Symmetric bi-pyridyl banana-shaped molecule and its intermolecular hydrogen bonding liquid-crystalline complexes

Science.gov (United States)

Sui, Dan; Hou, Qiufei; Chai, Jia; Ye, Ling; Zhao, Liyan; Li, Min; Jiang, Shimei

2008-11-01

A new symmetric bi-pyridyl banana-shaped molecule 1,3-phenylene diisonicotinate (PDI) was designed and synthesized. Its molecular structure was confirmed by FTIR, Elemental analysis and 1H NMR. X-ray crystallographic study reveals that there is an angle of approximate 118° among the centroids of the three rings (pyridyl-phenyl-pyridyl) in each PDI molecule indicating a desired banana shape. In addition, a series of liquid crystal complexes nBA:PDI:nBA induced by intermolecular hydrogen bonding between PDI (proton acceptor) and 4-alkoxybenzoic acids (nBA, proton donor) were synthesized and characterized. The mesomorphism properties and optical textures of the complex of nBA:PDI:nBA were investigated by differential scanning calorimetry, polarizing optical microscope and X-ray diffraction.

New insights into the dual fluorescence of methyl salicylate: effects of intermolecular hydrogen bonding and solvation.

Science.gov (United States)

Zhou, Panwang; Hoffmann, Mark R; Han, Keli; He, Guozhong

2015-02-12

In this paper, we propose a new and complete mechanism for dual fluorescence of methyl salicylate (MS) under different conditions using a combined experimental (i.e., steady-state absorption and emission spectra and time-resolved fluorescence spectra) and theoretical (i.e., time-dependent density function theory) study. First, our theoretical study indicates that the barrier height for excited state intramolecular proton transfer (ESIPT) reaction of ketoB depends on the solvent polarity. In nonpolar solvents, the ESIPT reaction of ketoB is barrierless; the barrier height will increase with increasing solvent polarity. Second, we found that, in alcoholic solvents, intermolecular hydrogen bonding plays a more important role. The ketoB form of MS can form two hydrogen bonds with alcoholic solvents; one will facilitate ESIPT and produce the emission band in the blue region; the other one precludes ESIPT and produces the emission band in the near-UV region. Our proposed new mechanism can well explain previous results as well as our new experimental results.

The Strength of Hydrogen Bonds between Fluoro-Organics and Alcohols, a Theoretical Study.

Science.gov (United States)

Rosenberg, Robert E

2018-05-10

Fluorinated organic compounds are ubiquitous in the pharmaceutical and agricultural industries. To better discern the mode of action of these compounds, it is critical to understand the strengths of hydrogen bonds involving fluorine. There are only a few published examples of the strengths of these bonds. This study provides a high level ab initio study of inter- and intramolecular hydrogen bonds between RF and R'OH, where R and R' are aryl, vinyl, alkyl, and cycloalkyl. Intermolecular binding energies average near 5 kcal/mol, while intramolecular binding energies average about 3 kcal/mol. Inclusion of zero-point energies and applying a counterpoise correction lessen the difference. In both series, modest increases in binding energies are seen with increased acidity of R'OH and increased electron donation of R in RF. In the intramolecular compounds, binding energy increases with the rigidity of the F-(C) n -OH ring. Inclusion of free energy corrections at 298 K results in exoergic binding energies for the intramolecular compounds and endoergic binding energies for the intermolecular compounds. Parameters such as bond lengths, vibrational frequencies, and atomic populations are consistent with formation of a hydrogen bond and with slightly stronger binding in the intermolecular cases over the intramolecular cases. However, these parameters correlated poorly with binding energies.

Unambiguous Determination of Intermolecular Hydrogen Bond of NMR Structure by Molecular Dynamics Refinement Using All-Atom Force Field and Implicit Solvent Model

International Nuclear Information System (INIS)

Jee, Jun Goo

2010-01-01

It has been shown that AMD refinement is very useful for defining an intermolecular hydrogen bond in NMR structure calculation. The refined structure also provides a clue for explaining the pH dependence in Ub and UIM complexes. As reported by Choi et al., serine-mediated hydrogen bonds are the third most populated hydrogen bonds found in protein-protein intermolecular interactions, after the backbone-backbone and backbone-aspartate ones. The abundance imposes the requirement of an method to determine the interface of protein-protein complexes. The precise geometry is particularly important in the complex structures between Ub and UBDs. Ub recognizes various targets with the same surface, where both hydrophobic and hydrophobic interactions are involved. Hence, the details of the hydrophilic interactions are necessary to find the common binding modes. The structure determination of a biomolecule by NMR depends heavily on the distance restraints derived by the NOE cross peaks that are observed between two protons within 6 A through space. Therefore, the existence of the NOE peaks and their correct assignments to two corresponding protons are essential for an accurate and precise structure determination. Recent developments of NOE assignment and calculation algorithms have enabled the determination of protein 3D structures without any manual interpretation, provided chemical shifts are assigned in most atoms and sufficient NOE peaks exist. Along with these advances, the necessity of determining complicated structures such as complexes is increasing

Intermolecular hydrogen bonds: From temperature-driven proton ...

Indian Academy of Sciences (India)

Abstract. We have combined neutron scattering and a range of numerical simulations to study hydrogen bonds in condensed matter. Two examples from a recent thesis will be presented. The first concerns proton transfer with increasing temperature in short inter- molecular hydrogen bonds [1,2]. These bonds have unique ...

Protein-ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes.

Science.gov (United States)

Raschka, Sebastian; Wolf, Alex J; Bemister-Buffington, Joseph; Kuhn, Leslie A

2018-04-01

Understanding how proteins encode ligand specificity is fascinating and similar in importance to deciphering the genetic code. For protein-ligand recognition, the combination of an almost infinite variety of interfacial shapes and patterns of chemical groups makes the problem especially challenging. Here we analyze data across non-homologous proteins in complex with small biological ligands to address observations made in our inhibitor discovery projects: that proteins favor donating H-bonds to ligands and avoid using groups with both H-bond donor and acceptor capacity. The resulting clear and significant chemical group matching preferences elucidate the code for protein-native ligand binding, similar to the dominant patterns found in nucleic acid base-pairing. On average, 90% of the keto and carboxylate oxygens occurring in the biological ligands formed direct H-bonds to the protein. A two-fold preference was found for protein atoms to act as H-bond donors and ligand atoms to act as acceptors, and 76% of all intermolecular H-bonds involved an amine donor. Together, the tight chemical and geometric constraints associated with satisfying donor groups generate a hydrogen-bonding lock that can be matched only by ligands bearing the right acceptor-rich key. Measuring an index of H-bond preference based on the observed chemical trends proved sufficient to predict other protein-ligand complexes and can be used to guide molecular design. The resulting Hbind and Protein Recognition Index software packages are being made available for rigorously defining intermolecular H-bonds and measuring the extent to which H-bonding patterns in a given complex match the preference key.

Protein-ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes

Science.gov (United States)

Raschka, Sebastian; Wolf, Alex J.; Bemister-Buffington, Joseph; Kuhn, Leslie A.

2018-02-01

Understanding how proteins encode ligand specificity is fascinating and similar in importance to deciphering the genetic code. For protein-ligand recognition, the combination of an almost infinite variety of interfacial shapes and patterns of chemical groups makes the problem especially challenging. Here we analyze data across non-homologous proteins in complex with small biological ligands to address observations made in our inhibitor discovery projects: that proteins favor donating H-bonds to ligands and avoid using groups with both H-bond donor and acceptor capacity. The resulting clear and significant chemical group matching preferences elucidate the code for protein-native ligand binding, similar to the dominant patterns found in nucleic acid base-pairing. On average, 90% of the keto and carboxylate oxygens occurring in the biological ligands formed direct H-bonds to the protein. A two-fold preference was found for protein atoms to act as H-bond donors and ligand atoms to act as acceptors, and 76% of all intermolecular H-bonds involved an amine donor. Together, the tight chemical and geometric constraints associated with satisfying donor groups generate a hydrogen-bonding lock that can be matched only by ligands bearing the right acceptor-rich key. Measuring an index of H-bond preference based on the observed chemical trends proved sufficient to predict other protein-ligand complexes and can be used to guide molecular design. The resulting Hbind and Protein Recognition Index software packages are being made available for rigorously defining intermolecular H-bonds and measuring the extent to which H-bonding patterns in a given complex match the preference key.

A general approach to intermolecular carbonylation of arene C-H bonds to ketones through catalytic aroyl triflate formation

Science.gov (United States)

Garrison Kinney, R.; Tjutrins, Jevgenijs; Torres, Gerardo M.; Liu, Nina Jiabao; Kulkarni, Omkar; Arndtsen, Bruce A.

2018-02-01

The development of metal-catalysed methods to functionalize inert C-H bonds has become a dominant research theme in the past decade as an approach to efficient synthesis. However, the incorporation of carbon monoxide into such reactions to form valuable ketones has to date proved a challenge, despite its potential as a straightforward and green alternative to Friedel-Crafts reactions. Here we describe a new approach to palladium-catalysed C-H bond functionalization in which carbon monoxide is used to drive the generation of high-energy electrophiles. This offers a method to couple the useful features of metal-catalysed C-H functionalization (stable and available reagents) and electrophilic acylations (broad scope and selectivity), and synthesize ketones simply from aryl iodides, CO and arenes. Notably, the reaction proceeds in an intermolecular fashion, without directing groups and at very low palladium-catalyst loadings. Mechanistic studies show that the reaction proceeds through the catalytic build-up of potent aroyl triflate electrophiles.

Hydrogen bonds of sodium alginate/Antarctic krill protein composite material.

Science.gov (United States)

Yang, Lijun; Guo, Jing; Yu, Yue; An, Qingda; Wang, Liyan; Li, Shenglin; Huang, Xuelin; Mu, Siyang; Qi, Shanwei

2016-05-20

Sodium alginate/Antarctic krill protein composite material (SA/AKP) was successfully obtained by blending method. The hydrogen bonds of SA/AKP composite material were analyzed by Fourier transform infrared spectroscopy (FT-IR) and Nuclear magnetic resonance hydrogen spectrum (HNMR). Experiment manifested the existence of intermolecular and intramolecular hydrogen bonds in SA/AKP system; strength of intermolecular hydrogen bond enhanced with the increase of AKP in the composite material and the interaction strength of hydrogen bonding followed the order: OH…Ether O>OH…π>OH…N. The percentage of intermolecular hydrogen bond decreased with increase of pH. At the same time, the effect of hydrogen bonds on properties of the composite material was discussed. The increase of intermolecular hydrogen bonding led to the decrease of crystallinity, increase of apparent viscosity and surface tension, as well as obvious decrease of heat resistance of SA/AKP composite material. SA/AKP fiber SEM images and energy spectrum showed that crystallized salt was separated from the fiber, which possibly led to the fibrillation of the composite fibers. Copyright © 2016 Elsevier Ltd. All rights reserved.

Intra- und intermolecular hydrogen bonds. Spectroscopic, quantum chemical and molecular dynamics studies

International Nuclear Information System (INIS)

Simperler, A.

1999-03-01

Intra- and intermolecular H-bonds have been investigated with spectroscopic, quantum chemical, and molecular dynamics methods. The work is divided into the following three parts: 1. Intramolecular interactions in ortho-substituted phenols. Theoretical and experimental data that characterizes the intramolecular hydrogen bonds in 48 different o-substituted phenols are discussed. The study covers various kinds of O-H ... Y -type interactions (Y= N, O, S, F, Cl, Br, I, C=C, C=-C, and C-=N). The bond strength sequences for several series of systematically related compounds as obtained from IR spectroscopy data (i.e., v(OH) stretching frequencies) are discussed and reproduced with several theoretical methods (B3LYP/6-31G(d,p), B3LYP/6-311G(d,p), B3LYP/6-31++G(d,p), B3LYP/DZVP, MP2/6-31G(d,p), and MP2/6-31++G(d,p) levels of theory). The experimentally determined sequences are interpreted in terms of the intrinsic properties of the molecules: hydrogen bond distances, Mulliken partial charges, van der Waals radii, and electron densities of the Y-proton acceptors. 2. Competitive hydrogen bonds and conformational equilibria in 2,6-disubstituted phenols containing two different carbonyl substituents. The rotational isomers of ten unsymmetrical 2,6-disubstituted phenols as obtained by combinations of five different carbonyl substituents (COOH, COOCH 3 , CHO, COCH 3 , and CONH 2 ) have been theoretically investigated at the B3LYP/6-31G(d,p) level of theory. The relative stability of four to five conformers of each compound were determined by full geometry optimization for free molecules as well as for molecules in reaction fields with dielectric constants up to ε=37.5. A comparison with IR spectroscopic data of available compounds revealed excellent agreement with the theoretically predicted stability sequences and conformational equilibria. The stability of a conformer could be interpreted to be governed by the following two contributions: (i) an attractive hydrogen bond

Mapping the force field of a hydrogen-bonded assembly

Science.gov (United States)

Sweetman, A. M.; Jarvis, S. P.; Sang, Hongqian; Lekkas, I.; Rahe, P.; Wang, Yu; Wang, Jianbo; Champness, N. R.; Kantorovich, L.; Moriarty, P.

2014-05-01

Hydrogen bonding underpins the properties of a vast array of systems spanning a wide variety of scientific fields. From the elegance of base pair interactions in DNA to the symmetry of extended supramolecular assemblies, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the hydrogen bond continue to be vigorously debated. Here we use dynamic force microscopy (DFM) to quantitatively map the tip-sample force field for naphthalene tetracarboxylic diimide molecules hydrogen-bonded in two-dimensional assemblies. A comparison of experimental images and force spectra with their simulated counterparts shows that intermolecular contrast arises from repulsive tip-sample interactions whose interpretation can be aided via an examination of charge density depletion across the molecular system. Interpreting DFM images of hydrogen-bonded systems therefore necessitates detailed consideration of the coupled tip-molecule system: analyses based on intermolecular charge density in the absence of the tip fail to capture the essential physical chemistry underpinning the imaging mechanism.

Competing intramolecular N-H⋯O=C hydrogen bonds and extended intermolecular network in 1-(4-chlorobenzoyl)-3-(2-methyl-4-oxopentan-2-yl) thiourea analyzed by experimental and theoretical methods

Energy Technology Data Exchange (ETDEWEB)

Saeed, Aamer, E-mail: aamersaeed@yahoo.com [Department of Chemistry, Quaid-I-Azam University, Islamabad 45320 (Pakistan); Khurshid, Asma [Department of Chemistry, Quaid-I-Azam University, Islamabad 45320 (Pakistan); Jasinski, Jerry P. [Department of Chemistry, Keene State College, 229 Main Street Keene, NH 03435-2001 (United States); Pozzi, C. Gustavo; Fantoni, Adolfo C. [Instituto de Física La Plata, Departamento de Física, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 49 y 115, La Plata, Buenos Aires (Argentina); Erben, Mauricio F., E-mail: erben@quimica.unlp.edu.ar [CEQUINOR (UNLP, CONICET-CCT La Plata), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, C.C. 962, (1900) La Plata, Buenos Aires (Argentina)

2014-03-18

Highlights: • Two distinct N-H⋯O=C intramolecular competing hydrogen bonds are feasible in the title molecule. • Crystal structures and vibrational properties were determined. • The C=O and C=S double bonds of the acyl-thiourea group are mutually oriented in opposite directions. • A strong hyperconjugative lpO1 → σ{sup ∗}(N2-H) remote interaction was detected. • Topological analysis reveals a Cl⋯N interaction playing a relevant role in crystal packing. - Abstract: The synthesis of a novel 1-acyl-thiourea species (C{sub 14}H{sub 17}N{sub 2}O{sub 2}SCl), has been tailored in such a way that two distinct N-H⋯O=C intramolecular competing hydrogen bonds are feasible. The X-ray structure analysis as well as the vibrational (FT-IR and FT-Raman) data reveal that the S conformation is preferred, with the C=O and C=S bonds of the acyl-thiourea group pointing in opposite directions. The preference for the intramolecular N-H⋯O=C hydrogen bond within the -C(O)NHC(S)NH- core is confirmed. The Natural Bond Orbital and the Atom in Molecule approaches demonstrate that a strong hyperconjugative lpO → σ{sup ∗}(N-H) remote interaction between the acyl and the thioamide N-H groups is responsible for the stabilization of the S conformation. Intermolecular interactions have been characterized in the periodic system electron density and the topological analysis reveals the presence of an extended intermolecular network in the crystal, including a Cl⋯N interaction playing a relevant role in crystal packing.

Induced Smectic X Phase Through Intermolecular Hydrogen-Bonded Liquid Crystals Formed Between Citric Acid and p- n-(Octyloxy)Benzoic Acid

Science.gov (United States)

Sundaram, S.; Subhasri, P.; Rajasekaran, T. R.; Jayaprakasam, R.; Senthil, T. S.; Vijayakumar, V. N.

2017-08-01

Hydrogen-bonded liquid crystal (HBLC) is synthesized from citric acid (CA) and 4-(octyloxy)benzoic acid (8OBA) with different mole ratios. Fourier transform infrared spectroscopy (FT-IR) confirms the presence of hydrogen bond between CA and 8OBA. Nuclear magnetic resonance (NMR) spectroscopic studies validate the intermolecular complementary, cyclic type of hydrogen bond, and molecular environment in the designed HBLC complex. Powder X-ray diffraction analysis reveals the monoclinic nature of liquid crystal complex in solid phase. Liquid crystal parameters such as phase transition temperature and enthalpy values for the corresponding mesogenic phases are investigated using a polarizing optical microscope (POM) and differential scanning calorimetry (DSC). It is observed that the change in chain length and steric hindrance while increasing the mole ratio in HBLC complex induces a new smectic X (Sm X) along with higher-order smectic G (Sm G) phases by quenching of smectic C (Sm C). From the experimental observations, induced Sm X phase has been identified as a finger print texture. Also, Sm G is a multi-colored mosaic texture in 1:1, 1:2, and 1:3 mol ratios. The optical tilt angle, thermal stability factor, and enhanced thermal span width of CA + 8OBA complex are discussed.

A Raman spectroscopy study on the effects of intermolecular hydrogen bonding on water molecules absorbed by borosilicate glass surface

Science.gov (United States)

Li, Fabing; Li, Zhanlong; Wang, Ying; Wang, Shenghan; Wang, Xiaojun; Sun, Chenglin; Men, Zhiwei

2018-05-01

The structural forms of water/deuterated water molecules located on the surface of borosilicate capillaries have been first investigated in this study on the basis of the Raman spectral data obtained at different temperatures and under atmospheric pressure for molecules in bulk and also for molecules absorbed by borosilicate glass surface. The strongest two fundamental bands locating at 3063 cm-1 (2438 cm-1) in the recorded Raman spectra are assigned here to the Osbnd H (Osbnd D) bond stretching vibrations and they are compared with the corresponding bands observed at 3124 cm-1 (2325 cm-1) in the Raman spectrum of ice Ih. Our spectroscopic observations have indicated that the structure of water and deuterated water molecules on borosilicate surface is similar to that of ice Ih (hexagonal phase of ice). These observations have also indicated that water molecules locate on the borosilicate surface so as to construct a bilayer structure and that strong and weak intermolecular hydrogen bonds are formed between water/deuterated molecules and silanol groups on borosilicate surface. In accordance with these findings, water and deuterated water molecules at the interface of capillary have a higher melting temperature.

Instantaneous normal mode analysis for intermolecular and intramolecular vibrations of water from atomic point of view.

Science.gov (United States)

Chen, Yu-Chun; Tang, Ping-Han; Wu, Ten-Ming

2013-11-28

By exploiting the instantaneous normal mode (INM) analysis for models of flexible molecules, we investigate intermolecular and intramolecular vibrations of water from the atomic point of view. With two flexible SPC/E models, our investigations include three aspects about their INM spectra, which are separated into the unstable, intermolecular, bending, and stretching bands. First, the O- and H-atom contributions in the four INM bands are calculated and their stable INM spectra are compared with the power spectra of the atomic velocity autocorrelation functions. The unstable and intermolecular bands of the flexible models are also compared with those of the SPC/E model of rigid molecules. Second, we formulate the inverse participation ratio (IPR) of the INMs, respectively, for the O- and H-atom and molecule. With the IPRs, the numbers of the three species participated in the INMs are estimated so that the localization characters of the INMs in each band are studied. Further, by the ratio of the IPR of the H atom to that of the O atom, we explore the number of involved OH bond per molecule participated in the INMs. Third, by classifying simulated molecules into subensembles according to the geometry of their local environments or their H-bond configurations, we examine the local-structure effects on the bending and stretching INM bands. All of our results are verified to be insensible to the definition of H-bond. Our conclusions about the intermolecular and intramolecular vibrations in water are given.

Thermophysical properties of supercritical water and bond flexibility.

Science.gov (United States)

Shvab, I; Sadus, Richard J

2015-07-01

Molecular dynamics results are reported for the thermodynamic properties of supercritical water using examples of both rigid (TIP4P/2005) and flexible (TIP4P/2005f) transferable interaction potentials. Data are reported for pressure, isochoric and isobaric heat capacities, the thermal expansion coefficient, isothermal and adiabatic compressibilities, Joule-Thomson coefficient, speed of sound, self-diffusion coefficient, viscosities, and thermal conductivity. Many of these properties have unusual behavior in the supercritical phase such as maximum and minimum values. The effectiveness of bond flexibility on predicting these properties is determined by comparing the results to experimental data. The influence of the intermolecular potential on these properties is both variable and state point dependent. In the vicinity of the critical density, the rigid and flexible potentials yield very different values for the compressibilities, heat capacities, and thermal expansion coefficient, whereas the self-diffusion coefficient, viscosities, and thermal conductivities are much less potential dependent. Although the introduction of bond flexibility is a computationally expedient way to improve the accuracy of an intermolecular potential, it can be counterproductive in some cases and it is not an adequate replacement for incorporating the effects of polarization.

On the intermolecular vibrational coupling, hydrogen bonding, and librational freedom of water in the hydration shell of mono- and bivalent anions.

Science.gov (United States)

Ahmed, Mohammed; Namboodiri, V; Singh, Ajay K; Mondal, Jahur A

2014-10-28

The hydration energy of an ion largely resides within the first few layers of water molecules in its hydration shell. Hence, it is important to understand the transformation of water properties, such as hydrogen-bonding, intermolecular vibrational coupling, and librational freedom in the hydration shell of ions. We investigated these properties in the hydration shell of mono- (Cl(-) and I(-)) and bivalent (SO4(2-) and CO3(2-)) anions by using Raman multivariate curve resolution (Raman-MCR) spectroscopy in the OH stretch, HOH bend, and [bend+librational] combination bands of water. Raman-MCR of aqueous Na-salt (NaCl, NaI, Na2SO4, and Na2CO3) solutions provides ion-correlated spectra (IC-spectrum) which predominantly bear the vibrational characteristics of water in the hydration shell of respective anions. Comparison of these IC-spectra with the Raman spectrum of bulk water in different spectral regions reveals that the water is vibrationally decoupled with its neighbors in the hydration shell. Hydrogen-bond strength and librational freedom also vary with the nature of anion: hydrogen-bond strength, for example, decreases as CO3(2-) > SO4(2-) > bulk water ≈ Cl(-) > I(-); and the librational freedom increases as CO3(2-) ≈ SO4(2-) water water in the hydration shell of anions.

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

Science.gov (United States)

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.

Intermolecular Interactions in Crystalline Theobromine as Reflected in Electron Deformation Density and (13)C NMR Chemical Shift Tensors.

Science.gov (United States)

Bouzková, Kateřina; Babinský, Martin; Novosadová, Lucie; Marek, Radek

2013-06-11

An understanding of the role of intermolecular interactions in crystal formation is essential to control the generation of diverse crystalline forms which is an important concern for pharmaceutical industry. Very recently, we reported a new approach to interpret the relationships between intermolecular hydrogen bonding, redistribution of electron density in the system, and NMR chemical shifts (Babinský et al. J. Phys. Chem. A, 2013, 117, 497). Here, we employ this approach to characterize a full set of crystal interactions in a sample of anhydrous theobromine as reflected in (13)C NMR chemical shift tensors (CSTs). The important intermolecular contacts are identified by comparing the DFT-calculated NMR CSTs for an isolated theobromine molecule and for clusters composed of several molecules as selected from the available X-ray diffraction data. Furthermore, electron deformation density (EDD) and shielding deformation density (SDD) in the proximity of the nuclei involved in the proposed interactions are calculated and visualized. In addition to the recently reported observations for hydrogen bonding, we focus here particularly on the stacking interactions. Although the principal relations between the EDD and CST for hydrogen bonding (HB) and stacking interactions are similar, the real-space consequences are rather different. Whereas the C-H···X hydrogen bonding influences predominantly and significantly the in-plane principal component of the (13)C CST perpendicular to the HB path and the C═O···H hydrogen bonding modulates both in-plane components of the carbonyl (13)C CST, the stacking modulates the out-of-plane electron density resulting in weak deshielding (2-8 ppm) of both in-plane principal components of the CST and weak shielding (∼ 5 ppm) of the out-of-plane component. The hydrogen-bonding and stacking interactions may add to or subtract from one another to produce total values observed experimentally. On the example of theobromine, we demonstrate

Vibrational polarizabilities of hydrogen-bonded water

International Nuclear Information System (INIS)

Torii, Hajime

2013-01-01

Highlights: ► Vibrational polarizabilities of hydrogen-bonded water are analyzed theoretically. ► Total vibrational polarizability is (at least) comparable to the electronic one. ► Molecular translations contribute to the vibrational polarizability below 300 cm −1 . ► Intermolecular charge fluxes along H bonds are induced by molecular translations. ► The results are discussed in relation to the observed dielectric properties. - Abstract: The vibrational polarizabilities and the related molecular properties of hydrogen-bonded water are analyzed theoretically, taking the case of (water) 30 clusters as an example case. It is shown that some off-diagonal dipole derivatives are large for the translations of incompletely hydrogen-bonded molecules, and this is reasonably explained by the scheme of intermolecular charge fluxes induced along hydrogen bonds. In total, because of these intermolecular charge fluxes, molecular translations give rise to the vibrational polarizability of 2.8–3.3 a 0 3 per molecule, which is as large as about 40% of the electronic polarizability, mainly in the frequency region below 300 cm −1 . Adding the contributions of the molecular rotations (librations) and the translation–rotation cross term, the total polarizability (electronic + vibrational) at ∼100 cm −1 is slightly larger than the double of that at >4000 cm −1 . The relation of these results to some observed time- and frequency-dependent dielectric properties of liquid water is briefly discussed

Intermolecular Dehydrative Coupling Reaction of Arylketones with Cyclic Alkenes Catalyzed by a Well-Defined Cationic Ruthenium-Hydride Complex: A Novel Ketone Olefination Method via Vinyl C–H Bond Activation

Science.gov (United States)

Yi, Chae S.; Lee, Do W.

2010-01-01

Summary The cationic ruthenium-hydride complex [(η6-C6H6)(PCy3)(CO)RuH]+BF4− was found to be a highly effective catalyst for the intermolecular olefination reaction of arylketones with cycloalkenes. The preliminary mechanistic analysis revealed that electrophilic ruthenium-vinyl complex is the key species for mediating both vinyl C–H bond activation and the dehydrative olefination steps of the coupling reaction. PMID:20567607

Criticality of the D=2 bond-dilute anisotropic Heisenberg ferromagnet

International Nuclear Information System (INIS)

Mariz, A.M.; Tsallis, C.; Caride, A.O.

