fully oxidized and fully reduced SH2 domains exhibit similar chemical shift patterns and are indicative of similar, well-defined tertiary structures. The solvent-accessible disulfide bond in the isolated SH2 domain is highly stable and far from the small lobe of the kinase domain. However, reduction of this bond results in chemical shift changes of resonances that map to a cluster of residues that extend from the disulfide bond across the molecule to a surface that is in direct contact with the small lobe of the kinase domain in the intact molecule. Normal mode analyses and molecular dynamics calculations suggest that disulfide bond formation has large effects on residues within the kinase domain, most notably within the active-site cleft. Overall, the data indicate that reversible cross-linking of two cysteine residues in the SH2 domain greatly impacts catalytic function and interdomain communication in Csk.

Bonding durability of dual-curing composite core material with different self-etching adhesive systems in a model complete vertical root fracture reconstruction.

PubMed

Waidyasekera, Kanchana; Nikaido, Toru; Weerasinghe, Dinesh; Nurrohman, Hamid; Tagami, Junji

2012-04-01

This study evaluated a dual-curing composite along with different dentin adhesive systems for 1 year under water storage, as a new bonding method of root fragments in complete vertical root fracture. Bovine root fragments were bonded with the dual-curing resin composite Clearfil DC Core Automix (DCA) and one of three adhesive systems: two-step self-etching adhesive Clearfil SE Bond (SE), one-step self-etching adhesive Tokuyama Bond Force (BF), one-step dual-curing self-etching adhesive Clearfil DC Bond (DC). Microtensile bond strength (µTBS)/ultimate tensile bond strength (UTS), FE-SEM ultramorphology of fracture modes, and adhesive dentin interface were observed after water storage for periods of up to one year. The data were analyzed with two-way ANOVA. µTBS was influenced by "dentin adhesive system" (F = 324.455, p < 0.001) and "length of water storage" (F = 8.470, p < 0.001). SE yielded significantly higher µTBS, regardless of storage period (p < 0.05) and maintained the initial µTBS without a significant change after 1 year of water storage (p > 0.05). From 24 h to 1 month, BF showed significantly higher bond strength than DC. UTS of DCA was influenced only by the curing mode of the material (F = 5.051, p = 0.027), but not by the length of water storage (F = 0.053, p > 0.05). Two-step self-etching adhesive systems and dual-curing composite core material can be considered as a suitable bonding method for complete root fractures.

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.

Hydrogen bonding between nitriles and hydrogen halides and the topological properties of molecular charge distributions

NASA Astrophysics Data System (ADS)

Boyd, Russell J.; Choi, Sai Cheng

1986-08-01

The topological properties of the charge density of the hydrogen-bonded complexes between nitrites and hydrogen chloride correlate linearly with theoretical estimates of the hydrogen-bond energy. At the 6-31G ** level, the hydrogenbond energies range from a low of 10 kJ/mol m NCCN—HC1 to a high of 38 kJ/mol in LiCN—HCl. A linear relationship between the charge density at the hydrogen-bond critical point and the NH internuclear distance of the RCN—HC1 complexes indicates that the generalization of the bond-length-bond-order relationship of CC bonds due to Bader, Tang, Tal and Biegler-König can be extended to intermolecular hydrogen bonding.

Orbital Exponent Optimization in Elementary VB Calculations of the Chemical Bond in the Ground State of Simple Molecular Systems

ERIC Educational Resources Information Center

Magnasco, Valerio

2008-01-01

Orbital exponent optimization in the elementary ab-initio VB calculation of the ground states of H[subscript 2][superscript +], H[subscript 2], He[subscript 2][superscript +], He[subscript 2] gives a fair description of the exchange-overlap component of the interatomic interaction that is important in the bond region. Correct bond lengths and…

The effects of chain length, embedded polar groups, pressure, and pore shape on structure and retention in reversed-phase liquid chromatography: molecular-level insights from Monte Carlo simulations.

PubMed

Rafferty, Jake L; Siepmann, J Ilja; Schure, Mark R

2009-03-20

Particle-based simulations using the configurational-bias and Gibbs ensemble Monte Carlo techniques are carried out to probe the effects of various chromatographic parameters on bonded-phase chain conformation, solvent penetration, and retention in reversed-phase liquid chromatography (RPLC). Specifically, we investigate the effects due to the length of the bonded-phase chains (C(18), C(8), and C(1)), the inclusion of embedded polar groups (amide and ether) near the base of the bonded-phase chains, the column pressure (1, 400, and 1000 atm), and the pore shape (planar slit pore versus cylindrical pore with a 60A diameter). These simulations utilize a bonded-phase coverage of 2.9 micromol/m(2)and a mobile phase containing methanol at a molfraction of 33% (about 50% by volume). The simulations show that chain length, embedded polar groups, and pore shape significantly alter structural and retentive properties of the model RPLC system, whereas the column pressure has a relatively small effect. The simulation results are extensively compared to retention measurements. A molecular view of the RPLC retention mechanism emerges that is more complex than can be inferred from thermodynamic measurements.

Contact and Length Dependent Effects in Single-Molecule Electronics

NASA Astrophysics Data System (ADS)

Hines, Thomas

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

Programmable Assembly of Peptide Amphiphile via Noncovalent-to-Covalent Bond Conversion

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

Sato, Kohei; Ji, Wei; Palmer, Liam C.

Controlling the number of monomers in a supramolecular polymer has been a great challenge in programmable self-assembly of organic molecules. One approach has been to make use of frustrated growth of the supramolecular assembly by tuning the balance of attractive and repulsive intermolecular forces. We report here on the use of covalent bond formation among monomers, compensating for intermolecular electrostatic repulsion, as a mechanism to control the length of a supramolecular nanofiber formed by self-assembly of peptide amphiphiles. Circular dichroism spectroscopy in combination with dynamic light scattering, size-exclusion chromatography, and transmittance electron microscope analyses revealed that hydrogen bonds between peptidesmore » were reinforced by covalent bond formation, enabling the fiber elongation. To examine these materials for their potential biomedical applications, cytotoxicity of nanofibers against C2C12 premyoblast cells was tested. We demonstrated that cell viability increased with an increase in fiber length, presumably because of the suppressed disruption of cell membranes by the fiber end-caps.« less

Crystal structure of 2-bromo-3-di­methyl­amino-N,N,N′,N′,4-penta­methyl-4-(tri­methyl­sil­yloxy)pent-2-eneamidinium bromide

PubMed Central

Tiritiris, Ioannis; Kress, Ralf; Kantlehner, Willi

2015-01-01

The reaction of the ortho­amide 1,1,1-tris­(di­methyl­amino)-4-methyl-4-(tri­methyl­sil­yloxy)pent-2-yne with bromine in benzene, yields the title salt, C15H33BrN3OSi+·Br−. The C—N bond lengths in the amidinium unit are 1.319 (6) and 1.333 (6) Å, indicating double-bond character, pointing towards charge delocalization within the NCN plane. The C—Br bond length of 1.926 (5) Å is characteristic for a C—Br single bond. Additionally, there is a bromine–bromine inter­action [3.229 (3) Å] present involving the anion and cation. In the crystal, weak C—H⋯Br inter­actions between the methyl H atoms of the cation and the bromide ions are present. PMID:26870498

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.

Programmable Assembly of Peptide Amphiphile via Noncovalent-to-Covalent Bond Conversion

DOE PAGES

Sato, Kohei; Ji, Wei; Palmer, Liam C.; ...

2017-06-22

Controlling the number of monomers in a supramolecular polymer has been a great challenge in programmable self-assembly of organic molecules. One approach has been to make use of frustrated growth of the supramolecular assembly by tuning the balance of attractive and repulsive intermolecular forces. We report here on the use of covalent bond formation among monomers, compensating for intermolecular electrostatic repulsion, as a mechanism to control the length of a supramolecular nanofiber formed by self-assembly of peptide amphiphiles. Circular dichroism spectroscopy in combination with dynamic light scattering, size-exclusion chromatography, and transmittance electron microscope analyses revealed that hydrogen bonds between peptidesmore » were reinforced by covalent bond formation, enabling the fiber elongation. To examine these materials for their potential biomedical applications, cytotoxicity of nanofibers against C2C12 premyoblast cells was tested. We demonstrated that cell viability increased with an increase in fiber length, presumably because of the suppressed disruption of cell membranes by the fiber end-caps.« less

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.

Real-space identification of intermolecular bonding with atomic force microscopy.

PubMed

Zhang, Jun; Chen, Pengcheng; Yuan, Bingkai; Ji, Wei; Cheng, Zhihai; Qiu, Xiaohui

2013-11-01

We report a real-space visualization of the formation of hydrogen bonding in 8-hydroxyquinoline (8-hq) molecular assemblies on a Cu(111) substrate, using noncontact atomic force microscopy (NC-AFM). The atomically resolved molecular structures enable a precise determination of the characteristics of hydrogen bonding networks, including the bonding sites, orientations, and lengths. The observation of bond contrast was interpreted by ab initio density functional calculations, which indicated the electron density contribution from the hybridized electronic state of the hydrogen bond. Intermolecular coordination between the dehydrogenated 8-hq and Cu adatoms was also revealed by the submolecular resolution AFM characterization. The direct identification of local bonding configurations by NC-AFM would facilitate detailed investigations of intermolecular interactions in complex molecules with multiple active sites.

Reaction of the thermo-labile triazenide Na[tBu3SiNNNSiMe3] with CO2: formation of the imido carbonate (tBu3SiO)(Me3SiO)C[double bond, length as m-dash]N-SitBu3 and carbamine acid (tBu3SiO)CONH2.

PubMed

Lerner, H-W; Bolte, M; Wagner, M

2017-07-11

The thermo-labile triazenide Na[tBu 3 SiNNNSiMe 3 ] was prepared by the reaction of Me 3 SiN 3 with Na(thf) 2 [SitBu 3 ] in pentane at -78 °C. Treatment of Na[tBu 3 SiNNNSiMe 3 ] with an excess of carbon dioxide in pentane at -78 °C yielded the imido carbonate (tBu 3 SiO)(Me 3 SiO)C[double bond, length as m-dash]N-SitBu 3 and the carbamine acid (tBu 3 SiO)CONH 2 along with other products. From the reaction solution we could isolate the imido carbonate (tBu 3 SiO)(Me 3 SiO)C[double bond, length as m-dash]N-SitBu 3 and carbamine acid (tBu 3 SiO)CONH 2 . At first single crystals of the carbamine acid (tBu 3 SiO)CONH 2 (triclinic, space group P1[combining macron]) were grown from this solution at room temperature. A second crop of crystals were obtained by concentrating the solution. The second charge consisted of the imido carbonate (tBu 3 SiO)(Me 3 SiO)C[double bond, length as m-dash]N-SitBu 3 (monoclinic, space group P2 1 /n).

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.

Monte Carlo simulations of lattice models for single polymer systems

NASA Astrophysics Data System (ADS)

Hsu, Hsiao-Ping

2014-10-01

Single linear polymer chains in dilute solutions under good solvent conditions are studied by Monte Carlo simulations with the pruned-enriched Rosenbluth method up to the chain length N ˜ O(10^4). Based on the standard simple cubic lattice model (SCLM) with fixed bond length and the bond fluctuation model (BFM) with bond lengths in a range between 2 and sqrt{10}, we investigate the conformations of polymer chains described by self-avoiding walks on the simple cubic lattice, and by random walks and non-reversible random walks in the absence of excluded volume interactions. In addition to flexible chains, we also extend our study to semiflexible chains for different stiffness controlled by a bending potential. The persistence lengths of chains extracted from the orientational correlations are estimated for all cases. We show that chains based on the BFM are more flexible than those based on the SCLM for a fixed bending energy. The microscopic differences between these two lattice models are discussed and the theoretical predictions of scaling laws given in the literature are checked and verified. Our simulations clarify that a different mapping ratio between the coarse-grained models and the atomistically realistic description of polymers is required in a coarse-graining approach due to the different crossovers to the asymptotic behavior.

Electric Field Effects on the Intermolecular Interactions in Water Whiskers: Insight from Structures, Energetics, and Properties

DOE PAGES

Bai, Yang; He, Hui-Min; Li, Ying; ...

2015-02-19

Modulation of intermolecular interactions in response to external electric fields could be fundamental to the formation of unusual forms of water, such as water whiskers. However, a detailed understanding of the nature of intermolecular interactions in such systems is lacking. In this study, we present novel theoretical results based on electron correlation calculations regarding the nature of H-bonds in water whiskers, which is revealed by studying their evolution under external electric fields with various field strengths. We find that the water whiskers consisting of 2-7 water molecules all have a chain-length dependent critical electric field. Under the critical electric field,more » the most compact chain structures are obtained, featuring very strong H-bonds, herein referred to as covalent H-bonds. In the case of a water dimer whisker, the bond length of the novel covalent H-bond shortens by 25%, the covalent bond order increases by 9 times, and accordingly the H-bond energy is strengthened by 5 times compared to the normal H-bond in a (H 2O) 2 cluster. Below the critical electric field, it is observed that with increasing field strength, H-bonding orbitals display gradual evolutions in the orbital energy, orbital ordering, and orbital nature (i.e., from typical -style orbital to unusual -style double H-bonding orbital). We also show that beyond the critical electric field, a single water whisker may disintegrate to form a loosely bound zwitterionic chain due to a relay-style proton transfer, whereas two water whiskers may undergo intermolecular cross-linking to form a quasi-two-dimensional water network. In conclusion, these results help shed new insight on the effects of electric fields on water whisker formation.« less

Density functional theory and chromium: Insights from the dimers

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

Würdemann, Rolf; Kristoffersen, Henrik H.; Moseler, Michael

2015-03-28

The binding in small Cr clusters is re-investigated, where the correct description of the dimer in three charge states is used as criterion to assign the most suitable density functional theory approximation. The difficulty in chromium arises from the subtle interplay between energy gain from hybridization and energetic cost due to exchange between s and d based molecular orbitals. Variations in published bond lengths and binding energies are shown to arise from insufficient numerical representation of electron density and Kohn-Sham wave-functions. The best functional performance is found for gradient corrected (GGA) functionals and meta-GGAs, where we find severe differences betweenmore » functionals from the same family due to the importance of exchange. Only the “best fit” from Bayesian error estimation is able to predict the correct energetics for all three charge states unambiguously. With this knowledge, we predict small bond-lengths to be exclusively present in Cr{sub 2} and Cr{sub 2}{sup −}. Already for the dimer cation, solely long bond-lengths appear, similar to what is found in the trimer and in chromium bulk.« less

Efficient Organometallic Spin Filter between Single-Wall Carbon Nanotube or Graphene Electrodes

NASA Astrophysics Data System (ADS)

Koleini, Mohammad; Paulsson, Magnus; Brandbyge, Mads

2007-05-01

We present a theoretical study of spin transport in a class of molecular systems consisting of an organometallic benzene-vanadium cluster placed in between graphene or single-wall carbon-nanotube-model contacts. Ab initio modeling is performed by combining spin density functional theory and nonequilibrium Green’s function techniques. We consider weak and strong cluster-contact bonds. Depending on the bonding we find from 73% (strong bonds) up to 99% (weak bonds) spin polarization of the electron transmission, and enhanced polarization with increased cluster length.

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

PubMed Central

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

2010-01-01

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

Noble gas bond and the behaviour of XeO3 under pressure.

PubMed

Hou, Chunju; Wang, Xianlong; Botana, Jorge; Miao, Maosheng

2017-10-18

Over the past few decades, the concept of hydrogen bonds, in which hydrogen is electrophilic, has been extended to halogen bonds, chalcogen bonds and pnicogen bonds. Herein, we show that such a non-covalent bonding also exists in noble gas compounds. Using first principles calculations, we illustrate the OXe-O bond in molecular crystal XeO 3 and its effect on the behavior of this compound under pressure. Our calculations show that the covalent Xe-O bond lengths were elongated with increasing pressure and correspondingly the Xe-O stretching vibration frequencies were red shifted, which is similar to the change of H-bonds under pressure. The OXe-O bond and related hopping of O between neighboring Xe sites also correspond to the structural changes in the XeO 3 compounds at about 2 GPa. Our study extends the concept of hydrogen bonding to include all p-block elements and show a new bonding type for Noble gas elements in which it acts as an electrophilic species.

Bond-strength inversion in (In,Ga)As semiconductor alloys

NASA Astrophysics Data System (ADS)

Eckner, Stefanie; Ritter, Konrad; Schöppe, Philipp; Haubold, Erik; Eckner, Erich; Rensberg, Jura; Röder, Robert; Ridgway, Mark C.; Schnohr, Claudia S.

2018-05-01

The atomic-scale structure and vibrational properties of semiconductor alloys are determined by the energy required for stretching and bending the individual bonds. Using temperature-dependent extended x-ray absorption fine-structure spectroscopy, we have determined the element-specific In-As and Ga-As effective bond-stretching force constants in (In,Ga)As as a function of the alloy composition. The results reveal a striking inversion of the bond strength where the originally stiffer bond in the parent materials becomes the softer bond in the alloy and vice versa. Our findings clearly demonstrate that changes of both the individual bond length and the surrounding matrix affect the bond-stretching force constants. We thus show that the previously used common assumptions about the element-specific force constants in semiconductor alloys do not reproduce the composition dependence determined experimentally for (In,Ga)As.

Microwave structure for the propiolic acid-formic acid complex.

PubMed

Kukolich, Stephen G; Mitchell, Erik G; Carey, Spencer J; Sun, Ming; Sargus, Bryan A

2013-10-03

New microwave spectra were measured to obtain rotational constants and centrifugal distortion constants for the DCCCOOH···HOOCH and HCCCOOD···DOOCH isotopologues. Rotational transitions were measured in the frequency range of 4.9-15.4 GHz, providing accurate rotational constants, which, combined with previous rotational constants, allowed an improved structural fit for the propiolic acid-formic acid complex. The new structural fit yields reasonably accurate orientations for both the propiolic and formic acid monomers in the complex and more accurate structural parameters describing the hydrogen bonding. The structure is planar, with a positive inertial defect of Δ = 1.33 amu Å(2). The experimental structure exhibits a greater asymmetry for the two hydrogen bond lengths than was obtained from the ab initio mp2 calculations. The best-fit hydrogen bond lengths have an r(O1-H1···O4) of 1.64 Å and an r(O3-H2···O2) of 1.87 Å. The average of the two hydrogen bond lengths is r(av)(exp) = 1.76 Å, in good agreement with r(av)(theory) = 1.72 Å. The center of mass separation of the monomers is R(CM) = 3.864 Å. Other structural parameters from the least-squares fit using the experimental rotational constants are compared with theoretical values. The spectra were obtained using two different pulsed beam Fourier transform microwave spectrometers.

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.

Bond, transfer length, and development length of prestressing strand in self-consolidating concrete.

DOT National Transportation Integrated Search

2014-07-01

Due to its economic advantages, the use of self-consolidating concrete (SCC) has increased rapidly in recent years. However, because : SCC mixes typically have decreased amounts of coarse aggregate and high amounts of admixtures, industry members hav...

The Hydrogen Bonded Structures of Two 5-Bromobarbituric Acids and Analysis of Unequal C5–X and C5–X′ Bond Lengths (X = X′ = F, Cl, Br or Me) in 5,5-Disubstituted Barbituric Acids

PubMed Central

Gelbrich, Thomas; Braun, Doris E.; Oberparleiter, Stefan; Schottenberger, Herwig; Griesser, Ulrich J.

2017-01-01

The crystal structure of the methanol hemisolvate of 5,5-dibromobarbituric acid (1MH) displays an H-bonded layer structure which is based on N–H⋯O=C, N–H⋯O(MeOH) and (MeOH)O–H⋯O interactions. The barbiturate molecules form an H-bonded substructure which has the fes topology. 5,5′-Methanediylbis(5-bromobarbituric acid) 2, obtained from a solution of 5,5-dibromobarbituric acid in nitromethane, displays a N–H⋯O=C bonded framework of the sxd type. The conformation of the pyridmidine ring and the lengths of the ring substituent bonds C5–X and C5–X′ in crystal forms of 5,5-dibromobarbituric acid and three closely related analogues (X = X′ = Br, Cl, F, Me) have been investigated. In each case, a conformation close to a C5-endo envelope is correlated with a significant lengthening of the axial C5–X′ in comparison to the equatorial C5–X bond. Isolated molecule geometry optimizations at different levels of theory confirm that the C5-endo envelope is the global conformational energy minimum of 5,5-dihalogenbarbituric acids. The relative lengthening of the axial bond is therefore interpreted as an inherent feature of the preferred envelope conformation of the pyrimidine ring, which minimizes repulsive interactions between the axial substituent and pyrimidine ring atoms. PMID:28670485

Site-specific binding of a water molecule to the sulfa drugs sulfamethoxazole and sulfisoxazole: a laser-desorption isomer-specific UV and IR study.

PubMed

Uhlemann, Thomas; Seidel, Sebastian; Müller, Christian W

2018-03-07

To determine the preferred water molecule binding sites of the polybasic sulfa drugs sulfamethoxazole (SMX) and sulfisoxazole (SIX), we have studied their monomers and monohydrated complexes through laser-desorption conformer-specific UV and IR spectroscopy. Both the SMX and SIX monomer adopt a single conformer in the molecular beam. On the basis of their conformer-specific IR spectra in the NH stretch region, these conformers were assigned to the SMX and SIX global minimum structures, both exhibiting a staggered sulfonamide group and an intramolecular C-HO[double bond, length as m-dash]S hydrogen bond. The SMX-H 2 O and SIX-H 2 O complexes each adopt a single isomer in the molecular beam. Their isomeric structures were determined based on their isomer-specific IR spectra in the NH/OH stretch region. Quantum Theory of Atoms in Molecules analysis of the calculated electron densities revealed that in the SMX-H 2 O complex the water molecule donates an O-HN hydrogen bond to the heterocycle nitrogen atom and accepts an N-HO hydrogen bond from the sulfonamide NH group. In the SIX-H 2 O complex, however, the water molecule does not bind to the heterocycle but instead donates an O-HO[double bond, length as m-dash]S hydrogen bond to the sulfonamide group and accepts an N-HO hydrogen bond from the sulfonamide NH group. Both water complexes are additionally stabilized by a C ph -HOH 2 hydrogen bond. Interacting Quantum Atoms analysis suggests that all intermolecular hydrogen bonds are dominated by the short-range exchange-correlation contribution.

Laser desorption single-conformation UV and IR spectroscopy of the sulfonamide drug sulfanilamide, the sulfanilamide-water complex, and the sulfanilamide dimer.

PubMed

Uhlemann, Thomas; Seidel, Sebastian; Müller, Christian W

2017-06-07

We have studied the conformational preferences of the sulfonamide drug sulfanilamide, its dimer, and its monohydrated complex through laser desorption single-conformation UV and IR spectroscopy in a molecular beam. Based on potential energy curves for the inversion of the anilinic and the sulfonamide NH 2 groups calculated at DFT level, we suggest that the zero-point level wave function of the sulfanilamide monomer is appreciably delocalized over all four conformer wells. The sulfanilamide dimer, and the monohydrated complex each exhibit a single isomer in the molecular beam. The isomeric structures of the sulfanilamide dimer and the monohydrated sulfanilamide complex were assigned based on their conformer-specific IR spectra in the NH and OH stretch region. Quantum Theory of Atoms in Molecules (QTAIM) analysis of the calculated electron density in the water complex suggests that the water molecule is bound side-on in a hydrogen bonding pocket, donating one O-HO[double bond, length as m-dash]S hydrogen bond and accepting two hydrogen bonds, a NHO and a CHO hydrogen bond. QTAIM analysis of the dimer electron density suggests that the C i symmetry dimer structure exhibits two dominating N-HO[double bond, length as m-dash]S hydrogen bonds, and three weaker types of interactions: two CHO bonds, two CHN bonds, and a chalcogen OO interaction. Most interestingly, the molecular beam dimer structure closely resembles the R dimer unit - the dimer unit with the greatest interaction energy - of the α, γ, and δ crystal polymorphs. Interacting Quantum Atoms analysis provides evidence that the total intermolecular interaction in the dimer is dominated by the short-range exchange-correlation contribution.

Conciliatory Inductive Model Explaining the Origin of Changes in the η(2)-SiH Bond Length Caused by Presence of Strongly Electronegative Atoms X (X = F, Cl) in Cp(OC)2Mn[η(2)-H(SiH3-nXn)] (n = 0-3) Complexes.

PubMed

Jabłoński, Mirosław

2016-06-23

Using three theoretical methods, QTAIM, IQA, and NCI, we analyze an influence of halogen atoms X (X = F, Cl) substituted at various positions in the -SiH3-nXn group on the charge density distribution within the η(2)-SiH bond and on the SiH bond energies in Cp(OC)2Mn[η(2)-H(SiH3-nXn)] complexes and isolated HSiH3-nXn molecules. It is shown that shortening of the η(2)-SiH bond in Cp(OC)2Mn[η(2)-H(SiH3-nXn)] complexes should be considered as a normal inductive result of halogenation. This η(2)-SiH bond's compression may, however, be overcome by a predominant elongation resulting from a contingent presence of a halogen atom at position trans to the η(2)-SiH bond. This trans effect is particularly large for bulky and highly polarizable chlorine. Moreover, peculiar properties of the trans chlorine atom are manifested in several ways. To explain the origin of all the observed changes in both the length and the electron charge distribution of the η(2)-SiH bond in investigated Cp(OC)2Mn[η(2)-H(SiH3-nXn)] complexes a new model, called the Conciliatory Inductive Model, is being proposed.

On the nature of the {SO2-4}/{Ag(111) } and {SO2-4}/{Au(111) } surface bonding

NASA Astrophysics Data System (ADS)

Patrito, E. M.; Olivera, P. Paredes; Sellers, Harrell

1997-05-01

The nature of sulfate-Ag(111) and sulfate-Au(111) surface bonding has been investigated at the SCF + MP2 level of theory. Convergence of binding energy with cluster size is investigated and, unlike neutral adsorbates, large clusters are required in order to obtain reliable binding energies. In the most stable adsorption mode, sulfate binds to the surface via three oxygen atoms (C 3v symmetry) with a binding energy of 159.3 kcal/mol on Ag(111) and 143.9 kcal/mol on Au(111). The geometry of adsorbed sulfate was optimized at the SCF level. While the bond length between sulfur and the oxygens coordinated to the surface increases, the sulfur-uncoordinated oxygen bond length decreases. This weakening and strengthening of the bonds, respectively, is consistent with bond order conservation in adsorbates on metal surfaces. Although a charge transfer of 0.4 electrons towards the metal is observed, the adsorbate remains very much sulfate-like. The molecular orbital analysis indicates that there is also some charge back-donation towards unoccupied orbitals of sulfate. This results in an increased electron density around sulfur as revealed in the electron density difference maps. Analysis of the Laplacian of the charge density of free sulfate provides a suitable framework to understand the nature of the different charge transfer processes and allows us to establish some similarities with the CO- and SO 2-metal bondings.

Local Bonding Influence on the Band Edge and Band Gap Formation in Quaternary Chalcopyrites.

PubMed

Miglio, Anna; Heinrich, Christophe P; Tremel, Wolfgang; Hautier, Geoffroy; Zeier, Wolfgang G

2017-09-01

Quaternary chalcopyrites have shown to exhibit tunable band gaps with changing anion composition. Inspired by these observations, the underlying structural and electronic considerations are investigated using a combination of experimentally obtained structural data, molecular orbital considerations, and density functional theory. Within the solid solution Cu 2 ZnGeS 4- x Se x , the anion bond alteration parameter changes, showing larger bond lengths for metal-selenium than for metal-sulfur bonds. The changing bonding interaction directly influences the valence and conduction band edges, which result from antibonding Cu-anion and Ge-anion interactions, respectively. The knowledge of the underlying bonding interactions at the band edges can help design properties of these quaternary chalcopyrites for photovoltaic and thermoelectric applications.

Driven translocation of Polymer through a nanopore: effect of heterogeneous flexibility

NASA Astrophysics Data System (ADS)

Adhikari, Ramesh; Bhattacharya, Aniket

2014-03-01

We have studied translocation of a model bead-spring polymer through a nanopore whose building blocks consist of alternate stiff and flexible segments and variable elastic bond potentials. For the case of uniform spring potential translocation of a symmetric periodic stiff-flexible chain of contour length N and segment length m (mod(N,2m)=0), we find that the end-to-end distance and the mean first passage time (MFPT) have weak dependence on the length m. The characteristic periodic pattern of the waiting time distribution captures the stiff and flexible segments of the chain with stiff segments taking longer time to translocate. But when we vary both the elastic bond energy, and the bending energy, as well as the length of stiff/flexible segments, we discover novel patterns in the waiting time distribution which brings out structural information of the building blocks of the translocating chain. Partially supported by UCF Office of Research and Commercialization & College of Science SEED grant.

31 CFR 321.12 - Redemption value of securities.

Code of Federal Regulations, 2014 CFR

2014-07-01

... value of each savings security is determined by the terms of its offering and the length of time it has been outstanding. The Bureau of the Fiscal Service determines redemption values for Series A-E bonds, eligible Series EE and I bonds, and savings notes, that should be used in redeeming savings securities. [63...

Efficient Transition State Optimization of Periodic Structures through Automated Relaxed Potential Energy Surface Scans.

PubMed

Plessow, Philipp N

2018-02-13

This work explores how constrained linear combinations of bond lengths can be used to optimize transition states in periodic structures. Scanning of constrained coordinates is a standard approach for molecular codes with localized basis functions, where a full set of internal coordinates is used for optimization. Common plane wave-codes for periodic boundary conditions almost exlusively rely on Cartesian coordinates. An implementation of constrained linear combinations of bond lengths with Cartesian coordinates is described. Along with an optimization of the value of the constrained coordinate toward the transition states, this allows transition optimization within a single calculation. The approach is suitable for transition states that can be well described in terms of broken and formed bonds. In particular, the implementation is shown to be effective and efficient in the optimization of transition states in zeolite-catalyzed reactions, which have high relevance in industrial processes.

Impact of hydrogen bonding on dynamics of hydroxyl-terminated polydimethylsiloxane

DOE PAGES

Xing, Kunyue; Chatterjee, Sabornie; Saito, Tomonori; ...

2016-04-06

Dielectric spectroscopy, rheology, and differential scanning calorimetry were employed to study the effect of chain-end hydrogen bonding on the dynamics of hydroxylterminated polydimethylsiloxane. We demonstrate that hydrogen bonding has a strong influence on both segmental and slower dynamics in the systems with low molecular weights. In particular, the decrease in the chain length leads to an increase of the glass transition temperature, viscosity, and fragility index, at variance with the usual behavior of nonassociating polymers. The supramolecular association of hydroxylterminated chains leads to the emergence in dielectric and mechanical relaxation spectra of the so-called Debye process traditionally observed in monohydroxymore » alcohols. Our analysis suggests that the hydroxyl-terminated PDMS oligomers may associate in brush-like or chain-like structures, depending on the size of their covalent chains. Finally, the effective length of the linear-associated chains was estimated from the rheological measurements.« less

Neutron and X-ray total scattering study of hydrogen disorder in fully hydrated hydrogrossular, Ca3Al2(O4H4)3

NASA Astrophysics Data System (ADS)

Keen, David A.; Keeble, Dean S.; Bennett, Thomas D.

2018-04-01

The structure of fully hydrated grossular, or katoite, contains an unusual arrangement of four O-H bonds within each O4 tetrahedra. Neutron and X-ray total scattering from a powdered deuterated sample have been measured to investigate the local arrangement of this O4D4 cluster. The O-D bond length determined directly from the pair distribution function is 0.954 Å, although the Rietveld-refined distance between average O and D positions was slightly smaller. Reverse Monte Carlo refinement of supercell models to the total scattering data show that other than the consequences of this correctly determined O-D bond length, there is little to suggest that the O4D4 structure is locally significantly different from that expected based on the average structure determined solely from Bragg diffraction.

Formation of {Co(dppe)}2{μ2-η(2):η(2)-η(2):η(2)-[(C60)2]} Dimers Bonded by Single C-C Bonds and Bridging η(2)-Coordinated Cobalt Atoms.

PubMed

Konarev, Dmitri V; Troyanov, Sergey I; Ustimenko, Kseniya A; Nakano, Yoshiaki; Shestakov, Alexander F; Otsuka, Akihiro; Yamochi, Hideki; Saito, Gunzi; Lyubovskaya, Rimma N

2015-05-18

Coordination of two bridging cobalt atoms to fullerenes by the η(2) type in {Co(dppe)}2{μ2-η(2):η(2)-η(2):η(2)-[(C60)2]}·3C6H4Cl2 [1; dppe = 1,2-bis(diphenylphosphino)ethane] triggers fullerene dimerization with the formation of two intercage C-C bonds of 1.571(4) Å length. Coordination-induced fullerene dimerization opens a path to the design of fullerene structures bonded by both covalent C-C bonds and η(2)-coordination-bridged metal atoms.

The effect of elastomer chain length on properties of silicone-modified polyimide adhesives

NASA Technical Reports Server (NTRS)

St.clair, A. K.; St.clair, T. L.; Ezzell, S.

1981-01-01

A series of polyimides containing silicone elastomers was synthesized in order to study the effects of the elastomer chain length on polymer properties. The elastomer with repeat units varying from n=10 to 105 was chemically reacted into the backbone of an addition polyimide oligomer via reactive aromatic amine groups. Glass transition temperatures of the elastomer and polyimide phases were observed by torsional braid analysis. The elastomer-modified polyimides were tested as adhesives for bonding titanium in order to determine their potential for aerospace applications. Adhesive lap shear tests were performed before and after aging bonded specimens at elevated temperatures.

Bio-inspired passive actuator simulating an abalone shell mechanism for structural control

NASA Astrophysics Data System (ADS)

Yang, Henry T. Y.; Lin, Chun-Hung; Bridges, Daniel; Randall, Connor J.; Hansma, Paul K.

2010-10-01

An energy dispersion mechanism called 'sacrificial bonds and hidden length', which is found in some biological systems, such as abalone shells and bones, is the inspiration for new strategies for structural control. Sacrificial bonds and hidden length can substantially increase the stiffness and enhance energy dissipation in the constituent molecules of abalone shells and bone. Having been inspired by the usefulness and effectiveness of such a mechanism, which has evolved over millions of years and countless cycles of evolutions, the authors employ the conceptual underpinnings of this mechanism to develop a bio-inspired passive actuator. This paper presents a fundamental method for optimally designing such bio-inspired passive actuators for structural control. To optimize the bio-inspired passive actuator, a simple method utilizing the force-displacement-velocity (FDV) plots based on LQR control is proposed. A linear regression approach is adopted in this research to find the initial values of the desired parameters for the bio-inspired passive actuator. The illustrative examples, conducted by numerical simulation with experimental validation, suggest that the bio-inspired passive actuator based on sacrificial bonds and hidden length may be comparable in performance to state-of-the-art semi-active actuators.

The Quest for Greater Chemical Energy Storage II: On the Relationship between Bond Length and Bond Energy

NASA Astrophysics Data System (ADS)

Lindsay, Michael; Buszek, Robert; Boatz, Jerry; Fajardo, Mario

2017-06-01

This is the second in a series of papers aimed at exploring the fundamental limitations to chemical energy storage. In the previous work, we summarized the lessons learned in various high energy density materials (HEDM) programs, the different degrees of freedom in which to store energy in materials, and the fundamental limitations and orders of magnitude of the energies involved.1 That discussion focused almost exclusively on the topic of molar energy density (J/mol) from the perspective of the energy of oxidation of the elements and Fritz Zwicky's ``free atom limit.''2 In this talk, we extend the analysis by considering a different, though equally important, aspect of the energy density calculation: the volumetric density of the energetic material. Specifically, we examine how the distances between individual atoms (i.e. intra- and inter-molecular bond lengths) are coupled to (in fact, approximately inversely proportional to) the energy stored in the bonds of the molecule. This relationship further limits the chemical energy that theoretically can be stored in a material below that predicted by the ``free atom limit.'' This talk will give specific examples of the trends with different bonding motifs and the implications to the fundamental limitations of chemical energy storage.

4-Bromo-N-(di-n-propyl-carbamothioyl)-benzamide.

PubMed

Binzet, Gün; Flörke, Ulrich; Külcü, Nevzat; Arslan, Hakan

2009-02-04

The synthesis of the title compound, C(14)H(19)BrN(2)OS, involves the reaction of 4-bromo-benzoyl chloride with potassium thio-cyanate in acetone followed by condensation of the resulting 4-bromo-benzoyl isothio-cyanate with di-n-propyl-amine. Typical thio-urea carbonyl and thio-carbonyl double bonds, as well as shortened C-N bonds, are observed in the title compound. The short C-N bond lengths in the centre of the mol-ecule reveal the effects of resonance in this part of the mol-ecule. The asymmetric unit of the title compound contains two crystallographically independent mol-ecules, A and B. There is very little difference between the bond lengths and angles of these mol-ecules. In mol-ecule B, one di-n-propyl group is twisted in a -anti-periplanar conformation with C-C-C-H = -179.1 (3)° and the other adopts a -synclinal conformation with C-C-C-H = -56.7 (4)°; in mol-ecule A the two di-n-propyl groups are twisted in + and -anti-periplanar conformations, with C-C-C-H = -179.9 (3) and 178.2 (3)°, respectively. In the crystal, the mol-ecules are linked into dimeric pairs via pairs of N-H⋯S hydrogen bonds.

Theoretical investigations on the structure and properties of p-n-alkoxy benzoic acid based liquid crystals

NASA Astrophysics Data System (ADS)

Subhapriya, P.; Dhanapal, V.; Sadasivam, K.; Vijayanand, P. S.

2016-05-01

The present study focused on the structural conformations, alkoxy chain lengths and mesogenic properties of two mole of alkoxy benzoic acid(nOBA) and one mole of suberic acid (SA) hydrogen bonded (nOBASA) complexes (n=8 to 10) by density functional theory (DFT) calculations and the Fourier Transform Infrared (FT-IR) spectrum. The intermolecular hydrogen bond formation was confirmed by the optimized geometric bond lengths and bond angles obtained by computation. Using the natural bond orbital (NBO) analysis, the stability of the molecule arising from hyper conjugative interactions and charge delocalization has been analyzed. Results obtained shows that the charge in electron density (ED) in σ*and π* antibonding orbital and second order delocalization energies E(2) authorizes the occurrence of intermolecular charge transfer. The molecular electrostatic potential (MEP) surface map is plotted over the optimized geometry of the molecule to obtain the chemical reactivity of the molecule. From the local charge distributions, the mesomorphic behavior and the nematic phase stabilities for each of the molecule have been predicted. Finally the calculated result is applied to simulated infrared spectra of 8OBASA mesogens which shows good agreement with the observed spectra. The comparison of the theoretical results obtained with the experimental ones shows the reliability of this DFT method.

Does time after pair bond disruption affect subsequent reproduction in the socially monogamous woodland vole (Microtus pinetorum)?

PubMed Central

Renfro, Caroline A.; Pesek, Daniel W.; Bobeck, Kelly; Solomon, Nancy G.

2010-01-01

Disruption of the pair bond between socially monogamous animals leads to changes in behavior, which may have reproductive consequences. There are two alternative hypotheses to explain the effect of the length of time since pair bond disruption on subsequent reproduction. One hypothesis predicts that voles housed immediately with a new opposite-sex conspecific will be as likely to produce litters and will produce them as quickly as voles separated from their initial mate for longer. Alternatively, if attachment between mates is enduring, we expect that more voles separated longer from their previous mates will produce litters and produce them sooner than voles re-paired immediately after separation from their initial mates. Woodland voles, paired with opposite-sex conspecifics, remained together until parturition. Mates were then separated for zero, seven, or fourteen days until re-pairing with an opposite-sex conspecific. Pair bond disruption did not prevent males and females from mating subsequently, which was consistent with data from our breeding colony. In addition, the length of time an individual remained alone after pair bond disruption did not affect the latency to produce a litter. Our results show that having been paired previously does not affect subsequent reproduction in this socially monogamous vole. PMID:19429197

Transient sheath overvoltages in armored power cables

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

Gustavsen, B.; Sletbak, J.