1984-01-01

The critical frontier and critical exponents associated with the quenched bond-dilute quantum anisotropic spin 1/2 Heisenberg ferromagnet in square lattice are described. To perform the calculations, an approximate real-space renormalization-group framework recently developed by some of us for the pure model (and analysed with some detail) is extended. Whenever comparison with available exact results is possible, the agreement is either perfect or quite satisfactory. Some effort has been dedicated to extract the main asymptotic behaviours of the critical frontier. Also several interesting quantum effects appearing in the composition laws of (Heisenberg) bond arrays are exhibited. (Author) [pt

Predictions of glass transition temperature for hydrogen bonding biomaterials.

Science.gov (United States)

van der Sman, R G M

2013-12-19

We show that the glass transition of a multitude of mixtures containing hydrogen bonding materials correlates strongly with the effective number of hydroxyl groups per molecule, which are available for intermolecular hydrogen bonding. This correlation is in compliance with the topological constraint theory, wherein the intermolecular hydrogen bonds constrain the mobility of the hydrogen bonded network. The finding that the glass transition relates to hydrogen bonding rather than free volume agrees with our recent finding that there is little difference in free volume among carbohydrates and polysaccharides. For binary and ternary mixtures of sugars, polyols, or biopolymers with water, our correlation states that the glass transition temperature is linear with the inverse of the number of effective hydroxyl groups per molecule. Only for dry biopolymer/sugar or sugar/polyol mixtures do we find deviations due to nonideal mixing, imposed by microheterogeneity.

The origins of the directionality of noncovalent intermolecular interactions.

Science.gov (United States)

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

2016-01-05

The recent σ-hole concept emphasizes the contribution of electrostatic attraction to noncovalent bonds, and implies that the electrostatic force has an angular dependency. Here a set of clusters, which includes hydrogen bonding, halogen bonding, chalcogen bonding, and pnicogen bonding systems, is investigated to probe the magnitude of covalency and its contribution to the directionality in noncovalent bonding. The study is based on the block-localized wavefunction (BLW) method that decomposes the binding energy into the steric and the charge transfer (CT) (hyperconjugation) contributions. One unique feature of the BLW method is its capability to derive optimal geometries with only steric effect taken into account, while excluding the CT interaction. The results reveal that the overall steric energy exhibits angular dependency notably in halogen bonding, chalcogen bonding, and pnicogen bonding systems. Turning on the CT interactions further shortens the intermolecular distances. This bond shortening enhances the Pauli repulsion, which in turn offsets the electrostatic attraction, such that in the final sum, the contribution of the steric effect to bonding is diminished, leaving the CT to dominate the binding energy. In several other systems particularly hydrogen bonding systems, the steric effect nevertheless still plays the major role whereas the CT interaction is minor. However, in all cases, the CT exhibits strong directionality, suggesting that the linearity or near linearity of noncovalent bonds is largely governed by the charge-transfer interaction whose magnitude determines the covalency in noncovalent bonds. © 2015 Wiley Periodicals, Inc.

Effect of intermolecular dipole-dipole interactions on interfacial supramolecular structures of C3-symmetric hexa-peri-hexabenzocoronene derivatives.

Science.gov (United States)

Mu, Zhongcheng; Shao, Qi; Ye, Jun; Zeng, Zebing; Zhao, Yang; Hng, Huey Hoon; Boey, Freddy Yin Chiang; Wu, Jishan; Chen, Xiaodong

2011-02-15

Two-dimensional (2D) supramolecular assemblies of a series of novel C(3)-symmetric hexa-peri-hexabenzocoronene (HBC) derivatives bearing different substituents adsorbed on highly oriented pyrolytic graphite were studied by using scanning tunneling microscopy at a solid-liquid interface. It was found that the intermolecular dipole-dipole interactions play a critical role in controlling the interfacial supramolecular assembly of these C(3)-symmetric HBC derivatives at the solid-liquid interface. The HBC molecule bearing three -CF(3) groups could form 2D honeycomb structures because of antiparallel dipole-dipole interactions, whereas HBC molecules bearing three -CN or -NO(2) groups could form hexagonal superstructures because of a special trimeric arrangement induced by dipole-dipole interactions and weak hydrogen bonding interactions ([C-H···NC-] or [C-H···O(2)N-]). Molecular mechanics and dynamics simulations were performed to reveal the physics behind the 2D structures as well as detailed functional group interactions. This work provides an example of how intermolecular dipole-dipole interactions could enable fine control over the self-assembly of disklike π-conjugated molecules.

A simple semi-empirical approximation for bond energy

International Nuclear Information System (INIS)

Jorge, F.E.; Giambiagi, M.; Giambiagi, M.S. de.

1985-01-01

A simple semi-empirical expression for bond energy, related with a generalized bond index, is proposed and applied within the IEH framework. The correlation with experimental data is good for the intermolecular bond energy of base pairs of nucleic acids and other hydrogen bonded systems. The intramolecular bond energies for a sample of molecules containing typical bonds and for hydrides are discussed. The results are compared with those obtained by other methods. (Author) [pt

The computation of bond percolation critical polynomials by the deletion–contraction algorithm

International Nuclear Information System (INIS)

Scullard, Christian R

2012-01-01

Although every exactly known bond percolation critical threshold is the root in [0,1] of a lattice-dependent polynomial, it has recently been shown that the notion of a critical polynomial can be extended to any periodic lattice. The polynomial is computed on a finite subgraph, called the base, of an infinite lattice. For any problem with exactly known solution, the prediction of the bond threshold is always correct for any base containing an arbitrary number of unit cells. For unsolved problems, the polynomial is referred to as the generalized critical polynomial and provides an approximation that becomes more accurate with increasing number of bonds in the base, appearing to approach the exact answer. The polynomials are computed using the deletion–contraction algorithm, which quickly becomes intractable by hand for more than about 18 bonds. Here, I present generalized critical polynomials calculated with a computer program for bases of up to 36 bonds for all the unsolved Archimedean lattices, except the kagome lattice, which was considered in an earlier work. The polynomial estimates are generally within 10 −5 –10 −7 of the numerical values, but the prediction for the (4,8 2 ) lattice, though not exact, is not ruled out by simulations. (paper)

Effects of hydrogen bonds on solid state TATB, RDX, and DATB under high pressures

International Nuclear Information System (INIS)

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

2014-01-01

To probe the behavior of hydrogen bonds in solid energetic materials, we conduct ReaxFF and SCC–DFTB molecular dynamics simulations of crystalline TATB, RDX, and DATB. By comparing the intra- and inter-molecular hydrogen bonding rates, we find that the crystal structures are stabilized by inter-molecular hydrogen bond networks. Under high-pressure, the inter- and intra-molecular hydrogen bonds in solid TATB and DATB are nearly equivalent. The hydrogen bonds in solid TATB and DATB are much shorter than in solid RDX, which suggests strong hydrogen bond interactions existing in these energetic materials. Stretching of the C–H bond is observed in solid RDX, which may lead to further decomposition and even detonation. (condensed matter: structural, mechanical, and thermal properties)

Hydrogen and dihydrogen bonding of transition metal hydrides

Science.gov (United States)

Jacobsen, Heiko

2008-04-01

Intermolecular interactions between a prototypical transition metal hydride WH(CO) 2NO(PH 3) 2 and a small proton donor H 2O have been studied using DFT methodology. The hydride, nitrosyl and carbonyl ligand have been considered as site of protonation. Further, DFT-D calculations in which empirical corrections for the dispersion energy are included, have been carried out. A variety of pure and hybrid density functionals (BP86, PW91, PBE, BLYP, OLYP, B3LYP, B1PW91, PBE0, X3LYP) have been considered, and our calculations indicate the PBE functional and its hybrid variation are well suited for the calculation of transition metal hydride hydrogen and dihydrogen bonding. Dispersive interactions make up for a sizeable portion of the intermolecular interaction, and amount to 20-30% of the bond energy and to 30-40% of the bond enthalpy. An energy decomposition analysis reveals that the H⋯H bond of transition metal hydrides contains both covalent and electrostatic contributions.

Hydrogen and dihydrogen bonding of transition metal hydrides

International Nuclear Information System (INIS)

Jacobsen, Heiko

2008-01-01

Intermolecular interactions between a prototypical transition metal hydride WH(CO) 2 NO(PH 3 ) 2 and a small proton donor H 2 O have been studied using DFT methodology. The hydride, nitrosyl and carbonyl ligand have been considered as site of protonation. Further, DFT-D calculations in which empirical corrections for the dispersion energy are included, have been carried out. A variety of pure and hybrid density functionals (BP86, PW91, PBE, BLYP, OLYP, B3LYP, B1PW91, PBE0, X3LYP) have been considered, and our calculations indicate the PBE functional and its hybrid variation are well suited for the calculation of transition metal hydride hydrogen and dihydrogen bonding. Dispersive interactions make up for a sizeable portion of the intermolecular interaction, and amount to 20-30% of the bond energy and to 30-40% of the bond enthalpy. An energy decomposition analysis reveals that the H...H bond of transition metal hydrides contains both covalent and electrostatic contributions

A quantitative analysis of weak intermolecular interactions & quantum chemical calculations (DFT) of novel chalcone derivatives

Energy Technology Data Exchange (ETDEWEB)

Chavda, Bhavin R., E-mail: chavdabhavin9@gmail.com; Dubey, Rahul P.; Patel, Urmila H. [Department of Physics, Sardar Patel University, Vallabh Vidyanagar-388120, Gujarat (India); Gandhi, Sahaj A. [Bhavan’s Shri I.L. Pandya Arts-Science and Smt. J.M. shah Commerce College, Dakar, Anand -388001, Gujarat, Indian (India); Barot, Vijay M. [P. G. Center in Chemistry, Smt. S. M. Panchal Science College, Talod, Gujarat 383 215 (India)

2016-05-06

The novel chalcone derivatives have widespread applications in material science and medicinal industries. The density functional theory (DFT) is used to optimized the molecular structure of the three chalcone derivatives (M-I, II, III). The observed discrepancies between the theoretical and experimental (X-ray data) results attributed to different environments of the molecules, the experimental values are of the molecule in solid state there by subjected to the intermolecular forces, like non-bonded hydrogen bond interactions, where as isolated state in gas phase for theoretical studies. The lattice energy of all the molecules have been calculated using PIXELC module in Coulomb –London –Pauli (CLP) package and is partitioned into corresponding coulombic, polarization, dispersion and repulsion contributions. Lattice energy data confirm and strengthen the finding of the X-ray results that the weak but significant intermolecular interactions like C-H…O, Π- Π and C-H… Π plays an important role in the stabilization of crystal packing.

Triangular and honeycomb lattices bond-diluted Ising ferromagnet: critical frontier

International Nuclear Information System (INIS)

Magalhaes, A.C.N. de; Schwaccheim, G.; Tsallis, C.

1982-01-01

Within a real space renormalization group framework (12 different procedures, all of them using star-triangle and duality-type transformations) accurate approximations for the critical frontiers associated with the quenched bond-diluted first-neighbour spin- 1 / 2 Ising ferromagnet on triangular and honeycomb lattices are calculated. All of them provide, in both pure bond percolation and pure Ising limits, the exact critical points and exact or almost exact derivatives in the p-t space (p is the bond independent occupancy probability and t tanh J/k(sub B)T). The best numerical proposals lead to the exact derivative in the pure percolation limit (p = p(sub c)) and, in what concerns the pure Ising limit (p = 1) derivative, to a 0.15% error for the triangular lattice and to a 0.96% error for the honeycomb one; in the intermediate region (p(sub c) [pt

Structural modeling and intermolecular correlation of liquid chlorine dioxide

International Nuclear Information System (INIS)

Ogata, Norio; Hironori, Shimakura; Kawakita, Yukinobu; Ohara, Yukoji; Kohara, Shinji; Takeda, Shinichi

2009-01-01

Chlorine dioxide (ClO 2 ) is water-soluble yellow gas at room temperature. It has long been used as a disinfectant of tap water and various commodities owing to its strong oxidizing activity against various microbial proteins. The oxidizing activity is believed to be due to the presence of unpaired electron in its molecular orbital. Despite wealth of physicochemical studies of gaseous ClO 2 , little is known about liquid ClO 2 , especially about fine molecular structure and intermolecular interactions of liquid ClO 2 . The purpose of this study is to elucidate the fine structure and intermolecular orientations of ClO 2 molecules in its liquid state using a high-energy X-ray diffraction technique. The measurements of liquid ClO 2 were carried out at -50 to 0 degree Celsius using a two-axis diffractometer installed at the BL04B2 beamline in the third-generation synchrotron radiation facility SPring-8 (Hyogo, Japan). The incident X-ray beamline was 113.4 keV in energy and 0.1093 Armstrong in wavelength from a Si(111) monochromator with the third harmonic reflection. Liquid ClO 2 held in a quartz capillary tube was placed in a temperature-controlled vacuum chamber. We obtained a structure factor S(Q) to a range of Q = 0.3-30 Amstrong -1 and a pair distribution function g(r) upon Fourier transform of the S(Q). The total g(r) showed peaks at 1.46, 2.08, 2.48, 3.16 and 4.24 Armstrong. From intramolecular bond lengths of 1.46 Armstrong for Cl-O and 2.48 Armstrong for O-O, O-Cl-O bond angle was estimated to be 116.1 degrees. Peaks at 3.16 and 4.24 Armstrong in the total g(r) strongly indicate presence of specific intermolecular orientations of ClO 2 molecules that are distinct from those observed as a dimer in the solid phase ClO 2 . This view was further supported by molecular simulation using a reverse Monte Carlo method (RMC). (author)

Quantifying intermolecular interactions of ionic liquids using cohesive energy densities

Science.gov (United States)

2017-01-01

For ionic liquids (ILs), both the large number of possible cation + anion combinations and their ionic nature provide a unique challenge for understanding intermolecular interactions. Cohesive energy density, ced, is used to quantify the strength of intermolecular interactions for molecular liquids, and is determined using the enthalpy of vaporization. A critical analysis of the experimental challenges and data to obtain ced for ILs is provided. For ILs there are two methods to judge the strength of intermolecular interactions, due to the presence of multiple constituents in the vapour phase of ILs. Firstly, cedIP, where the ionic vapour constituent is neutral ion pairs, the major constituent of the IL vapour. Secondly, cedC+A, where the ionic vapour constituents are isolated ions. A cedIP dataset is presented for 64 ILs. For the first time an experimental cedC+A, a measure of the strength of the total intermolecular interaction for an IL, is presented. cedC+A is significantly larger for ILs than ced for most molecular liquids, reflecting the need to break all of the relatively strong electrostatic interactions present in ILs. However, the van der Waals interactions contribute significantly to IL volatility due to the very strong electrostatic interaction in the neutral ion pair ionic vapour. An excellent linear correlation is found between cedIP and the inverse of the molecular volume. A good linear correlation is found between IL cedIP and IL Gordon parameter (which are dependent primarily on surface tension). ced values obtained through indirect methods gave similar magnitude values to cedIP. These findings show that cedIP is very important for understanding IL intermolecular interactions, in spite of cedIP not being a measure of the total intermolecular interactions of an IL. In the outlook section, remaining challenges for understanding IL intermolecular interactions are outlined. PMID:29308254

Quantifying intermolecular interactions of ionic liquids using cohesive energy densities.

Science.gov (United States)

Lovelock, Kevin R J

2017-12-01

For ionic liquids (ILs), both the large number of possible cation + anion combinations and their ionic nature provide a unique challenge for understanding intermolecular interactions. Cohesive energy density, ced , is used to quantify the strength of intermolecular interactions for molecular liquids, and is determined using the enthalpy of vaporization. A critical analysis of the experimental challenges and data to obtain ced for ILs is provided. For ILs there are two methods to judge the strength of intermolecular interactions, due to the presence of multiple constituents in the vapour phase of ILs. Firstly, ced IP , where the ionic vapour constituent is neutral ion pairs, the major constituent of the IL vapour. Secondly, ced C+A , where the ionic vapour constituents are isolated ions. A ced IP dataset is presented for 64 ILs. For the first time an experimental ced C+A , a measure of the strength of the total intermolecular interaction for an IL, is presented. ced C+A is significantly larger for ILs than ced for most molecular liquids, reflecting the need to break all of the relatively strong electrostatic interactions present in ILs. However, the van der Waals interactions contribute significantly to IL volatility due to the very strong electrostatic interaction in the neutral ion pair ionic vapour. An excellent linear correlation is found between ced IP and the inverse of the molecular volume. A good linear correlation is found between IL ced IP and IL Gordon parameter (which are dependent primarily on surface tension). ced values obtained through indirect methods gave similar magnitude values to ced IP . These findings show that ced IP is very important for understanding IL intermolecular interactions, in spite of ced IP not being a measure of the total intermolecular interactions of an IL. In the outlook section, remaining challenges for understanding IL intermolecular interactions are outlined.

Intermolecular interactions between σ- and π-holes of bromopentafluorobenzene and pyridine: computational and experimental investigations.

Science.gov (United States)

Yang, Fang-Ling; Yang, Xing; Wu, Rui-Zhi; Yan, Chao-Xian; Yang, Fan; Ye, Weichun; Zhang, Liang-Wei; Zhou, Pan-Pan

2018-04-25

The characters of σ- and π-holes of bromopentafluorobenzene (C6F5Br) enable it to interact with an electron-rich atom or group like pyridine which possesses an electron lone-pair N atom and a π ring. Theoretical studies of intermolecular interactions between C6F5Br and C5H5N have been carried out at the M06-2X/aug-cc-pVDZ level without and with the counterpoise method, together with single point calculations at M06-2X/TZVP, wB97-XD/aug-cc-pVDZ and CCSD(T)/aug-cc-pVDZ levels. The σ- and π-holes of C6F5Br exhibiting positive electrostatic potentials make these sites favorably interact with the N atom and the π ring of C5H5N with negative electrostatic potentials, leading to five different dimers connected by a σ-holen bond, a σ-holeπ bond or a π-holeπ bond. Their geometrical structures, characteristics, nature and spectroscopy behaviors were systematically investigated. EDA analyses reveal that the driving forces in these dimers are different. NCI, QTAIM and NBO analyses confirm the existence of intermolecular interactions formed via σ- and π-holes of C6F5Br and the N atom and the π ring of C5H5N. The experimental IR and Raman spectra gave us important information about the formation of molecular complexes between C6F5Br and C5H5N. We expect that the results could provide valuable insights into the investigation of intermolecular interactions involving σ- and π-holes.

Proton tunnelling in intermolecular hydrogen bonds

Energy Technology Data Exchange (ETDEWEB)

Horsewill, A J [Nottingham Univ. (United Kingdom); Johnson, M R [Institut Max von Laue - Paul Langevin (ILL), 38 - Grenoble (France); Trommsdorff, H P [Grenoble-1 Univ., 38 (France)

1997-04-01

The wavefunctions of particles extend beyond the classically accessible regions of potential energy-surfaces (PES). A manifestation of this partial delocalization is the quantum-mechanical tunneling effect which enables a particle to escape from a metastable potential-well. Tunnelling is most important for the lightest atoms, so that the determination of its contribution to proton transfer, one of the most fundamental chemical reactions, is an important issue. QENS and NMR techniques have been employed to study the motion of protons in the hydrogen bond of benzoic-acid crystals, a system which has emerged as a particularly suitable model since proton transfer occurs in a near symmetric double-well potential. The influence of quantum tunnelling was revealed and investigated in these experiments. This work provides an experimental benchmark for theoretical descriptions of translational proton-tunnelling. (author). 7 refs.

The effect of strong intermolecular and chemical interactions on the compatibility of polymers

International Nuclear Information System (INIS)

Askadskii, Andrei A

1999-01-01

The data on compatibility and on the properties of polymer blends are generalised. The emphasis is placed on the formation of strong intermolecular interactions (dipole-dipole interaction and hydrogen bonding) between the components of blends, as well as on the chemical reactions between them. A criterion for the prediction of compatibility of polymers is described in detail. Different cases of compatibility are considered and the dependences of the glass transition temperatures on the composition of blends are analysed. The published data on the effect of strong intermolecular interactions between the blend components on the glass transition temperature are considered. The preparation of interpolymers is described whose macromolecules are composed of incompatible polymers, which leads to the so-called 'forced compatibility.' The bibliography includes 80 references.

Performance of Several Density Functional Theory Methods on Describing Hydrogen-Bond Interactions.

Science.gov (United States)

Rao, Li; Ke, Hongwei; Fu, Gang; Xu, Xin; Yan, Yijing

2009-01-13

We have investigated eleven density functionals, including LDA, PBE, mPWPW91, TPSS, B3LYP, X3LYP, PBE0, O3LYP, B97-1, MPW1K, and TPSSh, for their performances on describing hydrogen bond (HB) interactions. The emphasis has been laid not only on their abilities to calculate the intermolecular hydrogen bonding energies but also on their performances in predicting the relative energies of intermolecular H-bonded complexes and the conformer stabilities due to intramolecular hydrogen bondings. As compared to the best theoretical values, we found that although PBE and PBE0 gave the best estimation of HB strengths, they might fail to predict the correct order of relative HB energies, which might lead to a wrong prediction of the global minimum for different conformers. TPSS and TPSSh did not always improve over PBE and PBE0. B3LYP was found to underestimate the intermolecular HB strengths but was among the best performers in calculating the relative HB energies. We showed here that X3LYP and B97-1 were able to give good values for both absolute HB strengths and relative HB energies, making these functionals good candidates for HB description.

High strength films from oriented, hydrogen-bonded "graphamid" 2D polymer molecular ensembles.

Science.gov (United States)

Sandoz-Rosado, Emil; Beaudet, Todd D; Andzelm, Jan W; Wetzel, Eric D

2018-02-27

The linear polymer poly(p-phenylene terephthalamide), better known by its tradename Kevlar, is an icon of modern materials science due to its remarkable strength, stiffness, and environmental resistance. Here, we propose a new two-dimensional (2D) polymer, "graphamid", that closely resembles Kevlar in chemical structure, but is mechanically advantaged by virtue of its 2D structure. Using atomistic calculations, we show that graphamid comprises covalently-bonded sheets bridged by a high population of strong intermolecular hydrogen bonds. Molecular and micromechanical calculations predict that these strong intermolecular interactions allow stiff, high strength (6-8 GPa), and tough films from ensembles of finite graphamid molecules. In contrast, traditional 2D materials like graphene have weak intermolecular interactions, leading to ensembles of low strength (0.1-0.5 GPa) and brittle fracture behavior. These results suggest that hydrogen-bonded 2D polymers like graphamid would be transformative in enabling scalable, lightweight, high performance polymer films of unprecedented mechanical performance.

Hydrogen bonding analysis of hydroxyl groups in glucose aqueous solutions by a molecular dynamics simulation study

International Nuclear Information System (INIS)

Chen, Cong; Li, Wei Zhong; Song, Yong Chen; Weng, Lin Dong; Zhang, Ning

2012-01-01

Molecular dynamics simulations have been performed to investigate hydrogen bonding characteristics of hydroxyl groups in glucose aqueous solutions with different concentrations. The hydrogen bonding abilities and strength of different O and H atom types have been calculated and compared. The acceptor/donor efficiencies have been predicted and it has been found that: (1) O2-HO2 and O3-HO3 are more efficient intramolecular hydrogen bonding acceptors than donors; (2) O1-HO1, O4-HO4 and O6-HO6 are more efficient intramolecular hydrogen bonding donors than acceptors; (5) O1-HO1 and O6-HO6 are more efficient intermolecular hydrogen bonding acceptors than donors while hydroxyl groups O2-HO2 and O4-HO4 are more efficient intermolecular hydrogen bonding donors than acceptors. The hydrogen bonding abilities of hydroxyl groups revealed that: (1) the hydrogen bonding ability of OH2-H w is larger than that of hydroxyl groups in glucose; (2) among the hydroxyl groups in glucose, the hydrogen bonding ability of O6-HO6 is the largest and the hydrogen bonding ability of O4-HO4 is the smallest; (3) the intermolecular hydrogen bonding ability of O6-HO6 is the largest; (4) the order for intramolecular hydrogen bonding abilities (from large to small) is O2-HO2, O1-HO1, O3-HO3, O6-HO6 and O4-HO4

Hydrogen and dihydrogen bonding of transition metal hydrides

Energy Technology Data Exchange (ETDEWEB)

Jacobsen, Heiko [KemKom, Libellenweg 2, 25917 Leck, Nordfriesland (Germany)], E-mail: jacobsen@kemkom.com

2008-04-03

Intermolecular interactions between a prototypical transition metal hydride WH(CO){sub 2}NO(PH{sub 3}){sub 2} and a small proton donor H{sub 2}O have been studied using DFT methodology. The hydride, nitrosyl and carbonyl ligand have been considered as site of protonation. Further, DFT-D calculations in which empirical corrections for the dispersion energy are included, have been carried out. A variety of pure and hybrid density functionals (BP86, PW91, PBE, BLYP, OLYP, B3LYP, B1PW91, PBE0, X3LYP) have been considered, and our calculations indicate the PBE functional and its hybrid variation are well suited for the calculation of transition metal hydride hydrogen and dihydrogen bonding. Dispersive interactions make up for a sizeable portion of the intermolecular interaction, and amount to 20-30% of the bond energy and to 30-40% of the bond enthalpy. An energy decomposition analysis reveals that the H...H bond of transition metal hydrides contains both covalent and electrostatic contributions.

Observation of aggregation triggered by Resonance Energy Transfer (RET) induced intermolecular pairing force.

Science.gov (United States)

Pan, Xiaoyong; Wang, Weizhi; Ke, Lin; Zhang, Nan

2017-07-20

In this report, we showed the existence of RET induced intermolecular pairing force by comparing their fluorescence behaviors under room illumination vs standing in dark area for either PFluAnt solution or PFluAnt&PFOBT mixture. Their prominent emission attenuation under room illumination brought out the critical role of photo, i.e. RET induced intermolecular pairing force in induction of polymer aggregation. Constant UV-Vis absorption and fluorescence spectra in terms of both peak shapes and maximum wavelengths implied no chemical decomposition was involved. Recoverable fluorescence intensity, fluorescence lifetime as well as NMR spectra further exclude photo induced decomposition. The controllable on/off state of RET induced intermolecular pairing force was verified by the masking effect of outside PFluAnt solution which function as filter to block the excitation of inside PFluAnt and thus off the RET induced intermolecular pairing force. Theoretical calculation suggest that magnitude of RET induced intermolecular pairing force is on the same scale as that of van der Waals interaction. Although the absolute magnitude of RET induced intermolecular pairing force was not tunable, its effect can be magnified by intentionally turn it "on", which was achieved by irradiance with 5 W desk lamp in this report.

Effects of sodium salt types on the intermolecular interaction of sodium alginate/antarctic krill protein composite fibers.

Science.gov (United States)

Zhang, Rui; Guo, Jing; Liu, Yuanfa; Chen, Shuang; Zhang, Sen; Yu, Yue

2018-06-01

Sodium alginate (SA) and antarctic krill protein (AKP) were blended to fabricate the SA/AKP composite fibers by the conventional wet spinning method using 5% CaCl 2 as coagulation solution. The sodium salt was added to the SA/AKP solution to adjust the ionization degree and intermolecular interaction of composite system. The main purpose of this study is to investigate the influences of sodium salt types (NaCl, CH 3 COONa, Na 2 SO 4 ) on the intermolecular interaction of SA/AKP composite fibers. The intermolecular interaction, morphology, crystallinity, thermal stability and mechanical properties of SA/AKP composite fibers were analyzed by fourier transform infrared spectroscopy (FT-IR), scanning electron microscope (SEM), x-ray diffraction (XRD), thermogravimetric analysis (TGA). The results show that the types of sodium salt have obvious influences on the content of both β-sheet, intermolecular hydrogen bond, breaking strength and surface morphology in SA/AKP composite fibers, but have a negligible effect on the crystallinity and thermal stability. Copyright © 2018 Elsevier Ltd. All rights reserved.

The pseudohydrogen bond structures between 2-F-epoxy-butane and three kinds of bimolecular

International Nuclear Information System (INIS)

Liu Yanzhi; Yuan Kun; Lu Lingling; Zhu Yuancheng; Dong Xiaoning

2012-01-01

The weak intermolecular interactions between 2-F-epoxy-butane and Iminazole, Thiazole and Oxazole were theoretically discussed by using density functional B3LYP (Becke, three-parameter, Lee- Yang-Parr)/6-311++G ** and HF (Hartree Fock)/6-311++G ** methods. The results showed that both the N…H conventional hydrogen bond and C-F…H-C pseudohydrogen bond (PHB) structures are coexisting in the three complexes. The weak intermolecular interactions energies indicate the relative stabilities of the three complexes are proportionable. The calculated results showed that the stretch vibrational frequency of C-H bond (electronic acceptor) presents blue shift, but that of C-F bond, which is intensely related to F group (electronic donor), presents red shift. Electron density topological properties demonstrates that the covalent and ionic characteristics of the C-F…H-C pseudohydrogen bond are proportional to that of convention hydrogen bond. (authors)

Theoretical study of hydrogen bond interactions of fluvastatin with ι-carrageenan and λ-carrageenan.

Science.gov (United States)

Papadopoulos, Anastasios G; Sigalas, Michael P

2011-07-01

The binding of the reductase inhibitor drug fluvastatin, hydroxy-3-methylglutaryl coenzyme A, with the hydrophilic ι- or λ-carrageenan polymers, serving as potential controllers of the drug's release rate, have been studied at the density functional level of theory with the B3LYP exchange correlation functional. Three low energy conformers of fluvastatin have been calculated. The vibrational spectroscopic properties calculated for the most stable conformer were in satisfactory agreement with the experimental data. A series of hydrogen bonded complexes of the most stable conformer of fluvastatin anion with low molecular weight models of the polymers have been fully optimized. In almost all, intermolecular H-bonds are formed between the sulfate groups of ι- or λ-carrageenan and fluvastatin's hydroxyls, resulting in a red shift of the fluvastatin's O - H stretching vibrations. Cooperative intramolecular H-bonds within fluvastatin or ι-, λ-carrageenan are also present. The BSSE and ZPE corrected interaction energies were estimated in the range 281-318 kJ mol⁻¹ for ι-carrageenan - fluvastatin and 145-200 kJ mol⁻¹ for λ-carrageenan - fluvastatin complexes. The electron density (ρ (bcp)) and Laplacian (∇²ρ (bcp)) properties at critical points of the intermolecular hydrogen bonds, estimated by AIM (atoms in molecules) calculations, have a low and positive character (∇²ρ(bcp) > 0), consistent with the electrostatic character of the hydrogen bonds. The structural and energetic data observed, as well as the extent of the red shift of the fluvastatin's O - H stretching vibrations upon complex formation and the properties of electron density show a stronger binding of fluvastatin to ι- than to λ-carrageenan.

Bond-diluted interface between semi-infinite Potts bulks: criticality

International Nuclear Information System (INIS)

Cavalcanti, S.B.; Tsallis, C.

1986-01-01

Within a real space renormalisation group framework, we discuss the criticality of a system constituted by two (not necessarily equal) semi-infinite ferromagnetic q-state Potts bulks separated by an interface. This interface is a bond-diluted Potts ferromagnet with a coupling constant which is in general different from those of both bulks. The phase diagram presents four physically different phases, namely the paramagnetic one, and the surface, single bulk and double bulk ferromagnetic ones. These various phases determine a multicritical surface which contains a higher order multicritical line. The critical concentration P c that is the concentration of the interface bonds which surface magnetic ordering is possible even if the bulks are disordered. An interesting feature comes out which is that P c varies continuously with J 1 /J s and J 2 /J s . The standard two-dimensional percolation concentration is recovered for J 1 =J 2 =0. (author) [pt

Connecting Protein Structure to Intermolecular Interactions: A Computer Modeling Laboratory

Science.gov (United States)

Abualia, Mohammed; Schroeder, Lianne; Garcia, Megan; Daubenmire, Patrick L.; Wink, Donald J.; Clark, Ginevra A.

2016-01-01

An understanding of protein folding relies on a solid foundation of a number of critical chemical concepts, such as molecular structure, intra-/intermolecular interactions, and relating structure to function. Recent reports show that students struggle on all levels to achieve these understandings and use them in meaningful ways. Further, several…

Room temperature ionic liquids: A simple model. Effect of chain length and size of intermolecular potential on critical temperature.

Science.gov (United States)

Chapela, Gustavo A; Guzmán, Orlando; Díaz-Herrera, Enrique; del Río, Fernando

2015-04-21

A model of a room temperature ionic liquid can be represented as an ion attached to an aliphatic chain mixed with a counter ion. The simple model used in this work is based on a short rigid tangent square well chain with an ion, represented by a hard sphere interacting with a Yukawa potential at the head of the chain, mixed with a counter ion represented as well by a hard sphere interacting with a Yukawa potential of the opposite sign. The length of the chain and the depth of the intermolecular forces are investigated in order to understand which of these factors are responsible for the lowering of the critical temperature. It is the large difference between the ionic and the dispersion potentials which explains this lowering of the critical temperature. Calculation of liquid-vapor equilibrium orthobaric curves is used to estimate the critical points of the model. Vapor pressures are used to obtain an estimate of the triple point of the different models in order to calculate the span of temperatures where they remain a liquid. Surface tensions and interfacial thicknesses are also reported.

Improving Erosion Resistance of Plasma-Sprayed Ceramic Coatings by Elevating the Deposition Temperature Based on the Critical Bonding Temperature

Science.gov (United States)

Yao, Shu-Wei; Yang, Guan-Jun; Li, Cheng-Xin; Li, Chang-Jiu

2018-01-01

Interlamellar bonding within plasma-sprayed coatings is one of the most important factors dominating the properties and performance of coatings. The interface bonding between lamellae significantly influences the erosion behavior of plasma-sprayed ceramic coatings. In this study, TiO2 and Al2O3 coatings with different microstructures were deposited at different deposition temperatures based on the critical bonding temperature concept. The erosion behavior of ceramic coatings was investigated. It was revealed that the coatings prepared at room temperature exhibit a typical lamellar structure with numerous unbonded interfaces, whereas the coatings deposited at the temperature above the critical bonding temperature present a dense structure with well-bonded interfaces. The erosion rate decreases sharply with the improvement of interlamellar bonding when the deposition temperature increases to the critical bonding temperature. In addition, the erosion mechanisms of ceramic coatings were examined. The unbonded interfaces in the conventional coatings act as pre-cracks accelerating the erosion of coatings. Thus, controlling interlamellar bonding formation based on the critical bonding temperature is an effective approach to improve the erosion resistance of plasma-sprayed ceramic coatings.

Percolation with first-and-second neighbour bonds: a renormalization-group calculation of critical exponents

International Nuclear Information System (INIS)

Riera, R.; Oliveira, P.M.C. de; Chaves, C.M.G.F.; Queiroz, S.L.A. de.

1980-04-01

A real-space renormalization group approach for the bond percolation problem in a square lattice with first- and second- neighbour bonds is proposed. The respective probabilities are treated, as independent variables. Two types of cells are constructed. In one of them the lattice is considered as two interpenetrating sublattices, first-neighbour bonds playing the role of intersublattice links. This allows the calculation of both critical exponents ν and γ, without resorting to any external field. Values found for the critical indices are in good agreement with data available in the literature. The phase diagram in parameter space is also obtained in each case. (Author) [pt

A chemical approach for site-specific identification of NMR signals from protein side-chain NH3+ groups forming intermolecular ion pairs in protein–nucleic acid complexes

International Nuclear Information System (INIS)

Anderson, Kurtis M.; Nguyen, Dan; Esadze, Alexandre; Zandrashvili, Levani; Gorenstein, David G.; Iwahara, Junji

2015-01-01

Protein–nucleic acid interactions involve intermolecular ion pairs of protein side-chain and DNA or RNA phosphate groups. Using three protein–DNA complexes, we demonstrate that site-specific oxygen-to-sulfur substitution in phosphate groups allows for identification of NMR signals from the protein side-chain NH 3 + groups forming the intermolecular ion pairs. A characteristic change in their 1 H and 15 N resonances upon this modification (i.e., substitution of phosphate to phosphorodithioate) can represent a signature of an intermolecular ion pair. Hydrogen-bond scalar coupling between protein side-chain 15 N and DNA phosphorodithiaote 31 P nuclei provides direct confirmation of the intermolecular ion pair. The same approach is likely applicable to protein–RNA complexes as well

Stability and Reactivity of Cyclometallated Naphthylamine Complexes in Pd-C Bond Insertion Reactions with Coordinated Alkynylphosphanes

KAUST Repository

Chen, Shuli; Chiew, Jun Xuan; Pullarkat, Sumod A.; Li, Yongxin; Leung, Pak Hing

2013-01-01

, whereas the P→Pd bond is labile. Upon heating of these phosphane complexes at 70 °C, one of the C≡C bonds in the coordinated PhP(C≡CPh)2 was activated towards an intermolecular Pd-C bond insertion reaction with an external ortho-palladated naphthylamine

Modeling Adsorption-Desorption Processes at the Intermolecular Interactions Level

Science.gov (United States)

Varfolomeeva, Vera V.; Terentev, Alexey V.

2018-01-01

Modeling of the surface adsorption and desorption processes, as well as the diffusion, are of considerable interest for the physical phenomenon under study in ground tests conditions. When imitating physical processes and phenomena, it is important to choose the correct parameters to describe the adsorption of gases and the formation of films on the structural materials surface. In the present research the adsorption-desorption processes on the gas-solid interface are modeled with allowance for diffusion. Approaches are proposed to describe the adsorbate distribution on the solid body surface at the intermolecular interactions level. The potentials of the intermolecular interaction of water-water, water-methane and methane-methane were used to adequately modeling the real physical and chemical processes. The energies calculated by the B3LYP/aug-cc-pVDZ method. Computational algorithms for determining the average molecule area in a dense monolayer, are considered here. Differences in modeling approaches are also given: that of the proposed in this work and the previously approved probabilistic cellular automaton (PCA) method. It has been shown that the main difference is due to certain limitations of the PCA method. The importance of accounting the intermolecular interactions via hydrogen bonding has been indicated. Further development of the adsorption-desorption processes modeling will allow to find the conditions for of surface processes regulation by means of quantity adsorbed molecules control. The proposed approach to representing the molecular system significantly shortens the calculation time in comparison with the use of atom-atom potentials. In the future, this will allow to modeling the multilayer adsorption at a reasonable computational cost.

Intermolecular cope-type hydroamination of alkenes and alkynes using hydroxylamines.

Science.gov (United States)

Moran, Joseph; Gorelsky, Serge I; Dimitrijevic, Elena; Lebrun, Marie-Eve; Bédard, Anne-Catherine; Séguin, Catherine; Beauchemin, André M

2008-12-31

The development of the Cope-type hydroamination as a method for the metal- and acid-free intermolecular hydroamination of hydroxylamines with alkenes and alkynes is described. Aqueous hydroxylamine reacts efficiently with alkynes in a Markovnikov fashion to give oximes and with strained alkenes to give N-alkylhydroxylamines, while unstrained alkenes are more challenging. N-Alkylhydroxylamines also display similar reactivity with strained alkenes and give modest to good yields with vinylarenes. Electron-rich vinylarenes lead to branched products while electron-deficient vinylarenes give linear products. A beneficial additive effect is observed with sodium cyanoborohydride, the extent of which is dependent on the structure of the hydroxylamine. The reaction conditions are found to be compatible with common protecting groups, free OH and NH bonds, as well as bromoarenes. Both experimental and theoretical results suggest the proton transfer step of the N-oxide intermediate is of vital importance in the intermolecular reactions of alkenes. Details are disclosed concerning optimization, reaction scope, limitations, and theoretical analysis by DFT, which includes a detailed molecular orbital description for the concerted hydroamination process and an exhaustive set of calculated potential energy surfaces for the reactions of various alkenes, alkynes, and hydroxylamines.

Desensitization of metastable intermolecular composites

Science.gov (United States)

Busse, James R [South Fork, CO; Dye, Robert C [Los Alamos, NM; Foley, Timothy J [Los Alamos, NM; Higa, Kelvin T [Ridgecrest, CA; Jorgensen, Betty S [Jemez Springs, NM; Sanders, Victor E [White Rock, NM; Son, Steven F [Los Alamos, NM

2011-04-26

A method to substantially desensitize a metastable intermolecular composite material to electrostatic discharge and friction comprising mixing the composite material with an organic diluent and removing enough organic diluent from the mixture to form a mixture with a substantially putty-like consistency, as well as a concomitant method of recovering the metastable intermolecular composite material.

Direct measurements of intermolecular forces by chemical force microscopy

Science.gov (United States)

Vezenov, Dmitri Vitalievich

1999-12-01

Detailed description of intermolecular forces is key to understanding a wide range of phenomena from molecular recognition to materials failure. The unique features of atomic force microscopy (AFM) to make point contact force measurements with ultra high sensitivity and to generate spatial maps of surface topography and forces have been extended to include measurements between well-defined organic molecular groups. Chemical modification of AFM probes with self-assembled monolayers (SAMs) was used to make them sensitive to specific molecular interactions. This novel chemical force microscopy (CFM) technique was used to probe forces between different molecular groups in a range of environments (vacuum, organic liquids and aqueous solutions); measure surface energetics on a nanometer scale; determine pK values of the surface acid and base groups; measure forces to stretch and unbind a short synthetic DNA duplex and map the spatial distribution of specific functional groups and their ionization state. Studies of adhesion forces demonstrated the important contribution of hydrogen bonding to interactions between simple organic functionalities. The chemical identity of the tip and substrate surfaces as well as the medium had a dramatic effect on adhesion between model monolayers. A direct correlation between surface free energy and adhesion forces was established. The adhesion between epoxy polymer and model mixed SAMs varied with the amount of hydrogen bonding component in the monolayers. A consistent interpretation of CFM measurements in polar solvents was provided by contact mechanics models and intermolecular force components theory. Forces between tips and surfaces functionalized with SAMs terminating in acid or base groups depended on their ionization state. A novel method of force titration was introduced for highly local characterization of the pK's of surface functional groups. The pH-dependent changes in friction forces were exploited to map spatially the

Critical properties of the D=3 bond-mixed quantum Heisenberg ferromagnet

International Nuclear Information System (INIS)

Tsallis, C.; Centro Brasileiro de Pesquisas Fisicas, Rio de Janeiro); Stinchcombe, R.B.; Buck, B.

1983-01-01

Within a Migdal-Kadanoff-like real-space renormalisation group procedure critical properties of the quenched bond-mixed spin 1/2 Heisenberg ferromagnet in simple cubic lattice are treated. It is verified that it is possible, within a very simple framework, to obtain quite reliable results for the critical temperatures. In addition to that, a general method for renormalising arbitrary clusters of Heisenberg-coupled spins 1/2 is outlined. (Author) [pt

A chemical approach for site-specific identification of NMR signals from protein side-chain NH{sub 3}{sup +} groups forming intermolecular ion pairs in protein–nucleic acid complexes

Energy Technology Data Exchange (ETDEWEB)

Anderson, Kurtis M. [University of Texas Health Science Center at Houston, Department of NanoMedicine and Biomedical Engineering and Institute of Molecular Medicine (United States); Nguyen, Dan; Esadze, Alexandre; Zandrashvili, Levani [University of Texas Medical Branch, Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics (United States); Gorenstein, David G. [University of Texas Health Science Center at Houston, Department of NanoMedicine and Biomedical Engineering and Institute of Molecular Medicine (United States); Iwahara, Junji, E-mail: juiwahar@utmb.edu, E-mail: j.iwahara@utmb.edu [University of Texas Medical Branch, Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics (United States)

2015-05-15

Protein–nucleic acid interactions involve intermolecular ion pairs of protein side-chain and DNA or RNA phosphate groups. Using three protein–DNA complexes, we demonstrate that site-specific oxygen-to-sulfur substitution in phosphate groups allows for identification of NMR signals from the protein side-chain NH{sub 3}{sup +} groups forming the intermolecular ion pairs. A characteristic change in their {sup 1}H and {sup 15}N resonances upon this modification (i.e., substitution of phosphate to phosphorodithioate) can represent a signature of an intermolecular ion pair. Hydrogen-bond scalar coupling between protein side-chain {sup 15}N and DNA phosphorodithiaote {sup 31}P nuclei provides direct confirmation of the intermolecular ion pair. The same approach is likely applicable to protein–RNA complexes as well.

Hydrogen-bonded structure in highly concentrated aqueous LiBr solutions

International Nuclear Information System (INIS)

Imano, Masahiro; Kameda, Yasuo; Usuki, Takeshi; Uemura, Osamu

2001-01-01

Neutron diffraction measurements were carried out for H/D isotopically substituted aqueous 10, 25 and 33 mol% LiBr solutions in order to obtain structural information on the intermolecular hydrogen bonds among water molecules in highly concentrated aqueous solutions. Observed scattering cross sections for D 2 O (99.9 % D), 0 H 2 O(35.9 % D) and 0-2 H 2 O(68.0 % D) solutions were combined to deduce partial structure factors, a HH (Q), a XH (Q) and a XX (Q) (X: O, Br and Li). The least squares fitting analysis was applied to the observed partial structure factors to determine the nearest neighbor interatomic distance, root-mean-square amplitude and coordination number. Intermolecular distances, r OH =1.91(1) A, r HH =2.38(1) A and r OO =3.02(1) A, between the nearest neighbor water molecules, were obtained for the 10 mol% LiBr solution. On the other hand, the intermolecular O···H interaction was found to almost disappear in concentrated 25 and 33 mol% LiBr solutions. The result implies that the hydrogen-bonded network is completely broken in highly concentrated aqueous LiBr solutions. (author)

High-energy, stable and recycled molecular solar thermal storage materials using AZO/graphene hybrids by optimizing hydrogen bonds.

Science.gov (United States)

Luo, Wen; Feng, Yiyu; Qin, Chengqun; Li, Man; Li, Shipei; Cao, Chen; Long, Peng; Liu, Enzuo; Hu, Wenping; Yoshino, Katsumi; Feng, Wei

2015-10-21

An important method for establishing a high-energy, stable and recycled molecular solar heat system is by designing and preparing novel photo-isomerizable molecules with a high enthalpy and a long thermal life by controlling molecular interactions. A meta- and ortho-bis-substituted azobenzene chromophore (AZO) is covalently grafted onto reduced graphene oxide (RGO) for solar thermal storage materials. High grafting degree and close-packed molecules enable intermolecular hydrogen bonds (H-bonds) for both trans-(E) and cis-(Z) isomers of AZO on the surface of nanosheets, resulting in a dramatic increase in enthalpy and lifetime. The metastable Z-form of AZO on RGO is thermally stabilized with a half-life of 52 days by steric hindrance and intermolecular H-bonds calculated using density functional theory (DFT). The AZO-RGO fuel shows a high storage capacity of 138 Wh kg(-1) by optimizing intermolecular H-bonds with a good cycling stability for 50 cycles induced by visible light at 520 nm. Our work opens up a new method for making advanced molecular solar thermal storage materials by tuning molecular interactions on a nano-template.

Characterizing the Polymer:Fullerene Intermolecular Interactions

KAUST Repository

Sweetnam, Sean

2016-02-02

Polymer:fullerene solar cells depend heavily on the electronic coupling of the polymer and fullerene molecular species from which they are composed. The intermolecular interaction between the polymer and fullerene tends to be strong in efficient photovoltaic systems, as evidenced by efficient charge transfer processes and by large changes in the energetics of the polymer and fullerene when they are molecularly mixed. Despite the clear presence of these strong intermolecular interactions between the polymer and fullerene, there is not a consensus on the nature of these interactions. In this work, we use a combination of Raman spectroscopy, charge transfer state absorption, and density functional theory calculations to show that the intermolecular interactions do not appear to be caused by ground state charge transfer between the polymer and fullerene. We conclude that these intermolecular interactions are primarily van der Waals in nature. © 2016 American Chemical Society.

Intermolecular spectroscopy

International Nuclear Information System (INIS)

Gelbart, W.M.

1980-01-01

In this article some of the theoretical background is presented for the following papers on 'Intermolecular Spectroscopy and Dynamical Properties of Dense Systems'. In Section 1 we outline a simple semi-classical description of the interaction between optical radiation and matter. The motion of a many-body polarizability is introduced; limiting forms of this complicated quantity lead to the familiar cases of light scattering spectra. In Section 2 we consider the linear response approximation, and the equation of motion for the many-body density matrix is solved to first order in the matter-radiation interaction. The often quoted fluctuation-dissipation theorem and the time-dependent, equilibrium correlation functions are discussed. Section 3 treats the problem of the local field. In Section 4 we consider the special case of collision-induced light scattering by atomic fluids in the low-density limit. This allows us to focus on determining the interaction polarizability for simple gases. Finally, in Section 5 we distinguish between collision-induced and multiple light scattering, and discuss the double-light-scattering analyses which provide new information about critical and thermodynamically unstable fluids. (KBE)

Intermolecular and surface forces

CERN Document Server

Israelachvili, Jacob N

2011-01-01

This reference describes the role of various intermolecular and interparticle forces in determining the properties of simple systems such as gases, liquids and solids, with a special focus on more complex colloidal, polymeric and biological systems. The book provides a thorough foundation in theories and concepts of intermolecular forces, allowing researchers and students to recognize which forces are important in any particular system, as well as how to control these forces. This third edition is expanded into three sections and contains five new chapters over the previous edition.· starts fr

Quantitative analysis of intermolecular interactions in orthorhombic rubrene

Directory of Open Access Journals (Sweden)

Venkatesha R. Hathwar

2015-09-01

Full Text Available Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically, the presence of Cπ...Cπ interactions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. The quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations.

Renormalization group critical frontier of the three-dimensional bond-dilute Ising ferromagnet

International Nuclear Information System (INIS)

Chao, N.-C.; Schwaccheim, G.; Tsallis, C.

1981-01-01

The critical frontier (as well as the thermal type critical exponents) associated to the quenched bond-dilute spin - 1/2 Ising ferromagnet in the simple cubic lattice is approximately calculated within a real space renormalization group framework in two different versions. Both lead to qualitatively satisfactory critical frontiers, although one of them provides an unphysical fixed point (which seem to be related to the three-dimensionality of the system) besides the expected pure ones; its effects tend to disappear for increasingly large clusters. Through an extrapolation procedure the (unknown) critical frontier is approximately located. (Author) [pt

Photophysics of Curcumin excited state in toluene-polar solvent mixtures: Role of H-bonding properties of the polar solvent

Energy Technology Data Exchange (ETDEWEB)

Saini, R.K.; Das, K., E-mail: kaustuv@rrcat.gov.in

2014-01-15

Excited state dynamics of Curcumin in binary solvent mixtures of toluene and polar H-bonding solvents were compared by using an instrument endowed with 40 ps time resolution. The solvation time constant of Curcumin increases significantly (and can therefore be measured) in polar solvents which have, either, both H-bond donating and accepting ability, or, only H-bond donating ability. These results suggest that the rate limiting step in the excited state dynamics of the pigment might be the formation and reorganization of the intermolecular H-bonding between the keto group of the pigment and the H-bond donating moieties of the polar solvent. -- Highlights: • Excited state dynamics of Curcumin in a binary solvent mixture of toluene and three polar H-bonding solvents were compared. • The solvation time constant increases significantly with polar solvents having, H-bond donating and accepting, or, H-bond donating ability. • Observed results suggest that H-bonding property of polar solvent plays an important role in the excited state dynamics. • Intermolecular H-bonding between the keto group of the pigment and polar solvent may be the rate limiting step.

Photophysics of Curcumin excited state in toluene-polar solvent mixtures: Role of H-bonding properties of the polar solvent

International Nuclear Information System (INIS)

Saini, R.K.; Das, K.

2014-01-01

Excited state dynamics of Curcumin in binary solvent mixtures of toluene and polar H-bonding solvents were compared by using an instrument endowed with 40 ps time resolution. The solvation time constant of Curcumin increases significantly (and can therefore be measured) in polar solvents which have, either, both H-bond donating and accepting ability, or, only H-bond donating ability. These results suggest that the rate limiting step in the excited state dynamics of the pigment might be the formation and reorganization of the intermolecular H-bonding between the keto group of the pigment and the H-bond donating moieties of the polar solvent. -- Highlights: • Excited state dynamics of Curcumin in a binary solvent mixture of toluene and three polar H-bonding solvents were compared. • The solvation time constant increases significantly with polar solvents having, H-bond donating and accepting, or, H-bond donating ability. • Observed results suggest that H-bonding property of polar solvent plays an important role in the excited state dynamics. • Intermolecular H-bonding between the keto group of the pigment and polar solvent may be the rate limiting step

Thz Spectroscopy and DFT Modeling of Intermolecular Vibrations in Hydrophobic Amino Acids

Science.gov (United States)

Williams, michael R. C.; Aschaffenburg, Daniel J.; Schmuttenmaer, Charles A.

2013-06-01

Vibrations that involve intermolecular displacements occur in molecular crystals at frequencies in the 0.5-5 THz range (˜15-165 cm^{-1}), and these motions are direct indicators of the interaction potential between the molecules. The intermolecular potential energy surface of crystalline hydrophobic amino acids is inherently interesting simply because of the wide variety of forces (electrostatic, dipole-dipole, hydrogen-bonding, van der Waals) that are present. Furthermore, an understanding of these particular interactions is immediately relevant to important topics like protein conformation and pharmaceutical polymorphism. We measured the low-frequency absorption spectra of several polycrystalline hydrophobic amino acids using THz time-domain spectroscopy, and in addition we carried out DFT calculations using periodic boundary conditions and an exchange-correlation functional that accounts for van der Waals dispersion forces. We chose to investigate a series of similar amino acids with closely analogous unit cells (leucine, isoleucine, and allo-isoleucine, in racemic or pseudo-racemic mixtures). This allows us to consider trends in the vibrational spectra as a function of small changes in molecular arrangement and/or crystal geometry. In this way, we gain confidence that peak assignments are not based on serendipitous similarities between calculated and observed features.

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

Science.gov (United States)

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.

The influence of large-amplitude librational motion on the hydrogen bond energy for alcohol–water complexes

DEFF Research Database (Denmark)

Andersen, Jonas; Heimdal, J.; Larsen, René Wugt

2015-01-01

is a superior hydrogen bond acceptor. The class of large-amplitude donor OH librational motion is shown to account for up to 5.1 kJ mol-1 of the destabilizing change of vibrational zero-point energy upon intermolecular OH...O hydrogen bond formation. The experimental findings are supported by complementary...