1996-07-01

This paper is concerned with methods of limiting the build-up of transient voltages between sheath and armor in long armored power cables. Calculations by a frequency dependent cable model demonstrate that this voltage can be efficiently limited to an acceptable level by introducing sheath-armor bondings at regular intervals, or by using a semiconductive sheath-armor interlayer. The paper investigates the required minimum length between bondings, as well as the required conductivity of the sheath-armor interlayer if the use of bondings is to be avoided.

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.

Stable Chloro- and Bromoxenate Cage Anions; [X3(XeO3)3]3- and [X4(XeO3)4]4- (X = Cl or Br).

PubMed

Goettel, James T; Haensch, Veit G; Schrobilgen, Gary J

2017-06-28

The number of isolable compounds which contain different noble-gas-element bonds is limited for xenon and even more so for krypton. Examples of Xe-Cl bonds are rare, and prior to this work, no Xe-Br bonded compound had been isolated in macroscopic quantities. The syntheses, isolation, and characterization of the first compounds to contain Xe-Br bonds and their chlorine analogues are described in the present work. The reactions of XeO 3 with [N(CH 3 ) 4 ]Br and [N(C 2 H 5 ) 4 ]Br have provided two bromoxenate salts, [N(C 2 H 5 ) 4 ] 3 [Br 3 (XeO 3 ) 3 ] and [N(CH 3 ) 4 ] 4 [Br 4 (XeO 3 ) 4 ], in which the cage anions have Xe-Br bond lengths that range from 3.0838(3) to 3.3181(8) Å. The isostructural chloroxenate anions (Xe-Cl bond lengths, 2.9316(2) to 3.101(4) Å) were synthesized by analogy with their bromine analogues. The bromo- and chloroxenate salts are stable in the atmosphere at room temperature and were characterized in the solid state by Raman spectroscopy and low-temperature single-crystal X-ray diffraction, and in the gas phase by quantum-chemical calculations. They are the only known examples of cage anions that contain a noble-gas element. The Xe-Br and Xe-Cl bonds are very weakly covalent and can be viewed as σ-hole interactions, similar to those encountered in halogen bonding. However, the halogen atoms in these cases are valence electron lone pair donors, and the σ* Xe-O orbitals are lone pair acceptors.

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

Structure determination from XAFS using high-accuracy measurements of x-ray mass attenuation coefficients of silver, 11 keV-28 keV, and development of an all-energies approach to local dynamical analysis of bond length, revealing variation of effective thermal contributions across the XAFS spectrum.

PubMed

Tantau, L J; Chantler, C T; Bourke, J D; Islam, M T; Payne, A T; Rae, N A; Tran, C Q

2015-07-08

We use the x-ray extended range technique (XERT) to experimentally determine the mass attenuation coefficient of silver in the x-ray energy range 11 kev-28 kev including the silver K absorption edge. The results are accurate to better than 0.1%, permitting critical tests of atomic and solid state theory. This is one of the most accurate demonstrations of cross-platform accuracy in synchrotron studies thus far. We derive the mass absorption coefficients and the imaginary component of the form factor over this range. We apply conventional XAFS analytic techniques, extended to include error propagation and uncertainty, yielding bond lengths accurate to approximately 0.24% and thermal Debye-Waller parameters accurate to 30%. We then introduce the FDMX technique for accurate analysis of such data across the full XAFS spectrum, built on full-potential theory, yielding a bond length accuracy of order 0.1% and the demonstration that a single Debye parameter is inadequate and inconsistent across the XAFS range. Two effective Debye-Waller parameters are determined: a high-energy value based on the highly-correlated motion of bonded atoms (σ(DW) = 0.1413(21) Å), and an uncorrelated bulk value (σ(DW) = 0.1766(9) Å) in good agreement with that derived from (room-temperature) crystallography.

Report B : self-consolidating concrete (SCC) for infrastructure elements - bond, transfer length, and development length of prestressing strand in SCC.

DOT National Transportation Integrated Search

2012-08-01

Due to its economic advantages, the use of self-consolidating concrete (SCC) has : increased rapidly in recent years. However, because SCC mixes typically have decreased : amounts of coarse aggregate and high amounts of admixtures, industry members h...

Insights into the crystal chemistry of Earth materials rendered by electron density distributions: Pauling's rules revisited

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

Gibbs, Gerald V.; Ross, Nancy L.; Cox, David F.

2014-05-20

Pauling's first two rules are examined in terms of the accumulation of the electron density between bonded pairs of atoms for a relatively large number of oxide and silicate crystals and siloxane molecules. The distribution of the electron density shows that the radius of the oxygen atom is not fixed, but that it actually decreases systematically from ~1.40 Å to ~ 0.65 Å as the polarizing power and the electronegativity of the bonded metal atoms increase and the distribution of the O atom is progressively polarized and contracted along the bond vectors by the impact of the bonded interactions. Themore » contractions result in an aspherical oxygen atom that displays as many different bonded “radii” as it has bonded interactions. The bonded radii for the metal atoms match the Shannon and Prewitt ionic radii for the more electropositive atoms like potassium and sodium, but they are systematically larger for the more electronegative atoms like aluminum, silicon and phosphorous. Pauling's first rule is based on the assumption that the radius of the oxide anion is fixed and that the radii of the cations are such that radius sum of the spherical oxide anion and a cation necessarily equals the separation between the cation-anion bonded pair with the coordination number of the cation being determined by the ratio of the radii of the cation and anion. In the case of the bonded radii, the sum of the bonded radii for the metal atoms and the oxide anion necessarily equals the bond lengths by virtue of the way that the bonded radii were determined in the partitioning of the electron density along the bond path into metal and O atom parts. But, the radius ratio for the O and M atoms is an unsatisfactory rule for determining the coordination number of the metal atom inasmuch as a bonded O atom is not, in general, spherical, and its size varies substantially along its bonded directions. But by counting the number of bond paths that radiate from a bonded atom, the coordination number of the atom is determined uniquely independent of the asphericity and sizes of the atom. A power law connection established between the bond lengths and bond strengths for crystals and molecules is mirrored by a comparable power law connection between bond length and the accumulation of the electron density between bonded pairs of atoms, a connection that is consistent with Pauling's electroneutrality postulate that the charges of the atoms in an oxide are negligibly small. The connection indicates that a one-to-one correspondence exists between the accumulation between a pair of bonded atoms and the Pauling bond strength for M-O bonded interaction for all atoms of the periodic table. The connection provides a common basis for understanding the success of the manifold applications that have been made with the bond valence theory model together with the modeling of crystal structures, chemical zoning, leaching and cation transport in batteries and the like. We believe that the wide spread applications of the model in mineralogy and material science owes much of its success to the direct connection between bond strength and the quantum mechanical observable, the electron density distribution. Comparable power law expressions established for the bonded interactions for both crystals and molecules support Pauling's assertion that his second rule has significance for molecules as well as for crystals. A simple expression is found that provides a one to one connection between the accumulation of the electron density between bonded M and O atoms and the Pauling bond strength for all M atoms of the periodic table with ~ 95 % of the variation of the bond strength being explained in terms of a linear dependence on the accumulated electron density. Compelling evidence is presented that supports the argument that the Si-O bonded interactions for tiny siloxane molecules and silicate crystals are chemically equivalent.« less

Nanoindentation methods for wood-adhesive bond lines

Treesearch

Joseph E. Jakes; Donald S. Stone; Charles R. Frihart

2008-01-01

As an adherend, wood is structurally, chemically, and mechanically more complex than metals or plastics, and the largest source of this complexity is wood’s chemical and mechanical inhomogeneities. Understanding and predicting the performance of adhesively bonded wood requires knowledge of the interactions occurring at length scales ranging from the macro down to the...

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.

Weak hydrogen bonds in complexes pairing monohalomethanes with neutral formic acid

NASA Astrophysics Data System (ADS)

Solimannejad, Mohammad; Scheiner, Steve

2006-06-01

Ab initio calculations are used to analyze the interaction between formic acid and CH 3X, for X equal to each of F, Cl, and Br. All minima are cyclic in that they contain more than one H-bond. The most strongly bound contain a OH⋯X bond, along with CH⋯O, and the others contain CH⋯X and CH⋯O interactions. Alterations of the covalent bond lengths within each subunit, and vibrational frequency shifts, coupled with electronic charge shifts, reveal fundamental features of these complexes, and the nature of the interactions. The OH⋯X bond is the strongest of those examined here, followed by CH⋯X and CH⋯O.

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

NASA Astrophysics Data System (ADS)

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

2002-02-01

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

Modeling single molecule junction mechanics as a probe of interface bonding

NASA Astrophysics Data System (ADS)

Hybertsen, Mark S.

2017-03-01

Using the atomic force microscope based break junction approach, applicable to metal point contacts and single molecule junctions, measurements can be repeated thousands of times resulting in rich data sets characterizing the properties of an ensemble of nanoscale junction structures. This paper focuses on the relationship between the measured force extension characteristics including bond rupture and the properties of the interface bonds in the junction. A set of exemplary model junction structures has been analyzed using density functional theory based calculations to simulate the adiabatic potential surface that governs the junction elongation. The junction structures include representative molecules that bond to the electrodes through amine, methylsulfide, and pyridine links. The force extension characteristics are shown to be most effectively analyzed in a scaled form with maximum sustainable force and the distance between the force zero and force maximum as scale factors. Widely used, two parameter models for chemical bond potential energy versus bond length are found to be nearly identical in scaled form. Furthermore, they fit well to the present calculations of N-Au and S-Au donor-acceptor bonds, provided no other degrees of freedom are allowed to relax. Examination of the reduced problem of a single interface, but including relaxation of atoms proximal to the interface bond, shows that a single-bond potential form renormalized by an effective harmonic potential in series fits well to the calculated results. This allows relatively accurate extraction of the interface bond energy. Analysis of full junction models shows cooperative effects that go beyond the mechanical series inclusion of the second bond in the junction, the spectator bond that does not rupture. Calculations for a series of diaminoalkanes as a function of molecule length indicate that the most important cooperative effect is due to the interactions between the dipoles induced by the donor-acceptor bond formation at the junction interfaces. The force extension characteristic of longer molecules such as diaminooctane, where the dipole interaction effects drop to a negligible level, accurately fit to the renormalized single-bond potential form. The results suggest that measured force extension characteristics for single molecule junctions could be analyzed with a modified potential form that accounts for the energy stored in deformable mechanical components in series.

Modeling single molecule junction mechanics as a probe of interface bonding

DOE PAGES

Hybertsen, Mark S.

2017-03-07

Using the atomic force microscope based break junction approach, applicable to metal point contacts and single molecule junctions, measurements can be repeated thousands of times resulting in rich data sets characterizing the properties of an ensemble of nanoscale junction structures. This paper focuses on the relationship between the measured force extension characteristics including bond rupture and the properties of the interface bonds in the junction. We analyzed a set of exemplary model junction structures using density functional theory based calculations to simulate the adiabatic potential surface that governs the junction elongation. The junction structures include representative molecules that bond tomore » the electrodes through amine, methylsulfide, and pyridine links. The force extension characteristics are shown to be most effectively analyzed in a scaled form with maximum sustainable force and the distance between the force zero and force maximum as scale factors. Widely used, two parameter models for chemical bond potential energy versus bond length are found to be nearly identical in scaled form. Furthermore, they fit well to the present calculations of N–Au and S–Au donor-acceptor bonds, provided no other degrees of freedom are allowed to relax. Examination of the reduced problem of a single interface, but including relaxation of atoms proximal to the interface bond, shows that a single-bond potential form renormalized by an effective harmonic potential in series fits well to the calculated results. This, then, allows relatively accurate extraction of the interface bond energy. Analysis of full junction models shows cooperative effects that go beyond the mechanical series inclusion of the second bond in the junction, the spectator bond that does not rupture. Calculations for a series of diaminoalkanes as a function of molecule length indicate that the most important cooperative effect is due to the interactions between the dipoles induced by the donor-acceptor bond formation at the junction interfaces. The force extension characteristic of longer molecules such as diaminooctane, where the dipole interaction effects drop to a negligible level, accurately fit to the renormalized single-bond potential form. Our results suggest that measured force extension characteristics for single molecule junctions could be analyzed with a modified potential form that accounts for the energy stored in deformable mechanical components in series.« less

Modeling single molecule junction mechanics as a probe of interface bonding

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

Hybertsen, Mark S.

Using the atomic force microscope based break junction approach, applicable to metal point contacts and single molecule junctions, measurements can be repeated thousands of times resulting in rich data sets characterizing the properties of an ensemble of nanoscale junction structures. This paper focuses on the relationship between the measured force extension characteristics including bond rupture and the properties of the interface bonds in the junction. We analyzed a set of exemplary model junction structures using density functional theory based calculations to simulate the adiabatic potential surface that governs the junction elongation. The junction structures include representative molecules that bond tomore » the electrodes through amine, methylsulfide, and pyridine links. The force extension characteristics are shown to be most effectively analyzed in a scaled form with maximum sustainable force and the distance between the force zero and force maximum as scale factors. Widely used, two parameter models for chemical bond potential energy versus bond length are found to be nearly identical in scaled form. Furthermore, they fit well to the present calculations of N–Au and S–Au donor-acceptor bonds, provided no other degrees of freedom are allowed to relax. Examination of the reduced problem of a single interface, but including relaxation of atoms proximal to the interface bond, shows that a single-bond potential form renormalized by an effective harmonic potential in series fits well to the calculated results. This, then, allows relatively accurate extraction of the interface bond energy. Analysis of full junction models shows cooperative effects that go beyond the mechanical series inclusion of the second bond in the junction, the spectator bond that does not rupture. Calculations for a series of diaminoalkanes as a function of molecule length indicate that the most important cooperative effect is due to the interactions between the dipoles induced by the donor-acceptor bond formation at the junction interfaces. The force extension characteristic of longer molecules such as diaminooctane, where the dipole interaction effects drop to a negligible level, accurately fit to the renormalized single-bond potential form. Our results suggest that measured force extension characteristics for single molecule junctions could be analyzed with a modified potential form that accounts for the energy stored in deformable mechanical components in series.« less

A Unified Theory for the Blue- and Red-Shifting Phenomena in Hydrogen and Halogen Bonds.

PubMed

Wang, Changwei; Danovich, David; Shaik, Sason; Mo, Yirong

2017-04-11

Typical hydrogen and halogen bonds exhibit red-shifts of their vibrational frequencies upon the formation of hydrogen and halogen bonding complexes (denoted as D···Y-A, Y = H and X). The finding of blue-shifts in certain complexes is of significant interest, which has led to numerous studies of the origins of the phenomenon. Because charge transfer mixing (i.e., hyperconjugation in bonding systems) has been regarded as one of the key forces, it would be illuminating to compare the structures and vibrational frequencies in bonding complexes with the charge transfer effect "turned on" and "turned off". Turning off the charge transfer mixing can be achieved by employing the block-localized wave function (BLW) method, which is an ab initio valence bond (VB) method. Further, with the BLW method, the overall stability gained in the formation of a complex can be analyzed in terms of a few physically meaningful terms. Thus, the BLW method provides a unified and physically lucid way to explore the nature of red- and blue-shifting phenomena in both hydrogen and halogen bonding complexes. In this study, a direct correlation between the total stability and the variation of the Y-A bond length is established based on our BLW computations, and the consistent roles of all energy components are clarified. The n(D) → σ*(Y-A) electron transfer stretches the Y-A bond, while the polarization due to the approach of interacting moieties reduces the HOMO-LUMO gap and results in a stronger orbital mixing within the YA monomer. As a consequence, both the charge transfer and polarization stabilize bonding systems with the Y-A bond stretched and red-shift the vibrational frequency of the Y-A bond. Notably, the energy of the frozen wave function is the only energy component which prefers the shrinking of the Y-A bond and thus is responsible for the associated blue-shifting. The total variations of the Y-A bond length and the corresponding stretching vibrational frequency are thus determined by the competition between the frozen-energy term and the sum of polarization and charge transfer energy terms. Because the frozen energy is composed of electrostatic and Pauli exchange interactions and frequency shifting is a long-range phenomenon, we conclude that long-range electrostatic interaction is the driving force behind the frozen energy term.

Structural Insights and the Surprisingly Low Mechanical Stability of the Au-S Bond in the Gold-Specific Protein GolB.

PubMed

Wei, Wei; Sun, Yang; Zhu, Mingli; Liu, Xiangzhi; Sun, Peiqing; Wang, Feng; Gui, Qiu; Meng, Wuyi; Cao, Yi; Zhao, Jing

2015-12-16

The coordination bond between gold and sulfur (Au-S) has been widely studied and utilized in many fields. However, detailed investigations on the basic nature of this bond are still lacking. A gold-specific binding protein, GolB, was recently identified, providing a unique opportunity for the study of the Au-S bond at the molecular level. We probed the mechanical strength of the gold-sulfur bond in GolB using single-molecule force spectroscopy. We measured the rupture force of the Au-S bond to be 165 pN, much lower than Au-S bonds measured on different gold surfaces (∼1000 pN). We further solved the structures of apo-GolB and Au(I)-GolB complex using X-ray crystallography. These structures showed that the average Au-S bond length in GolB is much longer than the reported average value of Au-S bonds. Our results highlight the dramatic influence of the unique biological environment on the stability and strength of metal coordination bonds in proteins.

Nonmetallic electronegativity equalization and point-dipole interaction model including exchange interactions for molecular dipole moments and polarizabilities.

PubMed

Smalø, Hans S; Astrand, Per-Olof; Jensen, Lasse

2009-07-28

The electronegativity equalization model (EEM) has been combined with a point-dipole interaction model to obtain a molecular mechanics model consisting of atomic charges, atomic dipole moments, and two-atom relay tensors to describe molecular dipole moments and molecular dipole-dipole polarizabilities. The EEM has been phrased as an atom-atom charge-transfer model allowing for a modification of the charge-transfer terms to avoid that the polarizability approaches infinity for two particles at infinite distance and for long chains. In the present work, these shortcomings have been resolved by adding an energy term for transporting charges through individual atoms. A Gaussian distribution is adopted for the atomic charge distributions, resulting in a damping of the electrostatic interactions at short distances. Assuming that an interatomic exchange term may be described as the overlap between two electronic charge distributions, the EEM has also been extended by a short-range exchange term. The result is a molecular mechanics model where the difference of charge transfer in insulating and metallic systems is modeled regarding the difference in bond length between different types of system. For example, the model is capable of modeling charge transfer in both alkanes and alkenes with alternating double bonds with the same set of carbon parameters only relying on the difference in bond length between carbon sigma- and pi-bonds. Analytical results have been obtained for the polarizability of a long linear chain. These results show that the model is capable of describing the polarizability scaling both linearly and nonlinearly with the size of the system. Similarly, a linear chain with an end atom with a high electronegativity has been analyzed analytically. The dipole moment of this model system can either be independent of the length or increase linearly with the length of the chain. In addition, the model has been parametrized for alkane and alkene chains with data from density functional theory calculations, where the polarizability behaves differently with the chain length. For the molecular dipole moment, the same two systems have been studied with an aldehyde end group. Both the molecular polarizability and the dipole moment are well described as a function of the chain length for both alkane and alkene chains demonstrating the power of the presented model.

Double bonds? Studies on the barrier to rotation about the cumulenic C=C bonds of tetraaryl[n]cumulenes (n = 3, 5, 7, 9).

PubMed

Buehringer, Martina U; Padberg, Kevin; Phleps, Martin; Maid, Harald; Placht, Christian; Neiss, Christian; Ferguson, Michael; Goerling, Andreas; Tykwinski, Rik R

2018-03-31

Bonding is the fundamental aspect of organic chemistry, yet the magnitude of C=C bonding in [n]cumulenes as a function of increasing chain length has yet to be experimentally verified for derivatives longer than n = 5. The synthesis of a series of apolar and unsymmetrically substituted tetraaryl[n]cumulenes (n = 3, 5, 7, 9) has been developed and rotational barriers for Z-/E-isomerization have been measured using dynamic VT-NMR spectroscopy. Both experiment and theory confirm a dramatic reduction of the rotational barrier (through estimation of G≠rot for the isomerization) from >24 to 19 to 15 to 11 kcal-1 in [n]cumulenes with n = 3, 5, 7, 9, respectively. Thus, the reduction of cumulenic bonding in longer cumulenes affords bond rotational barriers that are more characteristic of a sterically hindered single bond than that of a double bond. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effects of ligand electronegativity on recoupled pair bonds with application to sulfurane precursors.

PubMed

Lindquist, Beth A; Woon, David E; Dunning, Thom H

2014-07-31

Recoupled pair bonds (RPBs) are conditional bonds-they only form for selected central atoms and ligands. A complete theoretical description of RPBs requires an understanding of the properties of the central atom and ligands that enable such bonds to be formed. In this work, we show that ligand electronegativity is positively correlated with recoupled pair bond strength for a variety of ligands interacting with the 3p(2) pair of sulfur. We also describe substituent (X) effects on the SF(a(4)Σ(-)) state by investigating X2SF species. These effects generally mirror those observed for covalently bound analogues, but we found that recoupled pair bonding can lead to breakdowns in the expected relationships among bond length, strength, and force constant for some of these species. Finally, we compare the properties of two molecules of practical interest that are bound by recoupled pair bonds: the dimethyl sulfur fluoride and hydroxide radicals (DMS-F and DMS-OH).

Kinetics of the Multistep Rupture of Fibrin ‘A-a’ Polymerization Interactions Measured Using Atomic Force Microscopy

PubMed Central

Averett, Laurel E.; Schoenfisch, Mark H.; Akhremitchev, Boris B.; Gorkun, Oleg V.

2009-01-01

Abstract Fibrin, the structural scaffold of blood clots, spontaneously polymerizes through the formation of ‘A-a’ knob-hole bonds. When subjected to external force, the dissociation of this bond is accompanied by two to four abrupt changes in molecular dimension observable as rupture events in a force curve. Herein, the configuration, molecular extension, and kinetic parameters of each rupture event are examined. The increases in contour length indicate that the D region of fibrinogen can lengthen by ∼50% of the length of a fibrin monomer before rupture of the ‘A-a’ interaction. The dependence of the dissociation rate on applied force was obtained using probability distributions of rupture forces collected at different pull-off velocities. These distributions were fit using a model in which the effects of the shape of the binding potential are used to quantify the kinetic parameters of forced dissociation. We found that the weak initial rupture (i.e., event 1) was not well approximated by these models. The ruptured bonds comprising the strongest ruptures, events 2 and 3, had kinetic parameters similar to those commonly found for the mechanical unfolding of globular proteins. The bonds ruptured in event 4 were well described by these analyses, but were more loosely bound than the bonds in events 2 and 3. We propose that the first event represents the rupture of an unknown interaction parallel to the ‘A-a’ bond, events 2 and 3 represent unfolding of structures in the D region of fibrinogen, and event 4 is the rupture of the ‘A-a’ knob-hole bond weakened by prior structural unfolding. Comparison of the activation energy obtained via force spectroscopy measurements with the thermodynamic free energy of ‘A-a’ bond dissociation indicates that the ‘A-a’ bond may be more resistant to rupture by applied force than to rupture by thermal dissociation. PMID:19917237

Validating a Mentoring Relationship Quality Scale: Does Match Strength Predict Match Length?

ERIC Educational Resources Information Center

Rhodes, Jean E.; Schwartz, Sarah E. O.; Willis, Margaret M.; Wu, Max B.

2017-01-01

Youth mentoring relationships have significant potential for promoting positive youth development. Nonetheless, the benefits derived from such relationships depend considerably on the length and quality of the bonds that are created between mentors and youth. Although some attention has been paid to youth's experience of relationship quality, few…

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.

Molecular structure, vibrational spectra, NBO analysis and molecular packing prediction of 3-nitroacetanilide by ab initio HF and density functional theory.

PubMed

Li, Xiao-Hong; Li, Tong-Wei; Ju, Wei-Wei; Yong, Yong-Liang; Zhang, Xian-Zhou

2014-01-24

Quantum chemical calculations of geometries and vibrational wavenumbers of 3-nitroacetanilide (C8H8N2O3) in the ground state were carried out by using ab initio HF and density functional theory (DFT/B3LYP) methods with 6-31+G(*) basis set. The -311++G(**) basis set is also used for B3LYP level. The scaled harmonic vibrational frequencies have been compared with experimental FT-IR spectra. Theoretical vibrational spectra of the title compound were interpreted by means of potential energies distributions (PEDs) using MOLVIB program. The theoretical spectrograms for IR spectra of the title compound have been constructed. The shortening of C-H bond length and the elongation of N-H bond length suggest the existence of weak C-H⋯O and N-H⋯O hydrogen bonds, which is confirmed by the natural bond orbital analysis. In addition, the crystal structure obtained by molecular mechanics belongs to the P2(1) space group, with lattice parameters Z=4, a=14.9989 Å, b=4.0367 Å, c=12.9913 Å, ρ=0.998 g cm(-3). Copyright © 2013 Elsevier B.V. All rights reserved.

Molecular structure, vibrational spectra, NBO analysis and molecular packing prediction of 3-nitroacetanilide by ab initio HF and density functional theory

NASA Astrophysics Data System (ADS)

Li, Xiao-Hong; Li, Tong-Wei; Ju, Wei-Wei; Yong, Yong-Liang; Zhang, Xian-Zhou

2014-01-01

Quantum chemical calculations of geometries and vibrational wavenumbers of 3-nitroacetanilide (C8H8N2O3) in the ground state were carried out by using ab initio HF and density functional theory (DFT/B3LYP) methods with 6-31+G* basis set. The -311++G** basis set is also used for B3LYP level. The scaled harmonic vibrational frequencies have been compared with experimental FT-IR spectra. Theoretical vibrational spectra of the title compound were interpreted by means of potential energies distributions (PEDs) using MOLVIB program. The theoretical spectrograms for IR spectra of the title compound have been constructed. The shortening of Csbnd H bond length and the elongation of Nsbnd H bond length suggest the existence of weak Csbnd H⋯O and Nsbnd H⋯O hydrogen bonds, which is confirmed by the natural bond orbital analysis. In addition, the crystal structure obtained by molecular mechanics belongs to the P21 space group, with lattice parameters Z = 4, a = 14.9989 Å, b = 4.0367 Å, c = 12.9913 Å, ρ = 0.998 g cm-3.

Comprehensive derivation of bond-valence parameters for ion pairs involving oxygen

PubMed Central

Gagné, Olivier Charles; Hawthorne, Frank Christopher

2015-01-01

Published two-body bond-valence parameters for cation–oxygen bonds have been evaluated via the root mean-square deviation (RMSD) from the valence-sum rule for 128 cations, using 180 194 filtered bond lengths from 31 489 coordination polyhedra. Values of the RMSD range from 0.033–2.451 v.u. (1.1–40.9% per unit of charge) with a weighted mean of 0.174 v.u. (7.34% per unit of charge). The set of best published parameters has been determined for 128 ions and used as a benchmark for the determination of new bond-valence parameters in this paper. Two common methods for the derivation of bond-valence parameters have been evaluated: (1) fixing B and solving for R o; (2) the graphical method. On a subset of 90 ions observed in more than one coordination, fixing B at 0.37 Å leads to a mean weighted-RMSD of 0.139 v.u. (6.7% per unit of charge), while graphical derivation gives 0.161 v.u. (8.0% per unit of charge). The advantages and disadvantages of these (and other) methods of derivation have been considered, leading to the conclusion that current methods of derivation of bond-valence parameters are not satisfactory. A new method of derivation is introduced, the GRG (generalized reduced gradient) method, which leads to a mean weighted-RMSD of 0.128 v.u. (6.1% per unit of charge) over the same sample of 90 multiple-coordination ions. The evaluation of 19 two-parameter equations and 7 three-parameter equations to model the bond-valence–bond-length relation indicates that: (1) many equations can adequately describe the relation; (2) a plateau has been reached in the fit for two-parameter equations; (3) the equation of Brown & Altermatt (1985 ▸) is sufficiently good that use of any of the other equations tested is not warranted. Improved bond-valence parameters have been derived for 135 ions for the equation of Brown & Altermatt (1985 ▸) in terms of both the cation and anion bond-valence sums using the GRG method and our complete data set. PMID:26428406

Psychodynamic group psychotherapy: impact of group length and therapist professional characteristics on development of therapeutic alliance.

PubMed

Lorentzen, Steinar; Bakali, Jan Vegard; Hersoug, Anne Grete; Hagtvet, Knut A; Ruud, Torleif; Høglend, Per

2012-09-01

Little research has been done on therapeutic alliance in group psychotherapy, especially the impact of treatment duration and therapist professional characteristics. Therapeutic alliance was rated by patients on the Working Alliance Inventory-Short Form at three time points (sessions 3, 10 and 17) in a randomized controlled trial of short-term and long-term psychodynamic group psychotherapy. As predictors we selected therapist clinical experience and length of didactic training, which have demonstrated ambiguous results in previous research. Linear latent variable growth curve models (structural equation modeling) were developed for the three Working Alliance Inventory-Short Form subscales bond, task and goal. We found a significant variance in individual growth curves (intercepts and slopes) but no differential development due to group length. Longer therapist formal training had a negative impact on early values of subscale task in both treatments. There was an interaction between length of the therapists' clinical experience and group length on early bond, task and goal: therapists with longer clinical experience were rated lower on initial bond in the long-term group but less so in the short-term group. Longer clinical experience influenced initial task and goal positively in the short-term group but was unimportant for task or significantly negative for goal in the long-term group. There was no mean development of alliance, and group length did not differentially impact the alliance during 6 months. Early ratings of the three Working Alliance Inventory-Short Form subscales partly reflected different preparations of patients in the two group formats, partly therapist characteristics, but more research is needed to see how these aspects impact alliance development and outcome. Therapists should pay attention to all three aspects of the alliance, when they prepare patients for group therapy. In psychodynamic groups, length of therapy does not differentiate the overall level or the development of member-leader alliance. Within psychodynamic groups, each individual appear to have their unique perception of the member-leader alliance. Therapists with longer formal psychotherapy training may be less successful in establishing early agreement with patients on the tasks of psychodynamic group psychotherapy. Patients perceive a somewhat lower degree of early emotional bonding with the more clinically experienced therapists in long-term psychodynamics groups. Therapists with more clinical experience may contribute to a stronger degree of initial agreement with patients on the tasks and goals of short-term group psychotherapy. Copyright © 2011 John Wiley & Sons, Ltd.

Blood lead: Its effect on trace element levels and iron structure in hemoglobin

NASA Astrophysics Data System (ADS)

Jin, C.; Li, Y.; Li, Y. L.; Zou, Y.; Zhang, G. L.; Normura, M.; Zhu, G. Y.

2008-08-01

Lead is a ubiquitous environmental pollutant that induce a broad range of physiological and biochemical dysfunctions. The purpose of this study was to investigate its effects on trace elements and the iron structure in hemoglobin. Blood samples were collected from rats that had been exposed to lead. The concentration of trace elements in whole blood and blood plasma was determined by ICP-MS and the results indicate that lead exists mainly in the red blood cells and only about 1-3% in the blood plasma. Following lead exposure, the concentrations of zinc and iron in blood decrease, as does the hemoglobin level. This indicates that the heme biosynthetic pathway is inhibited by lead toxicity and that lead poisoning-associated anemia occurs. The selenium concentration also decreases after lead exposure, which may lead to an increased rate of free radical production. The effect of lead in the blood on iron structure in hemoglobin was determined by EXAFS. After lead exposure, the Fe-O bond length increases by about 0.07 Å and the Fe-Np bond length slightly increases, but the Fe-N ɛ bond length remains unchanged. This indicates that the blood content of Hb increases, but that the content of HbO 2 decreases.

Infrared study of matrix-isolated ethyl cyanide: simulation of the photochemistry in the atmosphere of Titan.

PubMed

Toumi, A; Piétri, N; Couturier-Tamburelli, I

2015-11-11

Low-temperature Ar matrix isolation has been carried out to investigate the infrared spectrum of ethyl cyanide (CH3CH2CN), a molecule present in the atmosphere of Titan. The λ > 120 nm and λ > 230 nm photolysis reactions of ethyl cyanide in an Ar matrix were also performed in order to compare the behaviour of this compound when it is submitted to high and low energetic radiations. These different wavelengths have been used with the aim to reproduce the radiation reaching the various parts of the atmosphere. Several photoproducts have been identified during photolysis such as vinyl cyanide (CH2[double bond, length as m-dash]CHCN), cyanoacetylene (HC3N), and ethylene/hydrogen cyanide (C2H4/HCN), ethylene/hydrogen isocyanide (C2H4/HNC), acetylene/hydrogen cyanide (C2H2/HCN), acetylene/hydrogen isocyanide (C2H2/HNC), and acetylene:methylenimine (C2H2:HNCH2) complexes. Ethyl isocyanide (CH3CH2NC) and a ketenimine form (CH3CH[double bond, length as m-dash]C[double bond, length as m-dash]NH) have been identified as well. Photoproduct identification and spectral assignments were done using previous studies and density functional theory (DFT) calculations with the B3LYP/cc-pVTZ basis set.

Bond length (Ti-O) dependence of nano ATO3-based (A = Pb, Ba, Sr) perovskite structures: Optical investigation in IR range

NASA Astrophysics Data System (ADS)

Ghasemifard, Mahdi; Ghamari, Misagh; Okay, Cengiz

2018-01-01

In the current study, ABO3 (A = Pb, Ba, Sr and B = Ti) perovskite structures are produced by the auto-combustion route by using citric acid (CA) and nitric acid (NA) as fuel and oxidizer. The X-ray diffraction (XRD) patterns confirmed the perovskite nanostructure with cubic, tetragonal, and rhombohedral for SrTiO3, PbTiO3, and BaTiO3, respectively. Using Scherrer’s equation and XRD pattern, the average crystallite size of the samples were acquired. The effect of Ti-O bond length on the structure of the samples was evaluated. The type of structures obtained depends on Ti-O bond length which is in turn influenced by A2+ substitutions. Microstructural studies of nanostructures calcined at 850∘C confirmed the formation of polyhedral particles with a narrow size distribution. The values of optical band gaps were measured and the impact of A2+ was discussed. The optical properties such as the complex refractive index and dielectric function were calculated by IR spectroscopy and Kramers-Kronig (K-K) relations. Lead, as the element with the highest density as compared to other elements, changes the optical constants, remarkably due to altering titanium and oxygen distance in TO6 groups.

The atomic geometries of GaP(110) and ZnS(110) revisited - A structural ambiguity and its resolution

NASA Technical Reports Server (NTRS)

Duke, C. B.; Paton, A.; Kahn, A.

1984-01-01

The atomic geometries of GaP(110) and ZnS(110) are reexamined using the R-factor minimization procedure, developed for GaAs(110) and previously applied to GaSb(110), ZnTe(110), InAs(110), and AlP(110), to analyze experimental elastic low-energy electron diffraction intensities. Unlike most of the earlier cases, both GaP(110) and ZnS(110) exhibit two distinct minimum-Rx structures which cannot be distinguished by analysis of the shapes of the intensity profiles alone. One region of best-fit structures exhibits top-layer displacements normal to the surface characterized by a small bond-length-conserving, top-layer rotation (omega aproximately 2-3 deg), a small relaxation of the top layer away from the surface, and a 10 percent expansion of the top-layer bond length. The other region of best-fit structures is the conventional one: nearly bond-length-conserving rotations of omega = 26-28 deg in the top layer and a small (approximately 0.1 A) contraction of the uppermost layer spacing. This ambiguity may be removed, however, by consideration of the integrated beam intensities. The conventional region of structural parameters provides a decisively better description of the relative magnitudes of the integrated beam intensities and hence is the preferred structure.

Both the stroma and thylakoid lumen of tobacco chloroplasts are competent for the formation of disulphide bonds in recombinant proteins.

PubMed

Bally, Julia; Paget, Eric; Droux, Michel; Job, Claudette; Job, Dominique; Dubald, Manuel

2008-01-01

Plant chloroplasts are promising vehicles for recombinant protein production, but the process of protein folding in these organelles is not well understood in comparison with that in prokaryotic systems, such as Escherichia coli. This is particularly true for disulphide bond formation which is crucial for the biological activity of many therapeutic proteins. We have investigated the capacity of tobacco (Nicotiana tabacum) chloroplasts to efficiently form disulphide bonds in proteins by expressing in this plant cell organelle a well-known bacterial enzyme, alkaline phosphatase, whose activity and stability strictly depend on the correct formation of two intramolecular disulphide bonds. Plastid transformants have been generated that express either the mature enzyme, localized in the stroma, or the full-length coding region, including its signal peptide. The latter has the potential to direct the recombinant alkaline phosphatase into the lumen of thylakoids, giving access to this even less well-characterized organellar compartment. We show that the chloroplast stroma supports the formation of an active enzyme, unlike a normal bacterial cytosol. Sorting of alkaline phosphatase to the thylakoid lumen occurs in the plastid transformants translating the full-length coding region, and leads to larger amounts and more active enzyme. These results are compared with those obtained in bacteria. The implications of these findings on protein folding properties and competency of chloroplasts for disulphide bond formation are discussed.

A computational study of hydrogen-bonded X3CH⋯YZ (X = Cl, F, NC; YZ = FLi, BF, CO, N2) complexes

NASA Astrophysics Data System (ADS)

McDowell, Sean A. C.

2018-03-01

An MP2/6-311++G(3df,3pd) computational study of a series of hydrogen-bonded complexes X3CH⋯YZ (X = Cl, F, NC; YZ = FLi, BF, CO, N2) was undertaken to assess the trends in the relative stability and other molecular properties with variation of both the X group and the chemical hardness of the Y atom of YZ. The red- and blue-shifting propensities of the proton donor X3CH were investigated by considering the Csbnd H bond length change and its associated vibrational frequency shift. The proton donor Cl3CH, which has a positive dipole moment derivative with respect to Csbnd H bond extension, tends to form red-shifted complexes, this tendency being modified by the hardness (and dipole moment) associated with the proton acceptor. On the other hand, F3CH has a negative dipole moment derivative and tends to form blue-shifted complexes, suggesting that as X becomes more electron-withdrawing, the proton donor should have a negative dipole moment derivative and form blue-shifted complexes. Surprisingly, the most polar proton donor (NC)3CH was found to have a positive dipole moment derivative and produces red-shifted complexes. A perturbative model was found useful in rationalizing the trends for the Csbnd H bond length change and associated frequency shift.

Molecular dynamics modeling of PPTA crystallite mechanical properties in the presence of defects

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

Mercer, Brian; Zywicz, Edward; Papadopoulos, Panayiotis

Here, the mechanical properties of PPTA crystallites, the fundamental building blocks of aramid polymer fibers such as Kevlar® and Twaron®, are studied here using molecular dynamics simulations. The ReaxFF interatomic potential is employed to study crystallite failure via covalent and hydrogen bond rupture in constant strain-rate tensile loading simulations. Emphasis is placed on analyzing how chain-end defects in the crystallite influence its mechanical response and fracture strength. Chain-end defects are found to affect the behavior of nearby chains in a region of the PPTA crystallite that is small relative to the typical crystallite size in manufactured aramid fibers. The centralmore » Csingle bondN bond along the backbone chain is identified as the weakest in the PPTA polymer chain backbone in dynamic strain-to-failure simulations of the crystallite. It is found that clustering of chain-ends leads to reduced crystallite strength and crystallite failure via hydrogen bond rupture and chain sliding, whereas randomly scattered defects impact the strength less and failure is by covalent bond rupture and chain scission. The axial crystallite modulus increases with increasing chain length and is independent of chain-end defect locations. On the basis of these findings, a theoretical model is proposed to predict the axial modulus as a function of chain length.« less

Molecular dynamics modeling of PPTA crystallite mechanical properties in the presence of defects

DOE PAGES

Mercer, Brian; Zywicz, Edward; Papadopoulos, Panayiotis

2017-03-11

Here, the mechanical properties of PPTA crystallites, the fundamental building blocks of aramid polymer fibers such as Kevlar® and Twaron®, are studied here using molecular dynamics simulations. The ReaxFF interatomic potential is employed to study crystallite failure via covalent and hydrogen bond rupture in constant strain-rate tensile loading simulations. Emphasis is placed on analyzing how chain-end defects in the crystallite influence its mechanical response and fracture strength. Chain-end defects are found to affect the behavior of nearby chains in a region of the PPTA crystallite that is small relative to the typical crystallite size in manufactured aramid fibers. The centralmore » Csingle bondN bond along the backbone chain is identified as the weakest in the PPTA polymer chain backbone in dynamic strain-to-failure simulations of the crystallite. It is found that clustering of chain-ends leads to reduced crystallite strength and crystallite failure via hydrogen bond rupture and chain sliding, whereas randomly scattered defects impact the strength less and failure is by covalent bond rupture and chain scission. The axial crystallite modulus increases with increasing chain length and is independent of chain-end defect locations. On the basis of these findings, a theoretical model is proposed to predict the axial modulus as a function of chain length.« less

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.