Concentration-dependent multiple chirality transition in halogen-bond-driven 2D self-assembly process

Science.gov (United States)

Miao, Xinrui; Li, Jinxing; Zha, Bao; Miao, Kai; Dong, Meiqiu; Wu, Juntian; Deng, Wenli

2018-03-01

The concentration-dependent self-assembly of iodine substituted thienophenanthrene derivative (5,10-DITD) is investigated at the 1-octanic acid/graphite interface using scanning tunneling microscopy. Three kinds of chiral arrangement and transition of 2D molecular assembly mainly driven by halogen bonding is clearly revealed. At high concentration the molecules self-assembled into a honeycomb-like chiral network. Except for the interchain van der Waals forces, this pattern is stabilized by intermolecular continuous Cdbnd O⋯I⋯S halogen bonds in each zigzag line. At moderate concentration, a chiral kite-like nanoarchitecture are observed, in which the Cdbnd O⋯I⋯S and I⋯Odbnd C halogen bonds, along with the molecule-solvent Cdbnd O⋯I⋯H halogen bonds are the dominated forces to determine the structural formation. At low concentration, the molecules form a chiral cyclic network resulting from the solvent coadsorption mainly by molecule-molecule Cdbnd O⋯I⋯S halogen bonds and molecule-solvent Cdbnd O⋯I⋯H halogen bonds. The density of molecular packing becomes lower with the decreasing of the solution concentration. The solution-concentration dependent self-assembly of thienophenanthrene derivative with iodine and ester chain moieties reveals that the type of intermolecular halogen bond and the number of the co-adsorbing 1-octanic acids by molecule-solvent Cdbnd O⋯I⋯H halogen bonds determine the formation and transformation of chirality. This research emphasizes the role of different types of halogen (I) bonds in the controllable supramolecular structures and provides an approach for the fabrication of chirality.

Near-infrared analysis of hydrogen-bonding in glass- and rubber-state amorphous saccharide solids.

Science.gov (United States)

Izutsu, Ken-ichi; Hiyama, Yukio; Yomota, Chikako; Kawanishi, Toru

2009-01-01

Near-infrared (NIR) spectroscopic analysis of noncrystalline polyols and saccharides (e.g., glycerol, sorbitol, maltitol, glucose, sucrose, maltose) was performed at different temperatures (30-80 degrees C) to elucidate the effect of glass transition on molecular interaction. Transmission NIR spectra (4,000-12,000 cm(-1)) of the liquids and cooled-melt amorphous solids showed broad absorption bands that indicate random configuration of molecules. Heating of the samples decreased an intermolecular hydrogen-bonding OH vibration band intensity (6,200-6,500 cm(-1)) with a concomitant increase in a free and intramolecular hydrogen-bonding OH group band (6,600-7,100 cm(-1)). Large reduction of the intermolecular hydrogen-bonding band intensity at temperatures above the glass transition (T(g)) of the individual solids should explain the higher molecular mobility and lower viscosity in the rubber state. Mixing of the polyols with a high T(g) saccharide (maltose) or an inorganic salt (sodium tetraborate) shifted both the glass transition and the inflection point of the hydrogen-bonding band intensity to higher temperatures. The implications of these results for pharmaceutical formulation design and process monitoring (PAT) are discussed.

Desensitization and recovery of metastable intermolecular composites

Science.gov (United States)

Busse, James R [South Fork, CO; Dye, Robert C [Los Alamos, NM; Foley, Timothy J [Los Alamos, NM; Higa, Kelvin T [Ridgecrest, CA; Jorgensen, Betty S [Jemez Springs, NM; Sanders, Victor E [White Rock, NM; Son, Steven F [Los Alamos, NM

2010-09-07

A method to substantially desensitize a metastable intermolecular composite material to electrostatic discharge and friction comprising mixing the composite material with an organic diluent and removing enough organic diluent from the mixture to form a mixture with a substantially putty-like consistency, as well as a concomitant method of recovering the metastable intermolecular composite material.

Scaling of the critical free length for progressive unfolding of self-bonded graphene

Energy Technology Data Exchange (ETDEWEB)

Kwan, Kenny; Cranford, Steven W., E-mail: s.cranford@neu.edu [Laboratory of Nanotechnology in Civil Engineering (NICE), Department of Civil and Environmental Engineering, Northeastern University, 400 Snell Engineering, 360 Huntington Avenue, Boston, Massachusetts 02115 (United States)

2014-05-19

Like filled pasta, rolled or folded graphene can form a large nanocapsule surrounding a hollow interior. Use as a molecular carrier, however, requires understanding of the opening of such vessels. Here, we investigate a monolayer sheet of graphene as a theoretical trial platform for such a nanocapsule. The graphene is bonded to itself via aligned disulfide (S-S) bonds. Through theoretical analysis and atomistic modeling, we probe the critical nonbonded length (free length, L{sub crit}) that induces fracture-like progressive unfolding as a function of folding radius (R{sub i}). We show a clear linear scaling relationship between the length and radius, which can be used to determine the necessary bond density to predict mechanical opening/closing. However, stochastic dissipated energy limits any exact elastic formulation, and the required energy far exceeds the dissociation energy of the S-S bond. We account for the necessary dissipated kinetic energy through a simple scaling factor (Ω), which agrees well with computational results.

Competition between weak OH···π and CH··O hydrogen bonds: THz spectroscopy of the C2H2—H2O and C2H4—H2O complexes

DEFF Research Database (Denmark)

Andersen, Jonas; Heimdal, Jimmy; Nelander, B.

2017-01-01

an intermolecular CH⋯O hydrogen-bonded configuration of C2v symmetry with the H2O subunit acting as the hydrogen bond acceptor. The observation and assignment of two large-amplitude donor OH librational modes of the C2H4—H2O complex at 255.0 and 187.5 cm−1, respectively, confirms an intermolecular OH⋯π hydrogen...

Crystal structures and intermolecular interactions of two novel antioxidant triazolyl-benzimidazole compounds

International Nuclear Information System (INIS)

Karayel, A.; Özbey, S.; Ayhan-Kılcıgil, G.; Kuş, C.

2015-01-01

The crystal structures of 5-(2-(p-chlorophenylbenzimidazol-1-yl-methyl)-4-(3-fluorophenyl)-2, 4-dihydro-[1,2,4]-triazole-3-thione (G6C) and 5-(2-(p-chlorophenylbenzimidazol-1-yl-methyl)-4-(2-methylphenyl)-2, 4-dihydro-[1,2,4]-triazole-3-thione (G4C) have been determined by single-crystal X-ray diffraction. Benzimidazole ring systems in both molecules are planar. The triazole part is almost perpendicular to the phenyl and the benzimidazole parts of the molecules in order to avoid steric interactions between the rings. The crystal structures are stabilized by intermolecular hydrogen bonds between the amino group of the triazole and the nitrogen atom of benzimidazole of a neighboring molecule

The structure of betaxolol studied by infrared spectroscopy and natural bond orbital theory.

Science.gov (United States)

Canotilho, João; Castro, Ricardo A E

2010-08-01

Betaxolol is a selective beta(1) receptor blocker used in the treatment of hypertension and glaucoma. A study of the betaxolol structure based on infrared spectroscopy and natural bond orbital (NBO) theory is the main aim of the present research. FTIR spectra of the solid betaxolol were recorded in the region from 4000 to 400cm(-1), in the temperature range between 25 and -170 degrees C. For spectral interpretation, spectrum of the deuterated betaxolol and the theoretical vibrational spectra of the conformer present in the solid obtained at the B3LYP/6-31G* level of theory, were used. Further insight into the structure was provided by natural bond orbital theory. NBO analysis of the conformer, before and after optimization, was carried out at the same level of theory referred above. Vibrational modes involved in hydrogen bond in the stretching and bending region were used in the estimation of the enthalpy using empirical correlations between enthalpy and the frequency shift that occurs as a result of the establishment of intermolecular hydrogen bonds. A detailed study of the structure of betaxolol and of its intermolecular interactions was obtained from the combination spectroscopy and NBO theory. Copyright 2010 Elsevier B.V. All rights reserved.

Using corresponding state theory to obtain intermolecular potentials to calculate pure liquid shock Hugoniots

Energy Technology Data Exchange (ETDEWEB)

Hobbs, M.L.

1997-12-01

Determination of product species, equations-of-state (EOS) and thermochemical properties of high explosives and pyrotechnics remains a major unsolved problem. Although, empirical EOS models may be calibrated to replicate detonation conditions within experimental variability (5--10%), different states, e.g. expansion, may produce significant discrepancy with data if the basic form of the EOS model is incorrect. A more physically realistic EOS model based on intermolecular potentials, such as the Jacobs Cowperthwaite Zwisler (JCZ3) EOS, is needed to predict detonation states as well as expanded states. Predictive capability for any EOS requires a large species data base composed of a wide variety of elements. Unfortunately, only 20 species have known JCZ3 molecular force constants. Of these 20 species, only 10 have been adequately compared to experimental data such as molecular scattering or shock Hugoniot data. Since data in the strongly repulsive region of the molecular potential is limited, alternative methods must be found to deduce force constants for a larger number of species. The objective of the present study is to determine JCZ3 product species force constants by using a corresponding states theory. Intermolecular potential parameters were obtained for a variety of gas species using a simple corresponding states technique with critical volume and critical temperature. A more complex, four parameter corresponding state method with shape and polarity corrections was also used to obtain intermolecular potential parameters. Both corresponding state methods were used to predict shock Hugoniot data obtained from pure liquids. The simple corresponding state method is shown to give adequate agreement with shock Hugoniot data.

Recent advances in C(sp3–H bond functionalization via metal–carbene insertions

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Bo Wang

2016-04-01

Full Text Available The recent development of intermolecular C–H insertion in the application of C(sp3–H bond functionalizations, especially for light alkanes, is reviewed. The challenging problem of regioselectivity in C–H bond insertions has been tackled by the use of sterically bulky metal catalysts, such as metal porphyrins and silver(I complexes. In some cases, high regioselectivity and enantioselectivity have been achieved in the C–H bond insertion of small alkanes. This review highlights the most recent accomplishments in this field.

Hydrogen Bonding: Between Strengthening the Crystal Packing and Improving Solubility of Three Haloperidol Derivatives.

Science.gov (United States)

Saluja, Hardeep; Mehanna, Ahmed; Panicucci, Riccardo; Atef, Eman

2016-06-01

The purpose of this study is to confirm the impact of polar functional groups on inter and intra-molecular hydrogen bonding in haloperidol (HP) and droperidol (DP) and, hence, their effects on dissolution using a new approach. To confirm our theory, a new molecule: deshydroxy-haloperidol (DHP) was designed and its synthesis was requested from a contract laboratory. The molecule was then studied and compared to DP and HP. Unlike DHP, both the HP and DP molecules have hydrogen donor groups, therefore, DHP was used to confirm the relative effects of the hydrogen donor group on solubility and crystal packing. The solid dispersions of the three structurally related molecules: HP, DP, and DHP were prepared using PVPK30, and characterized using XRPD and IR. A comparative dissolution study was carried out in aqueous medium. The absence of a hydrogen bonding donor group in DHP resulted in an unexpected increase in its aqueous solubility and dissolution rate from solid dispersion, which is attributed to weaker crystal pack. The increased dissolution rate of HP and DP from solid dispersions is attributed to drug-polymer hydrogen bonding that interferes with the drug-drug intermolecular hydrogen bonding and provides thermodynamic stability of the dispersed drug molecules. The drug-drug intermolecular hydrogen bond is the driving force for precipitation and crystal packing.

Hydrogen Bonding: Between Strengthening the Crystal Packing and Improving Solubility of Three Haloperidol Derivatives

Directory of Open Access Journals (Sweden)

Hardeep Saluja

2016-06-01

Full Text Available The purpose of this study is to confirm the impact of polar functional groups on inter and intra-molecular hydrogen bonding in haloperidol (HP and droperidol (DP and, hence, their effects on dissolution using a new approach. To confirm our theory, a new molecule: deshydroxy-haloperidol (DHP was designed and its synthesis was requested from a contract laboratory. The molecule was then studied and compared to DP and HP. Unlike DHP, both the HP and DP molecules have hydrogen donor groups, therefore, DHP was used to confirm the relative effects of the hydrogen donor group on solubility and crystal packing. The solid dispersions of the three structurally related molecules: HP, DP, and DHP were prepared using PVPK30, and characterized using XRPD and IR. A comparative dissolution study was carried out in aqueous medium. The absence of a hydrogen bonding donor group in DHP resulted in an unexpected increase in its aqueous solubility and dissolution rate from solid dispersion, which is attributed to weaker crystal pack. The increased dissolution rate of HP and DP from solid dispersions is attributed to drug-polymer hydrogen bonding that interferes with the drug-drug intermolecular hydrogen bonding and provides thermodynamic stability of the dispersed drug molecules. The drug-drug intermolecular hydrogen bond is the driving force for precipitation and crystal packing.

Measuring Intermolecular Binding Energies by Laser Spectroscopy.

Science.gov (United States)

Knochenmuss, Richard; Maity, Surajit; Féraud, Géraldine; Leutwyler, Samuel

2017-02-22

The ground-state dissociation energy, D0(S0), of isolated intermolecular complexes in the gas phase is a fundamental measure of the interaction strength between the molecules. We have developed a three-laser, triply resonant pump-dump-probe technique to measure dissociation energies of jet-cooled M•S complexes, where M is an aromatic chromophore and S is a closed-shell 'solvent' molecule. Stimulated emission pumping (SEP) via the S0→S1 electronic transition is used to precisely 'warm' the complex by populating high vibrational levels v" of the S0 state. If the deposited energy E(v") is less than D0(S0), the complex remains intact, and is then mass- and isomer-selectively detected by resonant two-photon ionization (R2PI) with a third (probe) laser. If the pumped level is above D0(S0), the hot complex dissociates and the probe signal disappears. Combining the fluorescence or SEP spectrum of the cold complex with the SEP breakoff of the hot complex brackets D0(S0). The UV chromophores 1-naphthol and carbazole were employed; these bind either dispersively via the aromatic rings, or form a hydrogen bond via the -OH or -NH group. Dissociation energies have been measured for dispersively bound complexes with noble gases (Ne, Kr, Ar, Xe), diatomics (N2, CO), alkanes (methane to n-butane), cycloalkanes (cyclopropane to cycloheptane), and unsaturated compounds (ethene, benzene). Hydrogen-bond dissociation energies have been measured for H2O, D2O, methanol, ethanol, ethers (oxirane, oxetane), NH3 and ND3.

Systematic study on intermolecular valence-band dispersion in molecular crystalline films

International Nuclear Information System (INIS)

Yamane, Hiroyuki; Kosugi, Nobuhiro

2015-01-01

Highlights: • Intermolecular valence-band dispersion of crystalline films of phthalocyanines. • Intermolecular transfer integral versus lattice constant. • Site-specific intermolecular interaction and resultant valence-band dispersion. • Band narrowing effect induced by elevated temperature. - Abstract: Functionalities of organic semiconductors are governed not only by individual properties of constituent molecules but also by solid-state electronic states near the Fermi level such as frontier molecular orbitals, depending on weak intermolecular interactions in various conformations. The individual molecular property has been widely investigated in detail; on the other hand, the weak intermolecular interaction is difficult to investigate precisely due to the presence of the structural and thermal energy broadenings in organic solids. Here we show quite small but essential intermolecular valence band dispersions and their temperature dependence of sub-0.1-eV scale in crystalline films of metal phthalocyanines (H_2Pc, ZnPc, CoPc, MnPc, and F_1_6ZnPc) by using angle-resolved photoemission spectroscopy (ARPES) with synchrotron radiation. The observed bands show intermolecular and site dependent dispersion widths, phases, and periodicities, for different chemical substitution of terminal groups and central metals in the phthalocyanine molecule. The precise and systematic band-dispersion measurement would be a credible approach toward the comprehensive understanding of intermolecular interactions and resultant charge transport properties as well as their tuning by substituents in organic molecular systems.

Intermolecular interactions

International Nuclear Information System (INIS)

Kaplan, I.G.; Rodimova, O.B.; AN SSSR, Tomsk. Inst. Optiki Atmosfery)

1978-01-01

The present state of the intermolecular interaction theory is described. The general physical picture of the molecular interactions is given, the relative contributions of interactions of different types are analyzed (electrostatic, resonance, induction, dispersion, relativistic, magnetostatic and exchange), and the main ones in each range of separations are picked out. The methods of the potential curve calculations are considered, specific for definite separations between the interacting systems. The special attention is paid to the analysis of approximations used in different theoretical calculation methods

Halogen Bonding from Dispersion-Corrected Density-Functional Theory: The Role of Delocalization Error.

Science.gov (United States)

Otero-de-la-Roza, A; Johnson, Erin R; DiLabio, Gino A

2014-12-09

Halogen bonds are formed when a Lewis base interacts with a halogen atom in a different molecule, which acts as an electron acceptor. Due to its charge transfer component, halogen bonding is difficult to model using many common density-functional approximations because they spuriously overstabilize halogen-bonded dimers. It has been suggested that dispersion-corrected density functionals are inadequate to describe halogen bonding. In this work, we show that the exchange-hole dipole moment (XDM) dispersion correction coupled with functionals that minimize delocalization error (for instance, BH&HLYP, but also other half-and-half functionals) accurately model halogen-bonded interactions, with average errors similar to other noncovalent dimers with less charge-transfer effects. The performance of XDM is evaluated for three previously proposed benchmarks (XB18 and XB51 by Kozuch and Martin, and the set proposed by Bauzá et al.) spanning a range of binding energies up to ∼50 kcal/mol. The good performance of BH&HLYP-XDM is comparable to M06-2X, and extends to the "extreme" cases in the Bauzá set. This set contains anionic electron donors where charge transfer occurs even at infinite separation, as well as other charge transfer dimers belonging to the pnictogen and chalcogen bonding classes. We also show that functional delocalization error results in an overly delocalized electron density and exact-exchange hole. We propose intermolecular Bader delocalization indices as an indicator of both the donor-acceptor character of an intermolecular interaction and the delocalization error coming from the underlying functional.

Dielectric behaviour and intermolecular association between L(+) ascorbic acid and ethanol

International Nuclear Information System (INIS)

Rudyk, R.A.; Torres, M.C.; Acuna Molina, M.A.

1990-01-01

In order to determine the dipole moment of L(+) ascorbic acid and the relation to its structure the experimental variations of permitivities, refractive indices and specific volumes of a series of dilute ethanolic solutions at 25 deg C were examined. The average moment (μ) using Buckingham equation was found to be 5,58 D considering the spherical approximation and 7,81 D if the ellipsoidal form factor was considered. The calculated μ value through vectorial addition was 4,98 D. The solute partial molal volume in the studied range was calculated to be 94,73 cm 3 instead of the theoretical value of 106,71 cm 3 . Both discrepancies are attributed to intermolecular solute-solvent interactions. A possible electronic displacement which favours hydrogen bonding with the solvent is postulated. (Author) [es

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

Science.gov (United States)

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

2015-06-28

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

An Ab Initio MP2 Study of HCN-HX Hydrogen Bonded Complexes

Directory of Open Access Journals (Sweden)

Araújo Regiane C.M.U.

1998-01-01

Full Text Available An ab initio MP2/6-311++G** study has been performed to obtain geometries, binding energies and vibrational properties of HCN-HX H-bonded complexes with X = F, Cl, NC, CN and CCH. These MP2/6-311++G** results have revealed that: (i the calculated H-bond lengths are in very good agreement with the experimental ones; (ii the H-bond strength is associated with the intermolecular charge transfer and follows the order: HCN-HNC ~ HCN-HF > HCN-HCl ~ HCN-HCN > HCN-HCCH; (iii BSSE correction introduces an average reduction of 2.4 kJ/mol on the MP2/6-311++G** binding energies, i.e. 11% of the uncorrected binding energy; (iv the calculated zero-point energies reduce the stability of these complexes and show a good agreement with the available experimental values; (v the H-X stretching frequency is shifted downward upon H-bond formation. This displacement is associated with the H-bond length; (vi The more pronounced effect on the infrared intensities occurs with the H-X stretching intensity. It is much enhanced after complexation due to the charge-flux term; (vii the calculated intermolecular stretching frequencies are in very good agreement with the experimental ones; and, finally, (viii the results obtained for the HCN-HX complexes follow the same profile as those found for the acetylene-HX series but, in the latter case, the effects on the properties of the free molecules due to complexation are less pronounced than those in HCN-HX.

A Protein Data Bank survey reveals shortening of intermolecular hydrogen bonds in ligand-protein complexes when a halogenated ligand is an H-bond donor.

Science.gov (United States)

Poznański, Jarosław; Poznańska, Anna; Shugar, David

2014-01-01

Halogen bonding in ligand-protein complexes is currently widely exploited, e.g. in drug design or supramolecular chemistry. But little attention has been directed to other effects that may result from replacement of a hydrogen by a strongly electronegative halogen. Analysis of almost 30000 hydrogen bonds between protein and ligand demonstrates that the length of a hydrogen bond depends on the type of donor-acceptor pair. Interestingly, lengths of hydrogen bonds between a protein and a halogenated ligand are visibly shorter than those estimated for the same family of proteins in complexes with non-halogenated ligands. Taking into account the effect of halogenation on hydrogen bonding is thus important when evaluating structural and/or energetic parameters of ligand-protein complexes. All these observations are consistent with the concept that halogenation increases the acidity of the proximal amino/imino/hydroxyl groups and thus makes them better, i.e. stronger, H-bond donors.

Z-H Bond Activation in (Di)hydrogen Bonding as a Way to Proton/Hydride Transfer and H2 Evolution.

Science.gov (United States)

Belkova, Natalia V; Filippov, Oleg A; Shubina, Elena S

2018-02-01

The ability of neutral transition-metal hydrides to serve as a source of hydride ion H - or proton H + is well appreciated. The hydride ligands possessing a partly negative charge are proton accepting sites, forming a dihydrogen bond, M-H δ- ⋅⋅⋅ δ+ HX (M=transition metal or metalloid). On the other hand, some metal hydrides are able to serve as a proton source and give hydrogen bond of M-H δ+ ⋅⋅⋅X type (X=organic base). In this paper we analyse recent works on transition-metal and boron hydrides showing i) how formation of an intermolecular complex between the reactants changes the Z-H (M-H and X-H) bond polarity and ii) what is the implication of such activation in the mechanisms of hydrides reactions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Intermolecular Modes between LH2 Bacteriochlorophylls and Protein Residues: The Effect on the Excitation Energies.

Science.gov (United States)

Anda, André; De Vico, Luca; Hansen, Thorsten

2017-06-08

Light-harvesting system 2 (LH2) executes the primary processes of photosynthesis in purple bacteria; photon absorption, and energy transportation to the reaction center. A detailed mechanistic insight into these operations is obscured by the complexity of the light-harvesting systems, particularly by the chromophore-environment interaction. In this work, we focus on the effects of the protein residues that are ligated to the bacteriochlorophylls (BChls) and construct potential energy surfaces of the ground and first optically excited state for the various BChl-residue systems where we in each case consider two degrees of freedom in the intermolecular region. We find that the excitation energies are only slightly affected by the considered modes. In addition, we see that axial ligands and hydrogen-bonded residues have opposite effects on both excitation energies and oscillator strengths by comparing to the isolated BChls. Our results indicate that only a small part of the chromophore-environment interaction can be associated with the intermolecular region between a BChl and an adjacent residue, but that it may be possible to selectively raise or lower the excitation energy at the axial and planar residue positions, respectively.

A Protein Data Bank survey reveals shortening of intermolecular hydrogen bonds in ligand-protein complexes when a halogenated ligand is an H-bond donor.

Directory of Open Access Journals (Sweden)

Jarosław Poznański

Full Text Available Halogen bonding in ligand-protein complexes is currently widely exploited, e.g. in drug design or supramolecular chemistry. But little attention has been directed to other effects that may result from replacement of a hydrogen by a strongly electronegative halogen. Analysis of almost 30000 hydrogen bonds between protein and ligand demonstrates that the length of a hydrogen bond depends on the type of donor-acceptor pair. Interestingly, lengths of hydrogen bonds between a protein and a halogenated ligand are visibly shorter than those estimated for the same family of proteins in complexes with non-halogenated ligands. Taking into account the effect of halogenation on hydrogen bonding is thus important when evaluating structural and/or energetic parameters of ligand-protein complexes. All these observations are consistent with the concept that halogenation increases the acidity of the proximal amino/imino/hydroxyl groups and thus makes them better, i.e. stronger, H-bond donors.

Probing the Watson-Crick, wobble, and sugar-edge hydrogen bond sites of uracil and thymine.

Science.gov (United States)

Müller, Andreas; Frey, Jann A; Leutwyler, Samuel

2005-06-16

The nucleobases uracil (U) and thymine (T) offer three hydrogen-bonding sites for double H-bond formation via neighboring N-H and C=O groups, giving rise to the Watson-Crick, wobble and sugar-edge hydrogen bond isomers. We probe the hydrogen bond properties of all three sites by forming hydrogen bonded dimers of U, 1-methyluracil (1MU), 3-methyluracil (3MU), and T with 2-pyridone (2PY). The mass- and isomer-specific S1 origins exhibit large spectral blue shifts relative to the 2PY monomer. Ab initio CIS calculations of the spectral shifts of the different hydrogen-bonded dimers show a linear correlation with experiment. This correlation allows us to identify the R2PI spectra of the weakly populated Watson-Crick and wobble isomers of both 2PY.U and 2PY.T. (3) PW91 density functional calculation of the ground-state binding and dissociation energies De and D0 are in agreement with the assignment of the dominant hydrogen bond isomers of 2PY.U, 2PY.3MU and 2PY.T as the sugar-edge form. For 2PY.U, 2PY.T and 2PY.1MU the measured wobble:Watson-Crick:sugar-edge isomer ratios are in good agreement with the calculated ratios, based on the ab initio dissociation energies and gas-phase statistical mechanics. The Watson-Crick and wobble isomers are thereby determined to be several kcal/mol less strongly bound than the sugar-edge isomers. The 36 observed intermolecular frequencies of the nine different H-bonded isomers give detailed insight into the intermolecular force field.

High-resolution synchrotron terahertz investigation of the large-amplitude hydrogen bond librational band of (HCN)2

DEFF Research Database (Denmark)

Mihrin, Dmytro; Jakobsen, P. W.; Voute, A.

2018-01-01

experimental value for the vibrational zero-point energy of 2.50 ± 0.05 kJ mol−1 arising from the entire class of large-amplitude intermolecular modes. The spectroscopic findings are complemented by CCSD(T)-F12b/aug-cc-pV5Z (electronic energies) and CCSD(T)-F12b/aug-cc-pVQZ (force fields) electronic structure...... calculations, providing a (semi)-experimental value of 17.20 ± 0.20 kJ mol−1 for the dissociation energy D0 of this strictly linear weak intermolecular CH⋯N hydrogen bond....

Single-molecule magnets ``without'' intermolecular interactions

Science.gov (United States)

Wernsdorfer, W.; Vergnani, L.; Rodriguez-Douton, M. J.; Cornia, A.; Neugebauer, P.; Barra, A. L.; Sorace, L.; Sessoli, R.