Fracture Behavior in Nylon 6 Fibers. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Lloyd, B. A.

1972-01-01

Electron paramagnetic resonance (EPR) techniques are used to determine the number of free radicals produced during deformation leading to fracture of nylon 6 fibers. A reaction rate molecular model is proposed to explain some of the deformation and bond rupture behavior leading to fracture. High-strength polymer fibers are assumed to consist of a sandwich structure of disordered and ordered regions along the fiber axis. In the disordered or critical flaw regions, tie chains connecting the ordered or crystalline block regions are assumed to have a statistical distribution in length. These chains are, therefore, subjected to different stresses. The effective length distribution was determined by EPR. The probability of bond rupture was assumed to be controlled by reaction-rate theory with a stress-aided activation energy and behavior of various loadings determined by numerical techniques. The model is successfully correlated with experimental stress, strain, and bond rupture results for creep, constant rate loadings, cyclic stress, stress relaxation and step strain tests at room temperature.

Driving force for hydrophobic interaction at different length scales.

PubMed

Zangi, Ronen

2011-03-17

We study by molecular dynamics simulations the driving force for the hydrophobic interaction between graphene sheets of different sizes down to the atomic scale. Similar to the prediction by Lum, Chandler, and Weeks for hard-sphere solvation [J. Phys. Chem. B 1999, 103, 4570-4577], we find the driving force to be length-scale dependent, despite the fact that our model systems do not exhibit dewetting. For small hydrophobic solutes, the association is purely entropic, while enthalpy favors dissociation. The latter is demonstrated to arise from the enhancement of hydrogen bonding between the water molecules around small hydrophobes. On the other hand, the attraction between large graphene sheets is dominated by enthalpy which mainly originates from direct solute-solute interactions. The crossover length is found to be inside the range of 0.3-1.5 nm(2) of the surface area of the hydrophobe that is eliminated in the association process. In the large-scale regime, different thermodynamic properties are scalable with this change of surface area. In particular, upon dimerization, a total and a water-induced stabilization of approximately 65 and 12 kJ/mol/nm(2) are obtained, respectively, and on average around one hydrogen bond is gained per 1 nm(2) of graphene sheet association. Furthermore, the potential of mean force between the sheets is also scalable except for interplate distances smaller than 0.64 nm which corresponds to the region around the barrier for removing the last layer of water. It turns out that, as the surface area increases, the relative height of the barrier for association decreases and the range of attraction increases. It is also shown that, around small hydrophobic solutes, the lifetime of the hydrogen bonds is longer than in the bulk, while around large hydrophobes it is the same. Nevertheless, the rearrangement of the hydrogen-bond network for both length-scale regimes is slower than in bulk water. © 2011 American Chemical Society

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.

Thermoplastic Ribbon-Ply Bonding Model

NASA Technical Reports Server (NTRS)

Hinkley, Jeffrey A.; Marchello, Joseph M.; Messier, Bernadette C.

1996-01-01

The aim of the present work was to identify key variables in rapid weldbonding of thermoplastic tow (ribbon) and their relationship to matrix polymer properties and to ribbon microstructure. Theoretical models for viscosity, establishment of ply-ply contact, instantaneous (Velcro) bonding, molecular interdiffusion (healing), void growth suppression, and gap filling were reviewed and synthesized. Consideration of the theoretical bonding mechanisms and length scales and of the experimental weld/peel data allow the prediction of such quantities as the time and pressure required to achieve good contact between a ribbon and a flat substrate, the time dependence of bond strength, pressures needed to prevent void growth from dissolved moisture and conditions for filling gaps and smoothing overlaps.

2-Acetyl-1,1,3,3-tetra­methyl­guanidine

PubMed Central

Tiritiris, Ioannis

2012-01-01

In the mol­ecule of the title compound, C7H15N3O, the central C atom is surrounded in a nearly ideal trigonal–planar geometry by three N atoms. The C—N bond lengths in the CN3 unit are 1.3353 (13), 1.3463 (12) and 1.3541 (13) Å, indicating an inter­mediate character between a single and a double bond for each C—N bond. The bonds between the N atoms and the terminal C-methyl groups all have values close to that of a typical single bond [1.4526 (13)–1.4614 (14) Å]. In the crystal, the guanidine mol­ecules are connected by weak C—H⋯O and C—H⋯N hydrogen bonds, generating layers parallel to the ab plane. PMID:23125768

Hydrogen bond asymmetric local potentials in compressed ice.

PubMed

Huang, Yongli; Ma, Zengsheng; Zhang, Xi; Zhou, Guanghui; Zhou, Yichun; Sun, Chang Q

2013-10-31

A combination of the Lagrangian mechanics of oscillators vibration, molecular dynamics decomposition of volume evolution, and Raman spectroscopy of phonon relaxation has enabled us to resolve the asymmetric, local, and short-range potentials pertaining to the hydrogen bond (O:H-O) in compressed ice. Results show that both oxygen atoms in the O:H-O bond shift initially outwardly with respect to the coordination origin (H), lengthening the O-O distance by 0.0136 nm from 0.2597 to 0.2733 nm by Coulomb repulsion between electron pairs on adjacent oxygen atoms. Both oxygen atoms then move toward right along the O:H-O bond by different amounts upon being compressed, approaching identical length of 0.11 nm. The van der Waals potential VL(r) for the O:H noncovalent bond reaches a valley at -0.25 eV, and the lowest exchange VH(r) for the H-O polar-covalent bond is valued at -3.97 eV.

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.

The effect of surface and interface on Neel transition temperature of low-dimensional antiferromagnetic materials

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

Zhang, Wen; Zhou, Zhaofeng, E-mail: zfzhou@xtu.edu.cn; Zhong, Yuan

2015-11-15

Incorporating the bond order-length-strength (BOLS) notion with the Ising premise, we have modeled the size dependence of the Neel transition temperature (T{sub N}) of antiferromagnetic nanomaterials. Reproduction of the size trends reveals that surface atomic undercoordination induces bond contraction, and interfacial hetero-coordination induces bond nature alteration. Both surface and interface of nanomaterials modulate the T{sub N} by adjusting the atomic cohesive energy. The T{sub N} is related to the atomic cohesive/exchange energy that is lowered by the coordination number (CN) imperfection of the undercoordinated atoms near the surface and altered by the changed bond nature of epitaxial interface. A numericalmore » match between predictions and measurements reveals that the T{sub N} of antiferromagnetic nanomaterials declines with reduced size and increases with both the strengthening of heterogeneous bond and the increase of the bond number.« less

Bond characteristics of reinforcing steel embedded in geopolymer concrete

NASA Astrophysics Data System (ADS)

Kathirvel, Parthiban; Thangavelu, Manju; Gopalan, Rashmi; Raja Mohan Kaliyaperumal, Saravana

2017-07-01

The force transferring between reinforcing steel and the surrounding concrete in reinforced concrete is influenced by several factors. Whereas, the study on bond behaviour of geopolymer concrete (GPC) is lagging. In this paper, an experimental attempt has been made to evaluate the geopolymer concrete bond with reinforcing steel of different diameter and embedded length using standard pull out test. The geopolymer concrete is made of ground granulated blast furnace slag (GGBFS) as geopolymer source material (GSM). The tests were conducted to evaluate the development of bond between steel and concrete of grade M40 and M50 with 12 and 16 mm diameter reinforcing steel for geopolymer and cement concrete mixes and to develop a relation between bond strength and compressive strength. From the experimental results, it has been observed that the bond strength of the geopolymer concrete mixes was more compared to the cement concrete mixes and increases with the reduction in the diameter of the bar.

Cis Effects in the Cobalt Corrins. 1. Crystal Structures of 10-Chloroaquacobalamin Perchlorate, 10-Chlorocyanocobalamin, and 10-Chloromethylcobalamin.

PubMed

Brown, Kenneth L.; Cheng, Shifa; Zou, Xiang; Zubkowski, Jeffrey D.; Valente, Edward J.; Knapton, Leanne; Marques, Helder M.

1997-08-13

The crystal structures of 10-chloroaquacobalamin perchlorate hydrate (10-Cl-H(2)OCbl.ClO(4)) (Mo Kalpha, 0.710 73 Å, monoclinic system, P2(1), a = 11.922(4) Å, b = 26.592(10) Å, c = 13.511(5) Å, beta = 93.05(3) degrees, 10 535 independent reflections, R(1) = 0.0426), 10-chlorocyanocobalamin-acetone hydrate (10-Cl-CNCbl) (Mo Kalpha, 0.710 73 Å, orthorhombic system, P2(1)2(1)2(1), a = 16.24(3) Å, b = 21.85(5) Å, c = 26.75(8) Å, 7699 independent reflections, R(1) = 0.0698), and 10-chloromethylcobalamin-acetone hydrate (10-Cl-MeCbl) (Mo Kalpha, 0.71073 Å, orthorhombic system, P2(1)2(1)2(1), a = 16.041(14) Å, b = 22.13(2) Å, c = 26.75(4) Å, 6792 independent reflections, R(1) = 0.0554), in which the C10 meso H is substituted by Cl, are reported. An unusual feature of the structures is disorder in the C ring, consistent with a two-site occupancy in which the major conformation has the C46 methyl group in the usual position, "upwardly" axial, and the C47 methyl group equatorial, while in the minor conformation both are pseudoequatorial, above and below the corrin ring. (13)C NMR chemical shifts of C46, C47, C12, and C13 suggest that the C ring disorder may persist in solution as a ring flip. Since molecular dynamics simulations fail to reveal any population of the minor conformation, the effect is likely to be electronic rather than steric. The axial bond lengths in 10-Cl-MeCbl are very similar to those in MeCbl (d(Co)(-)(C) = 1.979(7) vs 1.99(2); to 5,6-dimethylbenzimidazole, d(Co)(-)(NB3) = 2.200(7) vs 2.19(2)), but the bonds to the four equatorial N donors, d(Co)(-)(N(eq)), are on average 0.05 Å shorter. In 10-Cl-CNCbl, d(Co)(-)(C) and d(Co)(-)(NB3) are longer (by 0.10(2) and 0.03(1) Å, respectively) than the bond lengths observed in CNCbl itself, while conversely, the C-N bond length is shorter by 0.06(2) Å, but there is little difference in d(Co)(-)(N(eq)). The Co-O bond length to coordinated water in 10-Cl-H(2)OCbl(+) is very similar to that found in H(2)OCbl(+) itself, but the d(Co)(-)(NB3) bond is longer (1.967 vs1.925(2) Å), while the average d(Co)(-)(N(eq)) is very similar. The coordinated water molecule in 10-Cl-H(2)OCbl(+) is hydrogen bonded to the c side chain carbonyl oxygen, as in H(2)OCbl(+). NMR observations indicate that the H bond between coordinated H(2)O and the c side chain amide persists in solution. The equilibrium constant, K(Co), for coordination of bzm to Co(III) is smaller in 10-Cl-MeCbl and 10-Cl-CNCbl than in their C10-unsubstituted analogs (181 vs 452; 4.57 x 10(3) vs 3.35 x 10(5)), but could not be determined for 10-Cl-H(2)OCbl because hydrolysis of the phosphodiester is competitive with the establishment of the base-off equilibrium. Substitution of H by Cl at C10 causes the bands in the electronic spectrum of 10-Cl-XCbl complexes to move to lower energy, which is consistent with an increase in electron density in the corrin pi-conjugated system. This increased electron density is not due to greater electron donation from the axial ligand as bonds between these and the metal are either longer (not shorter) or unchanged, and it most probably arises from pi-donation to the corrin by Cl at C10. As the donor power of X increases (H(2)O < CN(-) < Me), the corrin ring becomes more flexible to deformation, and the number of bond lengths and bond angles that are significantly different in XCbl and 10-Cl-XCbl increases; importantly, the C10-Cl bond length, d(C10)(-)(Cl), increases as well. Thus, despite the fact that chlorine is an inductively electron withdrawing substituent, its resonance electron donation is the more important effect on electron distribution in the corrin ring. Mulliken charges obtained from semiempirical RHF-SCF MO calculations using the ZINDO/1 model on XCbl and their 10-Cl analogs at the crystal structure geometry are shown to correlate reasonably well with (13)C NMR shifts and may be used to determine the pattern of electron distribution in these complexes. Substitution by Cl at C10 causes an increase in charge density at Co when X = H(2)O and CN(-), while the charge density on the four equatorial N donors remains virtually unchanged, but a decrease when X = Me, while the charge density on the equatorial N donors also decreases. In response, d(Co)(-)(NB3) increases in the first two complexes but the equatorial bond lengths remain virtually unchanged, while d(Co)(-)(NB3) remains unchanged and the average d(Co)(-)(N(eq)) decreases in 10-Cl-MeCbl. Furthermore, the partial charge on chlorine increases as the donor power of X increases. The small decrease in the pK(a) of coordinated H(2)O in 10-Cl-H(2)OCbl(+) compared to H(2)OCbl(+) itself (7.65 vs 8.09) is due to a decreased charge density on oxygen in 10-Cl-OHCbl compared to OHCbl. The picture that emerges, therefore, is of competitive electron donation by X and Cl toward the corrin system. In 10-Cl-CNCbl, the decrease in the C&tbd1;N bond length as Co-C increases compared to CNCbl suggests that dpi-ppi bonding between cobalt and cyanide is important. (13)C and (15)N NMR observations on 10-Cl-(13)C(15)NCbl are consistent with these effects.

Possible steric control of the relative strength of chelation enhanced fluorescence for zinc(II) compared to cadmium(II): metal ion complexing properties of tris(2-quinolylmethyl)amine, a crystallographic, UV-visible, and fluorometric study.

PubMed

Williams, Neil J; Gan, Wei; Reibenspies, Joseph H; Hancock, Robert D

2009-02-16

The idea is examined that steric crowding in ligands can lead to diminution of the chelation enhanced fluorescence (CHEF) effect in complexes of the small Zn(II) ion as compared to the larger Cd(II) ion. Steric crowding is less severe for the larger ion and for the smaller Zn(II) ion leads to Zn-N bond length distortion, which allows some quenching of fluorescence by the photoinduced electron transfer (PET) mechanism. Some metal ion complexing properties of the ligand tris(2-quinolylmethyl)amine (TQA) are presented in support of the idea that more sterically efficient ligands, which lead to less M-N bond length distortion with the small Zn(II) ion, will lead to a greater CHEF effect with Zn(II) than Cd(II). The structures of [Zn(TQA)H(2)O](ClO(4))(2).1.5 H(2)O (1), ([Pb(TQA)(NO(3))(2)].C(2)H(5)OH) (2), ([Ag(TQA)(ClO(4))]) (3), and (TQA).C(2)H(5)OH (4) are reported. In 1, the Zn(II) is 5-coordinate, with four N-donors from the ligand and a water molecule making up the coordination sphere. The Zn-N bonds are all of normal length, showing that the level of steric crowding in 1 is not sufficient to cause significant Zn-N bond length distortion. This leads to the observation that, as expected, the CHEF effect in the Zn(II)/TQA complex is much stronger than that in the Cd(II)/TQA complex, in contrast to similar but more sterically crowded ligands, where the CHEF effect is stronger in the Cd(II) complex. The CHEF effect for TQA with the metal ions examined varies as Zn(II) > Cd(II) > Ni(II) > Pb(II) > Hg(II) > Cu(II). The structure of 2 shows an 8-coordinate Pb(II), with evidence of a stereochemically active lone pair, and normal Pb-N bond lengths. In 3, the Ag(I) is 5-coordinate, with four N-donors from the TQA and an oxygen from the perchlorate. The Ag(I) shows no distortion toward linear 2-coordinate geometry, and the Ag-N bonds fall slightly into the upper range for Ag-N bonds in 5-coordinate complexes. The structure of 4 shows the TQA ligand to be involved in pi-stacking between quinolyl groups from adjacent TQA molecules. Formation constants determined by UV-visible spectroscopy are reported in 0.1 M NaClO(4) at 25 degrees C for TQA with Zn(II), Cd(II), and Pb(II). When compared with other similar ligands, one sees that, as the level of steric crowding increases, the stability decreases most with the small Zn(II) ion and least with the large Pb(II) ion. This is in accordance with the idea that TQA has a moderate level of steric crowding and that steric crowding increases for TQA analogs tris(2-pyridylmethyl)amine (TPyA) < TQA < tris(6-methyl-2-pyridyl)amine (TMPyA).

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

NASA Astrophysics Data System (ADS)

Hansma, Paul

2007-03-01

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

Time-of-flight neutron powder diffraction study on the third row transition metal hexafluorides WF6, OsF6, and PtF6

NASA Astrophysics Data System (ADS)

Marx, R.; Seppelt, K.; Ibberson, R. M.

1996-05-01

A neutron diffraction study on the third-row transition metal hexafluorides MF6 (M≡W, Os, Pt) has been performed using the high resolution neutron powder diffractometer (HRPD) at the spallation source ISIS, England. The previously unknown structures of the low-temperature phases of OsF6 and PtF6 are reported. WF6, OsF6, and PtF6, which exhibit a (5dt2g)0, (5dt2g)2, and (5dt2g)4 electronic configuration, respectively, are found to be isostructural and crystallize in the UF6 structure, space group Pmnb, (No. 62). The geometry of the MF6 molecules is to good approximation octahedral for each compound, the mean M-F bond length increasing only slightly from 182.5 (W) to 185.0 (Pt). For WF6 deviations from ideal octahedral geometry are only marginally significant [181.8(2) to 183.2(2) pm] and may be interpreted on the basis of packing effects. Deviations for the d2 complex OsF6 are somewhat larger [181.5(2) to 184.4(3) pm] and may be assumed to be caused by packing effects essentially the same as for WF6, in addition to a first-order Jahn-Teller effect arising from the (5dt2g)2 electronic configuration. While eliminating the effects of packing by a comparison of individual M-F bond lengths for WF6 and OsF6, the OsF6 molecule shows to have D4h symmetry with two apical M-F bonds about 1.8 pm longer than the four equatorial bonds as a result of the Jahn-Teller distortion. Only small deviations from ideal octahedral geometry [184.4(3) to 185.8(3) pm] are found for the d4 complex PtF6. Within the series W to Pt a substantial shortening of the F...F van der Waals contact distances is observed. This shortening more than compensates for the increase in the M-F bond lengths and leads to unit cell volumes and cell parameters decreasing continuously from W to Pt. The variation of F...F contact distances and M-F bond lengths may be rationalized in terms of polarization of the F-ligands in the field of the highly charged nuclei of the central atoms which are only incompletely shielded by the 5d electrons.

Mathematical analysis of compressive/tensile molecular and nuclear structures

NASA Astrophysics Data System (ADS)

Wang, Dayu

Mathematical analysis in chemistry is a fascinating and critical tool to explain experimental observations. In this dissertation, mathematical methods to present chemical bonding and other structures for many-particle systems are discussed at different levels (molecular, atomic, and nuclear). First, the tetrahedral geometry of single, double, or triple carbon-carbon bonds gives an unsatisfying demonstration of bond lengths, compared to experimental trends. To correct this, Platonic solids and Archimedean solids were evaluated as atoms in covalent carbon or nitrogen bond systems in order to find the best solids for geometric fitting. Pentagonal solids, e.g. the dodecahedron and icosidodecahedron, give the best fit with experimental bond lengths; an ideal pyramidal solid which models covalent bonds was also generated. Second, the macroscopic compression/tension architectural approach was applied to forces at the molecular level, considering atomic interactions as compressive (repulsive) and tensile (attractive) forces. Two particle interactions were considered, followed by a model of the dihydrogen molecule (H2; two protons and two electrons). Dihydrogen was evaluated as two different types of compression/tension structures: a coaxial spring model and a ring model. Using similar methods, covalent diatomic molecules (made up of C, N, O, or F) were evaluated. Finally, the compression/tension model was extended to the nuclear level, based on the observation that nuclei with certain numbers of protons/neutrons (magic numbers) have extra stability compared to other nucleon ratios. A hollow spherical model was developed that combines elements of the classic nuclear shell model and liquid drop model. Nuclear structure and the trend of the "island of stability" for the current and extended periodic table were studied.

The effect of Ga vacancies on the defect and magnetic properties of Mn-doped GaN

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

Kang, Joongoo; Chang, K. J.; Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea and Korea Institute for Advanced Study, Seoul 130-722

2007-10-15

We perform first-principles theoretical calculations to investigate the effect of the presence of Ga vacancy on the defect and magnetic properties of Mn-doped GaN. When a Ga vacancy (V{sub Ga}) is introduced to the Mn ions occupying the Ga lattice sites, a charge transfer occurs from the Mn d band to the acceptor levels of V{sub Ga}, and strong Mn-N bonds are formed between the Mn ion and the N atoms in the neighborhood of V{sub Ga}. The charge transfer and chemical bonding effects significantly affect the defect and magnetic properties of Mn-doped GaN. In a Mn-V{sub Ga} complex, whichmore » consists of a Ga vacancy and one Mn ion, the dangling bond orbital of the N atom involved in the Mn-N bond is electrically deactivated, and the remaining dangling bond orbitals of V{sub Ga} lead to the shallowness of the defect level. When a Ga vacancy forms a complex with two Mn ions located at a distance of about 6 A, which corresponds to the percolation length in determining the Curie temperature in diluted Mn-doped GaN, the Mn d band is broadened and the density of states at the Fermi level is reduced due to two strong Mn-N bonds. Although the broadening and depopulation of the Mn d band weaken the ferromagnetic stability between the Mn ions, the ferromagnetism is still maintained because of the lack of antiferromagnetic superexchange interactions at the percolation length.« less

A quantum chemistry study of Qinghaosu

NASA Astrophysics Data System (ADS)

Gu, Jian-De; Chen, Kai-Xian; Jiang, Hua-Liang; Zhu, Wei-Liang; Chen, Jian-Zhong; Ji, Ru-Yun

1997-10-01

The powerful anti-malarial drug, Qinghaosu (Artemisinin), has been studied using ab initio methods. The DFT B3LYP method with the 6-31G ∗ basis set gives an excellent geometry compared to experiments, especially for the OO bond length and the 1,2,4-Trioxane ring subsystem. The R(OO) bond length predicted at this level is 1.460 Å, only 0.018 Å shorter than the experimental measurement. The vibrational analysis shows that the OO stretching mode is combined with the OC vibration mode, having the character of an OOC entity. The OO vibrational band at 722 cm -1 suggested in the experimental studies has been assigned as 1,2,4-trioxane ring breathing.

Dipropyl 3,6-diphenyl-1,2-dihydro-1,2,4,5-tetrazine-1,2-dicarboxylate.

PubMed

Rao, Guo-Wu; Hu, Wei-Xiao

2003-05-01

The title compound, C(22)H(24)N(4)O(4), was prepared from propyl chloroformate and 3,6-diphenyl-1,2-dihydro-s-tetrazine. This reaction yields the title compound rather than dipropyl 3,6-diphenyl-1,4-dihydro-s-tetrazine-1,4-dicarboxylate. The 2,3-diazabutadiene group in the central six-membered ring is not planar; the C=N double-bond length is 1.285 (2) A, and the average N-N single-bond length is 1.401 (3) A, indicating a lack of conjugation. The ring has a twist conformation, in which adjacent N atoms lie +/- 0.3268 (17) A from the plane of the ring. The molecule has twofold crystallographic symmetry.

All-electron molecular Dirac-Hartree-Fock calculations - The group IV tetrahydrides CH4, SiH4, GeH4, SnH4, and PbH4

NASA Technical Reports Server (NTRS)

Dyall, Kenneth G.; Taylor, Peter R.; Faegri, Knut, Jr.; Partridge, Harry

1991-01-01

A basis-set-expansion Dirac-Hartree-Fock program for molecules is described. Bond lengths and harmonic frequencies are presented for the ground states of the group 4 tetrahydrides, CH4, SiH4, GeH4, SnH4, and PbH4. The results are compared with relativistic effective core potential (RECP) calculations, first-order perturbation theory (PT) calculations and with experimental data. The bond lengths are well predicted by first-order perturbation theory for all molecules, but none of the RECP's considered provides a consistent prediction. Perturbation theory overestimates the relativistic correction to the harmonic frequencies; the RECP calculations underestimate the correction.

All-electron molecular Dirac-Hartree-Fock calculations: The group 4 tetrahydrides CH4, SiH4, GeH4, SnH4 and PbH4

NASA Technical Reports Server (NTRS)

Dyall, Kenneth G.; Taylor, Peter R.; Faegri, Knut, Jr.; Partridge, Harry

1990-01-01

A basis-set-expansion Dirac-Hartree-Fock program for molecules is described. Bond lengths and harmonic frequencies are presented for the ground states of the group 4 tetrahydrides, CH4, SiH4, GeH4, SnH4, and PbH4. The results are compared with relativistic effective core potential (RECP) calculations, first-order perturbation theory (PT) calculations and with experimental data. The bond lengths are well predicted by first-order perturbation theory for all molecules, but non of the RECP's considered provides a consistent prediction. Perturbation theory overestimates the relativistic correction to the harmonic frequencies; the RECP calculations underestimate the correction.

Quasiparticle and excitonic gaps of one-dimensional carbon chains.

PubMed

Mostaani, E; Monserrat, B; Drummond, N D; Lambert, C J

2016-06-01

We report diffusion quantum Monte Carlo (DMC) calculations of the quasiparticle and excitonic gaps of hydrogen-terminated oligoynes and extended polyyne. The electronic gaps are found to be very sensitive to the atomic structure in these systems. We have therefore optimised the geometry of polyyne by directly minimising the DMC energy with respect to the lattice constant and the Peierls-induced carbon-carbon bond-length alternation. We find the bond-length alternation of polyyne to be 0.136(2) Å and the excitonic and quasiparticle gaps to be 3.30(7) and 3.4(1) eV, respectively. The DMC zone-centre longitudinal optical phonon frequency of polyyne is 2084(5) cm(-1), which is consistent with Raman spectroscopic measurements for large oligoynes.

High temperature extended x-ray absorption fine structure study of multiferroic BiFeO3

NASA Astrophysics Data System (ADS)

Raghavendra Reddy, V.; Meneghini, Carlo; Kothari, Deepti; Gupta, Ajay; Aquilanti, Giuliana

2012-08-01

Local atomic structure modifications around Fe atoms in polycrystalline multiferroic BiFeO3 are studied by Fe K edge x-ray absorption spectroscopy as a function of temperature across the Néel temperature (TN = 643 K) in order to reveal local structure modifications related to the magnetic transition. This work demonstrates that on crossing TN the local structure around Fe shows peculiar changes: the Fe-O bond lengths get shorter, the ligand symmetry increases and the Fe-O bond length disorder (σ2) deviates from Debye behaviour. These results suggest that the structural transition at the ferroelectric Curie temperature (TC = 1103 K) is anticipated by early local rearrangement of the structure starting already at TN.

Concentration effect on inter-mineral equilibrium isotope fractionation: insights from Mg and Ca isotopic systems

NASA Astrophysics Data System (ADS)

Huang, F.; Wang, W.; Zhou, C.; Kang, J.; Wu, Z.

2017-12-01

Many naturally occurring minerals, such as carbonate, garnet, pyroxene, and feldspar, are solid solutions with large variations in chemical compositions. Such variations may affect mineral structures and modify the chemical bonding environment around atoms, which further impacts the equilibrium isotope fractionation factors among minerals. Here we investigated the effects of Mg content on equilibrium Mg and Ca isotope fractionation among carbonates and Ca content on equilibrium Ca isotope fractionation between orthopyroxene (opx) and clinopyroxene (cpx) using first-principles calculations. Our results show that the average Mg-O bond length increases with decreasing Mg/(Mg+Ca) in calcite when it is greater than 1/48[1] and the average Ca-O bond length significantly decreases with decreasing Ca/(Ca+Mg+Fe) in opx when it ranges from 2/16 to 1/48[2]. Equilibrium isotope fractionation is mainly controlled by bond strengths, which could be measured by bond lengths. Thus, 103lnα26Mg/24Mg between dolomite and calcite dramatically increases with decreasing Mg/(Mg+Ca) in calcite [1] and it reaches a constant value when it is lower than 1/48. 103lnα44Ca/40Ca between opx and cpx significantly increases with decreasing Ca content in opx when Ca/(Ca+Mg+Fe) ranges from 2/16 to 1/48 [2]. If Ca/(Ca+Mg+Fe) is below 1/48, 103lnα44Ca/40Ca is not sensitive to Ca content. Based on our results, we conclude that the concentration effect on equilibrium isotope fractionation could be significant within a certain range of chemical composition of minerals, which should be a ubiquitous phenomenon in solid solution systems. [1] Wang, W., Qin, T., Zhou, C., Huang, S., Wu, Z., Huang, F., 2017. GCA 208, 185-197. [2] Feng, C., Qin, T., Huang, S., Wu, Z., Huang, F., 2014. GCA 143, 132-142.

Estimating the hydraulic conductivity of two-dimensional fracture networks

NASA Astrophysics Data System (ADS)

Leung, C. T.; Zimmerman, R. W.

2010-12-01

Most oil and gas reservoirs, as well as most potential sites for nuclear waste disposal, are naturally fractured. In these sites, the network of fractures will provide the main path for fluid to flow through the rock mass. In many cases, the fracture density is so high as to make it impractical to model it with a discrete fracture network (DFN) approach. For such rock masses, it would be useful to have recourse to analytical, or semi-analytical, methods to estimate the macroscopic hydraulic conductivity of the fracture network. We have investigated single-phase fluid flow through stochastically generated two-dimensional fracture networks. The centres and orientations of the fractures are uniformly distributed, whereas their lengths follow either a lognormal distribution or a power law distribution. We have considered the case where the fractures in the network each have the same aperture, as well as the case where the aperture of each fracture is directly proportional to the fracture length. The discrete fracture network flow and transport simulator NAPSAC, developed by Serco (Didcot, UK), is used to establish the “true” macroscopic hydraulic conductivity of the network. We then attempt to match this conductivity using a simple estimation method that does not require extensive computation. For our calculations, fracture networks are represented as networks composed of conducting segments (bonds) between nodes. Each bond represents the region of a single fracture between two adjacent intersections with other fractures. We assume that the bonds are arranged on a kagome lattice, with some fraction of the bonds randomly missing. The conductance of each bond is then replaced with some effective conductance, Ceff, which we take to be the arithmetic mean of the individual conductances, averaged over each bond, rather than over each fracture. This is in contrast to the usual approximation used in effective medium theories, wherein the geometric mean is used. Our explanation is that the conductivities of the bonds that meet at a given node in a fracture network do not satisfy the usual assumption of being uncorrelated; rather, the conductances of at least two of these bonds are highly correlated, as they represent the incoming and outgoing branches of the same fracture. The effective conductance of our idealized “equivalent network” is then trivial to calculate. We find that this estimate of the hydraulic conductivity agrees very closely with the numerically computed value, essentially for all fracture densities that are not too close to the percolation threshold. Moreover, the same methodology applies regardless of whether the fracture lengths are distributed lognormally, or according to a power law.

Analysis of the vibronic structure of the trans-stilbene fluorescence and excitation spectra: the S0 and S1 PES along the Ce[double bond, length as m-dash]Ce and Ce-Cph torsions.

PubMed

Orlandi, Giorgio; Garavelli, Marco; Zerbetto, Francesco

2017-09-20

We analyze the highly resolved vibronic structure of the low energy (≤200 cm -1 ) region of the fluorescence and fluorescence excitation spectra of trans-stilbene in supersonic beams. In this spectral region the vibronic structure is associated mainly with vibrational levels of the C e -C e torsion (τ) and the a u combination of the two C e -C ph bond twisting (ϕ). We base this analysis on the well-established S 0 (τ, ϕ) two-dimensional potential energy surface (PES) and on a newly refined S 1 (τ, ϕ) PES. We obtain vibrational eigenvalues and eigenvectors of the anharmonic S 0 (τ, ϕ) and S 1 (τ, ϕ) PES using a numerical procedure based on the Meyer's flexible model [R. Meyer, J. Mol. Spectrosc., 1979, 76, 266]. Then we derive Franck-Condon factors and therefore intensities of the relevant vibronic bands for the S 0 → S 1 excitation and S 1 → S 0 fluorescence spectra. Furthermore, we assess the role of the b g combination of the two C e -C ph bond twisting (ν 48 ) in the structure of the S 1 → S 0 fluorescence spectra. By the use of these results we are able to assign most of the low energy vibrational levels of the S 0 → S 1 excitation spectra and of the fluorescence spectra of the emission from several low energy S 1 vibronic levels. The good agreement between the observed and the computed vibrational structure of the S 0 → S 1 and S 1 → S 0 spectra suggests that the proposed picture of the E 1 (τ, ϕ) and E 0 (τ, ϕ) PES, in particular along the coordinate τ governing trans-cis photo-isomerization in S 1 , is accurate. In S 0 , the barriers for the C e [double bond, length as m-dash]C e torsion and for the a u type C e -C ph bond twisting are 16 080 cm -1 and 3125 cm -1 , respectively, while in S 1 , where the bond orders of the C e [double bond, length as m-dash]C e and C e -C ph bonds are reversed, the two barriers become 1350 cm -1 and 8780 cm -1 , respectively.

Prediction of boiling points of organic compounds by QSPR tools.

PubMed

Dai, Yi-min; Zhu, Zhi-ping; Cao, Zhong; Zhang, Yue-fei; Zeng, Ju-lan; Li, Xun

2013-07-01

The novel electro-negativity topological descriptors of YC, WC were derived from molecular structure by equilibrium electro-negativity of atom and relative bond length of molecule. The quantitative structure-property relationships (QSPR) between descriptors of YC, WC as well as path number parameter P3 and the normal boiling points of 80 alkanes, 65 unsaturated hydrocarbons and 70 alcohols were obtained separately. The high-quality prediction models were evidenced by coefficient of determination (R(2)), the standard error (S), average absolute errors (AAE) and predictive parameters (Qext(2),RCV(2),Rm(2)). According to the regression equations, the influences of the length of carbon backbone, the size, the degree of branching of a molecule and the role of functional groups on the normal boiling point were analyzed. Comparison results with reference models demonstrated that novel topological descriptors based on the equilibrium electro-negativity of atom and the relative bond length were useful molecular descriptors for predicting the normal boiling points of organic compounds. Copyright © 2013 Elsevier Inc. All rights reserved.

Tunnel current across linear homocatenated germanium chains

NASA Astrophysics Data System (ADS)

Matsuura, Yukihito

2014-01-01

The electronic transport properties of germanium oligomers catenating into linear chains (linear Ge chains) have been theoretically studied using first principle methods. The conduction mechanism of a Ge chain sandwiched between gold electrodes was analyzed based on the density of states and the eigenstates of the molecule in a two-probe environment. Like that of silicon chains (Si chains), the highest occupied molecular orbital of Ge chains contains the extended σ-conjugation of Ge 4p orbitals at energy levels close to the Fermi level; this is in contrast to the electronic properties of linear carbon chains. Furthermore, the conductance of a Ge chain is expected to decrease exponentially with molecular length L. The decay constant β, which is defined as e-βL, of a Ge chain is similar to that of a Si chain, whereas the conductance of the Ge chains is higher than that of Si chains even though the Ge-Ge bond length is longer than the Si-Si bond length.

Molecular geometry as a source of chemical information. 5. Substituent effect on proton transfer in para-substituted phenol complexes with fluoride--a B3LYP/6-311+G study.

PubMed

Krygowski, Tadeusz M; Szatyłowicz, Halina; Zachara, Joanna E

2005-01-01

The simplified model system [p-X-PhO...H...F](-), where -X are -NO, -NO(2), -CHO, -H, -CH(3), -OCH(3), and -OH, with various O...F distance was used to simulate the wide range of the H-bond strength. Structural changes due to variation of the substituent as well as the H-bond strength are well monitored by the changes in the aromaticity index HOMA and by two empirical measures of the H-bond strength-the (1)H NMR chemical shift of proton involved and the C-O bond length. Changes in H-bonding strengths and the position of proton transfer while shortening the O...F distance are well described by the Hammett equation.

Electrochemical reduction of carbon fluorine bond in 4-fluorobenzonitrile Mechanistic analysis employing Marcus Hush quadratic activation-driving force relation

NASA Astrophysics Data System (ADS)

Muthukrishnan, A.; Sangaranarayanan, M. V.

2007-10-01

The reduction of carbon-fluorine bond in 4-fluorobenzonitrile in acetonitrile as the solvent, is analyzed using convolution potential sweep voltammetry and the dependence of the transfer coefficient on potential is investigated within the framework of Marcus-Hush quadratic activation-driving force theory. The validity of stepwise mechanism is inferred from solvent reorganization energy estimates as well as bond length calculations using B3LYP/6-31g(d) method. A novel method of estimating the standard reduction potential of the 4-fluorobenzonitrile in acetonitrile is proposed.

Stereoselective heterocycle synthesis through oxidative carbon-hydrogen bond activation.

PubMed

Liu, Lei; Floreancig, Paul E

2010-01-01

Heterocycles are ubiquitous structures in both drugs and natural products, and efficient methods for their construction are being pursued constantly. Carbon-hydrogen bond activation offers numerous advantages for the synthesis of heterocycles with respect to minimizing the length of synthetic routes and reducing waste. As interest in chiral medicinal leads increases, stereoselective methods for heterocycle synthesis must be developed. The use of carbon-hydrogen bond activation reactions for stereoselective heterocycle synthesis has produced a range of creative transformations that provide a wide array of structural motifs, selected examples of which are described in this review.

Exact valence bond entanglement entropy and probability distribution in the XXX spin chain and the potts model.

PubMed

Jacobsen, J L; Saleur, H

2008-02-29

We determine exactly the probability distribution of the number N_(c) of valence bonds connecting a subsystem of length L>1 to the rest of the system in the ground state of the XXX antiferromagnetic spin chain. This provides, in particular, the asymptotic behavior of the valence-bond entanglement entropy S_(VB)=N_(c)ln2=4ln2/pi(2)lnL disproving a recent conjecture that this should be related with the von Neumann entropy, and thus equal to 1/3lnL. Our results generalize to the Q-state Potts model.

Evidence for a novel chemisorption bond: Formate (HCO/sub 2/) on Cu(100)

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

Stoehr, J.; Outka, D.A.; Madix, R.J.

1985-03-25

Surface extended-x-ray-absorption fine-structure measurements reveal that formate (HCO/sub 2/) groups on Cu(100) chemisorb via the two oxygen atoms in adjacent fourfold hollow sites with an average O-Cu nearest-neighbor bond length of 2.38 +- 0.03 A. This distance is sig- nificantly (approx.0.4 A) longer than typical O-Cu bonds in bulk compounds and all known surface complexes. The unusually large O-Cu distance is attributed to a steric effect involving the C atom in HCO/sub 2/ and the nearest-neighbor Cu surface atoms.