2012-02-01

Intermolecular magnetic interactions (dipole-dipole and exchange) affect strongly the magnetic relaxation of crystals of single-molecule magnets (SMMs), especially at low temperature, where quantum tunneling of the magnetization (QTM) dominates. This leads to complex many-body problems [l]. Measurements on magnetically diluted samples are desirable to clearly sort out the behaviour of magnetically-isolated SMMs and to reveal, by comparison, the effect of intermolecular interactions. Here, we diluted a Fe4 SMM into a diamagnetic crystal lattice, affording arrays of independent and iso-oriented magnetic units. We found that the resonant tunnel transitions are much sharper, the tunneling efficiency changes significantly, and two-body QTM transitions disappear. These changes have been rationalized on the basis of a dipolar shuffling mechanism and of transverse dipolar fields, whose effect has been analyzed using a multispin model. Our findings directly prove the impact of intermolecular magnetic couplings on the SMM behaviour and disclose the magnetic response of truly-isolated giant spins in a diamagnetic crystalline environment.[4pt] [1] W. Wernsdorfer, at al, PRL 82, 3903 (1999); PRL 89, 197201 (2002); Nature 416, 406 (2002); IS Tupitsyn, PCE Stamp, NV Prokof'ev, PRB 69, 132406 (2004).

Spectroscopic study on the intermolecular interaction of SO{sub 2} absorption in poly-ethylene glycol+H{sub 2}O systems

Energy Technology Data Exchange (ETDEWEB)

He, Zhiqiang; Liu, Jinrong; Zhang, Jianbin; Zhang, Na [Inner Mongolia University of Technology, Huhhot (China)

2014-03-15

Poly-Ethylene Glycol (PEG) 300+H{sub 2}O solutions (PEGWs) has been used as a promising medium for the absorption of SO{sub 2}. We investigated the UV, FTIR, {sup 1}H-NMR, and fluorescence spectra in the absorption processes of SO{sub 2} in PEGWs to present an important absorption mechanism. Based on the spectral results, the possibility of intermolecular hydrogen bond formation by hydroxyl oxygen atom in the PEG molecule with hydrogen atom in H{sub 2}O and S…O interaction formation by the oxygen atoms in PEG with the sulfur atom in SO{sub 2} are discussed. This shows that the spectral changes may be due to the formation of -CH{sub 2}CH{sub 2}O(H)…HOH… and -CH{sub 2}-CH{sub 2}-O(CH{sub 2}-CH{sub 2}-)…HOH… in PEGWs and the formation of -CH{sub 2}CH{sub 2}OH…OSO…, and intermolecular S…O interaction between PEG and SO{sub 2} as the formation of -CH{sub 2}CH{sub 2}OCH{sub 2}CH{sub 2}O(H)…(O)S(O)… and -CH{sub 2}-CH{sub 2}-O(CH{sub 2}-CH{sub 2}-) …(O)S(O)…. The existence of these bonds benefits the absorption and desorption processes of SO{sub 2} in PEGWs.

Chemical bonding of hydrogen molecules to transition metal complexes

International Nuclear Information System (INIS)

Kubas, G.J.

1990-01-01

The complex W(CO) 3 (PR 3 ) 2 (H 2 ) (CO = carbonyl; PR 3 = organophosphine) was prepared and was found to be a stable crystalline solid under ambient conditions from which the hydrogen can be reversibly removed in vacuum or under an inert atmosphere. The weakly bonded H 2 exchanges easily with D 2 . This complex represents the first stable compound containing intermolecular interaction of a sigma-bond (H-H) with a metal. The primary interaction is reported to be donation of electron density from the H 2 bonding electron pair to a vacant metal d-orbital. A series of complexes of molybdenum of the type Mo(CO)(H 2 )(R 2 PCH 2 CH 2 PR 2 ) 2 were prepared by varying the organophosphine substitutent to demonstrate that it is possible to bond either dihydrogen or dihydride by adjusting the electron-donating properties of the co-ligands. Results of infrared and NMR spectroscopic studies are reported. 20 refs., 5 fig

Observation of paramorphic phenomenon and non-tilted orthogonal smectic phases in hydrogen bonded ferroelectric liquid crystals for photonic applications

Science.gov (United States)

Subhasri, P.; Venugopal, D.; Jayaprakasam, R.; Chitravel, T.; Vijayakumar, V. N.

2018-06-01

A new class of hydrogen bonded ferroelectric liquid crystals (HBFLC) have been designed and synthesized by intermolecular hydrogen bonds between mesogenic 4-decyloxybenzoic acid (10OBA) and non-mesogenic (R)-(+)-Methylsuccinic acid (MSA) which have been confirmed through experimental and theoretical studies. Further, Mulliken population analysis clearly reveals that the existence of hydrogen bonds, strength and dynamic properties. Textural observation and its corresponding enthalpy values are analyzed by polarizing optical microscope (POM) and differential scanning calorimetry (DSC) respectively. Paramorphic changes in Sm C* phase due to the change of refractive index, which clearly reveal that the complex could be used for filtering action in photonic devices. The transition from lone pair to π* with large stabilization energy evidently exposes the chiral phases in the present HBFLC complex. Intermolecular interaction is analyzed by using natural bond orbital (NBO) studies. The highest energy in the HOMO-LUMO shows the stable phase in the HBFLC complex. Molecular structure of the HBFLC complex possesses the monoclinic which has been evinced through x-ray analysis. The randomly oriented bunch of homogeneous molecules in Sm A* phase of the HBFLC complex is reported.

Electronic transitions and intermolecular forces

International Nuclear Information System (INIS)

Hemert, M.C. van.

1981-01-01

This thesis describes two different subjects - electronic transitions and intermolecular forces - that are related mainly by the following observation: The wavenumber at which an electronic transition in an atom or molecule occurs, depends on the environment of that atom or molecule. This implies, for instance, that when a molecule becomes solvated its absorption spectrum may be shifted either to the blue or to the red side of the original gasphase spectrum. In part I attention is paid to the experimental aspects of VUV spectroscopy, both in the gasphase and in the condensed phase. In part II a series of papers are presented, dealing with the calculation of intermolecular forces (and some related topics) both for the ground state and for the excited state interactions, using different non-empirical methods. The calculations provide, among other results, a semiquantitative interpretation of the spectral blue shifts encountered in our experiments. (Auth.)

IR-UV double resonance spectroscopic investigation of phenylacetylene-alcohol complexes. Alkyl group induced hydrogen bond switching.

Science.gov (United States)

Singh, Prashant Chandra; Patwari, G Naresh

2008-06-12

The electronic transitions of phenylacetylene complexes with water and trifluoroethanol are shifted to the blue, while the corresponding transitions for methanol and ethanol complexes are shifted to the red relative to the phenylacetylene monomer. Fluorescence dip infrared (FDIR) spectra in the O-H stretching region indicate that, in all the cases, phenylacetylene is acting as a hydrogen bond acceptor to the alcohols. The FDIR spectrum in the acetylenic C-H stretching region shows Fermi resonance bands for the bare phenylacetylene, which act as a sensitive tool to probe the intermolecular structures. The FDIR spectra reveal that water and trifluoroethanol interact with the pi electron density of the acetylene C-C triple bond, while methanol and ethanol interact with the pi electron density of the benzene ring. It can be inferred that the hydrogen bonding acceptor site on phenylacetylene switches from the acetylene pi to the benzene pi with lowering in the partial charge on the hydrogen atom of the OH group. The most significant finding is that the intermolecular structures of water and methanol complexes are notably distinct, which, to the best of our knowledge, this is first such observation in the case of complexes of substituted benzenes.

Effects of Weak Intermolecular Interactions on the Molecular Isomerism of Tricobalt Metal Chains

International Nuclear Information System (INIS)

Poulsen, R.; Overgaard, J.; Schulman, A.; Stergaard, C.; Murillo, C.; Spackman, M.; Iversen, B.

2009-01-01

Depending on the number of interstitial solvent molecules, n, crystals of the linear chain compound Co3(dipyridylamide)4Cl2·nCH2Cl2 adopt either symmetrical or unsymmetrical metal chain structures. We explore here the possible reasons for such behavior using Hirshfeld surface analysis of intermolecular interactions as well as the charge density determined from 100(1) K X-ray diffraction data on the unsymmetrical complex Co3(dipyridylamide)4Cl2·2.11CH2Cl2, u-1, and crystal structures of u-1 determined from single crystal synchrotron X-ray diffraction data at 20, 150, and 300 K. The new crystal structures are compared with previous structural results on a crystal with slightly different solvent content. This change in solvent content only affects the bond distances to atom Co(3), which are also strongly affected by temperature changes due to a spin crossover transition. Large differences in intermolecular interactions are revealed by the Hirshfeld surface analysis between symmetrical (s-1) and unsymmetrical (u-1) crystal solvates, suggesting that the molecular isomerism is strongly influenced by crystal packing effects. Topological analysis of the static electron density of u-1 suggests that there is direct metal-metal bonding for both the shorter Co(1)-Co(2) and the longer Co(2)-Co(3) contact. The approximate description of the system as a (Co2)2+-dimer and an isolated Co2+-ion is reflected in the character of the metal-ligand interactions, which are more ionic for the isolated Co(3) atom, and the topological charges Co(1)+0.50, Co(2)+0.77, and Co(3)+1.36. The two termini of u-1 are found to be very different, both in terms of structural surroundings as well as topology. The central Co(2) atom is similar to a cobalt atom in a tetragonally distorted octahedral environment resulting in preferred occupancy in the t2g orbitals. The Co(1) atom has significant deformation in the xz and yz planes (z along the chain axis, x and y toward ligands) reflecting covalent

Critical surface of the quenched bond-diluted cubic model in self-dual lattice: renormalisation group approach

International Nuclear Information System (INIS)

Silva, E.P. da; Tsallis, C.

1991-01-01

We propose a quite simple real space renormalisation group which enables us to calculate (for the first time as far as we know, and presumably with high precision) the critical surface of the quenched bond-diluted discrete N-vector ferromagnet. (author)

Theoretical investigation on hydrogen bond interaction of diketo/keto-enol form uracil and thymine tautomers with intercalators.

Science.gov (United States)

Anithaa, V S; Vijayakumar, S; Sudha, M; Shankar, R

2017-11-06

The interaction of diketo and keto-enol form of thymine and uracil tautomers with acridine (Acr), phenazine (Phen), benzo[c]cinnoline (Ben), 1,10-phenanthroline (1,10-Phe), and 4,7-phenenthroline (4,7-Phe) intercalating drug molecules was studied using density functional theory at B3LYP/6-311++G** and M05-2×/6-311++G** levels of theory. From the interaction energy, it is found that keto-enol form tautomers have stronger interaction with intercalators than diketone form tautomers. On complex formation of thymine and uracil tautomers with benzo[c]cinnoline the drug molecules have high interaction energy values of -20.14 (BenT3) and -20.55 (BenU3) kcal mol -1 , while phenazine has the least interaction energy values of -6.52 (PhenT2) and -6.67 (PhenU2) kcal mol -1 . The closed shell intermolecular type interaction between the molecules with minimum elliptical value of 0.018 and 0.019 a.u at both levels of theory has been found from topological analysis. The benzo[c]cinnoline drug molecule with thymine and uracil tautomers has short range intermolecular N-H…N, C-H…O, and O-H...N hydrogen bonds (H-bonds) resulting in higher stability than other drug molecules. The proper hydrogen bonds N-H..N and O-H..N have the frequency shifted toward the lower side (red shifted) with the elongation in their bond length while the improper hydrogen bond C-H...O has the frequency shifted toward the higher side (blue shifted) of the spectral region with the contraction in their bond length. Further, the charge transfer between proton acceptor and donor along with stability of the bond is studied using natural bond orbital (NBO) analysis. Graphical abstract Hydrogen bond interaction of diketo/keto-enol form uracil and thymine tautomers with intercalators.

Computational insights into the photocyclization of diclofenac in solution: effects of halogen and hydrogen bonding.

Science.gov (United States)

Bani-Yaseen, Abdulilah Dawoud

2016-08-21

The effects of noncovalent interactions, namely halogen and hydrogen bonding, on the photochemical conversion of the photosensitizing drug diclofenac (DCF) in solution were investigated computationally. Both explicit and implicit solvent effects were qualitatively and quantitatively assessed employing the DFT/6-31+G(d) and SQM(PM7) levels of theory. Full geometry optimizations were performed in solution for the reactant DCF, hypothesized radical-based intermediates, and the main product at both levels of theories. Notably, in good agreement with previous experimental results concerning the intermolecular halogen bonding of DCF, the SQM(PM7) method revealed different values for d(ClO, Å) and ∠(C-ClO, °) for the two chlorine-substituents of DCF, with values of 2.63 Å/162° and 3.13 Å/142° for the trans and cis orientations, respectively. Employing the DFT/6-31+G(d) method with implicit solvent effects was not conclusive; however, explicit solvent effects confirmed the key contribution of hydrogen and halogen bonding in stabilizing/destabilizing the reactant and hypothesized intermediates. Interestingly, the obtained results revealed that a protic solvent such as water can increase the rate of photocyclization of DCF not only through hydrogen bonding effects, but also through halogen bonding. Furthermore, the atomic charges of atoms majorly involved in the photocyclization of DCF were calculated using different methods, namely Mulliken, Hirshfeld, and natural bond orbital (NBO). The obtained results revealed that in all cases there is a notable nonequivalency in the noncovalent intermolecular interactions of the two chlorine substituents of DCF and the radical intermediates with the solvent, which in turn may account for the discrepancy of their reactivity in different media. These computational results provide insight into the importance of halogen and hydrogen bonding throughout the progression of the photochemical conversion of DCF in solution.

Effect of intermolecular cohesion on coal liquefaction. 3. Reactivity of oxygen methylated coal; Sekitan teibunshika hanno ni okeru bunshikan gyoshuryoku no koka. 3. O-methyl ka tan no hanno tokusei

Energy Technology Data Exchange (ETDEWEB)

Sasaki, M.; Nagaishi, H.; Yoshida, T. [Hokkaido National Industrial Research Institute, Sapporo (Japan)

1996-10-28

The reactivity of oxygen methylated coal was studied to control hydrogen bond in bituminous coal liquefaction and intermolecular cohesion such as van der Waals force. In experiment, crushed and dried Illinois coal of 100mesh or less was used as specimen, and oxygen methylated coal was prepared by Liotta`s method using tetrabutylammonium halide. Coal liquefaction was conducted in an electromagnetic agitation autoclave using tetralin solvent under initial hydrogen pressure of 100kg/cm{sup 2} while heating. The molecular weight distribution of the products obtained was measured by gel permeation chromatography (GPC) analysis. The experimental results are as follows. The effect of intermolecular cohesion in bituminous coal on the reactivity is mainly derived from decomposing reaction from preasphaltene to oil. Yields of oil fraction by methylation increase corresponding to release of intermolecular cohesion. Since the thermal release is promoted with temperature rise, the difference in yield due to different treatments decreases. 5 refs., 3 figs., 1 tab.

Unusually short chalcogen bonds involving organoselenium: insights into the Se-N bond cleavage mechanism of the antioxidant ebselen and analogues.

Science.gov (United States)

Thomas, Sajesh P; Satheeshkumar, K; Mugesh, Govindasamy; Guru Row, T N

2015-04-27

Structural studies on the polymorphs of the organoselenium antioxidant ebselen and its derivative show the potential of organic selenium to form unusually short Se⋅⋅⋅O chalcogen bonds that lead to conserved supramolecular recognition units. Se⋅⋅⋅O interactions observed in these polymorphs are the shortest such chalcogen bonds known for organoselenium compounds. The FTIR spectral evolution characteristics of this interaction from solution state to solid crystalline state further validates the robustness of this class of supramolecular recognition units. The strength and electronic nature of the Se⋅⋅⋅O chalcogen bonds were explored using high-resolution X-ray charge density analysis and atons-in-molecules (AIM) theoretical analysis. A charge density study unravels the strong electrostatic nature of Se⋅⋅⋅O chalcogen bonding and soft-metal-like behavior of organoselenium. An analysis of the charge density around Se-N and Se-C covalent bonds in conjunction with the Se⋅⋅⋅O chalcogen bonding modes in ebselen and its analogues provides insights into the mechanism of drug action in this class of organoselenium antioxidants. The potential role of the intermolecular Se⋅⋅⋅O chalcogen bonding in forming the intermediate supramolecular assembly that leads to the bond cleavage mechanism has been proposed in terms of electron density topological parameters in a series of molecular complexes of ebselen with reactive oxygen species (ROS). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural variability and the nature of intermolecular interactions in Watson-Crick B-DNA base pairs.

Science.gov (United States)

Czyznikowska, Z; Góra, R W; Zaleśny, R; Lipkowski, P; Jarzembska, K N; Dominiak, P M; Leszczynski, J

2010-07-29

A set of nearly 100 crystallographic structures was analyzed using ab initio methods in order to verify the effect of the conformational variability of Watson-Crick guanine-cytosine and adenine-thymine base pairs on the intermolecular interaction energy and its components. Furthermore, for the representative structures, a potential energy scan of the structural parameters describing mutual orientation of the base pairs was carried out. The results were obtained using the hybrid variational-perturbational interaction energy decomposition scheme. The electron correlation effects were estimated by means of the second-order Møller-Plesset perturbation theory and coupled clusters with singles and doubles method adopting AUG-cc-pVDZ basis set. Moreover, the characteristics of hydrogen bonds in complexes, mimicking those appearing in B-DNA, were evaluated using topological analysis of the electron density. Although the first-order electrostatic energy is usually the largest stabilizing component, it is canceled out by the associated exchange repulsion in majority of the studied crystallographic structures. Therefore, the analyzed complexes of the nucleic acid bases appeared to be stabilized mainly by the delocalization component of the intermolecular interaction energy which, in terms of symmetry adapted perturbation theory, encompasses the second- and higher-order induction and exchange-induction terms. Furthermore, it was found that the dispersion contribution, albeit much smaller in terms of magnitude, is also a vital stabilizing factor. It was also revealed that the intermolecular interaction energy and its components are strongly influenced by four (out of six) structural parameters describing mutual orientation of bases in Watson-Crick pairs, namely shear, stagger, stretch, and opening. Finally, as a part of a model study, much of the effort was devoted to an extensive testing of the UBDB databank. It was shown that the databank quite successfully reproduces the

Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: an ab initio study.

Science.gov (United States)

Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D

2014-10-07

We perform an ab initio computational study of molecular complexes with the general formula CF3X-B that involve one trifluorohalomethane CF3X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH3 and PH3), two n-pairs (H2O and H2S), two n-pairs with an unsaturated bond (H2CO and H2CS), and a single π-pair (C2H4) and two π-pairs (C2H2). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C-X bond lengths shorten, while the C-X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.

Effect of solvent on proton location and dynamic behavior in short intramolecular hydrogen bonds studied by molecular dynamics simulations and NMR experiments

International Nuclear Information System (INIS)

Mori, Yukie; Masuda, Yuichi

2015-01-01

Highlights: • MD simulations were performed to study dynamics of strong hydrogen bonds. • Nuclear magnetic relaxation times of proton were measured in solution. • The hydrogen bond of dibenzoylmethane enol is asymmetric in methanol solution. • Formation or breakage of intermolecular hydrogen bonds can trigger proton transfer. • Dimethylsulfoxide may form a bifurcated hydrogen bond with a hydrogen-bonded system. - Abstract: Hydrogen phthalate anion has a short strong O–H–O hydrogen bond (H-bond). According to previous experimental studies, the H-bond is asymmetric and two tautomers are interconverted in aqueous solutions. In the present study, the effects of polar solvents on the H-bond in a zwitterionic hydrogen phthalate derivative 1 were investigated by quantum mechanics/molecular mechanics molecular dynamics (MD) simulations. The analyses of the trajectories for the methanol solution showed that the H-bonding proton tends to be located closer to the carboxylate group that forms fewer intermolecular H-bonds, than to the other carboxylate group and that the intramolecular proton transfer in 1 is triggered by the breakage and/or formation of an intermolecular H-bond. The enol form of dibenzoylmethane (2) also has a short H-bond, and the OH bond is reported to be rather long (>1.1 Å) in the crystal. In the present study, the effects of the solvent on the H-bond in 2 were investigated by molecular orbital (MO) calculations, MD simulations and nuclear magnetic resonance (NMR) spectroscopy. Density functional theory (DFT) calculations for 2 in vacuum indicated that the barrier height for the intramolecular proton transfer is almost the same as the zero-point energy of the vibrational ground state, resulting in broad distribution of the proton density along the H-bond, owing to the nuclear quantum effect. The OH distances were determined in CCl 4 , acetonitrile, and dimethylsulfoxide solutions from the magnetic dipolar interactions between the 17 O and 1

Effect of solvent on proton location and dynamic behavior in short intramolecular hydrogen bonds studied by molecular dynamics simulations and NMR experiments

Energy Technology Data Exchange (ETDEWEB)

Mori, Yukie, E-mail: mori.yukie@ocha.ac.jp; Masuda, Yuichi

2015-09-08

Highlights: • MD simulations were performed to study dynamics of strong hydrogen bonds. • Nuclear magnetic relaxation times of proton were measured in solution. • The hydrogen bond of dibenzoylmethane enol is asymmetric in methanol solution. • Formation or breakage of intermolecular hydrogen bonds can trigger proton transfer. • Dimethylsulfoxide may form a bifurcated hydrogen bond with a hydrogen-bonded system. - Abstract: Hydrogen phthalate anion has a short strong O–H–O hydrogen bond (H-bond). According to previous experimental studies, the H-bond is asymmetric and two tautomers are interconverted in aqueous solutions. In the present study, the effects of polar solvents on the H-bond in a zwitterionic hydrogen phthalate derivative 1 were investigated by quantum mechanics/molecular mechanics molecular dynamics (MD) simulations. The analyses of the trajectories for the methanol solution showed that the H-bonding proton tends to be located closer to the carboxylate group that forms fewer intermolecular H-bonds, than to the other carboxylate group and that the intramolecular proton transfer in 1 is triggered by the breakage and/or formation of an intermolecular H-bond. The enol form of dibenzoylmethane (2) also has a short H-bond, and the OH bond is reported to be rather long (>1.1 Å) in the crystal. In the present study, the effects of the solvent on the H-bond in 2 were investigated by molecular orbital (MO) calculations, MD simulations and nuclear magnetic resonance (NMR) spectroscopy. Density functional theory (DFT) calculations for 2 in vacuum indicated that the barrier height for the intramolecular proton transfer is almost the same as the zero-point energy of the vibrational ground state, resulting in broad distribution of the proton density along the H-bond, owing to the nuclear quantum effect. The OH distances were determined in CCl{sub 4}, acetonitrile, and dimethylsulfoxide solutions from the magnetic dipolar interactions between the {sup 17

Characterizing the Polymer:Fullerene Intermolecular Interactions

KAUST Repository

Sweetnam, Sean; Vandewal, Koen; Cho, Eunkyung; Risko, Chad; Coropceanu, Veaceslav; Salleo, Alberto; Bredas, Jean-Luc; McGehee, Michael D.

2016-01-01

the polymer and fullerene, there is not a consensus on the nature of these interactions. In this work, we use a combination of Raman spectroscopy, charge transfer state absorption, and density functional theory calculations to show that the intermolecular

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

Science.gov (United States)

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.

He-, Ne-, and Ar-phosgene intermolecular potential energy surfaces

DEFF Research Database (Denmark)

Munteanu, Cristian R.; Henriksen, Christian; Felker, Peter M.

2013-01-01

Using the CCSD(T) model, we evaluated the intermolecular potential energy surfaces of the He-, Ne-, and Ar-phosgene complexes. We considered a representative number of intermolecular geometries for which we calculated the corresponding interaction energies with the augmented (He complex) and doub...... of the complexes, providing valuable results for future experimental investigations. Comparing our results to those previously available for other phosgene complexes, we suggest that the results for Cl2-phosgene should be revised....

Intermolecular cleavage by UmuD-like mutagenesis proteins

Science.gov (United States)

McDonald, John P.; Frank, Ekaterina G.; Levine, Arthur S.; Woodgate, Roger

1998-01-01

The activity of a number of proteins is regulated by self-processing reactions. Elegant examples are the cleavage of the prokaryotic LexA and λCI transcriptional repressors and the UmuD-like mutagenesis proteins. Various studies support the hypothesis that LexA and λCI cleavage reactions are predominantly intramolecular in nature. The recently described crystal structure of the Escherichia coli UmuD′ protein (the posttranslational cleavage product of the UmuD protein) suggests, however, that the region of the protein corresponding to the cleavage site is at least 50 Å away from the catalytic active site. We considered the possibility, therefore, that the UmuD-like proteins might undergo self-processing that, in contrast to LexA and λCI, occurs via an intermolecular rather than intramolecular reaction. To test this hypothesis, we introduced into E. coli compatible plasmids with mutations at either the cleavage or the catalytic site of three UmuD-like proteins. Cleavage of these proteins only occurs in the presence of both plasmids, indicating that the reaction is indeed intermolecular in nature. Furthermore, this intermolecular reaction is completely dependent upon the multifunctional RecA protein and leads to the restoration of cellular mutagenesis in nonmutable E. coli strains. Intermolecular cleavage of a biotinylated UmuD active site mutant was also observed in vitro in the presence of the wild-type UmuD′ protein, indicating that in addition to the intact UmuD protein, the normal cleavage product (UmuD′) can also act as a classical enzyme. PMID:9465040

Iodine bonding stabilizes iodomethane in MIDAS pesticide. Theoretical study of intermolecular interactions between iodomethane and chloropicrin.

Science.gov (United States)

Glaser, Rainer; Prugger, Kaitlan

2012-02-22

The results are reported of a theoretical study of iodomethane (H(3)C-I, 1) and chloropicrin (Cl(3)C-NO(2), 2), of the heterodimers 3-6 formed by aggregation of 1 and 2, and of their addition products 7 and 8 and their possible fragmentation reactions to 9-18. Mixtures of iodomethane and chloropicrin are not expected to show chemistry resulting from their reactions with each other. The structures and stabilities are discussed of the iodine-bonded molecular aggregates (IBMA) 3 and 4 and of the hydrogen- and iodine-bonded molecular aggregates (IHBMA) 5 and 6. The mixed aggregates 3-5 are bound on the free enthalpy surface relative to the homodimers of 1 and 2, and the IBMA structures 3 and 4 are most stable. This result suggests that the mixture of chloropicrin and iodomethane in the pesticide Midas is a good choice to reduce the volatility of iodomethane because of thermodynamically stabilizing iodine bonding.

Conjecture on the critical frontier of the fully anisotropic homogeneous quenched bond-mixed potts ferromagnet in square lattice

International Nuclear Information System (INIS)

Tsallis, C.

1980-01-01

It is conjectured that a logarithmic provides a very accurate approximation of the yet unknown critical frontier of a fully anisotropic homogeneous quenched bond-mixed q-state Potts ferromagnet in square lattice, where the random coupling constant J is distributed according to the laws P(J) and P'(J) for 'horizontal' and 'vertical' bonds respectively. Such an equation contains as particular cases a great number of exact results as well as a few recent conjectures (which are definitively only approximate). (Author) [pt

Determination of intermolecular transfer integrals from DFT calculations

Energy Technology Data Exchange (ETDEWEB)

Baumeier, Bjoern; Andrienko, Denis [Max-Planck Institute for Polymer Research, Mainz (Germany)

2010-07-01

Theoretical studies of charge transport in organic conducting systems pose a unique challenge since they require multiscale schemes that combine quantum-chemical, molecular dynamics and kinetic Monte-Carlo calculations. The description of the mobility of electrons and holes in the hopping regime relies on the determination of intermolecular hopping rates in large scale morphologies. Using Marcus theory these rates can be calculated from intermolecular transfer integrals and on-site energies. Here we present a detailed computational study on the accuracy and efficiency of density-functional theory based approaches to the determination of intermolecular transfer integrals. First, it is demonstrated how these can be obtained from quantum-chemistry calculations by forming the expectation value of a dimer Fock operator with frontier orbitals of two neighboring monomers based on a projective approach. We then consider the prototypical example of one pair out of a larger morphology of Tris(8-hydroxyquinolinato)aluminium (Alq3) and study the influence of computational parameters, e.g. the choice of basis sets, exchange-correlation functional, and convergence criteria, on the calculated transfer integrals. The respective accuracies and efficiencies are compared in order to derive an optimal strategy for future simulations based on the full morphology.