Bioremediation Using Dehaloperoxidase

DTIC Science & Technology

2011-02-01

distal pocket. The Fe—O bond length of 2.2 Å in the wild-type structure presented here is consistent with a chemical bond, while the longer distance in...130, 2128-2129 10.1021/ja0772952 CCC: $40.75 © 2008 American Chemical Society determination of the deuteron nuclei coupling constant. The assignment of...published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Article Characterization of Dehaloperoxidase Compound ES and

(But­oxy­methyl­idene)di­methyl­aza­nium tetra­phenyl­borate aceto­nitrile monosolvate

PubMed Central

Tiritiris, Ioannis; Saur, Stefan; Kantlehner, Willi

2014-01-01

In the title solvated salt, C7H16NO+·C24H20B−·C2H3N, the C—N bond lengths in the cation are 1.2831 (19), 1.467 (2) and 1.465 (2) Å, indicating double- and single-bond character, respectively. The C—O bond length of 1.2950 (18) Å shows a double-bond character, pointing towards charge delocalization within the NCO plane of the iminium ion. The two C atoms of the n-butyl group are disordered over the two sites, with refined occupancy ratios of 0.890 (5):0.110 (5) and 0.888 (4):0.112 (4). In the crystal, C—H⋯π inter­actions occur between the methine H atom, H atoms of the –N(CH3)2 and –CH2 groups of the cation, and two of the phenyl rings of the tetra­phenyl­borate anion. The latter inter­action forms an aromatic pocket in which the cation is embedded. Thus, a two-dimensional pattern is created in the ac plane. PMID:24826158

Role of Hydrogen Bonding on Nonlinear Mechano-Optical Behavior of L-Phenylalanine-based Poly(ester urea)s.

NASA Astrophysics Data System (ADS)

Chen, Keke; Yu, Jiayi; Guzman, Gustavo; Es-Haghi, S. Shams; Becker, Matthew L.; Cakmak, Miko

The uniaxial mechano-optical behavior of a series of amorphous L-phenylalanine-based poly(ester urea) (PEU) films was studied in the rubbery state using a custom real-time measurement system. When the materials were subjected to deformation at temperatures near the glass transition temperature (Tg) , the photoelastic behavior was manifested by a small increase in birefringence with a significant increase in true stress. At temperatures above Tg, PEUs with a shorter diol chain length exhibited a liquid-liquid (Tll) transition at about 1.06 Tg (K), above which the material transforms from a heterogeneous ``liquid of fixed-structure'' to a ``true liquid'' state. The initial photoelastic behavior disappears with increasing temperature, as the initial slope of the stress optical curves becomes temperature independent. Fourier transform infrared spectra of PEUs revealed that the average strength of hydrogen bonding diminishes with increasing temperature. For PEUs with the longest diol chain length, the area associated with N-H stretching region exhibits a linear temperature dependence. The presence of hydrogen bonding enhances the ``stiff'' segmental correlations between adjacent chains in the PEU structure. As a result, the photoelastic constant decreases with increasing hydrogen bonding strength. This work was supported by the Ohio Department of Development's Innovation Platform Program and The National Science Foundation.

Crystal structure of tetra­aqua­[2-(pyridin-2-yl)-1H-imidazole-κ2 N 2,N 3]iron(II) sulfate

PubMed Central

Setifi, Zouaoui; Setifi, Fatima; Francuski, Bojana M.; Novaković, Sladjana B.; Merazig, Hocine

2015-01-01

In the title compound, [Fe(C8H7N3)(H2O)4]SO4, the central FeII ion is octa­hedrally coordinated by two N atoms from the bidentate 2-(pyridin-2-yl)-1H-imidazole ligand and by four O atoms of the aqua ligands. The largest deviation from the ideal octa­hedral geometry is reflected by the small N—Fe—N bite angle of 76.0 (1)°. The Fe—N coordination bonds have markedly different lengths [2.1361 (17) and 2.243 (2) Å], with the shorter one to the pyrimidine N atom. The four Fe—O coordination bond lengths vary from 2.1191 (18) to 2.1340 (17) Å. In the crystal, the cations and anions are arranged by means of medium-strength O—H⋯O hydrogen bonds into layers parallel to the ab plane. Neighbouring layers further inter­connect by N—H⋯O hydrogen bonds involving the imidazole fragment as donor group to one sulfate O atom as an acceptor. The resulting three-dimensional network is consolidated by C—H⋯O, C—H⋯π and π–π inter­actions. PMID:26029386

Uranyl interaction with the hydrated (001) basal face of gibbsite: a combined theoretical and spectroscopic study.

PubMed

Veilly, Edouard; Roques, Jérôme; Jodin-Caumon, Marie-Camille; Humbert, Bernard; Drot, Romuald; Simoni, Eric

2008-12-28

The sorption of uranyl cations and water molecules on the basal (001) face of gibbsite was studied by combining vibrational and fluorescence spectroscopies together with density functional theory (DFT) computations. Both the calculated and experimental values of O-H bond lengths for the gibbsite bulk are in good agreement. In the second part, water sorption with this surface was studied to take into account the influence of hydration with respect to the uranyl adsorption. The computed water configurations agreed with previously published molecular dynamics studies. The uranyl adsorption in acidic media was followed by time-resolved laser-induced fluorescence spectroscopy and Raman spectrometry measurements. The existence of only one kind of adsorption site for the uranyl cation was then indicated in good agreement with the DFT calculations. The computation of the uranyl adsorption has been performed by means of a bidentate interaction with two surface oxygen atoms. The optimized structures displayed strong hydrogen bonds between the surface and the -yl oxygen of uranyl. The uranium-surface bond strength depends on the protonation state of the surface oxygen atoms. The calculated U-O(surface) bond lengths range between 2.1-2.2 and 2.6-2.7 A for the nonprotonated and protonated surface O atoms, respectively.

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.

A molecular scale perspective: Monte Carlo simulation for rupturing of ultra thin polymer film melts

NASA Astrophysics Data System (ADS)

Singh, Satya Pal

2017-04-01

Monte Carlo simulation has been performed to study the rupturing process of thin polymer film under strong confinement. The change in mean square displacement; pair correlation function; density distribution; average bond length and microscopic viscosity are sampled by varying the molecular interaction parameters such as the strength and the equilibrium positions of the bonding, non-bonding potentials and the sizes of the beads. The variation in mean square angular displacement χθ = [ < Δθ2 > - < Δθ>2 ] fits very well to a function of type y (t) = A + B *e-t/τ. This may help to study the viscous properties of the films and its dependence on different parameters. The ultra thin film annealed at high temperature gets ruptured and holes are created in the film mimicking spinodal dewetting. The pair correlation function and density profile reveal rich information about the equilibrium structure of the film. The strength and equilibrium bond length of finite extensible non-linear elastic potential (FENE) and non-bonding Morse potential have clear impact on microscopic rupturing of the film. The beads show Rouse or repetition motion forming rim like structures near the holes created inside the film. The higher order interaction as dipole-quadrupole may get prominence under strong confinement. The enhanced excluded volume interaction under strong confinement may overlap with the molecular dispersion forces. It can work to reorganize the molecules at the bottom of the scale and can imprint its signature in complex patterns evolved.

Does the 4f-shell contribute to bonding in tetravalent lanthanide halides?

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

Ji, Wen-Xin; School of Chemistry and Chemical Engineering, Ningxia University, 750015 Yinchuan; Xu, Wei

2014-12-28

Lanthanide tetrahalide molecules LnX{sub 4} (Ln = Ce, Pr, Tb; X = F, Cl, Br, I) have been investigated by density functional theory at the levels of the relativistic Zero Order Regular Approximation and the relativistic energy-consistent pseudopotentials, using frozen small- and medium-cores. The calculated bond lengths and vibrational frequencies are close to the experimental data. Our calculations indicate 4f shell contributions to bonding in LnX{sub 4}, in particular for the early lanthanides, which show significant overlap between the Ln 4f-shell and the halogen np-shells. The 4f shells contribute to Ln-X bonding in LnX{sub 4} about one third more thanmore » in LnX{sub 3}.« less

Anharmonic Potential Constants and Their Dependence Upon Bond Length

DOE R&D Accomplishments Database

Herschbach, D. R.; Laurie, V. W.

1961-01-01

Empirical study of cubic and quartic vibrational force constants for diatomic molecules shows them to be approximately exponential functions of internuclear distance. A family of curves is obtained, determined by the location of the bonded atoms in rows of the periodic table. Displacements between successive curves correspond closely to those in Badger's rule for quadratic force constants (for which the parameters are redetermined to accord with all data now available). Constants for excited electronic and ionic states appear on practically the same curves as those for the ground states. Predictions based on the diatomic correlations agree with the available cubic constants for bond stretching in polyatomic molecules, regardless of the type of bonding involved. Implications of these regularities are discussed. (auth)

Controlling formation of single-molecule junctions by electrochemical reduction of diazonium terminal groups.

PubMed

Hines, Thomas; Díez-Pérez, Ismael; Nakamura, Hisao; Shimazaki, Tomomi; Asai, Yoshihiro; Tao, Nongjian

2013-03-06

We report controlling the formation of single-molecule junctions by means of electrochemically reducing two axialdiazonium terminal groups on a molecule, thereby producing direct Au-C covalent bonds in situ between the molecule and gold electrodes. We report a yield enhancement in molecular junction formation as the electrochemical potential of both junction electrodes approach the reduction potential of the diazonium terminal groups. Step length analysis shows that the molecular junction is significantly more stable, and can be pulled over a longer distance than a comparable junction created with amine anchoring bonds. The stability of the junction is explained by the calculated lower binding energy associated with the direct Au-C bond compared with the Au-N bond.

Critical effects of alkyl chain length on fibril structures in benzene-trans(RR)- or (SS)-N,N'-alkanoyl-1,2-diaminocyclohexane gels.

PubMed

Sato, Hisako; Nakae, Takahiro; Morimoto, Kazuya; Tamura, Kenji

2012-02-28

Vibrational circular dichroism (VCD) spectra were recorded on benzene-d(6) gels formed by chiral low molecular mass gelators (LMGs), trans(RR)- or trans(SS)-N,N'-alkanoyl-1,2-diaminocyclohexane (denoted by RR-C(n) or SS-C(n), respectively; n = the number of carbon atoms in an introduced alkanoyl group). Attention was focused on the effects of alkyl chain length on the structures of the gels. When n was changed from 6 to 12, the signs of the coupled peaks around 1550 cm(-1) in the VCD spectra, which were assigned to the symmetric and asymmetric C=O stretching vibrations from the higher to lower wavenumber, respectively, critically depended on the alkyl chain length. In the case of RR-C(n), for example, the signs of the couplet were plus and minus for n = 8, 9, 10 and 12, while the signs of the same couplet were reversed for n = 6 and 7. The conformations of LMGs in fibrils were determined by comparing the observed IR and VCD spectra with those calculated for a monomeric molecule. The observed reversal of signs in the C=O couplet was rationalized in terms of the different modes of hydrogen bonding. In the case of C(8), C(9), C(10) and C(12), gelator molecules were stacked with their cyclohexyl rings in parallel, forming double anti-parallel chains of intermolecular hydrogen bonds using two pairs of >NH and >C=O groups. In case of C(6) and C(7), gelator molecules were stacked through a single chain of intermolecular hydrogen bonds using a pair of >NH and >C=O groups. The remaining pair of >NH and >C=O groups formed an intramolecular hydrogen bond.

Velocity modulation spectroscopy of molecular ions II: The millimeter/submillimeter-wave spectrum of TiF + ( X3Φr)

NASA Astrophysics Data System (ADS)

Halfen, D. T.; Ziurys, L. M.

2006-11-01

The pure rotational spectrum of the molecular ion TiF + in its 3Φr ground state has been measured in the range 327-542 GHz using millimeter-wave direct absorption techniques combined with velocity modulation spectroscopy. TiF + was made in an AC discharge from a mixture of TiCl 4, F 2 in He, and argon. Ten transitions of this ion were recorded. In every transition, fluorine hyperfine interactions, as well as the fine structure splittings, were resolved. The fine structure pattern was found to be regular with almost equal spacing in frequency between the three spin components, in contrast to TiCl +, which is perturbed in the ground state. The data were fit with a case ( a) Hamiltonian and rotational, fine structure, and hyperfine constants were determined. The bond length established for TiF +, r0 = 1.7775 Å, was found to be shorter than that of TiF, r0 = 1.8342 Å—also established from mm-wave data. The hyperfine parameters determined are consistent with a δ1π1 electron configuration with the electrons primarily located on the titanium nucleus. The nuclear spin-orbit constant a indicates that the unpaired electrons are closer to the fluorine nucleus in TiF + relative to TiF, as expected with the decrease in bond length for the ion. The shorter bond distance is thought to arise from increased charge on the titanium nucleus as a result of a Ti 2+F - configuration. A similar decrease in bond length was found for TiCl + relative to TiCl.

Effect of cutting temperature on hardness of SiC and diamond in the nano-cutting process of monocrystalline silicon

NASA Astrophysics Data System (ADS)

Wang, Jiachun; Li, Yuntao; Liu, Xiaoxuan; Lv, Maoqiang

2016-10-01

In the process of cutting silicon by natural diamond tools, groove wear happens on the flank face of cutting tool frequently.Scholars believe that one of the wear reasons is mechanical scratching effect by hard particles like SiC. To reveal the mechanical scratching mechanism, it is essential to study changes in the mechanical properties of hard particles and diamond, especially the effect of cutting temperature on hardness of diamond and hard particles. Molecular dynamics (MD) model that contact-zone temperature between tool and workpiece was calculated by dividing zone while nano-cutting monocrystalline silicon was established, cutting temperature values in different regions were computed as the simulation was carried out.On this basis, the models of molecular dynamics simulation of SiC and diamond were established separately with setting the initial temperature to room temperature. The laws of length change of C-C bond and Si-C bond varing with increase of simulation temperature were studied. And drawing on predecessors' research on theoretical calculation of hardness of covalent crystals and the relationship between crystal valence electron density and bond length, the curves that the hardness of diamond and SiC varing with bond length were obtained. The effect of temperature on the hardness was calculated. Results show that, local cutting temperature can reach 1300K.The rise in cutting temperature leaded to a decrease in the diamond local atomic clusters hardness,SiC local atomic clusters hardness increased. As the cutting temperature was more than 1100K,diamond began to soften, the local clusters hardness was less than that of SiC.

In-Situ Adhesive Bond Assessment

DTIC Science & Technology

2010-08-01

a list of AR coefficients. The use of the VCC metric , with appropriate extreme value statistics models as described in detail below, allowed...equivalent PZT with thickness equal to the MFC electrode spacing , a , and length equal to the MFC net electrode length, (p le), where p is the number of ...particular geometry of the test specimen and with MFC patches affixed to the

The influence of plain bar on bond strength of geopolymer concrete

NASA Astrophysics Data System (ADS)

Dewi, Evrianti Syntia; Ekaputri, Januarti Jaya

2017-06-01

This paper presents some results of experimental study of bond strength of plain bar embedded in geopolymer concrete. Fly ash class F was used as a raw material activated with alkali solutions. The combination of 8 Molar of sodium hydroxide (NaOH) and sodium silicate (Na2SiO3) as alkali activators was examined in the mixture with ratio of 2.5 by weight. Nine cubical specimens with a size of 150 × 150 × 150 mm were prepared to measure bond strength and slip between reinforcement and concrete. The influential factors studied for the experimental investigation were the diameter of reinforcement bar, bond area, and concrete cover to diameter (c/d) of reinforcement. The result showed that the average bond strength decreased as the diameter of plain bar and bonded length were increased from 16 mm to 19 mm. However, the 12 mm showed the different result allegedly caused by the effect of bond area and the passive confined provided by the concrete. Based on several equations used to compare the bond strength, it is clear that deformed bar of 12 mm in diameter is potential to increase the bond strength.

Significantly shorter Fe–S bond in cytochrome P450-I is consistent with greater reactivity relative to chloroperoxidase

DOE PAGES

Krest, Courtney M.; Silakov, Alexey; Rittle, Jonathan; ...

2015-08-03

Cytochrome P450 (P450) and chloroperoxidase (CPO) are thiolate-ligated haem proteins that catalyse the activation of carbon hydrogen bonds. The principal intermediate in these reactions is a ferryl radical species called compound I. P450 compound I (P450-I) is significantly more reactive than CPO-I, which only cleaves activated C–H bonds. In this paper, to provide insight into the differing reactivities of these intermediates, we examined CPO-I and P450-I using variable-temperature Mössbauer and X-ray absorption spectroscopies. These measurements indicate that the Fe–S bond is significantly shorter in P450-I than in CPO-I. This difference in Fe–S bond lengths can be understood in terms ofmore » variations in the hydrogen-bonding patterns within the ‘cys-pocket’ (a portion of the proximal helix that encircles the thiolate ligand). Weaker hydrogen bonding in P450-I results in a shorter Fe–S bond, which enables greater electron donation from the axial thiolate ligand. Finally, this observation may in part explain P450's greater propensity for C–H bond activation.« less

Consequences of theory level choice evaluated with new tools from QTAIM and the stress tensor for a dipeptide conformer

NASA Astrophysics Data System (ADS)

Li, Jiahui; Xu, Tianlv; Ping, Yang; van Mourik, Tanja; Früchtl, Herbert; Kirk, Steven R.; Jenkins, Samantha

2018-03-01

QTAIM and the stress tensor were used to provide a detailed analysis of the topology of the molecular graph, BCP and bond-path properties, including the new introduced helicity length H, of a Tyr-Gly dipeptide conformer subjected to a torsion with four levels of theory; MP2, M06-2X, B3LYP-D3 and B3LYP and a modest-sized basis set, 6-31+G(d). Structural effects and bonding properties are quantified and reflect differences in the BSSE and lack of inclusion of dispersion effects in the B3LYP calculations. The helicity length H demonstrated that MP2 produced a unique response to the torsion suggesting future use as a diagnostic tool.

Determination of the crystal structure and composition of Li6Be4OH12 by the stochastic method.

PubMed Central

Pauling, L

1990-01-01

Because of the failure to find a structure for LiBeH3 with a face-centered unit cube with edge 5.09 A, the x-ray powder pattern has been reindexed for a body-centered unit cube with edge 7.24 A. Application of the principles of structural chemistry leads to the formula Li6Be4OH12 and to a structure involving Be4OH12 clusters formed by 4 BeOH3 tetrahedra with their O corner shared, Be--(H,O) bond length 1.59 A, and with the clusters joined to one another by Li with octahedral or rectangular-planar coordination of 6 H or 4 H, Li-H bond lengths about 1.92 A. PMID:11607052

Determination of the crystal structure and composition of Li6Be4OH12 by the stochastic method.

PubMed

Pauling, L

1990-01-01

Because of the failure to find a structure for LiBeH3 with a face-centered unit cube with edge 5.09 A, the x-ray powder pattern has been reindexed for a body-centered unit cube with edge 7.24 A. Application of the principles of structural chemistry leads to the formula Li6Be4OH12 and to a structure involving Be4OH12 clusters formed by 4 BeOH3 tetrahedra with their O corner shared, Be--(H,O) bond length 1.59 A, and with the clusters joined to one another by Li with octahedral or rectangular-planar coordination of 6 H or 4 H, Li-H bond lengths about 1.92 A.

Study on the Connecting Length of CFRP

NASA Astrophysics Data System (ADS)

Liu, Xiongfei; Li, Yue; Li, Zhanguo

2018-05-01

The paper studied the varying mode of shear stress in the connecting zone of CFRP. Using epoxy resin (EP) as bond material, performance of specimens with different connecting length of CFRP was tested to obtain the conclusion. CFRP-confined concrete column was tested subsequently to verify the conclusion. The results show that: (1) The binding properties of modified epoxy resin with CFRP is good; (2) As the connecting length increased, the ultimate tensile strength of CFRP increased as well in the range of the experiment parameters; (3) Tensile strength of CFRP can reach the ultimate strength when the connecting length is 90mm;(4) The connecting length of 90mm of CFRP meet the reinforcement requirements.

Crystal structure of cis-aqua­bis­(2,2′-bi­pyridine-κ2 N,N′)chlorido­chromium(III) tetra­chlorido­zincate determined from synchrotron data

PubMed Central

Moon, Dohyun; Ryoo, Keon Sang; Choi, Jong-Ha

2016-01-01

The structure of the title salt, [CrCl(C10H8N2)2(H2O)][ZnCl4], has been determined from synchrotron data. The CrIII ion is coordinated by four N atoms from two 2,2′-bi­pyridine (bipy) ligands, one O atom from a water mol­ecule and a chloride anion in a cis arrangement, displaying a distorted octa­hedral geometry. The tetra­hedral [ZnCl4]2− anion is slightly distorted owing to its involvement in O—H⋯Cl hydrogen bonding with the coordinating water mol­ecule. The Cr—N(bipy) bond lengths are in the range 2.0485 (13)–2.0632 (12) Å, while the Cr—Cl and Cr—(OH2) bond lengths are 2.2732 (6) and 1.9876 (12) Å, respectively. In the crystal, mol­ecules are stacked along the a axis. PMID:27006786

Bis{2-meth­oxy-6-[tris­(hydroxy­meth­yl)methyl­imino­meth­yl]phenolato-κ3 O,N,O′}manganese(II) dimethanol solvate hemihydrate

PubMed Central

Zhang, Xiutang; Wei, Peihai; Dou, Jianmin; Li, Bin; Hu, Bo

2009-01-01

In the title complex, [Mn(C12H16NO5)2]·2CH3OH·0.5H2O, the MnII atom has a distorted octa­hedral coordination geometry in which two N atoms from two 6-meth­oxy-2-[tris­(hydroxy­meth­yl)methyl­imino­meth­yl]phenolate ligands adopt a trans arrangement. The Mn—O(H) bonds (mean length 2.134 Å) are significantly longer than the Mn—O and Mn—N bonds (mean length 2.011 and 2.027 Å, respectively), and the dihedral angle between the mean planes through the aromatic rings of the two ligands is 76.8 (1)°. A complex network of O—H⋯O hydrogen bonds is formed between the complexes and the uncoordinated methanol and water mol­ecules. The C and O atoms of one C—OH group are disordered with equal occupancies. PMID:21582076

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.

Spin-Orbit Effect on the Molecular Properties of TeXn (X = F, Cl, Br, and I; n = 1, 2, and 4): A Density Functional Theory and Ab Initio Study.

PubMed

Moon, Jiwon; Kim, Joonghan

2016-09-29

Density functional theory (DFT) and ab initio calculations, including spin-orbit coupling (SOC), were performed to investigate the spin-orbit (SO) effect on the molecular properties of tellurium halides, TeXn (X = F, Cl, Br, and I; n = 1, 2, and 4). SOC elongates the Te-X bond and slightly reduces the vibrational frequencies. Consideration of SOC leads to better agreement with experimental values. Møller-Plesset second-order perturbation theory (MP2) seriously underestimates the Te-X bond lengths. In contrast, B3LYP significantly overestimates them. SO-PBE0 and multireference configuration interactions with the Davidson correction (MRCI+Q), which include SOC via a state-interaction approach, give the Te-I bond length of TeI2 that matches the experimental value. On the basis of the calculated thermochemical energy and optimized molecular structure, TeI4 is unlikely to be stable. The use of PBE0 including SOC is strongly recommended for predicting the molecular properties of Te-containing compounds.

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.

Analysis of the bonding in XH3Cu+ (XB, Al, Ga) complexes

NASA Astrophysics Data System (ADS)

Corral, Inés; Mó, Otilia; Yáñez, Manuel

High-level density functional theory (DFT) calculations on XH3Cu+ (XB, Al, Ga) complexes show that the attachment of the metal cation to the base takes place through agostic-type interactions. These interactions that can be viewed as dative bonds from the σXH bonding orbitals of the base toward low-lying empty 4s orbitals of the metal cation, and back-donations from the lone pairs of the metal into the σ *XH antibonding orbitals of the neutral, are particularly favored when the XH bonds have a high X+δH-δ polarity. Accordingly, the AlH3 and GaH3 Cu+ binding energies are very similar, but much larger than that of BH3. Depopulation of the σXH bonding orbital and the concomitant population of the σ *XH antibonding orbital involved in the agostic interaction result in a significant weakening of the corresponding XH linkages, whose bond length increases and whose stretching frequency appears red-shifted.

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

Linking microscopic and macroscopic response in disordered solids

NASA Astrophysics Data System (ADS)

Hexner, Daniel; Liu, Andrea J.; Nagel, Sidney R.

2018-06-01

The modulus of a rigid network of harmonic springs depends on the sum of the energies in each of the bonds due to an applied distortion such as compression in the case of the bulk modulus or shear in the case of the shear modulus. However, the distortion need not be global. Here we introduce a local modulus, Li, associated with changing the equilibrium length of a single bond, i , in the network. We show that Li is useful for understanding many aspects of the mechanical response of the entire system. It allows an efficient computation of how the removal of any bond changes the global properties such as the bulk and shear moduli. Furthermore, it allows a prediction of the distribution of these changes and clarifies why the changes of these two moduli due to removal of a bond are uncorrelated; these are the essential ingredients necessary for the efficient manipulation of network properties by bond removal.

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.

Polyarylether composition and membrane

DOEpatents

Hung, Joyce; Brunelle, Daniel Joseph; Harmon, Marianne Elisabeth; Moore, David Roger; Stone, Joshua James; Zhou, Hongyi; Suriano, Joseph Anthony

2010-11-09

A composition including a polyarylether copolymer is provided. The copolymer includes a polyarylether backbone; and a sulfonated oligomeric group bonded to the polyarylether suitable for use as a cation conducting membrane. Method of bonding a sulfonated oligomeric group to the polyarylether backbone to form a polyarylether copolymer. The membrane may be formed from the polyarylether copolymer composition. The chain length of the sulfonated oligomeric group may be controlled to affect or control the ion conductivity of the membrane.

Topology of charge density of flucytosine and related molecules and characteristics of their bond charge distributions.

PubMed

Murgich, Juan; Franco, Héctor J; San-Blas, Gioconda

2006-08-24

The molecular charge distribution of flucytosine (4-amino-5-fluoro-2-pyrimidone), uracil, 5-fluorouracil, and thymine was studied by means of density functional theory calculations (DFT). The resulting distributions were analyzed by means of the atoms in molecules (AIM) theory. Bonds were characterized through vectors formed with the charge density value, its Laplacian, and the bond ellipticity calculated at the bond critical point (BCP). Within each set of C=O, C-H, and N-H bonds, these vectors showed little dispersion. C-C bonds formed three different subsets, one with a significant degree of double bonding, a second corresponding to single bonds with a finite ellipticity produced by hyperconjugation, and a third one formed by a pure single bond. In N-C bonds, a decrease in bond length (an increase in double bond character) was not reflected as an increase in their ellipticity, as in all C-C bonds studied. It was also found that substitution influenced the N-C, C-O, and C-C bond ellipticity much more than density and its Laplacian at the BCP. The Laplacian of charge density pointed to the existence of both bonding and nonbonding maxima in the valence shell charge concentration of N, O, and F, while only bonding ones were found for the C atoms. The nonbonding maxima related to the sites for electrophilic attack and H bonding in O and N, while sites of nucleophilic attack were suggested by the holes in the valence shell of the C atoms of the carbonyl groups.

History-dependence of muscle slack length following contraction and stretch in the human vastus lateralis.

PubMed

Stubbs, Peter W; Walsh, Lee D; D'Souza, Arkiev; Héroux, Martin E; Bolsterlee, Bart; Gandevia, Simon C; Herbert, Robert D

2018-06-01

In reduced muscle preparations, the slack length and passive stiffness of muscle fibres have been shown to be influenced by previous muscle contraction or stretch. In human muscles, such behaviours have been inferred from measures of muscle force, joint stiffness and reflex magnitudes and latencies. Using ultrasound imaging, we directly observed that isometric contraction of the vastus lateralis muscle at short lengths reduces the slack lengths of the muscle-tendon unit and muscle fascicles. The effect is apparent 60 s after the contraction. These observations imply that muscle contraction at short lengths causes the formation of bonds which reduce the effective length of structures that generate passive tension in muscles. In reduced muscle preparations, stretch and muscle contraction change the properties of relaxed muscle fibres. In humans, effects of stretch and contraction on properties of relaxed muscles have been inferred from measurements of time taken to develop force, joint stiffness and reflex latencies. The current study used ultrasound imaging to directly observe the effects of stretch and contraction on muscle-tendon slack length and fascicle slack length of the human vastus lateralis muscle in vivo. The muscle was conditioned by (a) strong isometric contractions at long muscle-tendon lengths, (b) strong isometric contractions at short muscle-tendon lengths, (c) weak isometric contractions at long muscle-tendon lengths and (d) slow stretches. One minute after conditioning, ultrasound images were acquired from the relaxed muscle as it was slowly lengthened through its physiological range. The ultrasound image sequences were used to identify muscle-tendon slack angles and fascicle slack lengths. Contraction at short muscle-tendon lengths caused a mean 13.5 degree (95% CI 11.8-15.0 degree) shift in the muscle-tendon slack angle towards shorter muscle-tendon lengths, and a mean 5 mm (95% CI 2-8 mm) reduction in fascicle slack length, compared to the other conditions. A supplementary experiment showed the effect could be demonstrated if the muscle was conditioned by contraction at short lengths but not if the relaxed muscle was held at short lengths, confirming the role of muscle contraction. These observations imply that muscle contraction at short lengths causes the formation of bonds which reduce the effective length of structures that generate passive tension in muscles. © 2018 The Authors. The Journal of Physiology © 2018 The Physiological Society.

Rotational dynamics of coumarin-153 and 4-aminophthalimide in 1-ethyl-3-methylimidazolium alkylsulfate ionic liquids: effect of alkyl chain length on the rotational dynamics.

PubMed

Das, Sudhir Kumar; Sarkar, Moloy

2012-01-12

Rotational dynamics of two neutral organic solutes, coumarin-153 (C-153) and 4-aminophthalimide (AP), with only the latter having hydrogen-bond-donating ability, has been investigated in a series of 1-ethyl-3-methylimidazolium alkyl sulfate ionic liquids as a function of temperature. The ionic liquids differ only in the length of the linear alkyl side chain (alkyl = ethyl, butyl, hexyl, and octyl) on the anionic moiety. The present study has been undertaken to examine the role of alkyl side chains on the rotational dynamics of the two solutes in these ionic liquids. Analysis of the results using Stokes-Einstein-Debye hydrodynamic theory indicates that the rotational dynamics of C-153 lies between the stick and slip boundary condition in the ethyl analogue and finally reaches subslip condition as in case of the octyl substituent. The observed rotational behavior of C-153 has been explained on the basis of an increase in the size of the solvent, which offers lower friction for solute rotation. On the other hand, AP shows superstick behavior in the ethyl system and exceeds the stick limit in the octyl derivative. Superstick behavior of AP has been attributed to the specific hydrogen-bonding interaction between AP and the sulfate moiety. Proton NMR investigation confirms the hydrogen-bonding interaction between the N-H hydrogen of AP and the ionic liquid. The decrease in rotational coupling constant values for AP with increasing length of alkyl side chains has been attributed to the decrease in the solute-solvent-specific interaction with an increase in the alkyl side chain length on the sulfate moiety.

Influence of chain length and double bond on the aqueous behavior of choline carboxylate soaps.

PubMed

Rengstl, Doris; Diat, Olivier; Klein, Regina; Kunz, Werner

2013-02-26

In preceding studies, we demonstrated that choline carboxylates ChC(m) with alkyl chain lengths of m = 12 - 18 are highly water-soluble (for m = 12, soluble up to 93 wt % soap and 0 °C). In addition, choline soaps are featured by an extraordinary lyotropic phase behavior. With decreasing water concentration, the following phases were found: micellar phase (L(1)), discontinuous cubic phase (I(1)' and I(1)"), hexagonal phase (H(1)), bicontinuous cubic phase (V(1)), and lamellar phase (L(α)). The present work is also focused on the lyotropic phase behavior of choline soaps but with shorter alkyl chains or different alkyl chain properties. We have investigated the aqueous phase behavior of choline soaps with C(8) and C(10) chain-lengths (choline octanoate and choline decanoate) and with a C(18) chain-length with a cis-double bond (choline oleate). We found that choline decanoate follows the lyotropic phase behavior of the longer-chain homologues mentioned above. Choline octanoate in water shows no discontinuous cubic phases, but an extended, isotropic micellar solution phase. In addition, choline octanoate is at the limit between a surfactant and a hydrotrope. The double bond in choline oleate leads also to a better solubility in water and a decrease of the solubilization temperature. It also influences the Gaussian curvature of the aggregates which results in a loss of discontinuous cubic phases in the binary phase diagram. The different lyotropic mesophases were identified by the penetration scan technique with polarizing light microscope and visual observations. To clarify the structural behavior small (SAXS) and wide (WAXS) angle X-ray scattering were performed. To further characterize the extended, isotropic micellar solution phase in the binary phase diagram of choline octanoate viscosity and conductivity measurements were also carried out.

Shear Bond Strengths and Morphological Evaluation of Filled and Unfilled Adhesive Interfaces to Enamel and Dentine

PubMed Central

Mortazavi, Vajihesadat; Fathi, Mohammadhosein; Ataei, Ebrahim; Khodaeian, Niloufar; Askari, Navid

2012-01-01

In this laboratory study shear bond strengths of three filled and one unfilled adhesive systems to enamel and dentine were compared. Forty-eight extracted intact noncarious human mandibular molars were randomly assigned to two groups of 24 one for bonding to enamel and the other for bonding to dentine. Buccal and lingual surfaces of each tooth were randomly assigned for application of each one of filled (Prime & Bond NT (PBNT), Optibond Solo Plus (OBSP), and Clearfil SE Bond (CSEB)) and unfilled (Single Bond (SB)) adhesive systems (n = 12). A universal resin composite was placed into the translucent plastic cylinders (3 mm in diameter and 2 mm in length) and seated against the enamel and dentine surfaces and polymerized for 40 seconds. Shear bond strength was determined using a universal testing machine, and the results were statistically analyzed using two-way ANOVA, one-way ANOVA, t-test, and Tukey HSD post hoc test with a 5% level of significance.There were no statistically significant differences in bond strength between the adhesive systems in enamel, but CSEB and SB exhibited significantly higher and lower bond strength to dentine, respectively, than the other tested adhesive systems while there were no statistically significant differences between PBNT and OBSP. PMID:23209471

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

Crystal structure details of La- and Bi-substituted hydroxyapatites: Evidence for LaO{sup +} and BiO{sup +} with a very short metal–oxygen bond

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

Kazin, Pavel E., E-mail: kazin@inorg.chem.msu.ru; Pogosova, Mariam A.; Trusov, Lev A.

Crystal structures of substituted apatites with general formula Ca{sub 10−x}M{sub x}(PO{sub 4}){sub 6}(OH{sub 1−δ}){sub 2−x}O{sub x}, where M=La, Bi, 0≤x<2, were refined using high-resolution X-ray powder diffraction patterns. Individual positions for Ca{sup 2+} and M{sup 3+}-ions localized near Ca2-site were determined. The M{sup 3+}-ion was found shifted toward the hexagonal channel center with respect to the Ca{sup 2+}-ion, forming very short bond with the intrachannel O{sup 2−}, while leaving considerably longer distances to other oxygen atoms, which suggested the existence of a MO{sup +} ion. Distinct bands of stretching M–O modes were observed in the Raman and FT-IR spectra ofmore » the compounds. The bond lengths for BiO{sup +} and LaO{sup +} were estimated to be 2.05(1) and 2.09(1) Å correspondingly. The latter was almost 0.3 Å lower than the shortest La–O bond in La{sub 2}O{sub 3}. The realization of such a strong lanthanide–oxygen bond in a crystal lattice could provide a very high axial ligand field and might be implemented to develop high-energy-barrier single-molecule magnets as well as to tune properties of lanthanide-based luminophores. - Graphical abstract: A fragment of the La-for-Ca substituted apatite crystal structure focusing on the La–O bond. - Highlights: • Individual positions in the apatite crystal lattice for a doping atom (La, Bi) and Ca. • The doping atom shifts toward the center of the hexagonal channel. • BiO{sup +} and LaO{sup +} with estimated short bond lengths of 2.05 and 2.09 Å respectively.« less

The Bacillus subtilis Acyl Lipid Desaturase Is a Δ5 Desaturase

PubMed Central

Altabe, Silvia G.; Aguilar, Pablo; Caballero, Gerardo M.; de Mendoza, Diego

2003-01-01

Bacillus subtilis was recently reported to synthesize unsaturated fatty acids (UFAs) with a double bond at positions Δ5, Δ7, and Δ9 (M. H. Weber, W. Klein, L. Muller, U. M. Niess, and M. A. Marahiel, Mol. Microbiol. 39:1321-1329, 2001). Since this finding would have considerable importance in the double-bond positional specificity displayed by the B. subtilis acyl lipid desaturase, we have attempted to confirm this observation. We report that the double bond of UFAs synthesized by B. subtilis is located exclusively at the Δ5 position, regardless of the growth temperature and the length chain of the fatty acids. PMID:12730185

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.

A DFT study of pure and lithium doped gold clusters

NASA Astrophysics Data System (ADS)

Rani, Babita

2018-05-01

First principles calculations on Aun and Aun-1Li (n=1-6) clusters are performed to understand the effect of size and composition on their structural and energy parameters. It has been found that binding energy increases continuously with increase in the size of pure Aun and doped Aun-1Li clusters and attains its maximum at n=6. Also, Li doping results in the improvement of relative stabilities of pure gold clusters, owing to higher bond strength (i.e. shorter bond length) of Au- Li bond as compared to Au-Au bonds. Moreover, Aun-1Li clusters are found to be more compact. Structural transformations are observed in case of gold clusters doped with Li atom which may affect their application in the field of catalysis.

Structural model of dioxouranium(VI) with hydrazono ligands.

PubMed

Mubarak, Ahmed T

2005-04-01

Synthesis and characterization of several new coordination compounds of dioxouranium(VI) heterochelates with bidentate hydrazono compounds derived from 1-phenyl-3-methyl-5-pyrazolone are described. The ligands and uranayl complexes have been characterized by various physico-chemical techniques. The bond lengths and the force constant have been calculated from asymmetric stretching frequency of OUO groups. The infrared spectral studies showed a monobasic bidentate behaviour with the oxygen and hydrazo nitrogen donor system. The effect of Hammett's constant on the bond distances and the force constants were also discussed and drawn. Wilson's matrix method, Badger's formula, Jones and El-Sonbati equations were used to determine the stretching and interaction force constant from which the UO bond distances were calculated. The bond distances of these complexes were also investigated.

Non-covalent synthesis of supermicelles with complex architectures using spatially confined hydrogen-bonding interactions

PubMed Central

Li, Xiaoyu; Gao, Yang; Boott, Charlotte E.; Winnik, Mitchell A.; Manners, Ian

2015-01-01

Nature uses orthogonal interactions over different length scales to construct structures with hierarchical levels of order and provides an important source of inspiration for the creation of synthetic functional materials. Here, we report the programmed assembly of monodisperse cylindrical block comicelle building blocks with crystalline cores to create supermicelles using spatially confined hydrogen-bonding interactions. We also demonstrate that it is possible to further program the self-assembly of these synthetic building blocks into structures of increased complexity by combining hydrogen-bonding interactions with segment solvophobicity. The overall approach offers an efficient, non-covalent synthesis method for the solution-phase fabrication of a range of complex and potentially functional supermicelle architectures in which the crystallization, hydrogen-bonding and solvophobic interactions are combined in an orthogonal manner. PMID:26337527

Structural model of dioxouranium(VI) with hydrazono ligands

NASA Astrophysics Data System (ADS)

Mubarak, Ahmed T.

2005-04-01

Synthesis and characterization of several new coordination compounds of dioxouranium(VI) heterochelates with bidentate hydrazono compounds derived from 1-phenyl-3-methyl-5-pyrazolone are described. The ligands and uranayl complexes have been characterized by various physico-chemical techniques. The bond lengths and the force constant have been calculated from asymmetric stretching frequency of O sbnd U sbnd O groups. The infrared spectral studies showed a monobasic bidentate behaviour with the oxygen and hydrazo nitrogen donor system. The effect of Hammett's constant on the bond distances and the force constants were also discussed and drawn. Wilson's matrix method, Badger's formula, Jones and El-Sonbati equations were used to determine the stretching and interaction force constant from which the U sbnd O bond distances were calculated. The bond distances of these complexes were also investigated.

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.

Raman and IR studies and DFT calculations of the vibrational spectra of 2,4-Dithiouracil and its cation and anion

NASA Astrophysics Data System (ADS)

Singh, R.; Yadav, R. A.

2014-09-01

Raman and FTIR spectra of solid 2,4-Dithiouracil (DTU) at room temperature have been recorded. DFT calculations were carried out to compute the optimized molecular geometries, GAPT charges and fundamental vibrational frequencies along with their corresponding IR intensities, Raman activities and depolarization ratios of the Raman bands for the neutral DTU molecule and its cation (DTU+) and anion (DTU-) using the Gaussian-03 software. Addition of one electron leads to increase in the atomic charges on the sites N1 and N3 and decrease in the atomic charges on the sites S8 and S10. Due to ionization of DTU molecule, the charge at the site C6 decreases in the cationic and anionic radicals of DTU as compared to its neutral species. As a result of anionic radicalization, the C5sbnd C6 bond length increases and loses its double bond character while the C4sbnd C5 bond length decreases. In the case of the DTU+ ion the IR and Raman band corresponding to the out-of-phase coupled Nsbnd H stretching mode is strongest amongst the three species. The anionic DTU radical is found to be the most stable. The two NH out-of-plane bending modes are found to originate due to out-of-phase and in-phase coupling of the two NH bonds in the anion and cation contrary to the case of the neutral DTU molecule in which the out-of-plane bending motions of the two NH bonds are not coupled.

Raman and IR studies and DFT calculations of the vibrational spectra of 2,4-Dithiouracil and its cation and anion.

PubMed

Singh, R; Yadav, R A

2014-09-15

Raman and FTIR spectra of solid 2,4-Dithiouracil (DTU) at room temperature have been recorded. DFT calculations were carried out to compute the optimized molecular geometries, GAPT charges and fundamental vibrational frequencies along with their corresponding IR intensities, Raman activities and depolarization ratios of the Raman bands for the neutral DTU molecule and its cation (DTU+) and anion (DTU-) using the Gaussian-03 software. Addition of one electron leads to increase in the atomic charges on the sites N1 and N3 and decrease in the atomic charges on the sites S8 and S10. Due to ionization of DTU molecule, the charge at the site C6 decreases in the cationic and anionic radicals of DTU as compared to its neutral species. As a result of anionic radicalization, the C5C6 bond length increases and loses its double bond character while the C4C5 bond length decreases. In the case of the DTU+ ion the IR and Raman band corresponding to the out-of-phase coupled NH stretching mode is strongest amongst the three species. The anionic DTU radical is found to be the most stable. The two NH out-of-plane bending modes are found to originate due to out-of-phase and in-phase coupling of the two NH bonds in the anion and cation contrary to the case of the neutral DTU molecule in which the out-of-plane bending motions of the two NH bonds are not coupled. Copyright © 2014 Elsevier B.V. All rights reserved.

Supramolecular structures for determination and identification of the bond lengths in novel uranyl complexes from their infrared spectra

NASA Astrophysics Data System (ADS)

El-Sonbati, A. Z.; Diab, M. A.; Morgan, Sh. M.; Seyam, H. A.

2018-02-01

Novel dioxouranium (VI) heterochelates with neutral bidentate compounds (Ln) have been synthesized. The ligands and the heterochelates [UO2(Ln)2(O2NO)2] were confirmed and characterized by elemental analysis, 1H NMR, UV.-Vis, IR, mass spectroscopy, X-ray diffraction and thermogravimetric analysis (TGA). IR spectral data suggest that the molecules of the Schiff base are coordinated to the central uranium atom (ON donor). The nitrato groups are coordinated as bidentate ligands. The thermodynamic parameters were calculated using Coats-Redfern and Horowitz-Metzger methods. The ligands (Ln) and their complexes (1-3) showed the υ3 frequency of UO22+ has been shown to be an excellent molecular probe for studying the coordinating power of the ligands. The values of υ3 of the prepared complexes containing UO22+ were successfully used to calculate the force constant, FUO (1n 10-8N/Å) and the bond length RUO (Å) of the Usbnd O bond. A strategy based upon both theoretical and experimental investigations has been adopted. The theoretical aspects are described in terms of the well-known theory of 5d-4f transitions. Wilson's, matrix method, Badger's formula, and Jones and El-Sonbati equations were used to calculate the Usbnd O bond distances from the values of the stretching and interaction force constants. The most probable correlation between Usbnd O force constant to Usbnd O bond distance were satisfactorily discussed in term of Badger's rule and the equations suggested by Jones and El-Sonbati. The effect of Hammett's constant is also discussed.

Adsorbate-induced reconstruction in the phase 1 × 2-3H/Rh(110)

NASA Astrophysics Data System (ADS)

Michl, M.; Nichtl-Pecher, W.; Oed, W.; Landskron, H.; Heinz, K.; Müller, K.

1989-10-01

The 1 × 2-3H superstructure of hydrogen on Rh(110) at coverage θ = {3}/{2} is analysed by low energy electron diffraction at 90 K. The spectra of eight beams are recorded with a computer-controlled TV measurement technique which yields low noise data even for weak superstructure spots by multiple averaging. Comparison to full dynamical calculations shows that a kinematic treatment of the hydrogen layer diffraction coupled to the full dynamical diffraction of the substrate is a very good approximation. Spectra computed in this way are compared with experimental data by R-factor evaluation. The three non-equivalent hydrogen atoms are found to adsorb in quasi-three-fold coordinated adsorption sites with slightly different local configurations and with H-Rh bond lengths between 1.87 and 1.93 Å to the first-layer rhodium atoms. Interaction between the adatoms seems to weaken the bonding to the adjacent atom in the second layer, so that H-Rh bond lengths larger than 2.17 Å result. A slight reconstruction of the substrate is necessary to bring superstructure spot intensities near the experimentally observed level. Rhodium atoms bonded to two hydrogen atoms are moved out of the surface by 0.03 ± 0.02 Å relative to Rh atoms bonded to only a single H atom. The relaxation of the first Rh layer spacing is determined to be {d 12}/{d 0} = -3.8 ± 1% and {d 22}/{d 0} = 0 ± 1% . The best fit Pendry R-factor is 0.33.

A Comparison of Cocrystal Structure Solutions from Powder and Single Crystal Techniques

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

S Lapidus; P Stephens; K Arora

We demonstrate the effectiveness and accuracy of high resolution powder diffraction for determination of cocrystal structures through a double-blind study. Structures of 10 cocrystals of varying complexity were determined independently using single crystal and powder techniques. The two methodologies give identical molecular packing and hydrogen bond topology, and an rms difference in covalent bond lengths of 0.035 {angstrom}. Powder techniques are clearly sufficient to establish a complete characterization of cocrystal geometry.

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

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.

A Sticky Chain Model of the Elongation and Unfolding of Escherichia coli P Pili under Stress

PubMed Central

Andersson, Magnus; Fällman, Erik; Uhlin, Bernt Eric; Axner, Ove

2006-01-01

A model of the elongation of P pili expressed by uropathogenic Escherichia coli exposed to stress is presented. The model is based upon the sticky chain concept, which is based upon Hooke's law for elongation of the layer-to-layer and head-to-tail bonds between neighboring units in the PapA rod and a kinetic description of the opening and closing of bonds, described by rate equations and an energy landscape model. It provides an accurate description of the elongation behavior of P pili under stress and supports a hypothesis that the PapA rod shows all three basic stereotypes of elongation/unfolding: elongation of bonds in parallel, the zipper mode of unfolding, and elongation and unfolding of bonds in series. The two first elongation regions are dominated by a cooperative bond opening, in which each bond is influenced by its neighbor, whereas the third region can be described by individual bond opening, in which the bonds open and close randomly. A methodology for a swift extraction of model parameters from force-versus-elongation measurements performed under equilibrium conditions is derived. Entities such as the free energy, the stiffness, the elastic elongation, the opening length of the various bonds, and the number of PapA units in the rod are determined. PMID:16361334

A sticky chain model of the elongation and unfolding of Escherichia coli P pili under stress.

PubMed

Andersson, Magnus; Fällman, Erik; Uhlin, Bernt Eric; Axner, Ove

2006-03-01

A model of the elongation of P pili expressed by uropathogenic Escherichia coli exposed to stress is presented. The model is based upon the sticky chain concept, which is based upon Hooke's law for elongation of the layer-to-layer and head-to-tail bonds between neighboring units in the PapA rod and a kinetic description of the opening and closing of bonds, described by rate equations and an energy landscape model. It provides an accurate description of the elongation behavior of P pili under stress and supports a hypothesis that the PapA rod shows all three basic stereotypes of elongation/unfolding: elongation of bonds in parallel, the zipper mode of unfolding, and elongation and unfolding of bonds in series. The two first elongation regions are dominated by a cooperative bond opening, in which each bond is influenced by its neighbor, whereas the third region can be described by individual bond opening, in which the bonds open and close randomly. A methodology for a swift extraction of model parameters from force-versus-elongation measurements performed under equilibrium conditions is derived. Entities such as the free energy, the stiffness, the elastic elongation, the opening length of the various bonds, and the number of PapA units in the rod are determined.

Synthesis, crystal structure and optical properties of BiMgVO 5

NASA Astrophysics Data System (ADS)

Benmokhtar, S.; El Jazouli, A.; Chaminade, J. P.; Gravereau, P.; Guillen, F.; de Waal, D.

2004-11-01

The new vanadate BiMgVO 5 has been prepared and its structure has been determined by single crystal X-ray diffraction: space group P21/n, a=7.542(6) Å, b=11.615(5) Å, c=5.305(3) Å, β=107.38(5)°, wR2=0.0447, R=0.0255. The structure consists of [Mg 2O 10] and [Bi 2O 10] dimers sharing their corners with [VO 4] tetrahedra. The ranges of bond lengths are 2.129-2.814 Å for Bi-O; 2.035-2.167 Å for Mg-O and 1.684-1.745 Å for V-O. V-O bond lengths determined from Raman band wavenumbers are between 1.679 and 1.747 Å. An emission band overlapping the entire visible region with a maximum around 650 nm is observed.

Local structure of In0.5Ga0.5As from joint high-resolution and differential pair distribution function analysis

NASA Astrophysics Data System (ADS)

Petkov, V.; Jeong, I.-K.; Mohiuddin-Jacobs, F.; Proffen, Th.; Billinge, S. J. L.; Dmowski, W.

2000-07-01

High resolution total and indium differential atomic pair distribution functions (PDFs) for In0.5Ga0.5As alloys have been obtained by high energy and anomalous x-ray diffraction experiments, respectively. The first peak in the total PDF is resolved as a doublet due to the presence of two distinct bond lengths, In-As and Ga-As. The In differential PDF, which involves only atomic pairs containing In, yields chemical specific information and helps ease the structure data interpretation. Both PDFs have been fit with structure models and the way in that the underlying cubic zinc-blende lattice of In0.5Ga0.5As semiconductor alloy distorts locally to accommodate the distinct In-As and Ga-As bond lengths present has been quantified.

Depressing thermal conductivity of fullerene by caging rare gas

NASA Astrophysics Data System (ADS)

Li, Jian; Zheng, Dong-Qin; Zhong, Wei-Rong

2016-01-01

We have investigated the thermal conductivity of C60 and its derivatives caged with rare gas by using the nonequilibrium molecular dynamics method. It is reported that embedding C60 with different rare gas atoms has a significant impact on its thermal conductivity. We analyze the phenomenon through the phonon spectra of rare gas atom and the C-C bonds length of C60. When the number of atoms inside the C60 increases, the phonon spectra band width of rare gas expands and the length of C-C bonds becomes longer, which contributes to the depression of the thermal conductivity of C60. The method is applied to control the thermal conductivity of C60 chains, which maybe a kind of potential materials in thermal circuits. Our results also provide a controllable method for the thermal management in nanoscale materials.

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

Xing, Kunyue; Chatterjee, Sabornie; Saito, Tomonori

Dielectric spectroscopy, rheology, and differential scanning calorimetry were employed to study the effect of chain-end hydrogen bonding on the dynamics of hydroxylterminated polydimethylsiloxane. We demonstrate that hydrogen bonding has a strong influence on both segmental and slower dynamics in the systems with low molecular weights. In particular, the decrease in the chain length leads to an increase of the glass transition temperature, viscosity, and fragility index, at variance with the usual behavior of nonassociating polymers. The supramolecular association of hydroxylterminated chains leads to the emergence in dielectric and mechanical relaxation spectra of the so-called Debye process traditionally observed in monohydroxymore » alcohols. Our analysis suggests that the hydroxyl-terminated PDMS oligomers may associate in brush-like or chain-like structures, depending on the size of their covalent chains. Finally, the effective length of the linear-associated chains was estimated from the rheological measurements.« less

In situ observation of electron beam-induced phase transformation of CaCO3 to CaO via ELNES at low electron beam energies.

PubMed

Golla-Schindler, Ute; Benner, Gerd; Orchowski, Alexander; Kaiser, Ute

2014-06-01

It is demonstrated that energy-filtered transmission electron microscope enables following of in situ changes of the Ca-L2,3 edge which can originate from variations in both local symmetry and bond lengths. Low accelerating voltages of 20 and 40 kV slow down radiation damage effects and enable study of the start and finish of phase transformations. We observed electron beam-induced phase transformation of single crystalline calcite (CaCO3) to polycrystalline calcium oxide (CaO) which occurs in different stages. The coordination of Ca in calcite is close to an octahedral one streched along the <111> direction. Changes during phase transformation to an octahedral coordination of Ca in CaO go along with a bond length increase by 5 pm, where oxygen is preserved as a binding partner. Electron loss near-edge structure of the Ca-L2,3 edge show four separated peaks, which all shift toward lower energies during phase transformation at the same time the energy level splitting increases. We suggest that these changes can be mainly addressed to the change of the bond length on the order of picometers. An important pre-condition for such studies is stability of the energy drift in the range of meV over at least 1 h, which is achieved with the sub-Ångström low-voltage transmission electron microscope I prototype microscope.

Theoretical characterization of the F(2)O(3) molecule by coupled-cluster methods.

PubMed

Huang, Ming-Ju; Watts, John D

2010-09-23

Coupled-cluster calculations with extended basis sets that include noniterative connected triple excitations (CCSD(T)) have been used to study the FOOOF isomer of F(2)O(3). Second-order Moller-Plessett perturbation theory (MP2) and density-functional theory (B3LYP functional) calculations have also been performed for comparison. Two local minima of similar energy, namely, conformers of C(2) and C(s) symmetry have been located. Structures, harmonic vibrational frequencies, and standard enthalpies and free energies of formation have been calculated. The calculated bond lengths of F(2)O(3) are more characteristic of those in F(2)O and a "normal" peroxide than the unusual bond lengths in F(2)O(2). Both conformers have equal F-O and O-O bond lengths, contrary to a recent suggestion of an unsymmetrical structure. The harmonic vibrational frequencies can aid possible identification of gaseous F(2)O(3). The calculated Δ(f)H° and Δ(f)G° are 110 and 173 kJ mol(-1), respectively. These values are based on extrapolation of CCSD(T) results with augmented triple- and quadruple-ζ basis sets and are expected to be within chemical accuracy (i.e., 1 kcal mol(-1) or 4 kJ mol(-1)). F(2)O(3) is calculated to be stable to decomposition to either FO + FOO or F(2) + O(3), but unstable to decomposition to its elements, to F(2)O(2) + (1)/(2)O(2), and to F(2)O + O(2).

Geometry, bonding and magnetism in planar triangulene graphene molecules with D3h symmetry: Zigzag Cm∗∗2+4m+1H3m+3 (m = 2, …, 15)

NASA Astrophysics Data System (ADS)

Philpott, Michael R.; Cimpoesu, Fanica; Kawazoe, Yoshiyuki

2008-12-01

Ab initio plane wave based all valence electron DFT calculations with geometry optimization are reported for the electronic structure of planar zigzag edged triangular shaped graphene molecules CH where the zigzag ring number m = 2, …, 15. The largest molecule C 286H 48 has a 3.8 nm side length and retains D3h symmetric geometry. The zone in the middle of the molecules, where the geometry and electronic properties resemble infinite single sheet graphite (graphene), expands with increasing ring number m, driving deviations in geometry, charge and spin to the perimeter. If a molecule is viewed as a set of nested triangular rings of carbon, then the zone where the lattice resembles an infinite sheet of graphene with CC = 142 pm, extends to the middle of the penultimate ring. The radial bonds joining the perimeter carbon atoms to the interior are long CC = 144 pm, except near the three apexes where the bonds are shorter. Isometric surfaces of the total charge density show that the two bonds joined at the apex have the highest valence charge. The perimeter CC bonds establish a simple pattern as the zigzag number increases, which shares some features with the zigzag edges in the D2h linear acenes C 4m+2H 2m+4 and the D6h hexangulenes CH6m but not the D6h symmetric annulenes (CH). The two CC bonds forming each apex are short (≈139 pm), next comes one long bond CC ≈ 142 pm and a middle region where all the CC bonds have length ≈141 pm. The homo-lumo gap declines from 0.53 eV at m = 2 to approximately 0.29 V at m = 15, the latter being larger than found for linear or hexagonal shaped graphenes with comparable edge lengths. Across the molecule the charge on the carbon atoms undergoes a small oscillation following the bipartite lattice. The magnitude of the charge in the same nested triangle decreases monotonically with the distance of the row from the center of the molecule. These systems are predicted to have spin polarized ground states with S = ½( m - 1), in accord with the theorems of Lieb for a bipartite lattice with unequal numbers of sub-lattice carbon atoms. The magnitude of the spin on the atoms increases monotonically from the center to the edges, this effect being greatest on the majority A-sub lattice atoms. The spins are delocalized, not confined to specific atoms as might result in geometries stabilized by islands of aromatic resonance. In the largest systems the magnetic non-bonding levels (NBL) occur as a narrowly distributed set of homos close to the Fermi level, separated from the lower lying valence bond manifold by a gap of about 1 eV. The NBL are a set of disjoint radical orbitals having charge only on atoms belonging to the A-lattice and this charge is concentrated on the perimeter and penultimate row atoms.

Non-destructive testing of full-length bonded rock bolts based on HHT signal analysis

NASA Astrophysics Data System (ADS)

Shi, Z. M.; Liu, L.; Peng, M.; Liu, C. C.; Tao, F. J.; Liu, C. S.

2018-04-01

Full-length bonded rock bolts are commonly used in mining, tunneling and slope engineering because of their simple design and resistance to corrosion. However, the length of a rock bolt and grouting quality do not often meet the required design standards in practice because of the concealment and complexity of bolt construction. Non-destructive testing is preferred when testing a rock bolt's quality because of the convenience, low cost and wide detection range. In this paper, a signal analysis method for the non-destructive sound wave testing of full-length bonded rock bolts is presented, which is based on the Hilbert-Huang transform (HHT). First, we introduce the HHT analysis method to calculate the bolt length and identify defect locations based on sound wave reflection test signals, which includes decomposing the test signal via empirical mode decomposition (EMD), selecting the intrinsic mode functions (IMF) using the Pearson Correlation Index (PCI) and calculating the instantaneous phase and frequency via the Hilbert transform (HT). Second, six model tests are conducted using different grouting defects and bolt protruding lengths to verify the effectiveness of the HHT analysis method. Lastly, the influence of the bolt protruding length on the test signal, identification of multiple reflections from defects, bolt end and protruding end, and mode mixing from EMD are discussed. The HHT analysis method can identify the bolt length and grouting defect locations from signals that contain noise at multiple reflected interfaces. The reflection from the long protruding end creates an irregular test signal with many frequency peaks on the spectrum. The reflections from defects barely change the original signal because they are low energy, which cannot be adequately resolved using existing methods. The HHT analysis method can identify reflections from the long protruding end of the bolt and multiple reflections from grouting defects based on mutations in the instantaneous frequency, which makes weak reflections more noticeable. The mode mixing phenomenon is observed in several tests, but this does not markedly affect the identification results due to the simple medium in bolt tests. The mode mixing can be reduced by ensemble EMD (EEMD) or complete ensemble EMD with adaptive noise (CEEMDAN), which are powerful tools to used analyze the test signal in a complex medium and may play an important role in future studies. The HHT bolt signal analysis method is a self-adaptive and automatic process, which can be programed as analysis software and will make bolt tests more convenient in practice.

High-resolution studies of tropolone in the S0 and S1 electronic states: isotope driven dynamics in the zero-point energy levels.

PubMed

Keske, John C; Lin, Wei; Pringle, Wallace C; Novick, Stewart E; Blake, Thomas A; Plusquellic, David F

2006-02-21

Rotationally resolved microwave (MW) and ultraviolet (UV) spectra of jet-cooled tropolone have been obtained in S(0) and S(1) electronic states using Fourier-transform microwave and UV-laser/molecular-beam spectrometers. In the ground electronic state, the MW spectra of all heavy-atom isotopomers including one (18)O and four (13)C isotopomers were observed in natural abundance. The OD isotopomer was obtained from isotopically enriched samples. The two lowest tunneling states of each isotopomer except (18)O have been assigned. The observed inversion splitting for the OD isotopomer is 1523.227(5) MHz. For the asymmetric (13)C structures, the magnitudes of tunneling-rotation interactions are found to diminish with decreasing distance between the heavy atom and the tunneling proton. In the limit of closest approach, the 0(+) state of (18)O was well fitted to an asymmetric rotor Hamiltonian, reflecting significant changes in the tautomerization dynamics. Comparisons of the substituted atom coordinates with theoretical predictions at the MP2/aug-cc-pVTZ level of theory suggest the localized 0(+) and 0(-) wave functions of the heavier isotopes favor the C-OH and C=O forms of tropolone, respectively. The only exception occurs for the (13)C-OH and (13)C[Double Bond]O structures which correlate to the 0(-) and 0(+) states, respectively. These preferences reflect kinetic isotope effects as quantitatively verified by the calculated zero-point energy differences between members of the asymmetric atom pairs. From rotationally resolved data of the 0(+) <--0(+) and 0(-) <--0(-) bands in S(1), line-shape fits have yielded Lorentzian linewidths that differ by 12.2(16) MHz over the 19.88(4) cm(-1) interval in S(1). The fluorescence decay rates together with previously reported quantum yield data give nonradiative decay rates of 7.7(5) x 10(8) and 8.5(5) x 10(8) s(-1) for the 0(+) and 0(-) levels of the S(1) state of tropolone.

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.

Energetic Analysis of Conjugated Hydrocarbons Using the Interacting Quantum Atoms Method.

PubMed

Jara-Cortés, Jesús; Hernández-Trujillo, Jesús

2018-07-05

A number of aromatic, antiaromatic, and nonaromatic organic molecules was analyzed in terms of the contributions to the electronic energy defined in the quantum theory of atoms in molecules and the interacting quantum atoms method. Regularities were found in the exchange and electrostatic interatomic energies showing trends that are closely related to those of the delocalization indices defined in the theory. In particular, the CC interaction energies between bonded atoms allow to rationalize the energetic stabilization associated with the bond length alternation in conjugated polyenes. This approach also provides support to Clar's sextet rules devised for aromatic systems. In addition, the H⋯H bonding found in some of the aromatic molecules studied was of an attractive nature, according to the stabilizing exchange interaction between the bonded H atoms. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Femtosecond x-ray scattering study of ultrafast photoinduced structural dynamics in solvated [ Co ( terpy ) 2 ] 2 +

DOE PAGES

Biasin, Elisa; van Driel, Tim Brandt; Kjær, Kasper S.; ...

2016-06-30

Here, we study the structural dynamics of photoexcited [Co(terpy) 2] 2+ in an aqueous solution with ultrafast x-ray diffuse scattering experiments conducted at the Linac Coherent Light Source. Through direct comparisons with density functional theory calculations, our analysis shows that the photoexcitation event leads to elongation of the Co-N bonds, followed by coherent Co-N bond length oscillations arising from the impulsive excitation of a vibrational mode dominated by the symmetrical stretch of all six Co-N bonds. This mode has a period of 0.33 ps and decays on a subpicosecond time scale. We find that the equilibrium bond-elongated structure of themore » high spin state is established on a single-picosecond time scale and that this state has a lifetime of ~7 ps.« less

Ultrastable assembly and integration technology for ground- and space-based optical systems.

PubMed

Ressel, Simon; Gohlke, Martin; Rauen, Dominik; Schuldt, Thilo; Kronast, Wolfgang; Mescheder, Ulrich; Johann, Ulrich; Weise, Dennis; Braxmaier, Claus

2010-08-01

Optical metrology systems crucially rely on the dimensional stability of the optical path between their individual optical components. We present in this paper a novel adhesive bonding technology for setup of quasi-monolithic systems and compare selected characteristics to the well-established state-of-the-art technique of hydroxide-catalysis bonding. It is demonstrated that within the measurement resolution of our ultraprecise custom heterodyne interferometer, both techniques achieve an equivalent passive path length and tilt stability for time scales between 0.1 mHz and 1 Hz. Furthermore, the robustness of the adhesive bonds against mechanical and thermal inputs has been tested, making this new bonding technique in particular a potential option for interferometric applications in future space missions. The integration process itself is eased by long time scales for alignment, as well as short curing times.

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.

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.

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

On the CH...Cu agostic interaction: chiral copper(II) compounds with ephedrine and pseudoephedrine derivatives.

PubMed

Castro, Miguel; Cruz, Julián; López-Sandoval, Horacio; Barba-Behrens, Norah

2005-08-14

The ephedrine derivative, (H2ceph), yields [Cu(Hceph)2], showing a CH...Cu(II) agostic interaction; while in the analogous compound [Cu(Hcpse)2], with pseudoephedrine (H2cpse), that interaction is absent, despite the fact that these two diasteromers differ only in the orientation of the methyl and phenyl groups: erythro in H2ceph and threo in H2cpse. The X-ray crystal structure of [Cu(Hceph)2], indicates a Cu...HC length of 2.454 A and the theoretical study reveals the formation of a Cu...HC bond since the associated electronic density shows both a bond critical point and a bond ring critical point.

Optical fiber pressure and acceleration sensor fabricated on a fiber endface

DOEpatents

Zhu, Yizheng; Wang, Xingwei; Xu, Juncheng; Wang, Anbo

2006-05-30

A fiber optic sensor has a hollow tube bonded to the endface of an optical fiber, and a diaphragm bonded to the hollow tube. The fiber endface and diaphragm comprise an etalon cavity. The length of the etalon cavity changes when applied pressure or acceleration flexes the diaphragm. The entire structure can be made of fused silica. The fiber, tube, and diaphragm can be bonded with a fusion splice. The present sensor is particularly well suited for measuring pressure or acceleration in high temperature, high pressure and corrosive environments (e.g., oil well downholes and jet engines). The present sensors are also suitable for use in biological and medical applications.

Improvement of modulation bandwidth in electroabsorption-modulated laser by utilizing the resonance property in bonding wire.

PubMed

Kwon, Oh Kee; Han, Young Tak; Baek, Yong Soon; Chung, Yun C

2012-05-21

We present and demonstrate a simple and cost-effective technique for improving the modulation bandwidth of electroabsorption-modulated laser (EML). This technique utilizes the RF resonance caused by the EML chip (i.e., junction capacitance) and bonding wire (i.e, wire inductance). We analyze the effects of the lengths of the bonding wires on the frequency responses of EML by using an equivalent circuit model. To verify this analysis, we package a lumped EML chip on the sub-mount and measure its frequency responses. The results show that, by using the proposed technique, we can increase the modulation bandwidth of EML from ~16 GHz to ~28 GHz.

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

NASA Astrophysics Data System (ADS)

Ramek, Michael; Tomić, Sanja

2001-09-01

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

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.

Evaluation of the interfacial bond properties between carbon phenolic and glass phenolic composites

NASA Technical Reports Server (NTRS)

Jordan, K.; Clinton, R.; Jeelani, S.

1991-01-01

The effects of moisture and surface finish on the mechanical and physical properties of the interfacial bond between carbon/phenolic (C/P) and glass/phenolic (G/P) composite materials have been studied. Test results indicate that moisture substantially degrades the integrity of the interfacial bond between C/P and G/P materials. The apparent effect of the autoclave curing of the C/P material reduces the ultimate interlaminar shear length of the C/P material by 20 percent compared to the hydroclave curing of the C/P material. The variation in applied surface finishes is found to have no appreciable effect on the ultimate interlaminar shear strength of the interface in the wet laminate.

A Mononuclear Nonheme Iron(V)-Imido Complex

DOE PAGES

Hong, Seungwoo; Sutherlin, Kyle D.; Vardhaman, Anil Kumar; ...

2017-06-19

Mononuclear nonheme iron(V)-oxo complexes have been reported previously. Herein, we report the first example of a mononuclear nonheme iron(V)-imido complex bearing a tetraamido macrocyclic ligand (TAML), [(TAML)Fe V(NTs)] – . The spectroscopic characterization of 1 revealed an S = 1/2 Fe(V) oxidation state, an Fe—N bond length of 1.65(4) Å, and an Fe—N vibration at 817 cm –1. In conclusion, the reactivity of 1 was demonstrated in C—H bond functionalization and nitrene transfer reactions.

Porous coatings from wire mesh for bone implants

DOEpatents

Sump, Kenneth R.

1986-01-01

A method of coating areas of bone implant elements and the resulting implant having a porous coating are described. Preselected surface areas are covered by a preform made from continuous woven lengths of wire. The preform is compressed and heated to assure that diffusion bonding occurs between the wire surfaces and between the surface boundaries of the implant element and the wire surfaces in contact with it. Porosity is achieved by control of the resulting voids between the bonded wire portions.

Thermal expansion compensator having an elastic conductive element bonded to two facing surfaces

NASA Technical Reports Server (NTRS)

Determan, William (Inventor); Matejczyk, Daniel Edward (Inventor)

2012-01-01

A thermal expansion compensator is provided and includes a first electrode structure having a first surface, a second electrode structure having a second surface facing the first surface and an elastic element bonded to the first and second surfaces and including a conductive element by which the first and second electrode structures electrically and/or thermally communicate, the conductive element having a length that is not substantially longer than a distance between the first and second surfaces.

Development of Flexible Extremities Protection utilizing Shear Thickening Fluid/Fabric Composites

DTIC Science & Technology

2012-01-19

absorption frequencies. With the addition of Gluta, the peak for each of the three bonds increased indicating that the total number of bonds (i.e., cross...fiber to be investigated a gage length of 127 mm. The fiber was clamped at one end and at a position of 127 mm at that end. A Celanese food ...general behavior of high performance fibers during cut resistance testing at normal incidence with a Celanese food processing blade. This data is the

A Mononuclear Nonheme Iron(V)-Imido Complex

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

Hong, Seungwoo; Sutherlin, Kyle D.; Vardhaman, Anil Kumar

Mononuclear nonheme iron(V)-oxo complexes have been reported previously. Herein, we report the first example of a mononuclear nonheme iron(V)-imido complex bearing a tetraamido macrocyclic ligand (TAML), [(TAML)Fe V(NTs)] – . The spectroscopic characterization of 1 revealed an S = 1/2 Fe(V) oxidation state, an Fe—N bond length of 1.65(4) Å, and an Fe—N vibration at 817 cm –1. In conclusion, the reactivity of 1 was demonstrated in C—H bond functionalization and nitrene transfer reactions.

Supramolecular Polymers Based on Non-Coplanar AAA-DDD Hydrogen-Bonded Complexes.

PubMed

Mendez, Iamnica J Linares; Wang, Hong-Bo; Yuan, Ying-Xue; Wisner, James A

2018-03-01

Non-coplanar triple-hydrogen-bond arrays are connected as telechelic groups to alkyl chains and their properties as AA/BB type supramolecular polymers are examined. Viscosity studies at three temperatures are used to study the ring-chain equilibrium and determine the critical concentrations where polymer chains are formed. It is observed that neither the temperature range studied nor the alkyl chain length of one component significantly affect the polymerization properties in this system. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Length-dependent structural stability of linear monatomic Cu wires

NASA Astrophysics Data System (ADS)

Singh, Gurvinder; Kumar, Krishan; Singh, Baljinder; Moudgil, R. K.

2018-05-01

We present first-principle calculations based on density functional theory for the finite-length monatomic Cu atom linear wires. The structure and its stability with increasing wire length in terms of number of atoms (N) is determined. Interestingly, the bond length is found to exhibit an oscillatory structure (the so-called magic length phenomenon), with a qualitative change in oscillatory behavior as one moves from even N wire to odd N wire. The even N wires follow simple even-odd oscillations whereas odd N wires show a phase change at the half length of the wires. The stability of the wire structure, determined in terms of the wire formation energy, also contains even-odd oscillation as a function of wire length. However, the oscillations in formation energy reverse its phase after the wire length is increased beyond N=12. Our findings are seen to be qualitatively consistent with recent simulations for a similar class finite-length metal atom wires.

Structural, electronic and spectral properties of carborane-containing boron dipyrromethenes (BODIPYs): A first-principles study

NASA Astrophysics Data System (ADS)

Li, Xiaojun

2017-10-01

In this work, we reported the geometrical structures, electronic and spectral properties of the carborane-containing BODIPYs complexes using the density functional theory calculations. In two structures, the calculated main bond lengths and bond angels of structural framework are consistent with X-ray experiment, and the two BODIPYs complexes are thermodynamically and kinetically stable. The strongest DOS band is mainly dominated by the Bsbnd B and Bsbnd H σ-bonds of carborane fragment, whereas the π-type MOs on the pyrromethene fragment contribute to the high-energy DOS bands. Analysis of the AdNDP chemical bonding indicates that the carborane cage can be stabilized by eleven delocalized 3csbnd 2e and two delocalized 4csbnd 2e σ-bonds, while the pyrromethene fragment corresponds to five delocalized 3csbnd 2e π-bonds. In addition, the main characteristic peaks of the two simulated IR spectra for the BODIPYs complexes are properly assigned. Hopefully, all these results will be helpful for understanding the electronic structures, and further stimulate the study on the biological and medical applications.

A dynamics prediction of nitromethane → methyl nitrite isomerization in external electric field.

PubMed

Ren, Fu-de; Cao, Duan-lin; Shi, Wen-jing

2016-04-01

As a follow-up to our investigation into the effect of external electric field on the chemical bond strength, the effects of external electric field on the CH3NO2 → CH3ONO isomerization dynamics were investigated using the MP2/6-311++G(2d,p) and CCSD/6-311++G(2d,p) methods. The rate constants in the absence and presence of various field strengths were calculated. The results show that, when the field strength is larger than +0.0060 a.u. along the C-NO2 bond axis, the barriers of the isomerization are lower than the C-NO2 bond dissociation energies, leading to the preferences of the isomerization over the C-NO2 bond dissociation. In this case, the sensitivities are higher than that in no field. However, in the other fields, the C-NO2 bond scission is favored and the sensitivities are almost equal to that in no field. Several good linear correlations are found between the field strengths and the changes of the bond lengths or corresponding electron densities.

Strength evaluation of butt joint by stress intensity factor of small edge crack near interface edge

NASA Astrophysics Data System (ADS)

Sato, T.; Oda, K.; Tsutsumi, N.

2018-06-01

Failure of the bonded dissimilar materials generally initiates near the interface, or just from the interface edge due to the stress singularity at the interface edge. In this study, the stress intensity factor of an edge crack close to the interface between the dissimilar materials is analyzed. The small edge crack is strongly dominated by the singular stress field near the interface edge. The analysis of stress intensity factor of small edge crack near the interface in bi-material and butt joint plates is carried out by changing the length and the location of the crack and the region dominated by the interface edge is examined. It is found that the dimensionless stress intensity factor of small crack, normalized by the singular stress at the crack tip point in the bonded plate without the crack, is equal to 1.12, independent of the material combination and adhesive layer thickness, when the relative crack length with respect to the crack location is less than 0.01. The adhesive strength of the bonded plate with various adhesive layer thicknesses can be expressed as the constant critical stress intensity factor of the small edge crack.

The pure rotational spectra of the open-shell diatomic molecules PbI and SnI

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

Evans, Corey J., E-mail: cje8@le.ac.uk, E-mail: nick.walker@newcastle.ac.uk; Needham, Lisa-Maria E.; Walker, Nicholas R., E-mail: cje8@le.ac.uk, E-mail: nick.walker@newcastle.ac.uk

2015-12-28

Pure rotational spectra of the ground electronic states of lead monoiodide and tin monoiodide have been measured using a chirped pulsed Fourier transform microwave spectrometer over the 7-18.5 GHz region for the first time. Each of PbI and SnI has a X {sup 2}Π{sub 1/2} ground electronic state and may have a hyperfine structure that aids the determination of the electron electric dipole moment. For each species, pure rotational transitions of a number of different isotopologues and their excited vibrational states have been assigned and fitted. A multi-isotopologue Dunham-type analysis was carried out on both species producing values for Y{submore » 01}, Y{sub 02}, Y{sub 11}, and Y{sub 21}, along with Λ-doubling constants, magnetic hyperfine constants and nuclear quadrupole coupling constants. The Born-Oppenheimer breakdown parameters for Pb have been evaluated and the parameter rationalized in terms of finite nuclear field effects. Analysis of the bond lengths and hyperfine interaction indicates that the bonding in both PbI and SnI is ionic in nature. Equilibrium bond lengths have been evaluated for both species.« 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.

Asymmetric oxidation of vinyl- and ethynyl terthiophene ligands in triruthenium complexes.

PubMed

Zhang, Jing; Sun, Chao-Fang; Zhang, Ming-Xing; Hartl, František; Yin, Jun; Yu, Guang-Ao; Rao, Li; Liu, Sheng Hua

2016-01-14

A series of ruthenium(ii) complexes [{RuCl(CO)(PMe3)3(-CH[double bond, length as m-dash]CH-)}nX], (: n = 3, X = 3,3''-dimethyl-2,2':3',2''-terthiophene; : n = 2, X = 2,2'-bithiophene; : n = 2, X = 2,3-bis(3-methylthiophen-2-yl)benzothiophene) and [{Cp*(dppe)2Ru(-C[triple bond, length as m-dash]C-)}3X], (X = 3,3''-dimethyl-2,2':3',2''-terthiophene), were prepared and characterized by (1)H, (13)C and (31)P NMR. Their redox, spectroscopic and bonding properties were studied with a range of spectro-electrochemical methods in combination with density functional theory calculations. The first two anodic steps observed for and are largely localized on the lateral frameworks of the molecular triangle, the direct conjugation between them being precluded due to the photostable open form of the dithienyl ethene moiety. The third anodic step is then mainly localized on the centerpiece of the triangular structure, affecting both bithiophene laterals. The experimental IR and UV-vis-NIR spectroelectrochemical data and, largely, also DFT calculations account for this explanation, being further supported by direct comparison with the anodic behavior of reference diruthenium complexes and .

Spin-crossover phenomena of the mononuclear Mn(III) complex tuned by metal dithiolene counteranions.

PubMed

Chen, Ying; Cao, Fan; Wei, Rong-Min; Zhang, Yang; Zhang, Yi-Quan; Song, You

2014-03-07

Three ion-pair complexes based on spin-crossover [Mn(5-Br-sal-N-1,5,8,12)]ClO4 with TBA2[Ni(mnt)2], TBA2[Pt(mnt)2] (mnt = maleonitriledithiolate) and TBA[Ni(dmit)2] respectively (dmit = 2-thioxo-1,3-dithiole-4,5-dithiolato) have been synthesized and structurally characterized. Complexes [Mn(5-Br-sal-N-1,5,8,12)]2[Ni(mnt)2] and [Mn(5-Br-sal-N-1,5,8,12)]2[Pt(mnt)2] are isomorphic and show the axial compression of the octahedral coordination environment of Mn(III) ions. With the temperature increasing the equatorial metal-ligand bond lengths show significant elongation, but the axial bond lengths remain unchanged. Complex [Mn(5-Br-sal-N-1,5,8,12)][Ni(dmit)2]·CH3CN contains π-π, p-π and H-bonds weak interactions. Magnetic investigation shows the spin-crossover phenomena for and , and T1/2 has been increased by 230 K comparing with the reactant complex. However, no spin-crossover was observed in complex , and theoretical calculations show that there are weak antiferromagnetic couplings mediated through π-π interactions.