Tuning the intermolecular proton bond in the H5O2+ `Zundel ion' scaffold

DEFF Research Database (Denmark)

Olesen, S. G.; Guasco, T. L.; Roscioli, J. R.

2011-01-01

a remarkably similar trend as the exterior OH groups are sequentially solvated or are replaced by methyl substituents. In effect, solvents H-bonding to exterior OH groups act to increase the proton affinity of the water to which they are bound in a roughly additive fashion. We discuss this behavior...

The Raman and vibronic activity of intermolecular vibrations in aromatic-containing complexes and clusters

International Nuclear Information System (INIS)

Maxton, P.M.; Schaeffer, M.W.; Ohline, S.M.; Kim, W.; Venturo, V.A.; Felker, P.M.

1994-01-01

Theoretical and experimental results pertaining to the excitation of intermolecular vibrations in the Raman and vibronic spectra of aromatic-containing, weakly bound complexes and clusters are reported. The theoretical analysis of intermolecular Raman activity is based on the assumption that the polarizability tensor of a weakly bound species is given by the sum of the polarizability tensors of its constituent monomers. The analysis shows that the van der Waals bending fundamentals in aromatic--rare gas complexes may be expected to be strongly Raman active. More generally, it predicts strong Raman activity for intermolecular vibrations that involve the libration or internal rotation of monomer moieties having appreciable permanent polarizability anisotropies. The vibronic activity of intermolecular vibrations in aromatic-rare gas complexes is analyzed under the assumption that every vibronic band gains its strength from an aromatic-localized transition. It is found that intermolecular vibrational excitations can accompany aromatic-localized vibronic excitations by the usual Franck--Condon mechanism or by a mechanism dependent on the librational amplitude of the aromatic moiety during the course of the pertinent intermolecular vibration. The latter mechanism can impart appreciable intensity to bands that are forbidden by rigid-molecule symmetry selection rules. The applicability of such rules is therefore called into question. Finally, experimental spectra of intermolecular transitions, obtained by mass-selective, ionization-detected stimulated Raman spectroscopies, are reported for benzene--X (X=Ar, --Ar 2 , N 2 , HCl, CO 2 , and --fluorene), fluorobenzene--Ar and --Kr, aniline--Ar, and fluorene--Ar and --Ar 2 . The results support the conclusions of the theoretical analyses and provide further evidence for the value of Raman methods in characterizing intermolecular vibrational level structures

Two-Order-Parameter Description of Liquids: Critical Phenomena and Phase Separation of Supercooled Liquids

OpenAIRE

Tanaka, Hajime

1997-01-01

Because of the isotropic and disordered nature of liquids, the anisotropy hidden in intermolecular interactions are often neglected. Accordingly, the order parameter describing a simple liquid has so far been believed to be only density. In contrast to this common sense, we propose that two order parameters, namely, density and bond order parameters, are required to describe the phase behavior of liquids since they intrinsically tend to form local bonds. This model gives us clear physical exp...

Hydrogen-Bonding Interactions in Luminescent Quinoline-Triazoles with Dominant 1D Crystals

Directory of Open Access Journals (Sweden)

Shi-Qiang Bai

2017-09-01

Full Text Available Quinoline-triazoles 2-((4-(diethoxymethyl-1H-1,2,3-triazol-1-ylmethylquinoline (1, 2-((4-(m-tolyl-1H-1,2,3-triazol-1-ylmethylquinoline (2 and 2-((4-(p-tolyl-1H-1,2,3-triazol-1-ylmethylquinoline (3 have been prepared with CuAAC click reactions and used as a model series to probe the relationship between lattice H-bonding interaction and crystal direction of growth. Crystals of 1–3 are 1D tape and prism shapes that correlate with their intermolecular and solvent 1D lattice H-bonding interactions. All compounds were thermally stable up to about 200 C and blue-green emissive in solution.

Characterizing agosticity using the quantum theory of atoms in molecules: bond critical points and their local properties.

Science.gov (United States)

Tognetti, Vincent; Joubert, Laurent; Raucoules, Roman; De Bruin, Theodorus; Adamo, Carlo

2012-06-07

In this paper, we extend the work of Popelier and Logothetis [J. Organomet. Chem. 1998, 555, 101] on the characterization of agosticity by considerably enlarging the set of the studied organometallic molecules. To this aim, 23 representative complexes have been considered, including all first line transition metals at various oxidation states and exhibiting four types of agosticity (α, β, γ, and δ). From these examples, the concepts of agostic atom, agostic bond, and agostic interaction are defined and discussed, notably by advocating Bader's analysis of the electron density. The nature and the local properties of the bond critical points are then investigated, and the relationships with the main geometric parameters of the complexes are particularly examined. Moreover, new local descriptors based on kinetic energy densities are developed in order to provide new tools for bond characterization.

Probing the role of backbone hydrogen bonds in protein-peptide interactions by amide-to-ester mutations

DEFF Research Database (Denmark)

Eildal, Jonas N N; Hultqvist, Greta; Balle, Thomas

2013-01-01

-protein interactions, those of the PDZ domain family involve formation of intermolecular hydrogen bonds: C-termini or internal linear motifs of proteins bind as β-strands to form an extended antiparallel β-sheet with the PDZ domain. Whereas extensive work has focused on the importance of the amino acid side chains...... of the protein ligand, the role of the backbone hydrogen bonds in the binding reaction is not known. Using amide-to-ester substitutions to perturb the backbone hydrogen-bonding pattern, we have systematically probed putative backbone hydrogen bonds between four different PDZ domains and peptides corresponding...... to natural protein ligands. Amide-to-ester mutations of the three C-terminal amides of the peptide ligand severely affected the affinity with the PDZ domain, demonstrating that hydrogen bonds contribute significantly to ligand binding (apparent changes in binding energy, ΔΔG = 1.3 to >3.8 kcal mol(-1...

A Closer Look at Trends in Boiling Points of Hydrides: Using an Inquiry-Based Approach to Teach Intermolecular Forces of Attraction

Science.gov (United States)

Glazier, Samantha; Marano, Nadia; Eisen, Laura

2010-01-01

We describe how we use boiling-point trends of group IV-VII hydrides to introduce intermolecular forces in our first-year general chemistry classes. Starting with the idea that molecules in the liquid state are held together by some kind of force that must be overcome for boiling to take place, students use data analysis and critical reasoning to…

Influence of chain topology and bond potential on the glass transition of polymer chains simulated with the bond fluctuation model

International Nuclear Information System (INIS)

Freire, J J

2008-01-01

The bond fluctuation model with a bond potential has been applied to investigation of the glass transition of linear chains and chains with a regular disposition of small branches. Cooling and subsequent heating curves are obtained for the chain energies and also for the mean acceptance probability of a bead jump. In order to mimic different trends to vitrification, a factor B gauging the strength of the bond potential with respect to the long-range potential (i.e. the intramolecular or intermolecular potential between indirectly bonded beads) has been introduced. (A higher value of B leads to a preference for the highest bond lengths and a higher total energy, implying a greater tendency to vitrify.) Different cases have been considered for linear chains: no long-range potential, no bond potential and several choices for B. Furthermore, two distinct values of B have been considered for alternate bonds in linear chains. In the case of the branched chains, mixed models with different values of B for bonds in the main chain and in the branches have also been investigated. The possible presence of ordering or crystallization has been characterized by calculating the collective light scattering function of the different samples after annealing at a convenient temperature below the onset of the abrupt change in the curves associated with a thermodynamic transition. It is concluded that ordering is inherited more efficiently in the systems with branched chains and also for higher values of B. The branched molecules with the highest B values in the main chain bonds exhibit two distinct transitions in the heating curves, which may be associated with two glass transitions. This behavior has been detected experimentally for chains with relatively long flexible branches

Influence of chain topology and bond potential on the glass transition of polymer chains simulated with the bond fluctuation model

Energy Technology Data Exchange (ETDEWEB)

Freire, J J [Departamento de Ciencias y Tecnicas FisicoquImicas, Facultad de Ciencias, Universidad Nacional de Educacion a Distancia (UNED), Senda del Rey 9, 28040 Madrid (Spain)], E-mail: jfreire@invi.uned.es

2008-07-16

The bond fluctuation model with a bond potential has been applied to investigation of the glass transition of linear chains and chains with a regular disposition of small branches. Cooling and subsequent heating curves are obtained for the chain energies and also for the mean acceptance probability of a bead jump. In order to mimic different trends to vitrification, a factor B gauging the strength of the bond potential with respect to the long-range potential (i.e. the intramolecular or intermolecular potential between indirectly bonded beads) has been introduced. (A higher value of B leads to a preference for the highest bond lengths and a higher total energy, implying a greater tendency to vitrify.) Different cases have been considered for linear chains: no long-range potential, no bond potential and several choices for B. Furthermore, two distinct values of B have been considered for alternate bonds in linear chains. In the case of the branched chains, mixed models with different values of B for bonds in the main chain and in the branches have also been investigated. The possible presence of ordering or crystallization has been characterized by calculating the collective light scattering function of the different samples after annealing at a convenient temperature below the onset of the abrupt change in the curves associated with a thermodynamic transition. It is concluded that ordering is inherited more efficiently in the systems with branched chains and also for higher values of B. The branched molecules with the highest B values in the main chain bonds exhibit two distinct transitions in the heating curves, which may be associated with two glass transitions. This behavior has been detected experimentally for chains with relatively long flexible branches.

Theoretical studies for the N2–N2O van der Waals complex: The potential energy surface, intermolecular vibrations, and rotational transition frequencies

International Nuclear Information System (INIS)

Zheng, Rui; Zheng, Limin; Yang, Minghui; Lu, Yunpeng

2015-01-01

Theoretical studies of the potential energy surface (PES) and bound states are performed for the N 2 –N 2 O van der Waals (vdW) complex. A four-dimensional intermolecular PES is constructed at the level of single and double excitation coupled-cluster method with a non-iterative perturbation treatment of triple excitations [CCSD(T)] with aug-cc-pVTZ basis set supplemented with bond functions. Two equivalent T-shaped global minima are located, in which the O atom of N 2 O monomer is near the N 2 monomer. The intermolecular fundamental vibrational states are assigned by inspecting the orientation of the nodal surface of the wavefunctions. The calculated frequency for intermolecular disrotation mode is 23.086 cm −1 , which is in good agreement with the available experimental data of 22.334 cm −1 . A negligible tunneling splitting with the value of 4.2 MHz is determined for the ground vibrational state and the tunneling splitting increases as the increment of the vibrational frequencies. Rotational levels and transition frequencies are calculated for both isotopomers 14 N 2 –N 2 O and 15 N 2 –N 2 O. The accuracy of the PES is validated by the good agreement between theoretical and experimental results for the transition frequencies and spectroscopic parameters

Ligand field and intermolecular interactions tuning the magnetic properties of spin-crossover Fe(II) polymer with 4,4′-bipyridine

Energy Technology Data Exchange (ETDEWEB)

Luo, Yang-Hui; Liu, Qing-Ling; Yang, Li-Jing; Ling, Yang; Wang, Wei; Sun, Bai-Wang, E-mail: chmsunbw@seu.edu.cn

2015-02-15

A new spin crossover coordination polymer (SCO-CPs) of Fe(II)-4,4′-bipyridine (4,4′-bipy) family: (Fe(4,4′-bipy){sub 2}(H{sub 2}O){sub 2})·(4,4′-bipy)· 8(H{sub 2}O)·2(ClO{sub 4}) (3), which displays half spin transitions between 100 and 300 K, has been synthesized and structurally characterized. Compound 3 featured with two-dimensional (2-D) grids connected by hydrogen bonds and π…π packing between one-dimensional (1-D) chains, the 2-D grids expand to three-dimensional (3-D) architecture supported by a “S-shaped holder” involving lattice 4-4′-bipy, water molecules and perchlorate anion. We compared 3 with the other two analogous complexes: ((Fe(4,4′-bipy) (H{sub 2}O){sub 2} (NCS){sub 2})·4,4′-bipy, 1 and (Fe(4,4′-bipy){sub 2}(NCS){sub 2})·mSolv, 2) through Hirshfeld surfaces analysis, which revealed that the low ligand field strength (NCS{sup −}) and lone-pair…H contacts contribute to the stabilization of HS (high-spin) state of the Fe(II) ion, while the high ligand field strength (4,4′-bipy) and strong intermolecular contacts (hydrogen bonds and π…π packing interactions) make for the LS (low-spin) state. - Highlights: ●A new member of Fe(||)-4,4′-bipy family has been prepared. ●It displays half spin transitions tuned by ligand field and intermolecular interactions. ●We have made a detailed comparison of this new member with two other analogous complexes.

Hydrogen bond dynamics governs the effective photoprotection mechanism of plant phenolic sunscreens.

Science.gov (United States)

Liu, Fang; Du, Likai; Lan, Zhenggang; Gao, Jun

2017-02-15

Sinapic acid derivatives are important sunscreen species in natural plants, which could provide protection from solar UV radiation. Using a combination of ultrafast excited state dynamics, together with classical molecular dynamics studies, we demonstrate that there is direct coupling of hydrogen bond motion with excited state photoprotection dynamics as part of the basic mechanism in solution. Beyond the intra-molecular degree of freedom, the inter-molecular motions on all timescales are potentially important for the photochemical or photophysical events, ranging from the ultrafast hydrogen bond motion to solvent rearrangements. This provides not only an enhanced understanding of the anomalous experimental spectroscopic results, but also the key idea in the development of sunscreen agents with improved photo-chemical properties. We suggest that the hydrogen bond dynamics coupled excited state photoprotection mechanism may also be possible in a broad range of bio-related molecules in the condensed phase.

The effect of the intermolecular potential formulation on the state-selected energy exchange rate coefficients in N2-N2 collisions.

Science.gov (United States)

Kurnosov, Alexander; Cacciatore, Mario; Laganà, Antonio; Pirani, Fernando; Bartolomei, Massimiliano; Garcia, Ernesto

2014-04-05

The rate coefficients for N2-N2 collision-induced vibrational energy exchange (important for the enhancement of several modern innovative technologies) have been computed over a wide range of temperature. Potential energy surfaces based on different formulations of the intramolecular and intermolecular components of the interaction have been used to compute quasiclassically and semiclassically some vibrational to vibrational energy transfer rate coefficients. Related outcomes have been rationalized in terms of state-to-state probabilities and cross sections for quasi-resonant transitions and deexcitations from the first excited vibrational level (for which experimental information are available). On this ground, it has been possible to spot critical differences on the vibrational energy exchange mechanisms supported by the different surfaces (mainly by their intermolecular components) in the low collision energy regime, though still effective for temperatures as high as 10,000 K. It was found, in particular, that the most recently proposed intermolecular potential becomes the most effective in promoting vibrational energy exchange near threshold temperatures and has a behavior opposite to the previously proposed one when varying the coupling of vibration with the other degrees of freedom. Copyright © 2014 Wiley Periodicals, Inc.

Copper wire bonding

CERN Document Server

Chauhan, Preeti S; Zhong, ZhaoWei; Pecht, Michael G

2014-01-01

This critical volume provides an in-depth presentation of copper wire bonding technologies, processes and equipment, along with the economic benefits and risks.  Due to the increasing cost of materials used to make electronic components, the electronics industry has been rapidly moving from high cost gold to significantly lower cost copper as a wire bonding material.  However, copper wire bonding has several process and reliability concerns due to its material properties.  Copper Wire Bonding book lays out the challenges involved in replacing gold with copper as a wire bond material, and includes the bonding process changes—bond force, electric flame off, current and ultrasonic energy optimization, and bonding tools and equipment changes for first and second bond formation.  In addition, the bond–pad metallurgies and the use of bare and palladium-coated copper wires on aluminum are presented, and gold, nickel and palladium surface finishes are discussed.  The book also discusses best practices and re...

Solid state synthesis, structural, physicochemical and optical properties of an inter-molecular compound: 2-hydroxy-1, 2-diphenylethanone-4-nitro-o-phenylenediamine system

Science.gov (United States)

Rai, U. S.; Singh, Manjeet; Rai, R. N.

2017-09-01

The phase diagram of 2-hydroxy-1, 2-diphenylethanone (HDPE)-4-nitro-o-phenylenediamine (NOPDA) system, determined by the thaw-melt method, gives two eutectics E1 (m p = 66.0 °C) and E2 (m p = 155.0 °C) with 0.30 and 0.55 mol fractions of NOPDA, respectively, and an 1:1 inter-molecular compound (IMC) (m p 162.0 °C). This IMC was synthesized by adopting the green synthetic method of solid state reaction. While its formation and structure were confirmed by the X-ray diffraction and spectroscopic methods, the ORTEP view gives mode of crystal packing, C‒H…O, C‒H…N, π-π stacking and the inter-molecular hydrogen bonding in the compound. The single crystal of the IMC shows 53% transmission and emits significantly higher dual fluorescence, and the band gap was computed to be 3.04 eV. The values of solubility of the IMC, measured in the temperature range 304-322 K, satisfy the mole fraction (X) and temperature equation: Xeq= 5.1324 × 10-7 e 0.01356T.

Intermolecular failure of L-type Ca2+ channel and ryanodine receptor signaling in hypertrophy.

Directory of Open Access Journals (Sweden)

Ming Xu

2007-02-01

Full Text Available Pressure overload-induced hypertrophy is a key step leading to heart failure. The Ca(2+-induced Ca(2+ release (CICR process that governs cardiac contractility is defective in hypertrophy/heart failure, but the molecular mechanisms remain elusive. To examine the intermolecular aspects of CICR during hypertrophy, we utilized loose-patch confocal imaging to visualize the signaling between a single L-type Ca(2+ channel (LCC and ryanodine receptors (RyRs in aortic stenosis rat models of compensated (CHT and decompensated (DHT hypertrophy. We found that the LCC-RyR intermolecular coupling showed a 49% prolongation in coupling latency, a 47% decrease in chance of hit, and a 72% increase in chance of miss in DHT, demonstrating a state of "intermolecular failure." Unexpectedly, these modifications also occurred robustly in CHT due at least partially to decreased expression of junctophilin, indicating that intermolecular failure occurs prior to cellular manifestations. As a result, cell-wide Ca(2+ release, visualized as "Ca(2+ spikes," became desynchronized, which contrasted sharply with unaltered spike integrals and whole-cell Ca(2+ transients in CHT. These data suggested that, within a certain limit, termed the "stability margin," mild intermolecular failure does not damage the cellular integrity of excitation-contraction coupling. Only when the modification steps beyond the stability margin does global failure occur. The discovery of "hidden" intermolecular failure in CHT has important clinical implications.

Triplet excited electronic state switching induced by hydrogen bonding: A transient absorption spectroscopy and time-dependent DFT study

Energy Technology Data Exchange (ETDEWEB)

Ravi Kumar, Venkatraman; Ariese, Freek; Umapathy, Siva, E-mail: umapathy@ipc.iisc.ernet.in [Inorganic and Physical Chemistry Department, Indian Institute of Science, Bangalore 560012 (India)

2016-03-21

The solvent plays a decisive role in the photochemistry and photophysics of aromatic ketones. Xanthone (XT) is one such aromatic ketone and its triplet-triplet (T-T) absorption spectra show intriguing solvatochromic behavior. Also, the reactivity of XT towards H-atom abstraction shows an unprecedented decrease in protic solvents relative to aprotic solvents. Therefore, a comprehensive solvatochromic analysis of the triplet-triplet absorption spectra of XT was carried out in conjunction with time dependent density functional theory using the ad hoc explicit solvent model approach. A detailed solvatochromic analysis of the T-T absorption bands of XT suggests that the hydrogen bonding interactions are different in the corresponding triplet excited states. Furthermore, the contributions of non-specific and hydrogen bonding interactions towards differential solvation of the triplet states in protic solvents were found to be of equal magnitude. The frontier molecular orbital and electron density difference analysis of the T{sub 1} and T{sub 2} states of XT indicates that the charge redistribution in these states leads to intermolecular hydrogen bond strengthening and weakening, respectively, relative to the S{sub 0} state. This is further supported by the vertical excitation energy calculations of the XT-methanol supra-molecular complex. The intermolecular hydrogen bonding potential energy curves obtained for this complex in the S{sub 0}, T{sub 1}, and T{sub 2} states support the model. In summary, we propose that the different hydrogen bonding mechanisms exhibited by the two lowest triplet excited states of XT result in a decreasing role of the nπ{sup ∗} triplet state, and are thus responsible for its reduced reactivity towards H-atom abstraction in protic solvents.

X-ray and Hydrogen-bonding Properties of 1-((1H-benzotriazol-1-ylmethylnaphthalen-2-ol

Directory of Open Access Journals (Sweden)

Jaime Ríos-Motta

2009-03-01

Full Text Available The solid state structure of 1-((1H-benzotriazol-1-ylmethylnaphthalen-2-ol, C17H13N3O, shows that this Mannich base crystallizes forming intermolecular N···HO hydrogen bonds, rather than intramolecular ones. Factors contributing to this choice of hydrogen-bonding mode are discussed. The compound crystallizes in the monoclinic system, P21/c space group, with lattice constants: a = 11.7934(9 Å, b = 14.3002(14 Å, c = 8.4444(8 Å, β = 106.243(5 deg, V = 1367.3(2 Å3, Z = 4, F(000 = 576, R1 = 6.96%, wR2 = 11.4%.

A combined experimental and theoretical approach to the study of hydrogen bond interaction in the binary mixture of N-methylimidazole with water

International Nuclear Information System (INIS)

Huang, Rongyi; Du, Rongbin; Liu, Guangxiang; Zhao, Xiuqin; Ye, Shiyong; Wu, Genhua

2012-01-01

Highlights: ► Densities of N-methylimidazole with water binary mixture were measured. ► Excess molar volumes were fitted to Redlich–Kister polynomial equation. ► Excess molar volumes are negative in the whole mole fraction range. ► 1:1 Hydrogen complex formation between the unlike components was observed. ► Formation of hydrogen bonds in the binary mixture was confirmed by DFT//B3LYP. - Abstract: The intermolecular hydrogen bond interactions in the N-methylimidazole (MeIm) with water binary mixture have been studied by a combined experimental and theoretical approach. The densities of the binary mixture have been measured at T = (288.15 to 323.15) K and at atmospheric pressure. From the experimental data, excess molar volumes were determined as a function of composition at each temperature. The results reveal the formation of 1:1 hydrogen bond complex between MeIm with water at the maximal excess molar volume. Meanwhile, the formation of hydrogen bonds in the binary mixture was further confirmed by high level theoretical calculation. The structures, interactional energies and bond characteristics of the hydrogen bond complexes were calculated in the gas phase using density functional theory (DFT) at the B3LYP/6-311++G(d, p) theory levels. The changes of thermodynamic properties from the monomers to hydrogen bond complexes with the temperature ranging from (288.15 to 323.15) K were obtained using the statistical thermodynamic method. Thermodynamic analyses have been interpreted in terms of intermolecular interactions and excess molar volume changes in the binary mixture. It was also found that the formation reaction of the hydrogen bond complex of MeIm with water was an exothermic, entropy reduced and spontaneous thermodynamic process at all the temperature studied.

Intermolecular Formation of Two C−C Bonds across Olefins Enabled by Boron-Based Relay Strategies

Czech Academy of Sciences Publication Activity Database

Hidasová, Denisa; Jahn, Ullrich

2017-01-01

Roč. 56, č. 33 (2017), s. 9656-9658 ISSN 1433-7851 Institutional support: RVO:61388963 Keywords : 1,2- metal ate rearrangement * C−C bond formation * radical reactions * transition metal catalysis * vinyl boronates Subject RIV: CC - Organic Chemistry OBOR OECD: Organic chemistry Impact factor: 11.994, year: 2016

Critical and subcritical damage monitoring of bonded composite repairs using innovative non-destructive techniques

Science.gov (United States)

Grammatikos, S. A.; Kordatos, E. Z.; Aggelis, D. G.; Matikas, T. E.; Paipetis, A. S.

2012-04-01

Infrared Thermography (IrT) has been shown to be capable of detecting and monitoring service induced damage of repair composite structures. Full-field imaging, along with portability are the primary benefits of the thermographic technique. On-line lock-in thermography has been reported to successfully monitor damage propagation or/and stress concentration in composite coupons, as mechanical stresses in structures induce heat concentration phenomena around flaws. During mechanical fatigue, cyclic loading plays the role of the heating source and this allows for critical and subcritical damage identification and monitoring using thermography. The Electrical Potential Change Technique (EPCT) is a new method for damage identification and monitoring during loading. The measurement of electrical potential changes at specific points of Carbon Fiber Reinforced Polymers (CFRPs) under load are reported to enable the monitoring of strain or/and damage accumulation. Along with the aforementioned techniques Finally, Acoustic Emission (AE) method is well known to provide information about the location and type of damage. Damage accumulation due to cyclic loading imposes differentiation of certain parameters of AE like duration and energy. Within the scope of this study, infrared thermography is employed along with AE and EPCT methods in order to assess the integrity of bonded repair patches on composite substrates and to monitor critical and subcritical damage induced by the mechanical loading. The combined methodologies were effective in identifying damage initiation and propagation of bonded composite repairs.

Determination of the conformation of 2-hydroxy- and 2-aminobenzoic acid dimers using 13C NMR and density functional theory/natural bond order analysis: the central importance of the carboxylic acid carbon.

Science.gov (United States)

Burnette, Ronald R; Weinhold, Frank

2006-07-20

The 13C chemical shift for the carboxylic acid carbon provides a powerful diagnostic probe to determine the preferred isomeric dimer structures of benzoic acid derivatives undergoing intra- and intermolecular H-bonding in the gas, solution and crystalline phases. We have employed hybrid density functional calculations and natural bond orbital analysis to elucidate the electronic origins of the observed 13C shieldings and their relationship to isomeric stability. We find that delocalizing interactions from the carbonyl oxygen lone pairs (nO) into vicinal carbon-oxygen and carbon-carbon antibonds (sigmaCO*,sigmaCC*) make critical contributions to the 13C shieldings, and these nO --> sigmaCO*, nO --> sigmaCC* interactions are in turn sensitive to the intramolecular interactions that dictate dimer structure and stability. The carboxyl carbon atom can thus serve as a useful detector of subtle structural and conformational features in this pharmacologically important class of carboxylic acid interactions.

All rights reserved Intermolecular Model Potentials and Virial ...

African Journals Online (AJOL)

ADOWIE PERE

Intermolecular Model Potentials and Virial Coefficients from Acoustic Data. 1* ... method of cluster expansion. Its merit is that, ... their determination is by the analyses of isothermal p- ρ-y data ... Carlo simulation method to calculate volumetric.