The pure rotational spectrum of ZnS (X 1Σ +)

NASA Astrophysics Data System (ADS)

Zack, L. N.; Ziurys, L. M.

2009-10-01

The pure rotational spectrum of ZnS (X 1Σ +) has been measured using direct-absorption millimeter/sub-millimeter techniques in the frequency range 372-471 GHz. This study is the first spectroscopic investigation of this molecule. Spectra originating in four zinc isotopologues ( 64ZnS, 66ZnS, 68ZnS, and 67ZnS) were recorded in natural abundance in the ground vibrational state, and data from the v = 1 state were also measured for the two most abundant zinc species. Spectroscopic constants have been subsequently determined, and equilibrium parameters have been estimated. The equilibrium bond length was calculated to be re ˜ 2.0464 Å, which agrees well with theoretical predictions. In contrast, the dissociation energy of DE ˜ 3.12 eV calculated for ZnS, assuming a Morse potential, was significantly higher than past experimental and theoretical estimates, suggesting diabatic interaction with other potentials that lower the effective dissociation energy. Although ZnS is isovalent with ZnO, there appear to be subtle differences in bonding between the two species, as suggested by their respective force constants and bond length trends in the 3d series.

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.

Strain engineering of the elasticity and the Raman shift of nanostructured TiO2

NASA Astrophysics Data System (ADS)

Liu, X. J.; Pan, L. K.; Sun, Z.; Chen, Y. M.; Yang, X. X.; Yang, L. W.; Zhou, Z. F.; Sun, Chang Q.

2011-08-01

Correlation between the elastic modulus (B) and the Raman shift (Δω) of TiO2 and their responses to the variation of crystal size, applied pressure, and measuring temperature have been established as a function depending on the order, length, and energy of a representative bond for the entire specimen. In addition to the derived fundamental information of the atomic cohesive energy, binding energy density, Debye temperature and nonlinear compressibility, theoretical reproduction of the observations clarified that (i) the size effect arises from the under-coordination induced cohesive energy loss and the energy density gain in the surface up to skin depth; (ii) the thermally softened B and Δω results from bond expansion and bond weakening due to vibration; and, (iii) the mechanically stiffened B and Δω results from bond compression and bond strengthening due to mechanical work hardening. With the developed premise, one can predict the changing trends of the concerned properties with derivatives of quantitative information as such from any single measurement alone.

Semitransparent bandages based on chitosan and extracellular matrix for photochemical tissue bonding.

PubMed

Frost, Samuel J; Mawad, Damia; Wuhrer, Richard; Myers, Simon; Lauto, Antonio

2018-01-22

Extracellular matrices (ECMs) are often used in reconstructive surgery to enhance tissue regeneration and remodeling. Sutures and staples are currently used to fix ECMs to tissue although they can be invasive devices. Other sutureless and less invasive techniques, such as photochemical tissue bonding, cannot be coupled to ECMs because of their intrinsic opacity to light. We succeeded in fabricating a biocompatible and adhesive device that is based on ovine forestomach matrix (OFM) and a chitosan adhesive. The natural opacity of the OFM has been overcome by adding the adhesive into the matrix that allows for the light to effectively penetrate through it. The OFM-chitosan device is semitransparent (attenuation length ~ 106 µm) and can be photoactivated by green light to bond to tissue. This device does not require sutures or staples and guarantees a bonding strength of ~ 23 kPa. A new semitransparent and biocompatible bandage has been successfully fabricated and characterized for sutureless tissue bonding.

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.

Cholesterol oxidase: ultrahigh-resolution crystal structure and multipolar atom model-based analysis.

PubMed

Zarychta, Bartosz; Lyubimov, Artem; Ahmed, Maqsood; Munshi, Parthapratim; Guillot, Benoît; Vrielink, Alice; Jelsch, Christian

2015-04-01

Examination of protein structure at the subatomic level is required to improve the understanding of enzymatic function. For this purpose, X-ray diffraction data have been collected at 100 K from cholesterol oxidase crystals using synchrotron radiation to an optical resolution of 0.94 Å. After refinement using the spherical atom model, nonmodelled bonding peaks were detected in the Fourier residual electron density on some of the individual bonds. Well defined bond density was observed in the peptide plane after averaging maps on the residues with the lowest thermal motion. The multipolar electron density of the protein-cofactor complex was modelled by transfer of the ELMAM2 charge-density database, and the topology of the intermolecular interactions between the protein and the flavin adenine dinucleotide (FAD) cofactor was subsequently investigated. Taking advantage of the high resolution of the structure, the stereochemistry of main-chain bond lengths and of C=O···H-N hydrogen bonds was analyzed with respect to the different secondary-structure elements.

LCGTO-Xα model cluster study for the chemisorption of CO on twofold sites of Ni surfaces

NASA Astrophysics Data System (ADS)

Jörg, H.; Rösch, N.

The cluster Ni 2CO is studied as a simplified model for the chemisorption of CO on twofold bridging sites of transition metal surfaces. Using the LCGTO-Xα method we have calculated the potential energy surface for the totally symmetric stretching motion keeping the Ni-Ni distance fixed at the bulk value. The minimum energy is found at a Ni-C distance of 1.72 Å and a C-O bond length of 1.19 Å. The vibrational frequency for the CO bond (1850 cm -1) shows reasonable agreement with EELS data (1810, 1870 cm -1), whereas the (Ni 2)-C frequency of 495 cm -1 is remarkably higher than the experimental values (380, 400 cm -1) indicating an overestimation of the chemisorption bond strength in this simple cluster model. The bonding between CO and Ni is analyzed using orbital correlations, ionization energies and Mulliken population analysis. Important bonding contributions from π backdonation are identified while the a 1 orbital manifold exhibits strong antibonding effects.

LCGTO-Xα model cluster study for the chemisorption of CO on twofold sites of Ni surfaces

NASA Astrophysics Data System (ADS)

Jörg, H.; Rösch, N.

1985-11-01

The cluster Ni 2CO is studied as a simplified model for the chemisorption of CO on twofold bridging sites of transition metal surfaces. Using the LCGTO-Xα method we have calculated the potential energy surface for the totally symmetric stretching motion keeping the NiNi distance fixed at the bulk value. The minimum energy is found at a NiC distance of 1.72 Å and a CO bond length of 1.19 Å. The vibrational frequency for the CO bond (1850 cm -1) shows reasonable agreement with EELS data (1810, 1870 cm -1), whereas the (Ni 2)C frequency of 495 cm -1 is remarkably higher than the experimental values (380, 400 cm -1) indicating an overestimation of the chemisorption bond strength in this simple cluster model. The bonding between CO and Ni is analyzed using orbital correlations, ionization energies and Mulliken population analysis. Important bonding contributions from π backdonation are identified while the a 1orbital manifold exhibits strong antibonding effects.

Interaction of benzene thiol and thiolate with small gold clusters.

PubMed

Letardi, Sara; Cleri, Fabrizio

2004-06-01

We studied the interaction between benzene thiol and thiolate molecules, and gold clusters made of 1 to 3 atoms, by means of ab initio density functional theory in the local density approximation. We find that the thiolate is energetically more stable than the thiol, however the process of detachment of H from the thiol appears to be possibly mediated by the intermediate step of H chemisorption on Au. Cleavage of the S-H bond is accompanied by a 90 degrees rotation of the molecule around the S-Au bond, showing a strong steric specificity. Such a rotation is induced by the relative energy shift of the S atom p orbitals with respect to the benzene pi ring and the Au d orbitals. By analyzing the correlation of the bond energy, bond lengths, and HOMO-LUMO gap with the number of S-Au bonds, we find that the thiolate S atom appears to prefer a low-coordination condition on Au clusters. (c) 2004 American Institute of Physics.

Metal-Metal Single Bonds with the Magnetic Anisotropy of Quadruple Bonds: A Systematic Series of Heterobimetallic Bismuth(II)-Rhodium(II) Formamidinate Complexes.

PubMed

Sunderland, Travis L; Berry, John F

2016-12-19

The first set of five heterobimetallic MM'(form) 4 (form=formamidinate) complexes containing a BiRh core has been successfully synthesized. The Bi-Rh bond lengths lie between 2.5196(6) and 2.572(2) Å, consistent with Bi-Rh single bonds. All complexes have rich electrochemistry, with the [BiRh] 4+/5+ redox couples spanning approximately 700 mV and showing a strong correlation to remote ligand substitution. Visible spectroscopy showed two features for complexes 1-5 at approximately 459 and 551 nm, unique to BiRh paddlewheel complexes that are attributed to LMCT bands into the Bi-Rh σ* orbital. The large spin-orbit coupling (SOC) of Bi creates a massive Bi-Rh magnetic anisotropy, Δχ, approximately -4800×10 -36  m 3 molecule -1 , which is the largest value reported for any single bond to date. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Kondo length in bosonic lattices

NASA Astrophysics Data System (ADS)

Giuliano, Domenico; Sodano, Pasquale; Trombettoni, Andrea

2017-09-01

Motivated by the fact that the low-energy properties of the Kondo model can be effectively simulated in spin chains, we study the realization of the effect with bond impurities in ultracold bosonic lattices at half filling. After presenting a discussion of the effective theory and of the mapping of the bosonic chain onto a lattice spin Hamiltonian, we provide estimates for the Kondo length as a function of the parameters of the bosonic model. We point out that the Kondo length can be extracted from the integrated real-space correlation functions, which are experimentally accessible quantities in experiments with cold atoms.

Effects of different overlap lengths and composite adherend thicknesses on the performance of adhesively-bonded joints under tensile and bending loadings

NASA Astrophysics Data System (ADS)

Kadioglu, F.; Avil, E.; Ercan, M. E.; Aydogan, T.

2018-05-01

Fiber-reinforced polymer composites are being used in an increasingly wide range of products. They are particularly popular in automotive and aerospace sectors because they offer an attractive combination of stiffness, strength and low mass. Adhesively-bonded joints of such materials are preferred by many designers due to their assembling advantages over other traditional mechanical joining systems, such as bolted and riveted joints. In this study, some experimental works have been carried out on adhesively-bonded adherends manufactured from a woven carbon fiber-reinforced polymer matrix composite (Hexply 8552S/A280-5H, produced by Hexcel), by using a film adhesive (AF163-2K produced by 3 M). The bonded specimens were prepared in the Single Lap Joint (SLJ) configuration, and tested in tensile and also in four-point bending loading. In order to assess the joint performance, three different overlap lengths, 15 mm, 25 mm and 40 mm, and two different thicknesses of the composite adherends, 2 mm and 3 mm, were used. The results shown that the parameters are controlled by the loading modes; while the overlap length increases the joint performance significantly in tensile loading, the opposite was the case for those in bending loading, which was affected mainly by the adherend thicknesses. The results were related to the mechanisms of joint failures; while the joints in the tensile failed in the adhesive layer with some exceptions, those in the bending mainly failed in the plies adjacent to the layer. The current study indicates that one of the important factors affecting the joint strength of the adherends manufactured from the laminated composites is the local failure of the plies. It is thought more focused-studies would be needed to lessen such problems, which would be possible via in-depth numerical analysis.

Syntheses of monomeric (. eta. sup 5 -pentamethylcyclopentadienyl)platinum(IV) methyl and bromo complexes and of (hydrotris(3,5-dimethyl-1-pyrazolyl)borato)trimethylplatinum

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

Roth, S.; Ramamoorthy, V.; Sharp, P.R.

1990-09-05

The reaction of Cp*MgCl{center dot}THF (Cp* = C{sub 5}Me{sub 5}) with 1 equiv of PtMe{sub 3}I and PtMe{sub 2}Br{sub 2} produces Cp*PtMe{sub 3} (1) and Cp*PtMe{sub 2}Br (2), respectively. Reaction of 2 with Br{sub 2} produces Cp*PtMeBr{sub 2} (3) in good yield. The structures of 2 and 3 have been determined by x-ray crystallography, and the crystal structure data are reported. Complex 2 crystallizes in the monoclinic space group, P2{sub 1}/m, and complex 3 crystallizes in the monoclinic space group, P2{sub 1}/m. The molecules reside on mirror planes and are monomeric pseudotetrahedral Pt(IV) complexes with piano stool type geometries andmore » {eta}{sup 5}-Cp* groups. Both molecules have Br atoms on the mirror. This leads to a disorder of the Me and the second Br positions in complex 3. The average Pt-C(Cp*) bond length is 2.25 (7) {angstrom} in 2 and 2.22 (4) {angstrom} in 3. The Pt-C(Me) and Pt-Br bond lengths in 2 are 2.07 (2) and 2.498 (2) {angstrom}, respectively. The ordered Pt-Br bond length in 3 is 2.496 (2) {angstrom}. Treatment of 1 with halogens results in the cleavage of the Pt-Cp* bond. The reaction of PtMe{sub 3}I with KTp* (Tp* = (HB(3,5-dimethylpyrazolyl){sub 3}){sup {minus}}) in thf gives Tp*PtMe{sub 3} (4) in almost quantitative yield. The reaction of 4 with Br{sub 2} brominates the 4-position of the pyrazolyl ring only. 28 refs., 2 figs., 5 tabs.« less

Electrical conductivity enhancement by boron-doping in diamond using first principle calculations

NASA Astrophysics Data System (ADS)

Ullah, Mahtab; Ahmed, Ejaz; Hussain, Fayyaz; Rana, Anwar Manzoor; Raza, Rizwan

2015-04-01

Boron doping in diamond plays a vital role in enhancing electrical conductivity of diamond by making it a semiconductor, a conductor or even a superconductor. To elucidate this fact, partial and total density of states has been determined as a function of B-content in diamond. Moreover, the orbital charge distributions, B-C bond lengths and their population have been studied for B-doping in pristine diamond thin films by applying density functional theory (DFT). These parameters have been found to be influenced by the addition of different percentages of boron atoms in diamond. The electronic density of states, B-C bond situations as well as variations in electrical conductivities of diamond films with different boron content and determination of some relationship between these parameters were the basic tasks of this study. Diamond with high boron concentration (∼5.88% B-atoms) showed maximum splitting of energy bands (caused by acceptor impurity states) at the Fermi level which resulted in the enhancement of electron/ion conductivities. Because B atoms either substitute carbon atoms and/or assemble at grain boundaries (interstitial sites) inducing impurity levels close to the top of the valence band. At very high B-concentration, impurity states combine to form an impurity band which accesses the top of the valence band yielding metal like conductivity. Moreover, bond length and charge distributions are found to decrease with increase in boron percentage in diamond. It is noted that charge distribution decreased from +1.89 to -1.90 eV whereas bond length reduced by 0.04 Å with increasing boron content in diamond films. These theoretical results support our earlier experimental findings on B-doped diamond polycrystalline films which depict that the addition of boron atoms to diamond films gives a sudden fall in resistivity even up to 105 Ω cm making it a good semiconductor for its applications in electrical devices.

Hyperpolarizabilities of Push-Pull Polyenes: Experimental Results and a New Two-State Model

NASA Technical Reports Server (NTRS)

Perry, J.; Bourhill, G.; Marder, S.; Lu, D.; Chen, G.; Goddard, W.

1994-01-01

Recent work has demonstrated a correlation between the geometry (i.e., the bond length alteration, BLA) and the first and second hyperpolarizabilities (betta and gamma) of donor-acceptor substituted (push-pull)polyenes.

31 CFR 321.12 - Redemption value of securities.

Code of Federal Regulations, 2010 CFR

2010-07-01

... each savings security is determined by the terms of its offering and the length of time it has been outstanding. The Bureau of the Public Debt determines redemption values for Series A-E bonds, eligible Series...

31 CFR 321.12 - Redemption value of securities.

Code of Federal Regulations, 2012 CFR

2012-07-01

... savings security is determined by the terms of its offering and the length of time it has been outstanding. The Bureau of the Public Debt determines redemption values for Series A-E bonds, eligible Series EE...

31 CFR 321.12 - Redemption value of securities.

Code of Federal Regulations, 2011 CFR

2011-07-01

... security is determined by the terms of its offering and the length of time it has been outstanding. The Bureau of the Public Debt determines redemption values for Series A-E bonds, eligible Series EE and I...

31 CFR 321.12 - Redemption value of securities.

Code of Federal Regulations, 2013 CFR

2013-07-01

... savings security is determined by the terms of its offering and the length of time it has been outstanding. The Bureau of the Public Debt determines redemption values for Series A-E bonds, eligible Series EE...

Local structure in solid solutions of stabilised zirconia with actinide dioxides (UO{sub 2}, NpO{sub 2})

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

Walter, Marcus, E-mail: marcus.walter@vkta.d; Somers, Joseph; Bouexiere, Daniel

2011-04-15

The local structure of (Zr,Lu,U)O{sub 2-x} and (Zr,Y,Np)O{sub 2-x} solid solutions has been investigated by extended X-ray absorption fine structure (EXAFS). Samples were prepared by mixing reactive (Zr,Lu)O{sub 2-x} and (Zr,Y)O{sub 2-x} precursor materials with the actinide oxide powders, respectively. Sintering at 1600 {sup o}C in Ar/H{sub 2} yields a fluorite structure with U(IV) and Np(IV). As typical for stabilised zirconia the metal-oxygen and metal-metal distances are characteristic for the different metal ions. The bond lengths increase with actinide concentration, whereas highest adaptation to the bulk stabilised zirconia structure was observed for U---O and Np---O bonds. The Zr---O bond showsmore » only a slight increase from 2.14 A at 6 mol% actinide to 2.18 A at infinite dilution in UO{sub 2} and NpO{sub 2}. The short interatomic distance between Zr and the surrounding oxygen and metal atoms indicate a low relaxation of Zr with respect to the bulk structure, i.e. a strong Pauling behaviour. -- Graphical abstract: Metal-oxygen bond distances in (Zr,Lu,U)O{sub 2-x} solid solutions with different oxygen vacancy concentrations (Lu/Zr=1 and Lu/Zr=0.5). Display Omitted Research Highlights: {yields} EXAFS indicates high U and Np adaption to the bulk structure of stabilised zirconia. {yields} Zr---O bond length is 2.18 A at infinite Zr dilution in UO{sub 2} and NpO{sub 2}. {yields} Low relaxation (strong Pauling behaviour) of Zr explains its low solubility in UO{sub 2}.« less

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

Ab-initio study of structural, electronic, and transport properties of zigzag GaP nanotubes.

PubMed

Srivastava, Anurag; Jain, Sumit Kumar; Khare, Purnima Swarup

2014-03-01

Stability and electronic properties of zigzag (3 ≤ n ≤ 16) gallium phosphide nanotubes (GaP NTs) have been analyzed by employing a systematic ab-intio approach based on density functional theory using generalized gradient approximation with revised Perdew Burke Ernzerhoff type parameterization. Diameter dependence of bond length, buckling, binding energy, and band gap has been investigated and the analysis shows that the bond length and buckling decreases with increasing diameter of the tube, highest binding energy of (16, 0) confirms this as the most stable amongst all the NTs taken into consideration. The present GaP NTs shows direct band gap and it increases with diameter of the tubes. Using a two probe model for (4, 0) NT the I-V relationship shows an exponential increase in current on applying bias voltage beyond 1.73 volt.

Bis[μ-N-(tert-butyl­dimethyl­silyl)-N-(pyridin-2-ylmeth­yl)amido]­bis­[methyl­cobalt(II)

PubMed Central

Malassa, Astrid; Agthe, Christine; Görls, Helmar; Westerhausen, Matthias

2012-01-01

The green title complex, [Co2(CH3)2(C12H21N2Si)2], was obtained from bis­{[μ-N-tert-butyl­dimethyl­silyl-N-(pyridin-2-ylmeth­yl)amido]­chloridocobalt(II)} and methyl­lithium in diethyl ether at 195 K via a metathesis reaction. The dimeric cobalt(II) complex exhibits a crystallographic center of inversion in the middle of the Co2N2 ring (average Co—N = 2.050 Å). The CoII atom shows a distorted tetra­hedral coordination sphere. The exocyclic Co—N bond length to the pyridyl group shows a similar value of 2.045 (4) Å. The exocyclic methyl group has a rather long Co—C bond length of 2.019 (5) Å. PMID:22969464

Modification of the G-phonon mode of graphene by nitrogen doping

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

Lukashev, Pavel V., E-mail: pavel.lukashev@uni.edu; Hurley, Noah; Zhao, Liuyan

2016-01-25

The effect of nitrogen doping on the phonon spectra of graphene is analyzed. In particular, we employ first-principles calculations and scanning Raman analysis to investigate the dependence of phonon frequencies in graphene on the concentration of nitrogen dopants. We demonstrate that the G phonon frequency shows oscillatory behavior as a function of nitrogen concentration. We analyze different mechanisms which could potentially be responsible for this behavior, such as Friedel charge oscillations around the localized nitrogen impurity atom, the bond length change between nitrogen impurity and its nearest neighbor carbon atoms, and the long-range interactions of the nitrogen point defects. Wemore » show that the bond length change and the long range interaction of point defects are possible mechanisms responsible for the oscillatory behavior of the G frequency as a function of nitrogen concentration. At the same time, Friedel charge oscillations are unlikely to contribute to this behavior.« less

Quantum conductance oscillation in linear monatomic silicon chains

NASA Astrophysics Data System (ADS)

Liu, Fu-Ti; Cheng, Yan; Yang, Fu-Bin; Chen, Xiang-Rong

2014-02-01

The conductance of linear silicon atomic chains with n=1-8 atoms sandwiched between Au electrodes is investigated by using the density functional theory combined with non-equilibrium Green's function. The results show that the conductance oscillates with a period of two atoms as the number of atoms in the chain is varied. We optimize the geometric structure of nanoscale junctions in different distances, and obtain that the average bond-length of silicon atoms in each chain at equilibrium positions is 2.15±0.03 Å. The oscillation of average Si-Si bond-length can explain the conductance oscillation from the geometric structure of atomic chains. We calculate the transmission spectrum of the chains in the equilibrium positions, and explain the conductance oscillation from the electronic structure. The transport channel is mainly contributed by px and py orbital electrons of silicon atoms. The even-odd oscillation is robust under external voltage up to 1.2 V.

Fragmentation-based QM/MM simulations: length dependence of chain dynamics and hydrogen bonding of polyethylene oxide and polyethylene in aqueous solutions.

PubMed

Li, Hui; Li, Wei; Li, Shuhua; Ma, Jing

2008-06-12

Molecular fragmentation quantum mechanics (QM) calculations have been combined with molecular mechanics (MM) to construct the fragmentation QM/MM method for simulations of dilute solutions of macromolecules. We adopt the electrostatics embedding QM/MM model, where the low-cost generalized energy-based fragmentation calculations are employed for the QM part. Conformation energy calculations, geometry optimizations, and Born-Oppenheimer molecular dynamics simulations of poly(ethylene oxide), PEO(n) (n = 6-20), and polyethylene, PE(n) ( n = 9-30), in aqueous solution have been performed within the framework of both fragmentation and conventional QM/MM methods. The intermolecular hydrogen bonding and chain configurations obtained from the fragmentation QM/MM simulations are consistent with the conventional QM/MM method. The length dependence of chain conformations and dynamics of PEO and PE oligomers in aqueous solutions is also investigated through the fragmentation QM/MM molecular dynamics simulations.

Thermodynamic properties of small aggregates of rare-gas atoms

NASA Technical Reports Server (NTRS)

Etters, R. D.; Kaelberer, J.

1975-01-01

The present work reports on the equilibrium thermodynamic properties of small clusters of xenon, krypton, and argon atoms, determined from a biased random-walk Monte Carlo procedure. Cluster sizes ranged from 3 to 13 atoms. Each cluster was found to have an abrupt liquid-gas phase transition at a temperature much less than for the bulk material. An abrupt solid-liquid transition is observed for thirteen- and eleven-particle clusters. For cluster sizes smaller than 11, a gradual transition from solid to liquid occurred over a fairly broad range of temperatures. Distribution of number of bond lengths as a function of bond length was calculated for several systems at various temperatures. The effects of box boundary conditions are discussed. Results show the importance of a correct description of boundary conditions. A surprising result is the slow rate at which system properties approach bulk behavior as cluster size is increased.

Dopant activation mechanism of Bi wire-δ-doping into Si crystal, investigated with wavelength dispersive fluorescence x-ray absorption fine structure and density functional theory.

PubMed

Murata, Koichi; Kirkham, Christopher; Shimomura, Masaru; Nitta, Kiyofumi; Uruga, Tomoya; Terada, Yasuko; Nittoh, Koh-Ichi; Bowler, David R; Miki, Kazushi

2017-04-20

We successfully characterized the local structures of Bi atoms in a wire-δ-doped layer (1/8 ML) in a Si crystal, using wavelength dispersive fluorescence x-ray absorption fine structure at the beamline BL37XU, in SPring-8, with the help of density functional theory calculations. It was found that the burial of Bi nanolines on the Si(0 0 1) surface, via growth of Si capping layer at 400 °C by molecular beam epitaxy, reduced the Bi-Si bond length from [Formula: see text] to [Formula: see text] Å. We infer that following epitaxial growth the Bi-Bi dimers of the nanoline are broken, and the Bi atoms are located at substitutional sites within the Si crystal, leading to the shorter Bi-Si bond lengths.

Tetrel Bonding as a Vehicle for Strong and Selective Anion Binding.

PubMed

Scheiner, Steve

2018-05-11

Tetrel atoms T (T = Si, Ge, Sn, and Pb) can engage in very strong noncovalent interactions with nucleophiles, which are commonly referred to as tetrel bonds. The ability of such bonds to bind various anions is assessed with a goal of designing an optimal receptor. The Sn atom seems to form the strongest bonds within the tetrel family. It is most effective in the context of a -SnF₃ group and a further enhancement is observed when a positive charge is placed on the receptor. Connection of the -SnF₃ group to either an imidazolium or triazolium provides a strong halide receptor, which can be improved if its point of attachment is changed from the C to an N atom of either ring. Aromaticity of the ring offers no advantage nor is a cyclic system superior to a simple alkyl amine of any chain length. Placing a pair of -SnF₃ groups on a single molecule to form a bipodal dicationic receptor with two tetrel bonds enhances the binding, but falls short of a simple doubling. These two tetrel groups can be placed on opposite ends of an alkyl diamine chain of any length although SnF₃⁺NH₂(CH₂) n NH₂SnF₃⁺ with n between 2 and 4 seems to offer the strongest halide binding. Of the various anions tested, OH − binds most strongly: OH − > F − > Cl − > Br − > I − . The binding energy of the larger NO₃ − and HCO₃ − anions is more dependent upon the charge of the receptor. This pattern translates into very strong selectivity of binding one anion over another. The tetrel-bonding receptors bind far more strongly to each anion than an equivalent number of K⁺ counterions, which leads to equilibrium ratios in favor of the former of many orders of magnitude.

Bi-directional ultrasonic wave coupling to FBGs in continuously bonded optical fiber sensing.

PubMed

Wee, Junghyun; Hackney, Drew; Bradford, Philip; Peters, Kara

2017-09-01

Fiber Bragg grating (FBG) sensors are typically spot-bonded onto the surface of a structure to detect ultrasonic waves in laboratory demonstrations. However, to protect the rest of the optical fiber from any environmental damage during real applications, bonding the entire length of fiber, called continuous bonding, is commonly done. In this paper, we investigate the impact of continuously bonding FBGs on the measured Lamb wave signal. In theory, the ultrasonic wave signal can bi-directionally transfer between the optical fiber and the plate at any adhered location, which could potentially produce output signal distortion for the continuous bonding case. Therefore, an experiment is performed to investigate the plate-to-fiber and fiber-to-plate signal transfer, from which the signal coupling coefficient of each case is theoretically estimated based on the experimental data. We demonstrate that the two coupling coefficients are comparable, with the plate-to-fiber case approximately 19% larger than the fiber-to-plate case. Finally, the signal waveform and arrival time of the output FBG responses are compared between the continuous and spot bonding cases. The results indicate that the resulting Lamb wave signal output is only that directly detected at the FBG location; however, a slight difference in signal waveform is observed between the two bonding configurations. This paper demonstrates the practicality of using continuously bonded FBGs for ultrasonic wave detection in structural health monitoring (SHM) applications.

Tensile Bond Strength of Self Adhesive Resin Cement After Various Surface Treatment of Enamel.

PubMed

Sekhri, Sahil; Mittal, Sanjeev; Garg, Sandeep

2016-01-01

In self adhesive resin cements adhesion is achieved to dental surface without surface pre-treatment, and requires only single step application. This makes the luting procedure less technique-sensitive and decreases postoperative sensitivity. The purpose of this study was to evaluate bond strength of self adhesive resin after surface treatment of enamel for bonding base metal alloy. On the labial surface of 64 central incisor rectangular base metal block of dimension 6 mm length, 5mm width and 1 mm height was cemented with RelyX U200 and Maxcem Elite self adhesive cements with and without surface treatment of enamel. Surface treatment of enamel was application of etchant, one step bonding agent and both. Tensile bond strength of specimen was measured with universal testing machine at a cross head speed of 1mm/min. Least tensile bond strength (MPa) was in control group i.e. 1.33 (0.32) & 1.59 (0.299), Highest bond strength observed when enamel treated with both etchant and bonding agent i.e. 2.72 (0.43) & 2.97 (0.19) for Relyx U200 and Elite cement. When alone etchant and bonding agent were applied alone bond strength is 2.19 (0.18) & 2.24 (0.47) for Relyx U200, and 2.38 (0.27) 2.49 (0.16) for Max-cem elite. Mean bond strength was higher in case of Max-cem Elite as compared to RelyX U200 resin cement, although differences were non-significant (p > 0.05). Surface treatment of enamel increases the bond strength of self adhesive resin cement.

Detailed microscopic unfolding pathways of an α-helix and a β-hairpin: direct observation and molecular dynamics.

PubMed

Jas, Gouri S; Hegefeld, Wendy A; Middaugh, C Russell; Johnson, Carey K; Kuczera, Krzysztof

2014-07-03

We present a combined experimental and computational study of unfolding pathways of a model 21-residue α-helical heteropeptide (W1H5-21) and a 16-residue β-hairpin (GB41-56). Experimentally, we measured fluorescence energy transfer efficiency as a function of temperature, employing natural tryptophans as donors and dansylated lysines as acceptors. Secondary structural analysis was performed with circular dichroism and Fourier transform infrared spectroscopy. Our studies present markedly different unfolding pathways of the two elementary secondary structural elements. During thermal denaturation, the helical peptide exhibits an initial decrease in length, followed by an increase, while the hairpin undergoes a systematic increase in length. In the complementary computational part of the project, we performed microsecond length replica-exchange molecular dynamics simulations of the peptides in explicit solvent, yielding a detailed microscopic picture of the unfolding processes. For the α-helical peptide, we found a large heterogeneous population of intermediates that are primarily frayed single helices or helix-turn-helix motifs. Unfolding starts at the termini and proceeds through a stable helical region in the interior of the peptide but shifted off-center toward the C-terminus. The simulations explain the experimentally observed non-monotonic variation of helix length with temperature as due primarily to the presence of frayed-end single-helix intermediate structures. For the β-hairpin peptide, our simulations indicate that folding is initiated at the turn, followed by formation of the hairpin in zipper-like fashion, with Cα···Cα contacts propagating from the turn to termini and hairpin hydrogen bonds forming in parallel with these contacts. In the early stages of hairpin formation, the hydrophobic side-chain contacts are only partly populated. Intermediate structures with low numbers of β-hairpin hydrogen bonds have very low populations. This is in accord with the "broken zipper" model of Scheraga. The monotonic increase in length with temperature may be explained by the zipper-like breaking of the hairpin hydrogen bonds and backbone contacts.

Significance of DNA bond strength in programmable nanoparticle thermodynamics and dynamics.

PubMed

Yu, Qiuyan; Hu, Jinglei; Hu, Yi; Wang, Rong

2018-04-04

Assembly of nanoparticles (NPs) coated with complementary DNA strands leads to novel crystals with nanosized basic units rather than classic atoms, ions or molecules. The assembly process is mediated by hybridization of DNA via specific base pairing interaction, and is kinetically linked to the disassociation of DNA duplexes. DNA-level physiochemical quantities, both thermodynamic and kinetic, are key to understanding this process and essential for the design of DNA-NP crystals. The melting transition properties are helpful to judge the thermostability and sensitivity of relative DNA probes or other applications. Three different cases are investigated by changing the linker length and the spacer length on which the melting properties depend using the molecular dynamics method. Melting temperature is determined by sigmoidal melting curves based on hybridization percentage versus temperature and the Lindemann melting rule simultaneously. We provide a computational strategy based on a coarse-grained model to estimate the hybridization enthalpy, entropy and free energy from percentages of hybridizations which are readily accessible in experiments. Importantly, the lifetime of DNA bond dehybridization based on temperature and the activation energy depending on DNA bond strength are also calculated. The simulation results are in good agreement with the theoretical analysis and the present experimental data. Our study provides a good strategy to predict the melting temperature which is important for the DNA-directed nanoparticle system, and bridges the dynamics and thermodynamics of DNA-directed nanoparticle systems by estimating the equilibrium constant from the hybridization of DNA bonds quantitatively.

Effect of Surface Treatment on Enamel Cracks After Orthodontic Bracket Debonding: Er,Cr:YSGG Laser-Etching Versus Acid-Etching

PubMed Central

Ghaffari, Hassanali; Mirhashemi, Amirhossein; Baherimoghadam, Tahereh; Azmi, Amir

2017-01-01

Objectives: This study sought to compare enamel cracks after orthodontic bracket debonding in the surfaces prepared with erbium, chromium: yttrium-scandium-galliumgarnet (Er,Cr:YSGG) laser and the conventional acid-etching technique. Materials and Methods: This in-vitro experimental study was conducted on 60 sound human premolars extracted for orthodontic purposes. The teeth were randomly divided into two groups (n=30). The teeth in group A were etched with 37% phosphoric acid gel, while the teeth in group B were subjected to Er,Cr:YSGG laser irradiation (gold handpiece, MZ8 tip, 50Hz, 4.5W, 60μs, 80% water and 60% air). Orthodontic brackets were bonded to the enamel surfaces and were then debonded in both groups. The samples were inspected under a stereomicroscope at ×38 magnification to assess the number and length of enamel cracks before bonding and after debonding. Independent-samples t-test was used to compare the frequency of enamel cracks in the two groups. Levene’s test was applied to assess the equality of variances. Results: No significant difference was noted in the frequency or length of enamel cracks between the two groups after debonding (P>0.05). Conclusions: Despite the same results of the frequency and length of enamel cracks in the two groups and by considering the side effects of acid-etching (demineralization and formation of white spot lesions), Er,Cr:YSGG laser may be used as an alternative to acid-etching for enamel surface preparation prior to bracket bonding. PMID:29296111

Test and analysis of Celion 3000/PMR-15, graphite/polyimide bonded composite joints: Data report

NASA Technical Reports Server (NTRS)

Cushman, J. B.; Mccleskey, S. F.; Ward, S. H.

1982-01-01

Standard single lap, double lap and symmetric step lap bonded joints of Celion 3000/PMR-15 graphite/polyimide composite were evaluated. Composite to composite and composite to titanium joints were tested at 116 K (-250 F), 294 K (70 F) and 561 K (550 F). Joint parameters evaluated are lap length, adherend thickness, adherend axial stiffness, lamina stacking sequence and adherend tapering. Advanced joint concepts were examined to establish the change in performance of preformed adherends, scalloped adherends and hybrid systems. The material properties of the high temperature adhesive, designated A7F, used for bonding were established. The bonded joint tests resulted in interlaminar shear or peel failures of the composite and there were very few adhesive failures. Average test results agree with expected performance trends for the various test parameters. Results of finite element analyses and of test/analysis correlations are also presented.

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

Using the Climbing Drum Peel (CDP) Test to Obtain a G(sub IC) value for Core/Facesheet Bonds

NASA Technical Reports Server (NTRS)

Nettles, A. T.; Gregory, Elizabeth D.; Jackson, Justin R.

2006-01-01

A method of measuring the Mode I fracture toughness of core/facesheet bonds in sandwich Structures is desired, particularly with the widespread use of models that need this data as input. This study examined if a critical strain energy release rate, G(sub IC), can be obtained from the climbing drum peel (CDP) test. The CDP test is relatively simple to perform and does not rely on measuring small crack lengths such as required by the double cantilever beam (DCB) test. Simple energy methods were used to calculate G(sub IC) from CDP test data on composite facesheets bonded to a honeycomb core. Facesheet thicknesses from 2 to 5 plies were tested to examine the upper and lower bounds on facesheet thickness requirements. Results from the study suggest that the CDP test, with certain provisions, can be used to find the GIG value of a core/facesheet bond.

Quantum Mechanical Metric for Internal Cohesion in Cement Crystals

PubMed Central

Dharmawardhana, C. C.; Misra, A.; Ching, Wai-Yim

2014-01-01

Calcium silicate hydrate (CSH) is the main binding phase of Portland cement, the single most important structural material in use worldwide. Due to the complex structure and chemistry of CSH at various length scales, the focus has progressively turned towards its atomic level comprehension. We study electronic structure and bonding of a large subset of the known CSH minerals. Our results reveal a wide range of contributions from each type of bonding, especially hydrogen bonding, which should enable critical analysis of spectroscopic measurements and construction of realistic C-S-H models. We find the total bond order density (TBOD) as the ideal overall metric for assessing crystal cohesion of these complex materials and should replace conventional measures such as Ca:Si ratio. A rarely known orthorhombic phase Suolunite is found to have higher cohesion (TBOD) in comparison to Jennite and Tobermorite, which are considered the backbone of hydrated Portland cement. PMID:25476741

Micro-Raman study on the softening and stiffening of phonons in rutile titanium dioxide film: Competing effects of structural defects, crystallite size, and lattice strain

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

Gautam, Subodh K.; Singh, Fouran, E-mail: fouran@gmail.com; Sulania, I.

2014-04-14

Softening and stiffening of phonons in rutile titanium dioxide films are investigated by in situ micro-Raman studies during energetic ion irradiation. The in situ study minimized other possible mechanisms of phonon dynamics. Initial softening and broadening of Raman shift are attributed to the phonon confinement by structural defects and loss of stoichiometry. The stiffening of A{sub 1g} mode is ascribed to large distortion of TiO{sub 6} octahedra under the influence of lattice strain in the (110) plane, which gives rise to lengthening of equatorial Ti-O bond and shortening of apical Ti-O bond. The shortening of apical Ti-O bond induces stiffeningmore » of A{sub 1g} mode in the framework of the bond-order-length-strength correlation mechanism.« less

Thermally controllable reflective characteristics from rupture and self-assembly of hydrogen bonds in cholesteric liquid crystals.

PubMed

Hu, Wang; Cao, Hui; Song, Li; Zhao, Haiyan; Li, Sijin; Yang, Zhou; Yang, Huai

2009-10-22

A cholesteric liquid crystal (Ch-LC) composite, made of a series of cholesteryl esters, a nematic LC, and a hydrogen bond (H-bond) chiral dopant (HCD), was prepared and filled into a planar treated cell. When the cell was heated, the selective reflection of the cell exhibited an unusual blue shift. One of the reasonable mechanisms was that the helical twisting power (HTP) value of cholesteryl esters increased with an increasing temperature. The other one was that the H-bonds of HCD were ruptured when the temperature was above 60.0 degrees C and HCD was split into two kinds of new chiral dopants, which made the HTP value of the chiral dopants change a lot, thus changing the pitch length of the composite greatly. On the basis of this mechanism, a novel thermally controllable reflective color paper could be achieved.