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

Science.gov (United States)

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

2005-06-01

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

Spectroscopic identification of ethanol-water conformers by large-amplitude hydrogen bond librational modes

DEFF Research Database (Denmark)

Andersen, Jonas; Heimdal, J.; Larsen, René Wugt

2015-01-01

⋯HO hydrogen bond acceptor in the two most stable conformations. In the most stable conformation, the water subunit forces the ethanol molecule into its less stable gauche configuration upon dimerization owing to a cooperative secondary weak O⋯HC hydrogen bondinteraction evidenced by a significantly blue......-shift of the low-frequency in-plane donor OH librational band origin. The strong correlation between the low-frequency in-plane donor OH librational motion and the secondary intermolecular O⋯HC hydrogen bond is demonstrated by electronic structure calculations. The experimental findings are further supported...... by CCSD(T)-F12/aug-cc-pVQZ calculations of the conformationalenergy differences together with second-order vibrational perturbation theory calculations of the large-amplitude donor OH librational band origins....

A quantum-chemical validation about the formation of hydrogen bonds and secondary interactions in intermolecular heterocyclic systems

Directory of Open Access Journals (Sweden)

Boaz Galdino Oliveira

2009-08-01

Full Text Available We have performed a detailed theoretical study in order to understand the charge density topology of the C2H4O···C2H2 and C2H4S···C2H2 heterocyclic hydrogen-bonded complexes. Through the calculations derived from Quantum Theory of Atoms in Molecules (QTAIM, it was observed the formation of hydrogen bonds and secondary interactions. Such analysis was performed through the determination of optimized geometries at B3LYP/6-31G(d,p level of theory, by which is that QTAIM topological operators were computed, such as the electronic density ρ(r, Laplacian Ñ2ρ(r, and ellipticity ε. The examination of the hydrogen bonds has been performed through the measurement of ρ(r, Ñ2ρ(r and ε between (O···H—C and (S···H—C, whereas the secondary interaction between axial hydrogen atoms Hα and carbon of acetylene. In this insight, it was verified the existence of secondary interaction only in C2H4S···C2H2 complex because its structure is propitious to form multiple interactions.

Characterization of the glass transition of water predicted by molecular dynamics simulations using nonpolarizable intermolecular potentials.

Science.gov (United States)

Kreck, Cara A; Mancera, Ricardo L

2014-02-20

Molecular dynamics simulations allow detailed study of the experimentally inaccessible liquid state of supercooled water below its homogeneous nucleation temperature and the characterization of the glass transition. Simple, nonpolarizable intermolecular potentials are commonly used in classical molecular dynamics simulations of water and aqueous systems due to their lower computational cost and their ability to reproduce a wide range of properties. Because the quality of these predictions varies between the potentials, the predicted glass transition of water is likely to be influenced by the choice of potential. We have thus conducted an extensive comparative investigation of various three-, four-, five-, and six-point water potentials in both the NPT and NVT ensembles. The T(g) predicted from NPT simulations is strongly correlated with the temperature of minimum density, whereas the maximum in the heat capacity plot corresponds to the minimum in the thermal expansion coefficient. In the NVT ensemble, these points are instead related to the maximum in the internal pressure and the minimum of its derivative, respectively. A detailed analysis of the hydrogen-bonding properties at the glass transition reveals that the extent of hydrogen-bonds lost upon the melting of the glassy state is related to the height of the heat capacity peak and varies between water potentials.

Direct α-C-H bond functionalization of unprotected cyclic amines

Science.gov (United States)

Chen, Weijie; Ma, Longle; Paul, Anirudra; Seidel, Daniel

2018-02-01

Cyclic amines are ubiquitous core structures of bioactive natural products and pharmaceutical drugs. Although the site-selective abstraction of C-H bonds is an attractive strategy for preparing valuable functionalized amines from their readily available parent heterocycles, this approach has largely been limited to substrates that require protection of the amine nitrogen atom. In addition, most methods rely on transition metals and are incompatible with the presence of amine N-H bonds. Here we introduce a protecting-group-free approach for the α-functionalization of cyclic secondary amines. An operationally simple one-pot procedure generates products via a process that involves intermolecular hydride transfer to generate an imine intermediate that is subsequently captured by a nucleophile, such as an alkyl or aryl lithium compound. Reactions are regioselective and stereospecific and enable the rapid preparation of bioactive amines, as exemplified by the facile synthesis of anabasine and (-)-solenopsin A.

Preventing disulfide bond formation weakens non-covalent forces among lysozyme aggregates.

Directory of Open Access Journals (Sweden)

Vijay Kumar Ravi

Full Text Available Nonnative disulfide bonds have been observed among protein aggregates in several diseases like amyotrophic lateral sclerosis, cataract and so on. The molecular mechanism by which formation of such bonds promotes protein aggregation is poorly understood. Here in this work we employ previously well characterized aggregation of hen eggwhite lysozyme (HEWL at alkaline pH to dissect the molecular role of nonnative disulfide bonds on growth of HEWL aggregates. We employed time-resolved fluorescence anisotropy, atomic force microscopy and single-molecule force spectroscopy to quantify the size, morphology and non-covalent interaction forces among the aggregates, respectively. These measurements were performed under conditions when disulfide bond formation was allowed (control and alternatively when it was prevented by alkylation of free thiols using iodoacetamide. Blocking disulfide bond formation affected growth but not growth kinetics of aggregates which were ∼50% reduced in volume, flatter in vertical dimension and non-fibrillar in comparison to control. Interestingly, single-molecule force spectroscopy data revealed that preventing disulfide bond formation weakened the non-covalent interaction forces among monomers in the aggregate by at least ten fold, thereby stalling their growth and yielding smaller aggregates in comparison to control. We conclude that while constrained protein chain dynamics in correctly disulfide bonded amyloidogenic proteins may protect them from venturing into partial folded conformations that can trigger entry into aggregation pathways, aberrant disulfide bonds in non-amyloidogenic proteins (like HEWL on the other hand, may strengthen non-covalent intermolecular forces among monomers and promote their aggregation.

Molecular Dynamics Investigation of the Effects of Concentration on Hydrogen Bonding in Aqueous Solutions of Methanol, Ethylene Glycol and Glycerol

International Nuclear Information System (INIS)

Zhang, Ning; Li, Weizhong; Chen, Cong; Zuo, Jianguo; Weng, Lindong

2013-01-01

Hydrogen bonding interaction between alcohols and water molecules is an important characteristic in the aqueous solutions of alcohols. In this paper, a series of molecular dynamics simulations have been performed to investigate the aqueous solutions of low molecular weight alcohols (methanol, ethylene glycol and glycerol) at the concentrations covering a broad range from 1 to 90 mol %. The work focuses on studying the effect of the alcohols molecules on the hydrogen bonding of water molecules in binary mixtures. By analyzing the hydrogen bonding ability of the hydroxyl (-OH) groups for the three alcohols, it is found that the hydroxyl group of methanol prefers to form more hydrogen bonds than that of ethylene glycol and glycerol due to the intra-and intermolecular effects. It is also shown that concentration has significant effect on the ability of alcohol molecule to hydrogen bond water molecules. Understanding the hydrogen bonding characteristics of the aqueous solutions is helpful to reveal the cryoprotective mechanisms of methanol, ethylene glycol and glycerol in aqueous solutions

Ab initio and Gordon--Kim intermolecular potentials for two nitrogen molecules

International Nuclear Information System (INIS)

Ree, F.H.; Winter, N.W.

1980-01-01

Both ab initio MO--LCAO--SCF and the electron-gas (or Gordon--Kim) methods have been used to compute the intermolecular potential (Phi) of N 2 molecules for seven different N 2 --N 2 orientations. The ab initio calculations were carried out using a [4s3p] contracted Gaussian basis set with and without 3d polarization functions. The larger basis set provides adequate results for Phi>0.002 hartree or intermolecular separations less than 6.5--7 bohr. We use a convenient analytic expression to represent the ab initio data in terms of the intermolecular distance and three angles defining the orientations of the two N 2 molecules. The Gordon--Kim method with Rae's self-exchange correction yields Phi, which agrees reasonably well over a large repulsive range. However, a detailed comparison of the electron kinetic energy contributions shows a large difference between the ab initio and the Gordon--Kim calculations. Using the ab initio data we derive an atom--atom potential of the two N 2 molecules. Although this expression does not accurately fit the data at some orientations, its spherical average agrees with the corresponding average of the ab initio Phi remarkably well. The spherically averaged ab initio Phi is also compared with the corresponding quantities derived from experimental considerations. The approach of the ab initio Phi to the classical quadrupole--quadrupole interaction at large intermolecular separation is also discussed

Relating hydrogen-bonding interactions with the phase behavior of naproxen/PVP K 25 solid dispersions: evaluation of solution-cast and quench-cooled films.

Science.gov (United States)

Paudel, Amrit; Nies, Erik; Van den Mooter, Guy

2012-11-05

In this work, we investigated the relationship between various intermolecular hydrogen-bonding (H-bonding) interactions and the miscibility of the model hydrophobic drug naproxen with the hydrophilic polymer polyvinylpyrrolidone (PVP) across an entire composition range of solid dispersions prepared by quasi-equilibrium film casting and nonequilibrium melt quench cooling. The binary phase behavior in solid dispersions exhibited substantial processing method dependence. The solid state solubility of crystalline naproxen in PVP to form amorphous solid dispersions was 35% and 70% w/w naproxen in solution-cast films and quench-cooled films, respectively. However, the presence of a single mixed phase glass transition indicated the amorphous miscibility to be 20% w/w naproxen for the films, beyond which amorphous-amorphous and/or crystalline phase separations were apparent. This was further supported by the solution state interactions data such as PVP globular size distribution and solution infrared spectral profiles. The borderline melt composition showed cooling rate dependence of amorphization. The glass transition and melting point depression profiles of the system were treated with the analytical expressions based on Flory-Huggins mixing theory to interpolate the equilibrium solid solubility. FTIR analysis and subsequent spectral deconvolution revealed composition and miscibility dependent variations in the strength of drug-polymer intermolecular H-bonding. Two types of H-bonded populations were evidenced from 25% w/w and 35% w/w naproxen in solution-cast films and quench-cooled films, respectively, with the higher fraction of strongly H-bonded population in the drug rich domains of phase separated amorphous film compositions and highly drug loaded amorphous quench-cooled dispersions.

Isomorphous Crystals from Diynes and Bromodiynes Involved in Hydrogen and Halogen Bonds

Directory of Open Access Journals (Sweden)

Pierre Baillargeon

2016-04-01

Full Text Available Isomorphous crystals of two diacetylene derivatives with carbamate functionality (BocNH-CH2-diyne-X, where X = H or Br have been obtained. The main feature of these structures is the original 2D arrangement (as supramolecular sheets or walls in which the H bond and halogen bond have a prominent effect on the whole architecture. The two diacetylene compounds harbor neighboring carbamate (Boc protected amine and conjugated alkyne functionalities. They differ only by the nature of the atom located at the penultimate position of the diyne moiety, either a hydrogen atom or a bromine atom. Both of them adopt very similar 2D wall organizations with antiparallel carbamates (as in antiparallel beta pleated sheets. Additional weak interactions inside the same walls between molecular bricks are H bond interactions (diyne-H···O=C or halogen bond interactions (diyne-Br···O=C, respectively. Based on crystallographic atom coordinates, DFT (B3LYP/6-31++G(d,p and DFT (M06-2X/6-31++G(d,p calculations were performed on these isostructural crystals to gain insight into the intermolecular interactions.

Cohesion: a scientific history of intermolecular forces

National Research Council Canada - National Science Library

Rowlinson, J. S

2002-01-01

.... The final section gives an account of the successful use in the 20th century of quantum mechanics and statistical mechanics to resolve most of the remaining problems. Throughout the last 300 years there have been periods of tremendous growth in our understanding of intermolecular forces but such interest proved to be unsustainable, and long periods of...

Ligand-accelerated activation of strong C-H bonds of alkanes by a (salen)ruthenium(VI)-nitrido complex.

Science.gov (United States)

Man, Wai-Lun; Lam, William W Y; Kwong, Hoi-Ki; Yiu, Shek-Man; Lau, Tai-Chu

2012-09-03

Kinetic and mechanistic studies on the intermolecular activation of strong C-H bonds of alkanes by a (salen)ruthenium(VI) nitride were performed. The initial, rate-limiting step, the hydrogen atom transfer (HAT) from the alkane to Ru(VI)≡N, generates Ru(V)=NH and RC·HCH(2)R. The following steps involve N-rebound and desaturation. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rewetting phenomena and their relation to intermolecular forces between a hot wall and the fluid

International Nuclear Information System (INIS)

Gerweck, V.

1989-12-01

The rewetting phenomena and the different physical concepts which are used in their modelisation are reviewed. The present work studies the effect of the intermolecular forces between the hot wall and the fluid on this phase transition. Using suitable approximations, a local equation of state is obtained by the treatment of the fluid-fluid and fluid-wall intermolecular interactions. This local equation of state depends on the distance from the wall, and the critical pressure and temperature become a function of the distance from the wall, whereas the critical density is left constant throughout the fluid. At the wall, the critical pressure and temperature are half their bulk values and increase towards the bulk value as the distance from the wall increases. The penetration of a temperature profile in this fluid is studied by assuming that the liquid density is not strongly affected by this temperature profile as long as there is no phase transition. It is shown that the phase transition will occur extremely rapidly when the interfacial temperature upon contact is higher than the minimum of the local spinodal temperature, which varies with the distance from the wall. The result ist cast in the form of an interfacial rewetting temperature fT c above which rewetting of the surface by liquid-wall contacts is not expected because these contacts will be terminated in extremely short times. Comparing the theory with available data shows that in the usual rewetting situations the theory reduces to the use of the bulk spinodal temperature. For surfaces coated with poorly wetted materials the correction factor due to surface effects applies, reducing the rewetting temperature, in agreement with the experimental data. For liquid metals it appears that the theory is applied in a region where the basic theoretical approximations are very coarse; but even in that case the experimental trend is qualitatively predicted by the theory. (author) 43 figs., 11 tabs., 105 refs

Self-assembly of Hydrazide-based Heterodimers Driven by Hydrogen Bonding and Donor-Acceptor Interaction

Institute of Scientific and Technical Information of China (English)

FENG,Dai-Jun; WANG,Peng; LI,Xiao-Qiang; LI,Zhan-Ting

2006-01-01

A new series of hydrogen bonding-driven heterodimers have been self-assembled in chloroform from hydrazide-based monomers. Additional intermolecular donor-acceptor interaction between the electron-rich bis(p-phenylene)-34-crown-10 unit and the electron-deficient naphthalene diimide unit has been utilized to increase the stability of the dimmers, and pronounced cooperativity of the two discrete non-covalent forces to stabilize the dimer has been revealed by the quantitative 1H (2D) NMR and UV-Vis experiments.

The iodine molecule insights into intra- and intermolecular perturbation in diatomic molecules

CERN Document Server

Lukashov, Sergey; Pravilov, Anatoly

2018-01-01

This book presents experimental and theoretical spectroscopic studies performed over the last 25 years on the iodine molecule’s excited states and their perturbations. It is going to be of interest to researchers who study intra- and intermolecular perturbations in diatomic molecules and more complex systems. The book offers a detailed treatment of the nonadiabatic perturbations of valence, ion pair and Rydberg states induced by intramolecular as well as intermolecular interactions in collisions or in weakly-bound complexes. It also provides an overview of current instrumentation and techniques as well as theoretical approaches describing intra- and intermolecular perturbations. The authors are experts in the use of spectroscopy for the study of intrinsic and collision-induced perturbations in diatomic iodine. They introduced new methods of two- and three-step optical population of the iodine ion-pair states. The iodine molecule has 23 valence states correlating with three dissociation limits, 20 so-called ...

Effective intermolecular potential and critical point for C60 molecule

Science.gov (United States)

Ramos, J. Eloy

2017-07-01

The approximate nonconformal (ANC) theory is applied to the C60 molecule. A new binary potential function is developed for C60, which has three parameters only and is obtained by averaging the site-site carbon interactions on the surface of two C60 molecules. It is shown that the C60 molecule follows, to a good approximation, the corresponding states principle with n-C8H18, n-C4F10 and n-C5F12. The critical point of C60 is estimated in two ways: first by applying the corresponding states principle under the framework of the ANC theory, and then by using previous computer simulations. The critical parameters obtained by applying the corresponding states principle, although very different from those reported in the literature, are consistent with the previous results of the ANC theory. It is shown that the Girifalco potential does not correspond to an average of the site-site carbon-carbon interaction.

Characterization of the hydrogen bond in molecular systems of biological interest by neutron scattering

International Nuclear Information System (INIS)

Cavillon, F.

2004-10-01

This work presents a methodology for the analysis of the scattering spectra of neutrons on molecular liquids. This method is based on the adjustment of the molecular form factor concerning great momentum transfer. The subtraction of the intra-molecular contributions gives access to information on inter-molecular interactions such as the hydrogen bond. 3 systems with increasing levels of difficulty have been studied: the ammonia molecule, the N-methyl-formamide (NMF) and the N-methyl-acetamide (NMA). The value we get for the N-D intermolecular distance of the liquid ammonia molecule is 1.7 angstrom, this value is different from the value generally admitted (2.3 angstrom) but we have validated it by studying the isotopic substitution N 14 /N 15 . The adjustment to the NMF is obtained with a good accuracy but the characterization of the hydrogen bound is more delicate to infer. A preliminary study of the NMA molecule shows that this method can give relevant results on complex molecules

Bondability of processed glass wafers

NARCIS (Netherlands)

Pandraud, G.; Gui, C.; Lambeck, Paul; Pigeon, F.; Parriaux, O.; Gorecki, Christophe

1999-01-01

The mechanism of direct bonding at room temperature has been attributed to the short range inter-molecular and inter-atomic attraction forces, such as Van der Waals forces. Consequently, the wafer surface smoothness becomes one of the most critical parameters in this process. High surface roughness

Orientation correlation and intermolecular structure of GeCl4, VCl4 and other tetrachloride liquids

International Nuclear Information System (INIS)

Nath, P.P.; Sarkar, S.; Joarder, R.N.

2007-01-01

The intermolecular structure and correlation of GeCl 4 , VCl 4 and other tetrachloride liquids can be well described by Misawa's orientation correlation model originally applied to liquid CCl 4 . The model supports on average a specific 'corner' to 'face' correlation, but evidently very different from 'Apollo' type model. The Misawa model appears to work, in some respect, even better than reference interaction site model (RISM) used for long to describe intermolecular structure of such molecular systems. The test and comparison are made through the calculation of small asymmetric part of the intermolecular structure and evaluation of partial atom-atom distribution functions

Raman Spectra and Intermolecular Hydrogen Bonds of Quinoline in Solutions

International Nuclear Information System (INIS)

Tukhvatullin, F.H.; Jumabayev, A.; Hushvaktov, H.; Absanov, A.; Hudoyberdiev, B.

2012-01-01

The half-widths of the 1014- and 1033-cm -1 bands of the Raman spectrum of quinoline at its dilution in neutral solvents (benzene, CCl 4 ) are narrowed by 1.3-1.5 times at high dilutions. This effect is associated with the increased time of the vibrational relaxation. For the 520-cm -1 band in pure liquid quinoline, the parallel polarized component at 20 o C is asymmetric in the high-frequency region. The shape of the perpendicular polarized component is complicated. A non-coincidence of the peak frequencies of the parallel and perpendicular polarized components is observed (∼ 2 cm -1 ). Quantum-chemical calculations showed that, in the region of 520 cm -1 for a monomer molecule, we should really have two near located lines with the wavenumbers 530 and 527 cm -1 (scaling factor 0.97), and with the depolarization ratios 0.61 and 0.26. In the solutions with propan-2-ol, the 1033.8-cm -1 band becomes of a doublet character. The resolution of the doublet becomes better by the dilution of a binary quinoline-alcohol solution with a large amount of a neutral solvent (benzene). The wavenumbers of bands in the triple mixture are 1033 cm -1 and 1039 cm -1 . The doublet nature of the band in the binary and triple mixtures is associated with the presence of monomer molecules and quinoline-propan-2-ol aggregates (the high-frequency line) in the liquid mixture. Quantum-chemical calculations showed that the hydrogen bonds with a length of 1.958 A and an energy gain of 22.0 kJ/mole can be formed between molecules of quinoline and alcohol. The formation of aggregates can be also detected in the 820-cm -1 band of propan-2-ol. A similar picture is observed for the 667-cm -1 band of chloroform in its solution with quinoline.

Conformations and Intermolecular Interactions in Cellulose/Silk Fibroin Blend Films: A Solid-State NMR Perspective.

Science.gov (United States)

Tian, Donglin; Li, Tao; Zhang, Rongchun; Wu, Qiang; Chen, Tiehong; Sun, Pingchuan; Ramamoorthy, Ayyalusamy

2017-06-29

Fabricating materials with excellent mechanical performance from the natural renewable and degradable biopolymers has drawn significant attention in recent decades due to the environmental concerns and energy crisis. As two of the most promising substitutes of synthetic polymers, silk fibroin (SF), and cellulose, have been widely used in the field of textile, biomedicine, biotechnology, etc. Particularly, the cellulose/SF blend film exhibits better strength and toughness than that of regenerated cellulose film. Herein, this study is aimed to understand the molecular origin of the enhanced mechanical properties for the cellulose/SF blend film, using solid-state NMR as a main tool to investigate the conformational changes, intermolecular interactions between cellulose and SF and the water organization. It is found that the content of the β-sheet structure is increased in the cellulose/SF blend film with respect to the regenerated SF film, accompanied by the reduction of the content of random coil structures. In addition, the strong hydrogen bonding interaction between the SF and cellulose is clearly elucidated by the two-dimensional (2D) 1 H- 13 C heteronuclear correlation (HETCOR) NMR experiments, demonstrating that the SF and cellulose are miscible at the molecular level. Moreover, it is also found that the -NH groups of SF prefer to form hydrogen bonds with the hydroxyl groups bonded to carbons C2 and C3 of cellulose, while the hydroxyl groups bonded to carbon C6 and the ether oxygen are less favorable for hydrogen bonding interactions with the -NH groups of SF. Interestingly, bound water is found to be present in the air-dried cellulose/SF blend film, which is predominantly associated with the cellulose backbones as determined by 2D 1 H- 13 C wide-line-separation (WISE) experiments with spin diffusion. This clearly reveals the presence of nanoheterogeneity in the cellulose/SF blend film, although cellulose and SF are miscible at a molecular level. Without doubt

Dancing Crystals: A Dramatic Illustration of Intermolecular Forces

Science.gov (United States)

Mundell, Donald W.

2007-01-01

Crystals of naphthalene form on the surface of an acetone solution and dance about in an animated fashion illustrating surface tension, crystallization, and intermolecular forces. Additional experiments reveal the properties of the solution. Flows within the solutions can be visualized by various means. Previous demonstrations of surface motion…

Chemical activation of molecules by metals: Experimental studies of electron distributions and bonding

International Nuclear Information System (INIS)

Lichienberger, D.L.

1990-10-01

This quarter has witnessed further progress both in our experimental methods of photoelectron spectroscopy and in our understanding the fundamental relationships between ionization energies and the chemistry of transition metal species. Progress continues on the new gas phase photoelectron spectrometer that combine improved capabilities for HeI/HeII UPS, XPS, and Auger investigations of organometallic molecules. Several measurements have been accomplished this year that were not possible previously. We have published the formal relationship between measured molecular ionization energies and thermodynamic bond dissociation energies, and applied the relationships to homonuclear and heteronuclear diatomic molecules, multiple bonds, and metal-ligand bonds. Studies of C-H bond activation have continued with examination of different degrees of Si-H bond addition to metals. the electronic effects of intermolecular interactions have been observed by comparing the ionizations of metal complexes in the gas phase with the ionizations of monolayer solid organometallic films prepared in ultra-high vacuum. The orientations of the molecules have been determined by scanning tunneling microscopy. Especially interesting has been the recent application of these techniques to the characterization of the soccer-ball shaped C 60 molecule, buckminsterfullerene. Studies of the following complexes are described : Fe, Os, Nb, Mo, Rh, Re, Al, and Mn. 19 refs

Radiation-induced cleavage of disulfide bonds in proteins. Clivage radiolytique des ponts disulfure des proteines

Energy Technology Data Exchange (ETDEWEB)

Favaudon, V; Tourbez, H; Lhoste, J M [Paris-11 Univ., 91 - Orsay (FR); Houee-Levin, C [Paris-5 Univ., 75 (FR)

1991-06-01

The reduction of the disulfide bonds in apo-Riboflavin-Binding Protein (apoRBP) by the CO{sub 2}{sup -}{center dot} radical occurred under {gamma}-ray irradiation as a chain reaction whose efficiency increased upon acidification of the medium. Pulse-radiolysis analysis showed a rapid one-electron oxidation of the disulfide bonds yielding the anionic or protonated form of the disulfide radical. The main decay path of this radical under acidic conditions consisted of the rapid formation of a thiyl radical intermediate in equilibrium with the closed, cyclic form. At pH 8 the disulfide radical anion decayed via intramolecular and/or intermolecular routes including disproportionation, protein-protein crosslinking, non-dismutative recombination processes, and reaction with sulfhydryl groups in pre-reduced systems.

Picture change error in quasirelativistic electron/spin density, Laplacian and bond critical points

KAUST Repository

Bučinský , Luká š; Kucková , Lenka; Malček, Michal; Koží šek, Jozef; Biskupič, Stanislav; Jayatilaka, Dylan; Bü chel, Gabriel E.; Arion, Vladimir B.

2014-01-01

The change of picture of the quasirelativistic Hartree-Fock wave functions is considered for electron/spin densities, the negative Laplacian of electron density and the appropriate bond critical point characteristics from the Quantum Theory of Atoms In Molecules (QTAIM). [OsCl5(Hpz)]- and [RuCl5(NO)]2- transition metal complexes are considered. Both, scalar relativistic and spin-orbit effects have been accounted for using the Infinite Order Two Component (IOTC) Hamiltonian. Picture change error (PCE) correction in the electron and spin densities and the Laplacian of electron density are treated analytically. Generally, PCE is found significant only in the core region of the atoms for the electron/spin density as well as Laplacian.©2014 Elsevier B.V. All rights reserved.

Picture change error in quasirelativistic electron/spin density, Laplacian and bond critical points

KAUST Repository

Bučinský, Lukáš

2014-06-01

The change of picture of the quasirelativistic Hartree-Fock wave functions is considered for electron/spin densities, the negative Laplacian of electron density and the appropriate bond critical point characteristics from the Quantum Theory of Atoms In Molecules (QTAIM). [OsCl5(Hpz)]- and [RuCl5(NO)]2- transition metal complexes are considered. Both, scalar relativistic and spin-orbit effects have been accounted for using the Infinite Order Two Component (IOTC) Hamiltonian. Picture change error (PCE) correction in the electron and spin densities and the Laplacian of electron density are treated analytically. Generally, PCE is found significant only in the core region of the atoms for the electron/spin density as well as Laplacian.©2014 Elsevier B.V. All rights reserved.

Chalcogen- and halogen-bonds involving SX2 (X = F, Cl, and Br) with formaldehyde.