Structures and interactions in N-methylacetamide-water mixtures studied by IR spectra and density functional theory

NASA Astrophysics Data System (ADS)

Zhang, Rong; Li, Haoran; Lei, Yi; Han, Shijun

2004-05-01

IR spectra have been performed to study the structures and interactions in N-methylacetamide and water mixtures. Because of the competitions of acceptor and donor of the strong hydrogen bonds, some interesting phenomena of red shifts and blue shifts are observed in νCO and νN-H. It is due to the blue-shifting C-H⋯O hydrogen bond, the νC-H blue shifts more obviously. Then some representative cluster structures are suggested and further investigated by density functional theory method. The changes in bond length and frequency shift of the structures give good reasons for the red shift and blue shift, which represents excellent agreement with the IR experiment. The investigations of IR spectra and DFT calculations reveal that the weak C-H⋯O interactions play different roles compared with the classical strong hydrogen bonds in the NMA-water mixtures.

Bond Ellipticity Alternation: An Accurate Descriptor of the Nonlinear Optical Properties of π-Conjugated Chromophores.

PubMed

Lopes, Thiago O; Machado, Daniel F Scalabrini; Risko, Chad; Brédas, Jean-Luc; de Oliveira, Heibbe C B

2018-03-15

Well-defined structure-property relationships offer a conceptual basis to afford a priori design principles to develop novel π-conjugated molecular and polymer materials for nonlinear optical (NLO) applications. Here, we introduce the bond ellipticity alternation (BEA) as a robust parameter to assess the NLO characteristics of organic chromophores and illustrate its effectiveness in the case of streptocyanines. BEA is based on the symmetry of the electron density, a physical observable that can be determined from experimental X-ray electron densities or from quantum-chemical calculations. Through comparisons to the well-established bond-length alternation and π-bond order alternation parameters, we demonstrate the generality of BEA to foreshadow NLO characteristics and underline that, in the case of large electric fields, BEA is a more reliable descriptor. Hence, this study introduces BEA as a prominent descriptor of organic chromophores of interest for NLO applications.

Excess entropy scaling for the segmental and global dynamics of polyethylene melts.

PubMed

Voyiatzis, Evangelos; Müller-Plathe, Florian; Böhm, Michael C

2014-11-28

The range of validity of the Rosenfeld and Dzugutov excess entropy scaling laws is analyzed for unentangled linear polyethylene chains. We consider two segmental dynamical quantities, i.e. the bond and the torsional relaxation times, and two global ones, i.e. the chain diffusion coefficient and the viscosity. The excess entropy is approximated by either a series expansion of the entropy in terms of the pair correlation function or by an equation of state for polymers developed in the context of the self associating fluid theory. For the whole range of temperatures and chain lengths considered, the two estimates of the excess entropy are linearly correlated. The scaled bond and torsional relaxation times fall into a master curve irrespective of the chain length and the employed scaling scheme. Both quantities depend non-linearly on the excess entropy. For a fixed chain length, the reduced diffusion coefficient and viscosity scale linearly with the excess entropy. An empirical reduction to a chain length-independent master curve is accessible for both dynamic quantities. The Dzugutov scheme predicts an increased value of the scaled diffusion coefficient with increasing chain length which contrasts physical expectations. The origin of this trend can be traced back to the density dependence of the scaling factors. This finding has not been observed previously for Lennard-Jones chain systems (Macromolecules, 2013, 46, 8710-8723). Thus, it limits the applicability of the Dzugutov approach to polymers. In connection with diffusion coefficients and viscosities, the Rosenfeld scaling law appears to be of higher quality than the Dzugutov approach. An empirical excess entropy scaling is also proposed which leads to a chain length-independent correlation. It is expected to be valid for polymers in the Rouse regime.

Bond Strength and Interfacial Morphology of Different Dentin Adhesives in Primary Teeth

PubMed Central

Vashisth, Pallavi; Mittal, Mudit; Goswami, Mousumi; Chaudhary, Seema; Dwivedi, Swati

2014-01-01

Objective: To evaluate the interfacial morphology and the bond strength produced by the three-step, two-step and single-step bonding systems in primary teeth. Materials and Methods: Occlusal surfaces of 72 extracted human deciduous teeth were ground to expose the dentin. The teeth were divided into four groups: (a) Scotchbond Multipurpose (3M, ESPE), (b) Adh Se (Vivadent), (d) OptiBond All-in-One (Kerr) and (e)Futurabond NR (VOCO, Cuxhaven, Germany). The adhesives were applied to each group following the manufacturer’s instructions. Then, teeth from each group were divided into two groups: (A) For viewing interfacial morphology (32 teeth), with 8 teeth in each group, and (B) For measurement of bond strength (40 teeth), with 10 teeth in each group. All the samples were prepared for viewing under SEM. The statistical analysis was done using SPSS version 15.0 software. Results: Observational measurement of tag length in different adhesives revealed that Scotchbond had the most widely spread values with a range from 12.20 to 89.10μm while OptiBond AIO had the narrowest range (0 to 22.50). The bond strength of Scotchbond Multipurpose was significantly higher (7.4744±1.88763) (p<0.001) as compared to Futurabond NR (3.8070±1.61345), Adhe SE (4.4478 ± 1.3820) and OptiBond-all-in-one (4.4856±1.07925). Conclusion: The three-step bonding system showed better results as compared to simplified studied bonding systems PMID:24910694

Social bonds and rank acquisition in raven nonbreeder aggregations

PubMed Central

Braun, Anna; Bugnyar, Thomas

2012-01-01

Complex social life has been characterized as cognitively challenging and recently, social relationships such as long-term social bonds and alliances have been identified as key elements for brain evolution. Whereas good evidence is available to support the link between social relations and cognition in mammals, it remains unsatisfying for birds. Here we investigated the role of avian social bonds in a nonbreeder aggregation of ravens, Corvus corax, in the Austrian Alps. We individually marked 138 wild ravens, representing approximately half of a population that uses the area of a local zoo for foraging. For 2 years, we observed the dynamics of group composition and the birds' agonistic and affiliative interactions. We identified two levels of organization: the formation of an unrelated local group and the individuals' engagement in social bonds of different length and reciprocity pattern. Whereas belonging to the local group had no significant effect on conflicts won during foraging, the individual bonding type did. Birds that engaged in affiliative relationships were more successful when competing for food than those without such bonds. Bonded birds did suffer from aggression by other bonded birds and, probably as a consequence, most of the ravens' social relations were not stable over time. These results support the idea that social bonding and selective cooperation and competition are prominent features in nonbreeding ravens. Proximately, bonding may qualify as a social manoeuvre that facilitates access to resources; ultimately it might function to assess the quality of a partner in these long-term monogamous birds. PMID:23264693

Anti-Caries Effects of Dental Adhesives Containing Quaternary Ammonium Methacrylates with Different Chain Lengths

PubMed Central

Han, Qi; Li, Bolei; Zhou, Xuedong; Ge, Yang; Wang, Suping; Li, Mingyun; Ren, Biao; Wang, Haohao; Zhang, Keke; Xu, Hockin H. K.; Peng, Xian; Feng, Mingye; Weir, Michael D.; Chen, Yu; Cheng, Lei

2017-01-01

The objectives of this study were to investigate the effects of dental adhesives containing quaternary ammonium methacrylates (QAMs) with different alkyl chain lengths (CL) on ecological caries prevention in vitro. Five QAMs were synthesized with a CL = 3, 6, 9, 12, and 16 and incorporated into adhesives. Micro-tensile bond strength and surface charge density were used to measure the physical properties of the adhesives. The proportion change in three-species biofilms consisting of Streptococcus mutans, Streptococcus sanguinis, and Streptococcus gordonii was tested using the TaqMan real-time polymerase chain reaction. Lactic acid assay, MTT [3-(4,5-dimethyl-thiazol-2-yl)-2,5-diphenyltetrazolium bromide] assay, exopolysaccharide staining, live/dead staining, scanning electron microscopy (SEM), and transverse microradiography (TMR) were performed to study the anti-biofilm and anti-demineralization effects of the dental adhesives. The results showed that incorporating QAMs with different alkyl chain lengths into the adhesives had no obvious effect on the dentin bond strength. The adhesives containing QAMs with a longer alkyl chain developed healthier biofilms. The surface charge density, anti-biofilm, and anti-demineralization effects of the adhesives increased with a CL of the QAMs from 3 to 12, but decreased slightly with a CL from 12 to 16. In conclusion, adhesives containing QAMs with a tailored chain length are promising for preventing secondary caries in an “ecological way”. PMID:28773004

Impact of Alkyl Spacer Length on Aggregation Pathways in Kinetically Controlled Supramolecular Polymerization.

PubMed

Ogi, Soichiro; Stepanenko, Vladimir; Thein, Johannes; Würthner, Frank

2016-01-20

We have investigated the kinetic and thermodynamic supramolecular polymerizations of a series of amide-functionalized perylene bisimide (PBI) organogelator molecules bearing alkyl spacers of varied lengths (ethylene to pentylene chains, PBI-1-C2 to PBI-1-C5) between the amide and PBI imide groups. These amide-functionalized PBIs form one-dimensional fibrous nanostructures as the thermodynamically favored states in solvents of low polarity. Our in-depth studies revealed, however, that the kinetic behavior of their supramolecular polymerization is dependent on the spacer length. Propylene- and pentylene-tethered PBIs follow a similar polymerization process as previously observed for the ethylene-tethered PBI. Thus, the monomers of these PBIs are kinetically trapped in conformationally restricted states through intramolecular hydrogen bonding between the amide and imide groups. In contrast, the intramolecularly hydrogen-bonded monomers of butylene-tethered PBI spontaneously self-assemble into nanoparticles, which constitute an off-pathway aggregate state with regard to the thermodynamically stable fibrous supramolecular polymers obtained. Thus, for this class of π-conjugated system, an unprecedented off-pathway aggregate with high kinetic stability could be realized for the first time by introducing an alkyl linker of optimum length (C4 chain) between the amide and imide groups. Our current system with an energy landscape of two competing nucleated aggregation pathways is applicable to the kinetic control over the supramolecular polymerization by the seeding approach.

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

PubMed

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

2017-01-25

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

Swift heavy ion irradiation of Pt nanocrystals: II. Structural changes and H desorption

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

Giulian, R.; Araujo, L.L.; Kluth, P.

2014-09-24

The structural properties and H desorption from embedded Pt nanocrystals (NCs) following irradiation with swift heavy ions were investigated as a function of energy and fluence. From x-ray absorption near-edge spectroscopy analysis, Pt-H bonding was identified in NCs annealed in a forming gas (95% N{sub 2} + 5% H{sub 2}) ambient. The H content decreased upon irradiation and the desorption process was NC-size dependent such that larger NCs required a higher fluence to achieve a H-free state. Pt-H bonding and NC dissolution both perturbed the NC structural parameters (coordination number, bond-length and mean-square relative displacement) as determined with extended x-raymore » absorption fine structure measurements.« less

Predicting the structural and electronic properties of two-dimensional single layer boron nitride sheets

NASA Astrophysics Data System (ADS)

Li, Xiao-Dong; Cheng, Xin-Lu

2018-02-01

Three two-dimensional (2D) single layer boron nitride sheets have been predicted based on the first-principles calculations. These 2D boron nitride sheets are comprised of equivalent boron atoms and nitride atoms with sp2 and sp bond hybridization. The geometry optimization reflects that they all possess stable planar crystal structures with the space group P 6 bar 2 m (D3h3) symmetry. The charge density distribution manifests that the B-N bonds in these boron nitride sheets are covalent in nature but with ionic characteristics. The tunable band gaps indicate their potential applications in nanoscale electronic and optoelectronic devices by changing the length of sp-bonded Bsbnd N linkages.

Mechanical properties investigation on single-wall ZrO2 nanotubes: A finite element method with equivalent Poisson's ratio for chemical bonds

NASA Astrophysics Data System (ADS)

Yang, Xiao; Li, Huijian; Hu, Minzheng; Liu, Zeliang; Wärnå, John; Cao, Yuying; Ahuja, Rajeev; Luo, Wei

2018-04-01

A method to obtain the equivalent Poisson's ratio in chemical bonds as classical beams with finite element method was proposed from experimental data. The UFF (Universal Force Field) method was employed to calculate the elastic force constants of Zrsbnd O bonds. By applying the equivalent Poisson's ratio, the mechanical properties of single-wall ZrNTs (ZrO2 nanotubes) were investigated by finite element analysis. The nanotubes' Young's modulus (Y), Poisson's ratio (ν) of ZrNTs as function of diameters, length and chirality have been discussed, respectively. We found that the Young's modulus of single-wall ZrNTs is calculated to be between 350 and 420 GPa.

Crystal structure of fac-tri-chlorido-[tris-(pyridin-2-yl-N)amine]-chromium(III).

PubMed

Yamaguchi-Terasaki, Yukiko; Fujihara, Takashi; Nagasawa, Akira; Kaizaki, Sumio

2015-01-01

In the neutral complex mol-ecule of the title compound, fac-[CrCl3(tpa)] [tpa is tris-(pyridin-2-yl)amine; C15H12N4], the Cr(III) ion is bonded to three N atoms that are constrained to a facial arrangement by the tpa ligand and by three chloride ligands, leading to a distorted octa-hedral coordination sphere. The average Cr-N and Cr-Cl bond lengths are 2.086 (5) and 2.296 (4) Å, respectively. The complex mol-ecule is located on a mirror plane. In the crystal, a combination of C-H⋯N and C-H⋯Cl hydrogen-bonding inter-actions connect the mol-ecules into a three-dimensional network.

Effect of the substituent and hydrogen bond on the geometry and electronic properties of OH and O(-) groups in para-substituted phenol and phenolate derivatives.

PubMed

Szatylowicz, Halina; Krygowski, Tadeusz M

2010-10-14

Interrelations between intra- and intermolecular interactions were analyzed by using computational modeling of the para-X-substituted derivatives of phenol and phenolate (where X = NO, NO(2), CHO, COMe, COOH, CONH(2), Cl, F, H, Me, OMe, and OH) and their equilibrium H-bonded complexes with HB and B(-) (where HB = HF and HCN and B(-) = F(-) and CN(-)). B3LYP/6-311++G** computation was applied. Both the substituent effect and H-bonding changed the electronic properties of the -O(-) and -OH groups and geometric parameters of phenol and phenolate derivatives and their H-bonded complexes. C-O bond lengths and aromaticity indices of the ring were found to depend linearly on σ(p)(-) of the substituents. In the first case the greatest sensitivity on the substituent effect was for 4-X-C(6)H(4)OH···CN(-) and 4-X-C(6)H(4)O(-)···HF complexes, whereas for 4-X-C(6)H(4)O(-)···HCN systems it was comparable with that for phenol derivatives and a little smaller than that for 4-X-C(6)H(4)O(-) derivatives. This means that the strength of H-bonding may considerably change the sensitivity of the C-O bond length to the substituent effect. The greatest sensitivity of the aromaticity indices, both HOMA and NICS(1)zz, to σ(p)(-) was found for phenolate and then for phenolate H-bonded complexes, followed by phenol complexes, and the lowest sensitivity was observed for phenol derivatives. The interatomic proton-acceptor distance, being a measure of the H-bond strength, was found to depend linearly on σ(p)(-) of the substituents with a positive slope for O···HB (HF or HCN) interactions and a negative slope for OH···B(-) interactions. NBO charges on the oxygen and hydrogen atoms also depend on σ(p)(-) of the substituents. In the latter case for strong H-bonded complexes (energy less than ∼-20 kcal/mol) the substituent effect works oppositely for 4-X-C(6)H(4)OH···B(-) in comparison with the 4-X-C(6)H(4)O(-)···HB systems. Moreover, following the Espinoza et al. [J. Chem. Phys. 2002, 117, 5529] and Grabowski et al. [J. Phys. Chem. B 2006, 110, 6444] classifications, the above and q(H) vs proton-acceptor distance relationships suggest a partially covalent character of the hydrogen bond for these complexes and the degree of its covalent nature depending on the substituent.

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

Lebrilla, C.B.; Schulze, C.; Schwarz, H.

The gas-phase reaction of bare Fe/sup +/ atoms with linear alkyl nitriles generates end-on complexes which, depending on geometrical constraints, specifically interact with remote C-H bonds. Based on chain length effect studies and the investigation of labeled precursors, a mechanism is suggested which accounts for the chemospecificity observed for the loss of H/sub 2/ and C/sub 2/H/sub 4/ from RCN/Fe/sup +/ complexes. This mechanism does not follow the analogous reaction of Fe/sup +/ with alkenes and alkynes but involves an initial C-H insertion of the remote CH bonds followed by a C-C insertion.

The bonding of FeN2, FeCO, and Fe2N2 - Model systems for side-on bonding of CO and N2

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Pettersson, Lars G. M.; Siegbahn, Per E. M.

1987-01-01

Qualitative calculations are performed to elucidate the nature of the side-on interaction of both N2 and CO with a single Fe atom. The systems are found to be quite similar, with bonding leading to an increase in the CO or N2 bond length and a decrease in the vibrational frequency. The CO or N2 stretching modes lead to a large dipole derivative along the metal-ligand bond axis. The populations show an almost identical, large donation from the Fe 3d orbitals into the CO or N2 Pi-asterisk. The larger system Fe2N2 is then considered, with the N2 bridging the Fe2, both parallel and perpendicular to the Fe2 bond axis for two different Fe-Fe distances. For FeN2, the shift in the observed N2 frequency is smaller than observed for the alpha state of N2/Fe(111). The shift in the N2 vibrational frequency increases when the N2 interacts with two Fe atoms, either at the Fe-Fe nearest neighbor distance or at the first layer Fe-Fe distance, when the side-on N2 axis is oriented perpendicular to an Fe-Fe bond.

Influence of Hot-Etching Surface Treatment on Zirconia/Resin Shear Bond Strength

PubMed Central

Lv, Pin; Yang, Xin; Jiang, Ting

2015-01-01

This study was designed to evaluate the effect of hot-etching surface treatment on the shear bond strength between zirconia ceramics and two commercial resin cements. Ceramic cylinders (120 units; length: 2.5 mm; diameter: 4.7 mm) were randomly divided into 12 groups (n = 10) according to different surface treatments (blank control; airborne-particle-abrasion; hot-etching) and different resin cements (Panavia F2.0; Superbond C and B) and whether or not a thermal cycling fatigue test (5°–55° for 5000 cycles) was performed. Flat enamel surfaces, mounted in acrylic resin, were bonded to the zirconia discs (diameter: 4.7 mm). All specimens were subjected to shear bond strength testing using a universal testing machine with a crosshead speed of 1 mm/min. All data were statistically analyzed using one-way analysis of variance and multiple-comparison least significant difference tests (α = 0.05). Hot-etching treatment produced higher bond strengths than the other treatment with both resin cements. The shear bond strength of all groups significantly decreased after the thermal cycling test; except for the hot-etching group that was cemented with Panavia F2.0 (p < 0.05). Surface treatment of zirconia with hot-etching solution enhanced the surface roughness and bond strength between the zirconia and the resin cement. PMID:28793699

Compressive buckling of black phosphorene nanotubes: an atomistic study

NASA Astrophysics Data System (ADS)

Nguyen, Van-Trang; Le, Minh-Quy

2018-04-01

We investigate through molecular dynamics finite element method with Stillinger-Weber potential the uniaxial compression of armchair and zigzag black phosphorene nanotubes. We focus especially on the effects of the tube’s diameter with fixed length-diameter ratio, effects of the tube’s length for a pair of armchair and zigzag tubes of equal diameters, and effects of the tube’s diameter with fixed lengths. Their Young’s modulus, critical compressive stress and critical compressive strain are studied and discussed for these 3 case studies. Compressive buckling was clearly observed in the armchair nanotubes. Local bond breaking near the boundary occurred in the zigzag ones under compression.

Equation of state of wet granular matter.

PubMed

Fingerle, A; Herminghaus, S

2008-01-01

An expression for the near-contact pair correlation function of D -dimensional weakly polydisperse hard spheres is presented, which arises from elementary free-volume arguments. Its derivative at contact agrees very well with our simulations for D=2 . For jammed states, the expression predicts that the number of exact contacts is equal to 2D, in agreement with established simulations. When the particles are wetted, they interact by the formation and rupture of liquid capillary bridges. Since formation and rupture events of capillary bonds are well separated in configuration space, the interaction is hysteretic with a characteristic energy loss Ecb. The pair correlation is strongly affected by this capillary interaction depending on the liquid-bond status of neighboring particles. A theory is derived for the nonequilibrium probability currents of the capillary interaction which determines the pair correlation function near contact. This finally yields an analytic expression for the equation of state, P=P(N/V,T), of wet granular matter for D=2, valid in the complete density range from gas to jamming. Driven wet granular matter exhibits a van der Waals-like unstable branch at granular temperatures TT, is of relevance for aggregation in general, simulations have been performed which show very good agreement with the theoretically predicted coordination K of capillary bonds as a function of the bond length scrit. This result implies that particles that stick at the surface, scrit=0, form isostatic clusters. An extension of the theory in which the bridge coordination number K plays the role of a self-consistent mean-field is proposed.

Equation of state of wet granular matter

NASA Astrophysics Data System (ADS)

Fingerle, A.; Herminghaus, S.

2008-01-01

An expression for the near-contact pair correlation function of D -dimensional weakly polydisperse hard spheres is presented, which arises from elementary free-volume arguments. Its derivative at contact agrees very well with our simulations for D=2 . For jammed states, the expression predicts that the number of exact contacts is equal to 2D, in agreement with established simulations. When the particles are wetted, they interact by the formation and rupture of liquid capillary bridges. Since formation and rupture events of capillary bonds are well separated in configuration space, the interaction is hysteretic with a characteristic energy loss Ecb . The pair correlation is strongly affected by this capillary interaction depending on the liquid-bond status of neighboring particles. A theory is derived for the nonequilibrium probability currents of the capillary interaction which determines the pair correlation function near contact. This finally yields an analytic expression for the equation of state, P=P(N/V,T) , of wet granular matter for D=2 , valid in the complete density range from gas to jamming. Driven wet granular matter exhibits a van der Waals-like unstable branch at granular temperatures T

How cellulose stretches: synergism between covalent and hydrogen bonding.

PubMed

Altaner, Clemens M; Thomas, Lynne H; Fernandes, Anwesha N; Jarvis, Michael C

2014-03-10

Cellulose is the most familiar and most abundant strong biopolymer, but the reasons for its outstanding mechanical performance are not well understood. Each glucose unit in a cellulose chain is joined to the next by a covalent C-O-C linkage flanked by two hydrogen bonds. This geometry suggests some form of cooperativity between covalent and hydrogen bonding. Using infrared spectroscopy and X-ray diffraction, we show that mechanical tension straightens out the zigzag conformation of the cellulose chain, with each glucose unit pivoting around a fulcrum at either end. Straightening the chain leads to a small increase in its length and is resisted by one of the flanking hydrogen bonds. This constitutes a simple form of molecular leverage with the covalent structure providing the fulcrum and gives the hydrogen bond an unexpectedly amplified effect on the tensile stiffness of the chain. The principle of molecular leverage can be directly applied to certain other carbohydrate polymers, including the animal polysaccharide chitin. Related but more complex effects are possible in some proteins and nucleic acids. The stiffening of cellulose by this mechanism is, however, in complete contrast to the way in which hydrogen bonding provides toughness combined with extensibility in protein materials like spider silk.

Covalent bond force profile and cleavage in a single polymer chain

NASA Astrophysics Data System (ADS)

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

2000-08-01

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

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.

Tensile Bond Strength of Self Adhesive Resin Cement After Various Surface Treatment of Enamel

PubMed Central

Sekhri, Sahil; Garg, Sandeep

2016-01-01

Introduction In self adhesive resin cements adhesion is achieved to dental surface without surface pre-treatment, and requires only single step application. This makes the luting procedure less technique-sensitive and decreases postoperative sensitivity. Aim The purpose of this study was to evaluate bond strength of self adhesive resin after surface treatment of enamel for bonding base metal alloy. Materials and Methods On the labial surface of 64 central incisor rectangular base metal block of dimension 6 mm length, 5mm width and 1 mm height was cemented with RelyX U200 and Maxcem Elite self adhesive cements with and without surface treatment of enamel. Surface treatment of enamel was application of etchant, one step bonding agent and both. Tensile bond strength of specimen was measured with universal testing machine at a cross head speed of 1mm/min. Results Least tensile bond strength (MPa) was in control group i.e. 1.33 (0.32) & 1.59 (0.299), Highest bond strength observed when enamel treated with both etchant and bonding agent i.e. 2.72 (0.43) & 2.97 (0.19) for Relyx U200 and Elite cement. When alone etchant and bonding agent were applied alone bond strength is 2.19 (0.18) & 2.24 (0.47) for Relyx U200, and 2.38 (0.27) 2.49 (0.16) for Max-cem elite. Mean bond strength was higher in case of Max-cem Elite as compared to RelyX U200 resin cement, although differences were non–significant (p > 0.05). Conclusion Surface treatment of enamel increases the bond strength of self adhesive resin cement. PMID:26894165

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

Structural and optical properties of (Ag,Cu)(In,Ga)Se{sub 2} polycrystalline thin film alloys

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

Boyle, J. H.; Shafarman, W. N.; Birkmire, R. W.

2014-06-14

The structural and optical properties of pentenary alloy (Ag,Cu)(In,Ga)Se{sub 2} polycrystalline thin films were characterized over the entire compositional range at a fixed (Cu + Ag)/(In + Ga) ratio. Films deposited at 550 °C on bare and molybdenum coated soda-lime glass by elemental co-evaporation in a single-stage process with constant incident fluxes exhibit single phase chalcopyrite structure, corresponding to 122 spacegroup (I-42d) over the entire compositional space. Unit cell refinement of the diffraction patterns show that increasing Ag substitution for Cu, the refined a{sub o} lattice constant, (Ag,Cu)-Se bond length, and anion displacement increase in accordance with the theoretical model proposed by Jaffe, Wei, andmore » Zunger. However, the refined c{sub o} lattice constant and (In,Ga)-Se bond length deviated from theoretical expectations for films with mid-range Ag and Ga compositions and are attributed to influences from crystallographic bond chain ordering or cation electronegativity. The optical band gap, derived from transmission and reflection measurements, widened with increasing Ag and Ga content, due to influences from anion displacement and cation electronegativity, as expected from theoretical considerations for pseudo-binary chalcopyrite compounds.« less

Gel Electrophoresis of Gold-DNA Nanoconjugates

DOE PAGES

Pellegrino, T.; Sperling, R. A.; Alivisatos, A. P.; ...

2007-01-01

Gold-DNA conjugates were investigated in detail by a comprehensive gel electrophoresis study based on 1200 gels. A controlled number of single-stranded DNA of different length was attached specifically via thiol-Au bonds to phosphine-stabilized colloidal gold nanoparticles. Alternatively, the surface of the gold particles was saturated with single stranded DNA of different length either specifically via thiol-Au bonds or by nonspecific adsorption. From the experimentally determined electrophoretic mobilities, estimates for the effective diameters of the gold-DNA conjugates were derived by applying two different data treatment approaches. The first method is based on making a calibration curve for the relation between effectivemore » diameters and mobilities with gold nanoparticles of known diameter. The second method is based on Ferguson analysis which uses gold nanoparticles of known diameter as reference database. Our study shows that effective diameters derived from gel electrophoresis measurements are affected with a high error bar as the determined values strongly depend on the method of evaluation, though relative changes in size upon binding of molecules can be detected with high precision. Furthermore, in this study, the specific attachment of DNA via gold-thiol bonds to Au nanoparticles is compared to nonspecific adsorption of DNA. Also, the maximum number of DNA molecules that can be bound per particle was determined.« less

Diode-Pumped Long-Pulse-Length Ho:Tm:YLiF4 Laser at 10 Hz

NASA Technical Reports Server (NTRS)

Jani, Mahendra G.; Naranjo, Felipe L.; Barnes, Norman P.; Murray, Keith E.; Lockard, George E.

1995-01-01

An optical efficiency of 0.052 under normal mode operation for diode-pumped Ho:Tm:YLiF4 at a pulse repetition frequency of 10 Hz has been achieved. Laser output energy of 30 mJ in single Q-switched pulses with 600-ns pulse length were obtained for an input energy of 3 J. A diffusion-bonded birefringent laser rod consisting of Ho:Tm-doped and undoped pieces of YLF was utilized for 10-Hz operation.

3c/4e [small sigma, Greek, circumflex]-type long-bonding competes with ω-bonding in noble-gas hydrides HNgY (Ng = He, Ne, Ar, Kr, Xe, Rn; Y = F, Cl, Br, I): a NBO/NRT perspective.

PubMed

Zhang, Guiqiu; Li, Hong; Weinhold, Frank; Chen, Dezhan

2016-03-21

Noble-gas hydrides HNgY are frequently described as a single ionic form (H-Ng)(+)Y(-). We apply natural bond orbital (NBO) and natural resonance theory (NRT) analyses to a series of noble-gas hydrides HNgY (Ng = He, Ne, Ar, Kr, Xe, Rn; Y = F, Cl, Br, I) to gain quantitative insight into the resonance bonding of these hypervalent molecules. We find that each of the studied species should be better represented as a resonance hybrid of three leading resonance structures, namely, H-Ng(+ -):Y (I), H:(- +)Ng-Y (II), and H^Y (III), in which the "ω-bonded" structures I and II arise from the complementary donor-acceptor interactions nY → σ*HNg and nH → σ*NgY, while the "long-bond" ([small sigma, Greek, circumflex]-type) structure III arises from the nNg → [small sigma, Greek, circumflex]*HY/[small sigma, Greek, circumflex]HY interaction. The bonding for all of the studied molecules can be well described in terms of the continuously variable resonance weightings of 3c/4e ω-bonding and [small sigma, Greek, circumflex]-type long-bonding motifs. Furthermore, we find that the calculated bond orders satisfy a generalized form of "conservation of bond order" that incorporates both ω-bonding and long-bonding contributions [viz., (bHNg + bNgY) + bHY = bω-bonding + blong-bonding = 1]. Such "conservation" throughout the title series implies a competitive relationship between ω-bonding and [small sigma, Greek, circumflex]-type long-bonding, whose variations are found to depend in a chemically reasonable manner on the electronegativity of Y and the outer valence-shell character of the central Ng atom. The calculated bond orders are also found to exhibit chemically reasonable correlations with bond lengths, vibrational frequencies, and bond dissociation energies, in accord with Badger's rule and related empirical relationships. Overall, the results provide electronic principles and chemical insight that may prove useful in the rational design of noble-gas hydrides of technological interest.

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

PubMed

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

2018-06-06

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

Correlation between the band gap expansion and melting temperature depression of nanostructured semiconductors

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

Li, Jianwei, E-mail: jwl189@163.com; Zhao, Xinsheng; Liu, Xinjuan

The band gap and melting temperature of a semiconductor are tunable with the size and shape of the specimen at the nanometer scale, and related mechanisms remain as yet unclear. In order to understand the common origin of the size and shape effect on these two seemingly irrelevant properties, we clarify, correlate, formulate, and quantify these two properties of GaAs, GaN, InP, and InN nanocrystals from the perspectives of bond order-length-strength correlation using the core-shell configuration. The consistency in the theoretical predictions, experimental observations, and numerical calculations verify that the broken-bond-induced local bond contraction and strength gain dictates the bandmore » gap expansion, while the atomic cohesive energy loss due to bond number reduction depresses the melting point. The fraction of the under-coordinated atoms in the skin shell quantitatively determines the shape and size dependency. The atomic under-coordination in the skin down to a depth of two atomic layers inducing a change in the local chemical bond is the common physical origin.« less

Phase behaviors of supramolecular graft copolymers with reversible bonding

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

Zhang, Xu; Wang, Liquan, E-mail: jlin@ecust.edu.cn, E-mail: lq-wang@ecust.edu.cn; Jiang, Tao

2013-11-14

Phase behaviors of supramolecular graft copolymers with reversible bonding interactions were examined by the random-phase approximation and real-space implemented self-consistent field theory. The studied supramolecular graft copolymers consist of two different types of mutually incompatible yet reactive homopolymers, where one homopolymer (backbone) possesses multifunctional groups that allow second homopolymers (grafts) to be placed on. The calculations carried out show that the bonding strength exerts a pronounced effect on the phase behaviors of supramolecular graft copolymers. The length ratio of backbone to graft and the positions of functional groups along the backbone are also of importance to determine the phase behaviors.more » Phase diagrams were constructed at high bonding strength to illustrate this architectural dependence. It was found that the excess unbounded homopolymers swell the phase domains and shift the phase boundaries. The results were finally compared with the available experimental observations, and a well agreement is shown. The present work could, in principle, provide a general understanding of the phase behaviors of supramolecular graft copolymers with reversible bonding.« less

Hydrogen bonding in water clusters and their ionized counterparts.

PubMed

Neela, Y Indra; Mahadevi, A Subha; Sastry, G Narahari

2010-12-30

Ab initio and DFT computations were carried out on four distinct hydrogen-bonded arrangements of water clusters (H(2)O)(n), n = 2-20, represented as W1D, W2D, W2DH, and W3D. The variation in the strength of hydrogen bond as a function of the chain length is studied. In all the four cases, there is a substantial cooperative interaction, albeit in different degrees. The effect of basis set superposition error (BSSE) on the complexation energy of water clusters has been analyzed. Atoms in molecules (AIM) analysis performed to evaluate the nature of the hydrogen bonding shows a high correlation between hydrogen bond strength and the trends in complexation energy. Solvated water clusters exhibit lower complexation energies compared to corresponding gas-phase geometries on PCM (polarized continuum model) optimization. The feasibility of stripping an electron or addition of an electron increases dramatically as the cluster size increases. Although W3D caged structures are stable for neutral clusters, the helical W2DH arrangement appeared to be an optimal choice for its ionized counterparts.

Viscous friction of hydrogen-bonded matter

NASA Astrophysics Data System (ADS)

Erbas, Aykut; Horinek, Dominik; Netz, Roland R.

2012-02-01

Amontons' law successfully describes friction between macroscopic solid bodies for a wide range of velocities and normal forces. For the diffusion and forced sliding of adhering or entangled macromolecules, proteins and biological complexes, temperature effects are invariably important and a similarly successful friction law at biological length and velocity scales is missing. Hydrogen bonds are key to the specific binding of bio-matter. Here we show that friction between hydrogen-bonded matter obeys in the biologically relevant low-velocity viscous regime a simple equations: the friction force is proportional to the number of hydrogen bonds, the sliding velocity, and a friction coefficient γHB. This law is deduced from atomistic molecular dynamics simulations for short peptide chains that are laterally pulled over hydroxylated substrates in the presence of water and holds for widely different peptides, surface polarities and applied normal forces. The value of γHB is extrapolated from simulations at sliding velocities in the range from v=10-2 m/s to 100 m/s by mapping on a simple stochastic model and turns out to be of the order of γHB˜10-8 kg/s. 3 hydrogen bonds act collectively.

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

Fabrication of sophisticated two-dimensional organic nanoarchitectures thought hydrogen bond mediated molecular self assembly

NASA Astrophysics Data System (ADS)

Silly, Fabien

2012-02-01

Complex supramolecular two-dimensional (2D) networks are attracting considerable interest as highly ordered functional materials for applications in nanotechnology. The challenge consists in tailoring the ordering of one or more molecular species into specific architectures over an extended length scale with molecular precision. Highly organized supramolecular arrays can be obtained through self-assembly of complementary molecules which can interlock via intermolecular interactions. Molecules forming hydrogen bonds (H-bonds) are especially interesting building blocks for creating sophisticated organic architectures due to high selectivity and directionality of these bindings. We used scanning tunnelling microscopy to investigate at the atomic scale the formation of H-bonded 2D organic nanoarchitectures on surfaces. We mixed perylene derivatives having rectangular shape with melamine and DNA base having triangular and non symmetric shape respectively. We observe that molecule substituents play a key role in formation of the multicomponent H-bonded architectures. We show that the 2D self-assembly of these molecules can be tailored by adjusting the temperature and molecular ratio. We used these stimuli to successfully create numerous close-packed and porous 2D multicomponent structures.

Performance of prestressed girders cast with LWSCC.

DOT National Transportation Integrated Search

2012-08-01

Bond of prestressing steel has been a much debated topic since the 1950s. Limited data are available on the transfer and development length of strands cast in self : consolidating concrete (SCC) and even less for strands cast in light weight, self-co...

Structure and Properties of Polysaccharide Based BioPolymer Gels

NASA Astrophysics Data System (ADS)

Prud'Homme, Robert K.

2000-03-01

Nature uses the pyranose ring as the basic building unit for a wideclass of biopolymers. Because of their biological origin these biopolymers naturally find application as food additives, rheology modifiers. These polymers range from being rigid skeletal material, such as cellulose that resist dissolution in water, to water soluble polymers, such as guar or carrageenan. The flexibility of the basic pyranose ring structure to provide materials with such a wide range of properties comes from the specific interactions that can be engineered by nature into the structure. We will present several examples of specific interactions for these systems: hydrogen bonding, hydrophobic interactions, and specific ion interactions. The relationship between molecular interations and rheology will be emphasized. Hydrogen bonding mediated by steric interference is used to control of solubility of starch and the rheology of guar gels. A more interesting example is the hydrogen bonding induced by chemical modification in konjac glucomannan that results in a gel that melts upon cooling. Hydrogen bonding interactions in xanthan lead to gel formation at very low polymer concentrations which is a result of the fine tuning of the polymer persistence length and total contour length. Given the function of xanthan in nature its molecular architecture has been optimized. Hydrophobic interactions in methylcellulose show a reverse temperature dependence arising from solution entropy. Carrageenan gelation upon the addition of specific cations will be addressed to show the interplay of polymer secondary structure on chemical reactivity. And finally the cis-hydroxyls on galactomannans permit crosslinking by a variety of metal ions some of which lead to "living gels" and some of which lead to permanently crosslinked networks.

Hydrogen atoms can be located accurately and precisely by x-ray crystallography.

PubMed

Woińska, Magdalena; Grabowsky, Simon; Dominiak, Paulina M; Woźniak, Krzysztof; Jayatilaka, Dylan

2016-05-01

Precise and accurate structural information on hydrogen atoms is crucial to the study of energies of interactions important for crystal engineering, materials science, medicine, and pharmacy, and to the estimation of physical and chemical properties in solids. However, hydrogen atoms only scatter x-radiation weakly, so x-rays have not been used routinely to locate them accurately. Textbooks and teaching classes still emphasize that hydrogen atoms cannot be located with x-rays close to heavy elements; instead, neutron diffraction is needed. We show that, contrary to widespread expectation, hydrogen atoms can be located very accurately using x-ray diffraction, yielding bond lengths involving hydrogen atoms (A-H) that are in agreement with results from neutron diffraction mostly within a single standard deviation. The precision of the determination is also comparable between x-ray and neutron diffraction results. This has been achieved at resolutions as low as 0.8 Å using Hirshfeld atom refinement (HAR). We have applied HAR to 81 crystal structures of organic molecules and compared the A-H bond lengths with those from neutron measurements for A-H bonds sorted into bonds of the same class. We further show in a selection of inorganic compounds that hydrogen atoms can be located in bridging positions and close to heavy transition metals accurately and precisely. We anticipate that, in the future, conventional x-radiation sources at in-house diffractometers can be used routinely for locating hydrogen atoms in small molecules accurately instead of large-scale facilities such as spallation sources or nuclear reactors.

Hydrogen atoms can be located accurately and precisely by x-ray crystallography

PubMed Central

Woińska, Magdalena; Grabowsky, Simon; Dominiak, Paulina M.; Woźniak, Krzysztof; Jayatilaka, Dylan

2016-01-01

Precise and accurate structural information on hydrogen atoms is crucial to the study of energies of interactions important for crystal engineering, materials science, medicine, and pharmacy, and to the estimation of physical and chemical properties in solids. However, hydrogen atoms only scatter x-radiation weakly, so x-rays have not been used routinely to locate them accurately. Textbooks and teaching classes still emphasize that hydrogen atoms cannot be located with x-rays close to heavy elements; instead, neutron diffraction is needed. We show that, contrary to widespread expectation, hydrogen atoms can be located very accurately using x-ray diffraction, yielding bond lengths involving hydrogen atoms (A–H) that are in agreement with results from neutron diffraction mostly within a single standard deviation. The precision of the determination is also comparable between x-ray and neutron diffraction results. This has been achieved at resolutions as low as 0.8 Å using Hirshfeld atom refinement (HAR). We have applied HAR to 81 crystal structures of organic molecules and compared the A–H bond lengths with those from neutron measurements for A–H bonds sorted into bonds of the same class. We further show in a selection of inorganic compounds that hydrogen atoms can be located in bridging positions and close to heavy transition metals accurately and precisely. We anticipate that, in the future, conventional x-radiation sources at in-house diffractometers can be used routinely for locating hydrogen atoms in small molecules accurately instead of large-scale facilities such as spallation sources or nuclear reactors. PMID:27386545

NASA Astrophysics Data System (ADS)

Knight, Kevin S.; Marshall, William G.; Hawkins, Philip M.

2014-06-01

The fluoroperovskite phase RbCaF3 has been investigated using high-pressure neutron powder diffraction in the pressure range ~0-7.9 GPa at room temperature. It has been found to undergo a first-order high-pressure structural phase transition at ~2.8 GPa from the cubic aristotype phase to a hettotype phase in the tetragonal space group I4/ mcm. This transition, which also occurs at ~200 K at ambient pressure, is characterised by a linear phase boundary and a Clapeyron slope of 2.96 × 10-5 GPa K-1, which is in excellent agreement with earlier, low-pressure EPR investigations. The bulk modulus of the high-pressure phase (49.1 GPa) is very close to that determined for the low-pressure phase (50.0 GPa), and both are comparable with those determined for the aristotype phases of CsCdF3, TlCdF3, RbCdF3, and KCaF3. The evolution of the order parameter with pressure is consistent with recent modifications to Landau theory and, in conjunction with polynomial approximations to the pressure dependence of the lattice parameters, permits the pressure variation of the bond lengths and angles to be predicted. On entering the high-pressure phase, the Rb-F bond lengths decrease from their extrapolated values based on a third-order Birch-Murnaghan fit to the aristotype equation of state. By contrast, the Ca-F bond lengths behave atypically by exhibiting an increase from their extrapolated magnitudes, resulting in the volume and the effective bulk modulus of the CaF6 octahedron being larger than the cubic phase. The bulk moduli for the two component polyhedra in the tetragonal phase are comparable with those determined for the constituent binary fluorides, RbF and CaF2.

Models for mean bonding length, melting point and lattice thermal expansion of nanoparticle materials

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

Omar, M.S., E-mail: dr_m_s_omar@yahoo.com

2012-11-15

Graphical abstract: Three models are derived to explain the nanoparticles size dependence of mean bonding length, melting temperature and lattice thermal expansion applied on Sn, Si and Au. The following figures are shown as an example for Sn nanoparticles indicates hilly applicable models for nanoparticles radius larger than 3 nm. Highlights: ► A model for a size dependent mean bonding length is derived. ► The size dependent melting point of nanoparticles is modified. ► The bulk model for lattice thermal expansion is successfully used on nanoparticles. -- Abstract: A model, based on the ratio number of surface atoms to thatmore » of its internal, is derived to calculate the size dependence of lattice volume of nanoscaled materials. The model is applied to Si, Sn and Au nanoparticles. For Si, that the lattice volume is increases from 20 Å{sup 3} for bulk to 57 Å{sup 3} for a 2 nm size nanocrystals. A model, for calculating melting point of nanoscaled materials, is modified by considering the effect of lattice volume. A good approach of calculating size-dependent melting point begins from the bulk state down to about 2 nm diameter nanoparticle. Both values of lattice volume and melting point obtained for nanosized materials are used to calculate lattice thermal expansion by using a formula applicable for tetrahedral semiconductors. Results for Si, change from 3.7 × 10{sup −6} K{sup −1} for a bulk crystal down to a minimum value of 0.1 × 10{sup −6} K{sup −1} for a 6 nm diameter nanoparticle.« less

Molecular Dynamics Simulation of the Titration of Polyoxocations in Aqueous Solution

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

Rustad, James R.

The aqueous complex ion Al30O8(OH)56(H2O)26 18+(Al30) has a variety of bridging and terminal amphoteric surface functional groups which deprotonate over a pH range of 4–7. Their relative degree of protonation is calculated here from a series of molecular dynamics simulations in what appear to be the first molecular dynamics simulations of an acidometric titration. In these simulations, a model M30O8(OH)56(H2O)26 18+ ion is embedded in aqueous solution and titrated with hydroxide ions in the presence of a charge-compensating background of perchlorate ions. Comparison with titration of a model M13O4(OH)24(H2O)12 7+ reveals that the M30 ion is more acidic than themore » M13 ion due to the presence of acidic nH2O functional groups. The higher acidities of the functional groups on the M30 ion appear to result from enhanced hydration. Metal–oxygen bond lengths are calculated for the ion in solution, an isolated ion in the gas phase, and in its crystalline hydrate sulfate salt. Gas-phase and crystalline bond lengths do not correlate well with those calculated in solution. The acidities do not relate in any simple way to the number of metals coordinating the surface functional group or the M-O bond length. Moreover, the calculated acidity in solution does not correlate with proton affinities calculated for the isolated ion in the absence of solvent. It is concluded that the search for simple indicators of structure–reactivity relationships at the level of individual reactive sites faces major limitations, unless specific information on the hydration states of the functional groups is available.« less

Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field

PubMed Central

Buck, Patrick M.; Bystroff, Christopher

2015-01-01

Protein folding is a hierarchical process where structure forms locally first, then globally. Some short sequence segments initiate folding through strong structural preferences that are independent of their three-dimensional context in proteins. We have constructed a knowledge-based force field in which the energy functions are conditional on local sequence patterns, as expressed in the hidden Markov model for local structure (HMMSTR). Carbon-alpha force field (CALF) builds sequence specific statistical potentials based on database frequencies for α-carbon virtual bond opening and dihedral angles, pairwise contacts and hydrogen bond donor-acceptor pairs, and simulates folding via Brownian dynamics. We introduce hydrogen bond donor and acceptor potentials as α-carbon probability fields that are conditional on the predicted local sequence. Constant temperature simulations were carried out using 27 peptides selected as putative folding initiation sites, each 12 residues in length, representing several different local structure motifs. Each 0.6 μs trajectory was clustered based on structure. Simulation convergence or representativeness was assessed by subdividing trajectories and comparing clusters. For 21 of the 27 sequences, the largest cluster made up more than half of the total trajectory. Of these 21 sequences, 14 had cluster centers that were at most 2.6 Å root mean square deviation (RMSD) from their native structure in the corresponding full-length protein. To assess the adequacy of the energy function on nonlocal interactions, 11 full length native structures were relaxed using Brownian dynamics simulations. Equilibrated structures deviated from their native states but retained their overall topology and compactness. A simple potential that folds proteins locally and stabilizes proteins globally may enable a more realistic understanding of hierarchical folding pathways. PMID:19137613

Effects of Diode Laser Debonding of Ceramic Brackets on Enamel Surface and Pulpal Temperature.

PubMed

Yassaei, Soghra; Soleimanian, Azadeh; Nik, Zahra Ebrahimi

2015-04-01

Debonding of ceramic brackets due to their high bond strength and low fracture toughness is one of the most challenging complications of orthodontic clinicians. Application of lasers might be effective in the debonding of ceramic brackets as they reduce bond strength of resins and, therefore, can eliminate the risk of enamel damage. However, the thermal effects of laser radiation on dental tissue can cause undesirable results. The aim of this study is to evaluate the enamel surface characteristics and pulpal temperature changes of teeth after debonding of ceramic brackets with or without laser light. Thirty polycrystalline brackets were bonded to 30 intact extracted premolars, and later debonded conventionally or through a diode laser (2.5 W, 980 nm). The laser was applied for 10 seconds with sweeping movement. After debonding, the adhesive remnant index (ARI), the lengths and frequency of enamel cracks were compared among the groups. The increase in intrapulpal temperature was also measured. The collected data were analyzed by Chi-squared test and paired t-test using Statistical Package for Social Sciences (SPSS) software. There was no case of enamel fracture in none of the groups. Laser debonding caused a significant decrease in the frequency and lengths of enamel cracks, compared to conventional debonding. In laser debonding group, the increase in intrapulpal temperature (1.46°C) was significantly below the benchmark of 5.5°C for all the specimens. No significant difference was observed in ARI scores among the groups. Laser-assisted debonding of ceramic brackets could reduce the risk of enamel damage, without causing thermal damage to the pulp. However, some increases in the length and frequency of enamel cracks should be expected with all debonding methods.

A convenient and accurate wide-range parameter relationship between Buckingham and Morse potential energy functions

NASA Astrophysics Data System (ADS)

Lim, Teik-Cheng; Dawson, James Alexander

2018-05-01

This study explores the close-range, short-range and long-range relationships between the parameters of the Morse and Buckingham potential energy functions. The results show that the close-range and short-range relationships are valid for bond compression and for very small changes in bond length, respectively, while the long-range relationship is valid for bond stretching. A wide-range relationship is proposed to combine the comparative advantages of the close-range, short-range and long-range parameter relationships. The wide-range relationship is useful for replacing the close-range, short-range and long-range parameter relationships, thereby preventing the undesired effects of potential energy jumps resulting from functional switching between the close-range, short-range and long-range interaction energies.

A Triatomic Silicon(0) Cluster Stabilized by a Cyclic Alkyl(amino) Carbene.

PubMed

Mondal, Kartik Chandra; Roy, Sudipta; Dittrich, Birger; Andrada, Diego M; Frenking, Gernot; Roesky, Herbert W

2016-02-24

Reduction of the neutral carbene tetrachlorosilane adduct (cAAC)SiCl4 (cAAC=cyclic alkyl(amino) carbene :C(CMe2)2 (CH2)N(2,6-iPr2C6H3) with potassium graphite produces stable (cAAC)3Si3, a carbene-stabilized triatomic silicon(0) molecule. The Si-Si bond lengths in (cAAC)3Si3 are 2.399(8), 2.369(8) and 2.398(8) Å, which are in the range of Si-Si single bonds. Each trigonal pyramidal silicon atom of the triangular molecule (cAAC)3Si3 possesses a lone pair of electrons. Its bonding, stability, and electron density distributions were studied by quantum chemical calculations. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Aromatic thiol-mediated cleavage of N-O bonds enables chemical ubiquitylation of folded proteins

NASA Astrophysics Data System (ADS)

Weller, Caroline E.; Dhall, Abhinav; Ding, Feizhi; Linares, Edlaine; Whedon, Samuel D.; Senger, Nicholas A.; Tyson, Elizabeth L.; Bagert, John D.; Li, Xiaosong; Augusto, Ohara; Chatterjee, Champak

2016-09-01

Access to protein substrates homogenously modified by ubiquitin (Ub) is critical for biophysical and biochemical investigations aimed at deconvoluting the myriad biological roles for Ub. Current chemical strategies for protein ubiquitylation, however, employ temporary ligation auxiliaries that are removed under harsh denaturing conditions and have limited applicability. We report an unprecedented aromatic thiol-mediated N-O bond cleavage and its application towards native chemical ubiquitylation with the ligation auxiliary 2-aminooxyethanethiol. Our interrogation of the reaction mechanism suggests a disulfide radical anion as the active species capable of cleaving the N-O bond. The successful semisynthesis of full-length histone H2B modified by the small ubiquitin-like modifier-3 (SUMO-3) protein further demonstrates the generalizability and compatibility of our strategy with folded proteins.

A tensegrity model for hydrogen bond networks in proteins.

PubMed

Bywater, Robert P

2017-05-01

Hydrogen-bonding networks in proteins considered as structural tensile elements are in balance separately from any other stabilising interactions that may be in operation. The hydrogen bond arrangement in the network is reminiscent of tensegrity structures in architecture and sculpture. Tensegrity has been discussed before in cells and tissues and in proteins. In contrast to previous work only hydrogen bonds are studied here. The other interactions within proteins are either much stronger - covalent bonds connecting the atoms in the molecular skeleton or weaker forces like the so-called hydrophobic interactions. It has been demonstrated that the latter operate independently from hydrogen bonds. Each category of interaction must, if the protein is to have a stable structure, balance out. The hypothesis here is that the entire hydrogen bond network is in balance without any compensating contributions from other types of interaction. For sidechain-sidechain, sidechain-backbone and backbone-backbone hydrogen bonds in proteins, tensegrity balance ("closure") is required over the entire length of the polypeptide chain that defines individually folding units in globular proteins ("domains") as well as within the repeating elements in fibrous proteins that consist of extended chain structures. There is no closure to be found in extended structures that do not have repeating elements. This suggests an explanation as to why globular domains, as well as the repeat units in fibrous proteins, have to have a defined number of residues. Apart from networks of sidechain-sidechain hydrogen bonds there are certain key points at which this closure is achieved in the sidechain-backbone hydrogen bonds and these are associated with demarcation points at the start or end of stretches of secondary structure. Together, these three categories of hydrogen bond achieve the closure that is necessary for the stability of globular protein domains as well as repeating elements in fibrous proteins.

Relationship between x-ray emission and absorption spectroscopy and the local H-bond environment in water

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

Zhovtobriukh, Iurii; Besley, Nicholas A.; Fransson, Thomas

Here, the connection between specific features in the water X-ray absorption spectrum and X-ray emission spectrum (XES) and the local H-bond coordination is studied based on structures obtained from path-integral molecular dynamics simulations using either the opt-PBE-vdW density functional or the MB-pol force field. Computing the XES spectrum using all molecules in a snapshot results in only one peak in the lone-pair (1b 1) region, while the experiment shows two peaks separated by 0.8-0.9 eV. Different H-bond configurations were classified based on the local structure index (LSI) and a geometrical H-bond cone criterion. We find that tetrahedrally coordinated molecules characterizedmore » by high LSI values and two strong donated and two strong accepted H-bonds contribute to the low energy 1b 1 emission peak and to the post-edge region in absorption. Molecules with the asymmetric H-bond environment with one strong accepted H-bond and one strong donated H-bond and low LSI values give rise to the high energy 1b 1 peak in the emission spectrum and mainly contribute to the pre-edge and main-edge in the absorption spectrum. The 1b 1 peak splitting can be increased to 0.62 eV by imposing constraints on the H-bond length, i.e., for very tetrahedral structures short H-bonds (less than 2.68 Å) and for very asymmetric structures elongated H-bonds (longer than 2.8 Å). Such structures are present, but underrepresented, in the simulations which give more of an average of the two extremes.« less

Relationship between x-ray emission and absorption spectroscopy and the local H-bond environment in water

DOE PAGES

Zhovtobriukh, Iurii; Besley, Nicholas A.; Fransson, Thomas; ...

2018-04-14

Here, the connection between specific features in the water X-ray absorption spectrum and X-ray emission spectrum (XES) and the local H-bond coordination is studied based on structures obtained from path-integral molecular dynamics simulations using either the opt-PBE-vdW density functional or the MB-pol force field. Computing the XES spectrum using all molecules in a snapshot results in only one peak in the lone-pair (1b 1) region, while the experiment shows two peaks separated by 0.8-0.9 eV. Different H-bond configurations were classified based on the local structure index (LSI) and a geometrical H-bond cone criterion. We find that tetrahedrally coordinated molecules characterizedmore » by high LSI values and two strong donated and two strong accepted H-bonds contribute to the low energy 1b 1 emission peak and to the post-edge region in absorption. Molecules with the asymmetric H-bond environment with one strong accepted H-bond and one strong donated H-bond and low LSI values give rise to the high energy 1b 1 peak in the emission spectrum and mainly contribute to the pre-edge and main-edge in the absorption spectrum. The 1b 1 peak splitting can be increased to 0.62 eV by imposing constraints on the H-bond length, i.e., for very tetrahedral structures short H-bonds (less than 2.68 Å) and for very asymmetric structures elongated H-bonds (longer than 2.8 Å). Such structures are present, but underrepresented, in the simulations which give more of an average of the two extremes.« less

Periodic trends in bond dissociation energies. A theoretical study.

PubMed

Mó, Otilia; Yáñez, Manuel; Eckert-Maksić, Mirjana; Maksić, Zvonimir B; Alkorta, Ibón; Elguero, José

2005-05-19

Bond dissociation energies (BDEs) of all possible A-X single bonds involving the first- and second-row atoms, from Li to Cl, where the free valences are saturated by hydrogens, have been estimated through the use of the G3-theory and at the B3LYP/6-311+G(3df,2pd)//B3LYP/6-31G(2df,p) DFT level of theory. BDEs exhibit a periodical behavior. The A-X (A = Li, Be, B, Na, Mg, Al, and Si) BDEs show a steady increase along the first and the second row of the periodic table as a function of the atomic number Z(X). For A-X bonds involving electronegative atoms (A = C, N, O, F, P, S, and Cl) the bond energies achieve a maximum around Z(X) = 5. The same behavior is observed when BDEs are plotted against the electronegativity chi(X) of the atom X. Thus, for A-X bonds (A = Li, Be, B, Na, Mg, Al, Si), the BDEs for a fixed A increases, grosso modo, as the electronegativity differences between X and A increase, with some exceptions, which reflect the differences in the relaxation energies of the radicals produced upon the bond cleavage. A similar trend, albeit less pronounced, is found for single A-X bonds, where A = C, N, O, F, P, S, and Cl. However, there is an additional feature embodied in the enhancement of the strength of the A-boron bonds due to the ability of boron to act as a strong electron acceptor. The trends in bond lengths and charge densities at the bond critical points are in line with the aforementioned behavior.

Composition-dependent bonding and hardness of γ-aluminum oxynitride: A first-principles investigation

NASA Astrophysics Data System (ADS)

Tu, Bingtian; Wang, Hao; Liu, Xiao; Khan, Shahzad A.; Wang, Weimin; Fu, Zhengyi

2014-06-01

Spinel phase aluminum oxynitride solid solution (γ-alon, with formula of Al(8+x)/3O4-xNx) exists in the narrow Al2O3-rich region of Al2O3-AlN systems. The first-principles calculations were developed to investigate the composition-dependent bonding and hardness of γ-alon. Six supercell model for Al(8+x)/3O4-xNx (x = 0, 0.25, 0.44, 0.63, 0.81, and 1) was constructed to perform our calculations with high accuracy. It was found that the lattice constant increases with increasing composition of nitrogen in γ-alon. The bond lengths of AlIV-O, AlVI-O, AlIV-N, and AlVI-N all increase with the expansion of crystal structure. The well-known Mulliken overlap populations were calculated to estimate the bonding and hardness. As the content of nitrogen substitute increases, the Al-N bonds present more covalent characteristic, while the Al-O bonds present more ionic characteristic. The AlIV-N is the hardest bond in γ-alon. The theoretical hardness of γ-alon could be slightly enhanced from 17.16 GPa to 17.97 GPa by increasing content of nitrogen in full solubility range. The contribution ratio, CHμ, was proposed to quantify the contribution of bonds to hardness of γ-alon. The Al-O bonds are found to contribute more to the hardness. The Al-N bonds are the main influencing factor to enhance the hardness of γ-alon. These calculated results provide the basis for understanding the composition-dependent bonding and hardness of γ-alon.

Nb2©Au6: a molecular wheel with a short Nb 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 Nb triple bond coordinated by an Au6 ring and reinforced by σ aromaticity† †Electronic supplementary information (ESI) available: Photoelectron spectra of Nb2Au6– at (a) 616.86 nm, (b) 610.55 nm, (c) 603.38 nm, and (d) 589.58 nm; relative energies of low-lying isomers of Nb2Au6– within 1.5 eV at the PW91, PBE0 (in square brackets), CCSD (in braces) and CCSD(T) (in angle brackets) levels; the four lowest-lying isomers of Nb2Au6 at the levels of PW91 and PBE0; valence canonical molecular orbital contours for the D6h Nb2Au6– at the PBE0 level; comparison between the 193 nm spectrum of Nb2Au6– with the simulated spectra of isomers I and II at the PW91/Def2-TZVPPD and BP86/Def2-TZVPPD levels; comparison between the 193 nm spectrum of Nb2Au6– with the simulated spectra of isomer I at PBE0/Def2-TZVPPD and TPSSh/Def2-TZVPPD levels; the energy difference between isomers I and II of Nb2Au6– calculated at various levels of theory; the first VDEs of isomers I, II, III, IV and V of Nb2Au6– computed at the PW91 and PBE0 levels; calculated vibrational frequencies for the D6h global minimum of Nb2Au6 at PW91 and PBE0 levels; calculated bond orders and charges of D∞h Nb2, D6h Au6, and D6h Nb2Au6 at the PBE0/Def2-TZVP level. See DOI: 10.1039/c7sc02881d

PubMed Central

Jian, Tian; Cheung, Ling Fung; Czekner, Joseph; Chen, Teng-Teng; Lopez, Gary V.; Li, Wei-Li

2017-01-01

We report a photoelectron spectroscopy and high-resolution photoelectron imaging study of a bimetallic Nb2Au6– cluster. Theoretical calculations, in conjunction with the experimental data, reveal that Nb2Au6–/0 possess high-symmetry D6h structures featuring a Nb–Nb axis coordinated equatorially by an Au6 ring. Chemical bonding analyses show that there are two π bonds and one σ bond in the Nb2 moiety in Nb2©Au6, as well as five totally delocalized σ bonds. The Nb 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 Nb triple bond is strengthened significantly by the delocalized σ bonds, resulting in an extremely short Nb–Nb bond length comparable to the quintuple bond in gaseous Nb2. The totally delocalized σ bonding in Nb2©Au6 is reminiscent of σ aromaticity, representing a new bonding mode in metal–ligand systems. The unusually short Nb–Nb bond length in Nb2©Au6 shows that the Au6 ring can serve as a bridging ligand to facilitate multiple bonding in transition metal dimers via delocalized σ bonding. PMID:29163907

Synthesis of carbon nanotubes via Fe-catalyzed pyrolysis of phenolic resin

NASA Astrophysics Data System (ADS)

Wang, Junkai; Deng, Xiangong; Zhang, Haijun; Zhang, Yuanzhuo; Duan, Hongjuan; Lu, Lilin; Song, Jianbo; Tian, Liang; Song, Shupeng; Zhang, Shaowei

2017-02-01

Carbon nanotubes (CNTs) with 40-100 nm in diameter and tens of micrometers in length were prepared via catalytic pyrolysis of phenol resin in Ar at 673-1273 K using ferric nitrate as a catalyst precursor. Structure and morphology of pyrolyzed resin were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and Raman spectroscopy. Ferric nitrate was transformed to Fe3O4 at 673 K, and to metallic Fe and FexC carbide at 873-1273 K. The optimal weight ratio of Fe catalyst to phenol resin for growing CNTs was 1.00 wt%, and the optimal temperature was 1073 K. In addition, use of a high pressure increased the yield of CNTs. Density functional theory (DFT) calculations suggest that Fe catalysts facilitate the CNTs growth by increasing the bond length and weakening the bond strength in C2H4 via donating electrons to the C atoms in it.

Characterization of Barium Borate Frameworks Using Raman Spectroscopy.

PubMed

Gharavi-Naeini, Jafar; Yoo, Kyung W; Stump, Nathan A

2018-04-01

Systematic micro-Raman scattering investigations have been carried out on Sm +2 doped 2(BaO)-n(B 2 O 3 ) matrices for n = 4, 5, 8, and 2(BaO)-(Na 2 O)-9(B 2 O 3 ) using the 364 nm excitation of an Ar + laser. The Raman results have been compared with the known structures of barium tetraborate, barium pentaborate, barium octaborate, and barium sodium nonaborate. An excellent correlation has been found between the BO 4 /BO 3 composition ratios for each product and intensity ratios of the designated BO 4 and BO 3 Raman peaks. Furthermore, the Raman frequencies of both BO 4 and BO 3 groups undergo a systematic blueshift as n increases from four to nine. The shift results from a decrease of the B-O bond lengths for both BO 4 and BO 3 groups as the samples transition from the tetraborate to nonaborate structures. Linear relations (with negative slopes) have been determined between the measured Raman frequencies and B-O bond lengths in the frameworks.

Chemical Speciation and Bond Lengths of Organic Solutes by Core-Level Spectroscopy: pH and Solvent Influence on p-Aminobenzoic Acid.

PubMed

Stevens, Joanna S; Gainar, Adrian; Suljoti, Edlira; Xiao, Jie; Golnak, Ronny; Aziz, Emad F; Schroeder, Sven L M

2015-05-04

Through X-ray absorption and emission spectroscopies, the chemical, electronic and structural properties of organic species in solution can be observed. Near-edge X-ray absorption fine structure (NEXAFS) and resonant inelastic X-ray scattering (RIXS) measurements at the nitrogen K-edge of para-aminobenzoic acid reveal both pH- and solvent-dependent variations in the ionisation potential (IP), 1s→π* resonances and HOMO-LUMO gap. These changes unequivocally identify the chemical species (neutral, cationic or anionic) present in solution. It is shown how this incisive chemical state sensitivity is further enhanced by the possibility of quantitative bond length determination, based on the analysis of chemical shifts in IPs and σ* shape resonances in the NEXAFS spectra. This provides experimental access to detecting even minor variations in the molecular structure of solutes in solution, thereby providing an avenue to examining computational predictions of solute properties and solute-solvent interactions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Differential Microscopic Mobility of Components within a Deep Eutectic Solvent

DOE PAGES

Wagle, Durgesh V.; Baker, Gary A.; Mamontov, Eugene

2015-07-13

From macroscopic measurements of deep eutectic solvents such as glyceline (1:2 molar ratio of choline chloride to glycerol), the long-range translational diffusion of the larger cation (choline) is known to be slower compared to that of the smaller hydrogen bond donor (glycerol). However, when the diffusion dynamics are analyzed on the subnanometer length scale, we discover that the displacements associated with the localized diffusive motions are actually larger for choline. This counterintuitive diffusive behavior can be understood as follows. The localized diffusive motions confined in the transient cage of neighbor particles, which precede the cage-breaking long-range diffusion jumps, are moremore » spatially constrained for glycerol than for choline because of the stronger hydrogen bonds the former makes with chloride anions. The implications of differential localized mobility of the constituents should be especially important for applications where deep eutectic solvents are confined on the nanometer length scale and their long-range translational diffusion is strongly inhibited (e.g., within microporous media).« less

Analysis of wax esters by silver-ion high-performance liquid chromatography-tandem mass spectrometry.

PubMed

Vrkoslav, Vladimír; Urbanová, Klára; Háková, Matina; Cvačka, Josef

2013-08-09

Wax esters (WEs), esters of long-chain fatty acids and long-chain alcohols, were analysed by Ag-HPLC/APCI-MS/MS. Two ChromSpher Lipids columns connected in series (a total length of 50cm) and hexane-2-propanol-acetonitrile mobile phases were used to achieve good separation of the molecular species. The chromatographic behaviour of WEs was studied under optimised conditions: retention increased with the number of double bonds and with the temperature (15-35°C); retention times were affected by the double-bond position, trans isomers eluted earlier than cis isomers, and the WEs were partially separated depending on the aliphatic-chain length. The WEs provided simple APCI spectra with [M+H](+) ions, the MS/MS spectra showed fragments, which allowed their identification. The method was applied for an analysis of the WE mixtures from jojoba oil and human hair and the results were compared with analogous data from an optimised RP-HPLC system. Copyright © 2013 Elsevier B.V. All rights reserved.

Chemical Speciation and Bond Lengths of Organic Solutes by Core-Level Spectroscopy: pH and Solvent Influence on p -Aminobenzoic Acid

DOE PAGES

Stevens, Joanna S.; Gainar, Adrian; Suljoti, Edlira; ...

2015-03-18

Through X-ray absorption and emission spectroscopies, the chemical, electronic and structural properties of organic species in solution can be observed. Near-edge X-ray absorption fine structure (NEXAFS) and resonant inelastic X-ray scattering (RIXS) measurements at the nitrogen K-edge of para-aminobenzoic acid reveal both pH- and solvent-dependent variations in the ionisation potential (IP), 1s→π* resonances and HOMO–LUMO gap. These changes unequivocally identify the chemical species (neutral, cationic or anionic) present in solution. It is shown how this incisive chemical state sensitivity is further enhanced by the possibility of quantitative bond length determination, based on the analysis of chemical shifts in IPs andmore » σ* shape resonances in the NEXAFS spectra. Finally, this provides experimental access to detecting even minor variations in the molecular structure of solutes in solution, thereby providing an avenue to examining computational predictions of solute properties and solute–solvent interactions.« less

Structure and screening in molecular and metallic hydrogen at high pressure

NASA Technical Reports Server (NTRS)

Wood, D. M.; Ashcroft, N. W.

1981-01-01

A variational wavefunction is used to express the (spin restricted) Hartree-Fock energy as reciprocal lattice sums for static lattice FCC monatomic hydrogen and diatomic Pa3 molecular hydrogen. In the monatomic phase the hydrogenic orbital range closely parallels the inverse Thomas-Fermi wavevector; the corresponding energy E has a minimum of -0.929 Ryd/electron at r sub s = 1.67. For the diatomic phase E(r sub s) is similar, but the constituent energies, screening, and bond length reflect a qualitative change in the nature of the solid at r sub s = 2.8. This change is interpreted in terms of a transition from protons as structural units (at high density) to weakly interacting models (at low density). Insensitivity of the total energy to a rapid fall in the bond length suggests association with the rotational transition where the rapid molecular orientations characteristic of high pressures disappear and the molecules rotate freely at low pressure.

HIV/AIDS, childhood and governance: sundering the bonds of human society.

PubMed

Barnett, Tony

2005-12-01

There is a disharmonious resonance between the length of HIV infection in the individual human host and the length of a human generation. In brief, an infected person may have children, these may be orphaned and grow up to become infected, and afterwards they themselves may have children, who can be orphaned in turn. Hence, a basic unit of social structure in most human societies, the three-generation bond between grandparents, parents and the current generation - and on into the future - is repeatedly torn apart in the absence of treatment, a vaccine or behaviour change. This situation should be read against the threat of growing viral resistance. Certain implications of these processes for the future are outlined and discussed. The paper notes the uncertain future confronting societies that already have a relatively high number of orphans, and considers some otherwise unexpected possibilities, as well as the dangers of assuming that large-scale orphaning necessarily leads to social unrest and disorder.

Bond Length Equalization with molecular aromaticity-A new measurement of aromaticity.

PubMed

Shen, Chen-Fei; Liu, Zi-Zhong; Liu, Hong-Xia; Zhang, Hui-Qing

2018-05-08

A new method to measure the amount of aromaticity is presented through the process of Bond Length Equalization (BLE). Degree of Aromaticity (DOA), a two-dimensional intensive quantity including geometric and energetic factors, as a new measurement of aromaticity is proposed. The unique characteristic of DOA and the formation of DOA will be displayed. The calculation of the geometrical optimization, DOA, Nucleus Independent Chemical Shifts (NICS) and Ring Stretching Vibration Raman Spectroscopy Frequency (RSVRSF) for the aromatic ring molecules - G n H n m (G = C, Si, Ge, n = 3, 5-8, m = +1, -1, 0, +1, +2) were calculated using the method of Density Functional Theory (DFT). The correlation between radius angle and molecular energy is absolute quadratic in the process of BLE. As the increasing of the number of ring atoms, the value of DOA decreasing gradually, the aromaticity decreased gradually, which was a same conclusion as NICS and RSVRSF concluded. Copyright © 2018 Elsevier B.V. All rights reserved.

N,N,N′,N′,N′′-Penta­methyl-N′′-[3-(1,3,3-trimethyl­ureido)prop­yl]guanidinium tetra­phenyl­borate

PubMed Central

Tiritiris, Ioannis; Kantlehner, Willi

2012-01-01

In the crystal structure of the title molecular salt, C13H30N5O+·C24H20B−, discrete guanidinium cations and tetra­phenyl­borate anions are present. The C—N bond lengths in the CN3 unit are 1.3427 (12), 1.3445 (12) and 1.3453 (13) Å, indicating double-bond character. The central C atom is surrounded in a nearly ideal trigonal-planar geometry by three N atoms and the positive charge is delocalized on the CN3 plane. The bonds between the N atoms and the terminal C-methyl groups all have values close to a typical single bond [1.4595 (15)–1.4688 (12) Å]. In the crystal, cations are connected by C—H⋯O contacts generating a chain along the c axis. PMID:22798881

On the Extraction of Aromatic Compounds from Hydrocarbons by Imidazolium Ionic Liquids

PubMed Central

Cassol, Cláudia C.; Umpierre, Alexandre P.; Ebeling, Günter; Ferrera, Bauer; Chiaro, Sandra S. X.; Dupont, Jairton

2007-01-01

The liquid-liquid equilibrium for the ternary system formed by n-octane and aromatic (alkylbenzenes) and heteroaromatic compounds (nitrogen and sulfur containing heterocyles) and 1-alkyl-3-methylimidazolium ionic liquids (ILs) associated with various anions has been investigated. The selectivity on the extraction of a specific aromatic compound is influenced by anion volume, hydrogen bond strength between the anion and the imidazolium cation and the length of the 1-methyl-3-alkylimidazolium alkyl side chain. The interaction of alkylbenzenes and sulfur heterocyles with the IL is preferentially through CH-π hydrogen bonds and the quantity of these aromatics in the IL phase decreases with the increase of the steric hindrance imposed by the substituents on the aromatic nucleus. In the case of nitrogen heterocycles the interaction occurs preferentially through N(heteroaromatic)-H(imidazolium) hydrogen bonds and the extraction process is largely controlled by the nitrogen heterocycle pKa. Competitive extraction experiments suggest that benzene, pyridine and dibenzothiophene do not compete for the same hydrogen bond sites of the IL.

Nature and potency interactions of the hydrogen bond through the NBO analysis for charge transfer complex between 2-amino-4-hydroxy-6-methylpyrimidine and 2,3-pyrazinedicarboxylic acid

NASA Astrophysics Data System (ADS)

Faizan, Mohd; Afroz, Ziya; Alam, Mohammad Jane; Bhat, Sheeraz Ahmad; Ahmad, Shabbir; Ahmad, Afaq

2018-05-01

The intermolecular interactions in complex formation between 2-amino-4-hydroxy-6-methylpyrimidine (AHMP) and 2,3-pyrazinedicarboxylicacid (PDCA) have been explored using density functional theory calculations. The isolated 1:1 molecular geometry of proton transfer (PT) complex between AHMP and PDCA has been optimized on a counterpoise corrected potential energy surface (PES) at DFT-B3LYP/6-31G(d,p) level of theory in the gaseous phase. Further, the formation of hydrogen bonded charge transfer (HBCT) complex between PDCA and AHMP has been also discussed. PT energy barrier between two extremes is calculated using potential energy surface (PES) scan by varying bond length. The intermolecular interactions have been analyzed from theoretical perspective of natural bond orbital (NBO) analysis. In addition, the interaction energy between molecular fragments involved in the complex formation has been also computed by counterpoise procedure at same level of theory.

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

Recrystallization texture in nickel heavily deformed by accumulative roll bonding

NASA Astrophysics Data System (ADS)

Mishin, O. V.; Zhang, Y. B.; Godfrey, A.

2017-07-01

The recrystallization behavior of Ni processed by accumulative roll bonding to a total accumulated von Mises strain of 4.8 has been examined, and analyzed with respect to heterogeneity in the deformation microstructure. The regions near the bonding interface are found to be more refined and contain particle deformation zones around fragments of the steel wire brush used to prepare the surface for bonding. Sample-scale gradients are also observed, manifested as differences between the subsurface, intermediate and central layers, where the distributions of texture components are different. These heterogeneities affect the progress of recrystallization. While the subsurface and near-interface regions typically contain lower frequencies of cube-oriented grains than anywhere else in the sample, a strong cube texture forms in the sample during recrystallization, attributed to both a high nucleation rate and fast growth rate of cube-oriented grains. The observations highlight the sensitivity of recrystallization to heterogeneity in the deformation microstructure and demonstrate the importance of characterizing this heterogeneity over several length scales.

[A development of FRP frame for crown and bridge resin. (2) Rigidity and adaptability of FRP frame].

PubMed

Kimura, H; Teraoka, F

1990-05-01

Retainer and pontic of FRP frame for crown and bridge resin were constructed with two different prepregs, used glass cloth and roving as reinforcement. Rigidity and adaptability of the FRP frame and bonding strength of jointing of retainer and pontic were investigated. The glass content was about 50 wt% for both kinds of prepregs. Bonding strength and modulus of FRP plate reinforced with glass roving were about 1.5 times larger than that of the FRP plate reinforced with glass cloth. Bonding strength of FRP specimen constructed by curing the prepreg put on the FRP plate was about 3 kgf/mm2. However, the bonding strength of specimen constructed by curing simultaneously the two prepregs was about 12 kgf/mm2. Though discrepancy of the FRP frame to stone cast of abutment tooth was proportional to the length of pontic, that of the FRP frame with a 50 mm pontic was less than 0.05 mm.

Molecular dynamics of acetamide based ionic deep eutectic solvents

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

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.

Vibrational tug-of-war: The pKA dependence of the broad vibrational features of strongly hydrogen-bonded carboxylic acids

NASA Astrophysics Data System (ADS)

Van Hoozen, Brian L.; Petersen, Poul B.

2018-04-01

Medium and strong hydrogen bonds give rise to broad vibrational features frequently spanning several hundred wavenumbers and oftentimes exhibiting unusual substructures. These broad vibrational features can be modeled from first principles, in a reduced dimensional calculation, that adiabatically separates low-frequency modes, which modulate the hydrogen bond length, from high-frequency OH stretch and bend modes that contribute to the vibrational structure. Previously this method was used to investigate the origin of an unusual vibrational feature frequently found in the spectra of dimers between carboxylic acids and nitrogen-containing aromatic bases that spans over 900 cm-1 and contains two broad peaks. It was found that the width of this feature largely originates from low-frequency modes modulating the hydrogen bond length and that the structure results from Fermi resonance interactions. In this report, we examine how these features change with the relative acid and base strength of the components as reflected by their aqueous pKA values. Dimers with large pKA differences are found to have features that can extend to frequencies below 1000 cm-1. The relationships between mean OH/NH frequency, aqueous pKA, and O-N distance are examined in order to obtain a more rigorous understanding of the origin and shape of the vibrational features. The mean OH/NH frequencies are found to correlate well with O-N distances. The lowest OH stretch frequencies are found in dimer geometries with O-N distances between 2.5 and 2.6 Å. At larger O-N distances, the hydrogen bonding interaction is not as strong, resulting in higher OH stretch frequencies. When the O-N distance is smaller than 2.5 Å, the limited space between the O and N determines the OH stretch frequency, which gives rise to frequencies that decrease with O-N distances. These two effects place a lower limit on the OH stretch frequency which is calculated to be near 700 cm-1. Understanding how the vibrational features of strongly hydrogen-bonded structures depend on the relative pKA and other structural parameters will guide studies of biological structures and analysis of proton transfer studies using photoacids.

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.

Bonded and Stitched Composite Structure

NASA Technical Reports Server (NTRS)

Zalewski, Bart F. (Inventor); Dial, William B. (Inventor)

2014-01-01

A method of forming a composite structure can include providing a plurality of composite panels of material, each composite panel having a plurality of holes extending through the panel. An adhesive layer is applied to each composite panel and a adjoining layer is applied over the adhesive layer. The method also includes stitching the composite panels, adhesive layer, and adjoining layer together by passing a length of a flexible connecting element into the plurality of holes in the composite panels of material. At least the adhesive layer is cured to bond the composite panels together and thereby form the composite structure.