Science.gov (United States)

Mo, Lixin; Zeng, Yanli; Li, Xiaoyan; Zhang, Xueying; Meng, Lingpeng

2016-07-01

The capacity of SX2 (X = F, Cl, and Br) to engage in different kinds of noncovalent bonds was investigated by ab initio calculations. SCl2 (SBr2) has two σ-holes upon extension of Cl (Br)-S bonds, and two σ-holes upon extension of S-Cl (Br) bonds. SF2 contains only two σ-holes upon extension of the F-S bond. Consequently, SCl2 and SBr2 form chalcogen and halogen bonds with the electron donor H2CO while SF2 forms only a chalcogen bond, i.e., no F···O halogen bond was found in the SF2:H2CO complex. The S···O chalcogen bond between SF2 and H2CO is the strongest, while the strongest halogen bond is Br···O between SBr2 and H2CO. The nature of these two types of noncovalent interaction was probed by a variety of methods, including molecular electrostatic potentials, QTAIM, energy decomposition, and electron density shift maps. Termolecular complexes X2S···H2CO···SX'2 (X = F, Cl, Br, and X' = Cl, Br) were constructed to study the interplay between chalcogen bonds and halogen bonds. All these complexes contained S···O and Cl (Br)···O bonds, with longer intermolecular distances, smaller values of electron density, and more positive three-body interaction energies, indicating negative cooperativity between the chalcogen bond and the halogen bond. In addition, for all complexes studied, interactions involving chalcogen bonds were more favorable than those involving halogen bonds. Graphical Abstract Molecular electrostatic potential and contour map of the Laplacian of the electron density in Cl2S···H2CO···SCl2 complex.

Experimental studies on the nature of bonding of DNA/bipyridyl-(ethylenediamine)platinum(II) and DNA/netropsin complexes in solution and oriented wet-spun films

Science.gov (United States)

Marlowe, R. L.; Szabo, A.; Lee, S. A.; Rupprecht, A.

2002-03-01

The stability of complexes of NaDNA with bipyridyl-(ethylenediamine)platinum(II) (abbreviated [(bipy)Pt(en)]) and with netropsin has been studied using two techniques: (i) ultraviolet melting experiments were done on NaDNA/[(bipy)Pt(en)], showing that the [(bipy)Pt(en)] ligand stabilizes the DNA double helix structure; and (ii) swelling measurements (via optical microscopy) as a function of relative humidity were done on wet-spun oriented films of NaDNA/[(bipy)Pt(en)] and of NaDNA/netropsin. The swelling data shows that an irreversible transition of the films occurs at high relative humidity, first for the NaDNA/netropsin, then for pure NaDNA, and lastly for the NaDNA/[(bipy)Pt(en)]. These results are indicative that the [(bipy)Pt(en)] complex stabilizes the intermolecular bonds which mediate the film swelling characteristics. A model is suggested for the binding of [(bipy)Pt(en)] to DNA to explain why the swelling experiments show this ligand as increasing the intermolecular bond strength between the DNA double helices, while netropsin decreases this degree of stabilization.

Arginine-phosphate salt bridges between histones and DNA: Intermolecular actuators that control nucleosome architecture

Science.gov (United States)

Yusufaly, Tahir I.; Li, Yun; Singh, Gautam; Olson, Wilma K.

2014-10-01

Structural bioinformatics and van der Waals density functional theory are combined to investigate the mechanochemical impact of a major class of histone-DNA interactions, namely, the formation of salt bridges between arginine residues in histones and phosphate groups on the DNA backbone. Principal component analysis reveals that the configurational fluctuations of the sugar-phosphate backbone display sequence-specific directionality and variability, and clustering of nucleosome crystal structures identifies two major salt-bridge configurations: a monodentate form in which the arginine end-group guanidinium only forms one hydrogen bond with the phosphate, and a bidentate form in which it forms two. Density functional theory calculations highlight that the combination of sequence, denticity, and salt-bridge positioning enables the histones to apply a tunable mechanochemical stress to the DNA via precise and specific activation of backbone deformations. The results suggest that selection for specific placements of van der Waals contacts, with high-precision control of the spatial distribution of intermolecular forces, may serve as an underlying evolutionary design principle for the structure and function of nucleosomes, a conjecture that is corroborated by previous experimental studies.

Chemical activation of molecules by metals: Experimental studies of electron distributions and bonding

International Nuclear Information System (INIS)

Lichtenberger, D.L.

1991-10-01

The formal relationship between measured molecular ionization energies and thermodynamic bond dissociation energies has been developed into a single equation which unifies the treatment of covalent bonds, ionic bonds, and partially ionic bonds. This relationship has been used to clarify the fundamental thermodynamic information relating to metal-hydrogen, metal-alkyl, and metal-metal bond energies. We have been able to obtain a direct observation and measurement of the stabilization energy provided by the agostic interaction of the C-H bond with the metal. The ionization energies have also been used to correlate the rates of carbonyl substitution reactions of (η 5 -C 5 H 4 X)Rh(CO) 2 complexes, and to reveal the electronic factors that control the stability of the transition state. The extent that the electronic features of these bonding interactions transfer to other chemical systems is being investigated in terms of the principle of additivity of ligand electronic effects. Specific examples under study include metal- phosphines, metal-halides, and metallocenes. Especially interesting has been the recent application of these techniques to the characterization of the soccer-ball shaped C 60 molecule, buckminsterfullerene, and its interaction with a metal surface. The high-resolution valence ionizations in the gas phase reveal the high symmetry of the molecule, and studies of thin films of C 60 reveal weak intermolecular interactions. Scanning tunneling and atomic force microscopy reveal the arrangement of spherical molecules on gold substrates, with significant delocalization of charge from the metal surface. 21 refs

Digital communication through intermolecular fluorescence modulation.

Science.gov (United States)

Raymo, F M; Giordani, S

2001-06-14

[see reaction]. Ultraminiaturized processors incorporating molecular components can be developed only after devising efficient strategies to communicate signals at the molecular level. We have demonstrated that a three-state molecular switch responds to ultraviolet light, visible light, and H+, attenuating the emission intensity of a fluorescent probe. Intermolecular communication is responsible for the transduction of three input signals into a single optical output. The behavior of the communicating ensemble of molecules corresponds to that of a logic circuit incorporating seven gates.

How overdrying wood reduces its bonding to phenol-formaldehyde adhesives : a critical review of the literature. Part II, Chemical reactions

Science.gov (United States)

Alfred W. Christiansen

1991-01-01

Literature dealing with the effect of excessive drying (overdrying) on wood surface inactivation to bonding is reviewed in two parts and critically evaluated, primarily for phenolic adhesives. Part 1 of the review, published earlier, covers physical mechanisms that could contribute to surface inactivation. The principal physical mechanism is the migration to the...

How overdrying wood reduces its bonding to phenol-formaldehyde adhesives : a critical review of the literature. Part I, Physical responses

Science.gov (United States)

Alfred W. Christiansen

1990-01-01

This review critically evaluates literature on the ways in which excessive drying (overdrying) inactivates wood surfaces to bonding, primarily for phenolic adhesives. In Part I of a two-part review, three inactivation mechanisms involving physical responses to overdrying are considered: (1) exudation of extractives to the surface, which lowers the wettability or hides...

Influencing the bonding and assembly of a multiterminal molecule on a metal surface

Energy Technology Data Exchange (ETDEWEB)

Lukas, Maya; Doessel, Kerrin; Fink, Karin; Fuhr, Olaf [Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology, D-76021 Karlsruhe (Germany); DFG Center of Functional Nanostructures (CFN), D-76049 Karlsruhe (Germany); Schramm, Alexandrina; Stroh, Christophe [Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology, D-76021 Karlsruhe (Germany); Mayor, Marcel [Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology, D-76021 Karlsruhe (Germany); DFG Center of Functional Nanostructures (CFN), D-76049 Karlsruhe (Germany); University of Basel, Department of Chemistry, CH-4056 Basel (Switzerland); Loehneysen, Hilbert von [Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology, D-76021 Karlsruhe (Germany); DFG Center of Functional Nanostructures (CFN), D-76049 Karlsruhe (Germany); Karlsruhe Institute of Technology (KIT), Physics Institute and Institute for Solid State Physics, D-76049 Karlsruhe (Germany)

2011-07-01

The bond of a molecule to a metallic electrode is known to have a crucial influence on the molecular conductance. As electronic functionalities are integrated into molecules or several subunits are connected to a three-dimensional multiterminal molecule, it is not obvious that a ''well-known'' chemical linker group will lead to the bonding configuration known from simpler molecules. We investigated a series of tripodal molecules on metal surfaces by STM. The chemical linker groups and the complex connecting the three wire-units are varied. We find that the position of molecules on the surface is governed by a subtle balance of intermolecular and molecule-surface interactions, partly in strong contrast to expectations. This emphasizes the need to characterize the nature of molecule-electrode contacts along with the investigation of the electronic conductance.

Ab initio path-integral molecular dynamics and the quantum nature of hydrogen bonds

International Nuclear Information System (INIS)

Feng Yexin; Chen Ji; Wang Enge; Li Xin-Zheng

2016-01-01

The hydrogen bond (HB) is an important type of intermolecular interaction, which is generally weak, ubiquitous, and essential to life on earth. The small mass of hydrogen means that many properties of HBs are quantum mechanical in nature. In recent years, because of the development of computer simulation methods and computational power, the influence of nuclear quantum effects (NQEs) on the structural and energetic properties of some hydrogen bonded systems has been intensively studied. Here, we present a review of these studies by focussing on the explanation of the principles underlying the simulation methods, i.e., the ab initio path-integral molecular dynamics. Its extension in combination with the thermodynamic integration method for the calculation of free energies will also be introduced. We use two examples to show how this influence of NQEs in realistic systems is simulated in practice. (topical review)

Intermolecular interactions in the condensed phase

DEFF Research Database (Denmark)

Christensen, Anders S.; Kromann, Jimmy Charnley; Jensen, Jan Halborg

2017-01-01

To facilitate further development of approximate quantum mechanical methods for condensed phase applications, we present a new benchmark dataset of intermolecular interaction energies in the solution phase for a set of 15 dimers, each containing one charged monomer. The reference interaction energy...... and solution phases. As most approximate QM methods are parametrized and evaluated using data measured or calculated in the gas phase, the dataset represents an important first step toward calibrating QM based methods for application in the condensed phase where polarization and exchange repulsion need...

Chalcogen and Pnicogen Bonds in Complexes of Neutral Icosahedral and Bicapped Square-Antiprismatic Heteroboranes

Czech Academy of Sciences Publication Activity Database

Pecina, Adam; Lepšík, Martin; Hnyk, Drahomír; Hobza, Pavel; Fanfrlík, Jindřich

2015-01-01

Roč. 119, č. 8 (2015), s. 1388-1395 ISSN 1089-5639 R&D Projects: GA ČR GBP208/12/G016; GA ČR GAP208/10/2269 Grant - others:GA MŠk(CZ) LM2011033; GA MŠk(CZ) ED2.1.00/03.0058; GA MŠk(CZ) ED1.1.00/02.0070 Program:ED; ED Institutional support: RVO:61388963 ; RVO:61388980 Keywords : intermolecular interaction energies * Kohn-Sham orbitals * halogen bond Subject RIV: CF - Physical ; Theoretical Chemistry; CA - Inorganic Chemistry (UACH-T) Impact factor: 2.883, year: 2015

Intermolecular interaction potentials of the methane dimer from the local density approximation

International Nuclear Information System (INIS)

Chen Xiangrong; Bai Yulin; Zhu Jun; Yang Xiangdong

2004-01-01

The intermolecular interaction potentials of methane (CH 4 ) dimer are calculated within the density functional theory in the local density approximation (LDA). It is found that the calculated potentials have minima when the intermolecular distance of CH 4 dimer is about 7.0 a.u., which is in good agreement with the experiment. The depth of the potential is 0.017 eV. The results obtained by our LDA calculations seem to agree well with those obtained by MP2, MP3, and CCSD from the Moeller-Plesset and coupled cluster methods by Tsuzuki et al. and with the experimental data

Study of intermolecular interactions in binary mixtures of ethanol in methanol

Science.gov (United States)

Maharolkar, Aruna P.; Khirade, P. W.; Murugkar, A. G.

2016-05-01

Present paper deals with study of physicochemical properties like viscosity, density and refractive index for the binary mixtures of ethanol and methanol over the entire concentration range were measured at 298.15 K. The experimental data further used to determine the excess properties viz. excess molar volume, excess viscosity, excess molar refraction. The values of excess properties further fitted with Redlich-Kister (R-K Fit) equation to calculate the binary coefficients and standard deviation. The resulting excess parameters are used to indicate the presence of intermolecular interactions and strength of intermolecular interactions between the molecules in the binary mixtures. Excess parameters indicate structure making factor in the mixture predominates in the system.

Molecular dynamics simulation of nonlinear spectroscopies of intermolecular motions in liquid water.

Science.gov (United States)

Yagasaki, Takuma; Saito, Shinji

2009-09-15

Water is the most extensively studied of liquids because of both its ubiquity and its anomalous thermodynamic and dynamic properties. The properties of water are dominated by hydrogen bonds and hydrogen bond network rearrangements. Fundamental information on the dynamics of liquid water has been provided by linear infrared (IR), Raman, and neutron-scattering experiments; molecular dynamics simulations have also provided insights. Recently developed higher-order nonlinear spectroscopies open new windows into the study of the hydrogen bond dynamics of liquid water. For example, the vibrational lifetimes of stretches and a bend, intramolecular features of water dynamics, can be accurately measured and are found to be on the femtosecond time scale at room temperature. Higher-order nonlinear spectroscopy is expressed by a multitime correlation function, whereas traditional linear spectroscopy is given by a one-time correlation function. Thus, nonlinear spectroscopy yields more detailed information on the dynamics of condensed media than linear spectroscopy. In this Account, we describe the theoretical background and methods for calculating higher order nonlinear spectroscopy; equilibrium and nonequilibrium molecular dynamics simulations, and a combination of both, are used. We also present the intermolecular dynamics of liquid water revealed by fifth-order two-dimensional (2D) Raman spectroscopy and third-order IR spectroscopy. 2D Raman spectroscopy is sensitive to couplings between modes; the calculated 2D Raman signal of liquid water shows large anharmonicity in the translational motion and strong coupling between the translational and librational motions. Third-order IR spectroscopy makes it possible to examine the time-dependent couplings. The 2D IR spectra and three-pulse photon echo peak shift show the fast frequency modulation of the librational motion. A significant effect of the translational motion on the fast frequency modulation of the librational motion is

Hexacoordinate bonding and aromaticity in silicon phthalocyanine.

Science.gov (United States)

Yang, Yang

2010-12-23

Si-E bondings in hexacoordinate silicon phthalocyanine were analyzed using bond order (BO), energy partition, atoms in molecules (AIM), electron localization function (ELF), and localized orbital locator (LOL). Bond models were proposed to explain differences between hexacoordinate and tetracoordinate Si-E bondings. Aromaticity of silicon phthalocyanine was investigated using nucleus-independent chemical shift (NICS), harmonic oscillator model of aromaticity (HOMA), conceptual density functional theory (DFT), ring critical point (RCP) descriptors, and delocalization index (DI). Structure, energy, bonding, and aromaticity of tetracoordinate silicon phthalocyanine were studied and compared with hexacoordinate one.

Hydrogen Bonding, (1)H NMR, and Molecular Electron Density Topographical Characteristics of Ionic Liquids Based on Amino Acid Cations and Their Ester Derivatives.

Science.gov (United States)

Rao, Soniya S; Bejoy, Namitha Brijit; Gejji, Shridhar P

2015-08-13

Amino acid ionic liquids (AAILs) have attracted significant attention in the recent literature owing to their ubiquitous applications in diversifying areas of modern chemistry, materials science, and biosciences. The present work focuses on unraveling the molecular interactions underlying AAILs. Electronic structures of ion pairs consisting of amino acid cations ([AA(+)], AA = Gly, Ala, Val, Leu, Ile, Pro, Ser, Thr) and their ester substituted derivatives [AAE(+)] interacting with nitrate anion [NO3(-)] have been obtained from the dispersion corrected M06-2x density functional theory. The formation of ion pair is accompanied by the transfer of proton from quaternary nitrogen to anion facilitated via hydrogen bonding. The [Ile], [Pro], [Ser], and [Thr] and their esters reveal relatively strong inter- as well as intramolecular hydrogen-bonding interactions. Consequently, the hierarchy in binding energies of [AA][NO3] ion pairs and their ester analogues turns out to be [Gly] > [Ala] > [Ser] ∼ [Val] ∼ [Ile] > [Leu] ∼ [Thr] > [Pro]. The work underlines how the interplay of intra- as well as intermolecular hydrogen-bonding interactions in [AA]- and [AAE]-based ILs manifest in their infrared and (1)H NMR spectra. Substitution of -OCH3 functional group in [AA][NO3] ILs lowers the melting point attributed to weaker hydrogen-bonding interactions, making them suitable for room temperature applications. As opposed to gas phase structures, the presence of solvent (DMSO) does not bring about any proton transfer in the ion pairs or their ester analogues. Calculated (1)H NMR chemical shifts of the solvated structures agree well with those from experiment. Correlations of decomposition temperatures in [AA]- and [AAE]-based ILs with binding energies and electron densities at the bond critical point(s) in molecular electron density topography, have been established.

Tunable differentiation of tertiary C-H bonds in intramolecular transition metal-catalyzed nitrene transfer reactions.

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Corbin, Joshua R; Schomaker, Jennifer M

2017-04-13

Metal-catalyzed nitrene transfer reactions are an appealing and efficient strategy for accessing tetrasubstituted amines through the direct amination of tertiary C-H bonds. Traditional catalysts for these reactions rely on substrate control to achieve site-selectivity in the C-H amination event; thus, tunability is challenging when competing C-H bonds have similar steric or electronic features. One consequence of this fact is that the impact of catalyst identity on the selectivity in the competitive amination of tertiary C-H bonds has not been well-explored, despite the potential for progress towards predictable and catalyst-controlled C-N bond formation. In this communication, we report investigations into tunable and site-selective nitrene transfers between tertiary C(sp 3 )-H bonds using a combination of transition metal catalysts, including complexes based on Ag, Mn, Rh and Ru. Particularly striking was the ability to reverse the selectivity of nitrene transfer by a simple change in the identity of the N-donor ligand supporting the Ag(i) complex. The combination of our Ag(i) catalysts with known Rh 2 (ii) complexes expands the scope of successful catalyst-controlled intramolecular nitrene transfer and represents a promising springboard for the future development of intermolecular C-H N-group transfer methods.

Spectroscopic, DFT, and XRD Studies of Hydrogen Bonds in N-Unsubstituted 2-Aminobenzamides.

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Mphahlele, Malose Jack; Maluleka, Marole Maria; Rhyman, Lydia; Ramasami, Ponnadurai; Mampa, Richard Mokome

2017-01-04

The structures of the mono- and the dihalogenated N -unsubstituted 2-aminobenzamides were characterized by means of the spectroscopic (¹H-NMR, UV-Vis, FT-IR, and FT-Raman) and X-ray crystallographic techniques complemented with a density functional theory (DFT) method. The hindered rotation of the C(O)-NH₂ single bond resulted in non-equivalence of the amide protons and therefore two distinct resonances of different chemical shift values in the ¹H-NMR spectra of these compounds were observed. 2-Amino-5-bromobenzamide ( ABB ) as a model confirmed the presence of strong intramolecular hydrogen bonds between oxygen and the amine hydrogen. However, intramolecular hydrogen bonding between the carbonyl oxygen and the amine protons was not observed in the solution phase due to a rapid exchange of these two protons with the solvent and fast rotation of the Ar-NH₂ single bond. XRD also revealed the ability of the amide unit of these compounds to function as a hydrogen bond donor and acceptor simultaneously to form strong intermolecular hydrogen bonding between oxygen of one molecule and the NH moiety of the amine or amide group of the other molecule and between the amine nitrogen and the amide hydrogen of different molecules. DFT calculations using the B3LYP/6-311++G(d,p) basis set revealed that the conformer ( A ) with oxygen and 2-amine on the same side predominates possibly due to the formation of a six-membered intramolecular ring, which is assisted by hydrogen bonding as observed in the single crystal XRD structure.

Spectroscopic, DFT, and XRD Studies of Hydrogen Bonds in N-Unsubstituted 2-Aminobenzamides

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Malose Jack Mphahlele

2017-01-01

Full Text Available The structures of the mono- and the dihalogenated N-unsubstituted 2-aminobenzamides were characterized by means of the spectroscopic (1H-NMR, UV-Vis, FT-IR, and FT-Raman and X-ray crystallographic techniques complemented with a density functional theory (DFT method. The hindered rotation of the C(O–NH2 single bond resulted in non-equivalence of the amide protons and therefore two distinct resonances of different chemical shift values in the 1H-NMR spectra of these compounds were observed. 2-Amino-5-bromobenzamide (ABB as a model confirmed the presence of strong intramolecular hydrogen bonds between oxygen and the amine hydrogen. However, intramolecular hydrogen bonding between the carbonyl oxygen and the amine protons was not observed in the solution phase due to a rapid exchange of these two protons with the solvent and fast rotation of the Ar–NH2 single bond. XRD also revealed the ability of the amide unit of these compounds to function as a hydrogen bond donor and acceptor simultaneously to form strong intermolecular hydrogen bonding between oxygen of one molecule and the NH moiety of the amine or amide group of the other molecule and between the amine nitrogen and the amide hydrogen of different molecules. DFT calculations using the B3LYP/6-311++G(d,p basis set revealed that the conformer (A with oxygen and 2-amine on the same side predominates possibly due to the formation of a six-membered intramolecular ring, which is assisted by hydrogen bonding as observed in the single crystal XRD structure.

Local electronic and geometrical structures of hydrogen-bonded complexes studied by soft X-ray spectroscopy

International Nuclear Information System (INIS)

Luo, Y.

2004-01-01

Full text: The hydrogen bond is one of the most important forms of intermolecular interactions. It occurs in all-important components of life. However, the electronic structures of hydrogen-bonded complexes in liquid phases have long been difficult to determine due to the lack of proper experimental techniques. In this talk, a recent joint theoretical and experimental effort to understand hydrogen bonding in liquid water and alcohol/water mixtures using synchrotron radiation based soft-X-ray spectroscopy will be presented. The complexity of the liquid systems has made it impossible to interpret the spectra with physical intuition alone. Theoretical simulations have thus played an essential role in understanding the spectra and providing valuable insights on the local geometrical and electronic structures of these liquids. Our study sheds light on a 40-year controversy over what kinds of molecular structures are formed in pure liquid methanol. It also suggests an explanation for the well-known puzzle of why alcohol and water do not mix completely: the system must balance nature's tendency toward greater disorder (entropy) with the molecules' tendency to form hydrogen bonds. The observation of electron sharing and broken hydrogen bonding local structures in liquid water will be presented. The possible use of X-ray spectroscopy to determinate the local arrangements of hydrogen-bonded nanostructures will also been discussed

On the critical point of the fully-anisotropic quenched bond-random Potts ferromagnet in triangular and honeycomb lattices

International Nuclear Information System (INIS)

Tsallis, C.; Santos, R.J.V. dos

1983-01-01

On conjectural grounds an equation that provides a very good approximation for the critical temperature of the fully-anisotropic homogeneous quenched bond-random q-state Potts ferromagnet in triangular and honeycomb lattices is presented. Almost all the exact particular results presently known for the square, triangular and honeycomb lattices are recovered; the numerical discrepancy is quite small for the few exceptions. Some predictions that we believe to be exact are made explicite as well. (Author) [pt

N-Oxide-N-oxide interactions and Cl...Cl halogen bonds in pentachloropyridine N-oxide: the many-body approach to interactions in the crystal state.

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Wzgarda-Raj, Kinga; Rybarczyk-Pirek, Agnieszka J; Wojtulewski, Sławomir; Palusiak, Marcin

2018-02-01

Pentachloropyridine N-oxide, C 5 Cl 5 NO, crystallizes in the monoclinic space group P2 1 /c. In the crystal structure, molecules are linked by C-Cl...Cl halogen bonds into infinite ribbons extending along the crystallographic [100] direction. These molecular aggregates are further stabilized by very short intermolecular N-oxide-N-oxide interactions into herringbone motifs. Computations based on quantum chemistry methods allowed for a more detailed description of the N-oxide-N-oxide interactions and Cl...Cl halogen bonds. For this purpose, Hirshfeld surface analysis and the many-body approach to interaction energy were applied.

Hydrogen-Bonded Polymer-Small Molecule Complexes with Tunable Mechanical Properties.

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Liu, Tianqi; Peng, Xin; Chen, Ya-Nan; Bai, Qing-Wen; Shang, Cong; Zhang, Lin; Wang, Huiliang

2018-03-13

A novel type of polymeric material with tunable mechanical properties is fabricated from polymers and small molecules that can form hydrogen-bonded intermolecular complexes (IMCs). In this work, poly(vinyl alcohol) (PVA)-glycerol hydrogels are first prepared, and then they are dried to form IMCs. The tensile strengths and moduli of IMCs decrease dramatically with increasing glycerol content, while the elongations increase gradually. The mechanical properties are comparable with or even superior to those of common engineering plastics and rubbers. The IMCs with high glycerol content also show excellent flexibility and cold-resistance at subzero temperatures. Cyclic tensile and stress relaxation tests prove that there is an effective energy dissipation mechanism in IMCs and dynamic mechanical analysis confirms their physical crosslinking nature. FTIR and NMR characterizations prove the existence of hydrogen bonding between glycerol and PVA chains, which suppresses the crystallization of PVA from X-ray diffraction measurement. These PVA-glycerol IMCs may find potential applications in barrier films, biomedical packaging, etc., in the future. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Insights into the Diels-Alder Reaction between 3-Vinylindoles and Methyleneindolinone without and with the Assistance of Hydrogen-Bonding Catalyst Bisthiourea: Mechanism, Origin of Stereoselectivity, and Role of Catalyst.

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Yan, Chao-Xian; Yang, Fan; Yang, Xing; Zhou, Da-Gang; Zhou, Pan-Pan

2017-03-17

The Diels-Alder reaction between 3-vinylindoles and methyleneindolinone can proceed both under catalyst-free conditions and with bisthiourea as the catalyst. The reaction with bisthiourea is much faster and results in higher stereoselectivity of the product. The reaction mechanism, origin of stereoselectivity, and role of the catalyst were elaborated based on quantum mechanical calculations and theoretical methods of reactivity indices, NCI, QTAIM, and distortion/interaction models. In the uncatalyzed reaction, the two C-C bonds that are formed undergo conversion from noncovalent to covalent bonding via a concerted asynchronous mechanism. The weak intermolecular interactions formed in the transition state play important roles. The difference between the interaction and distortion energies is responsible for the stereoselectivity. In the catalyzed reaction, bisthiourea induces both the diene and dienophile to approach it via weak intermolecular interactions, which greatly lowers the energy barrier of the reaction and leads to the product with excellent stereoselectivity. The possible pathways of this reaction were explored, which suggested that the formation of the two C-C bonds goes through either a stepwise or concerted asynchronous mechanism. These results detail the reaction mechanism and shed light on both the significant role of the bisthiourea catalyst and the origin of stereoselectivity for this type of Diels-Alder reaction and related ones.

Effect of donor orientation on ultrafast intermolecular electron transfer in coumarin-amine systems

International Nuclear Information System (INIS)

Singh, P. K.; Nath, S.; Bhasikuttan, A. C.; Kumbhakar, M.; Mohanty, J.; Sarkar, S. K.; Mukherjee, T.; Pal, H.

2008-01-01

Effect of donor amine orientation on nondiffusive ultrafast intermolecular electron transfer (ET) reactions in coumarin-amine systems has been investigated using femtosecond fluorescence upconversion measurements. Intermolecular ET from different aromatic and aliphatic amines used as donor solvents to the excited coumarin-151 (C151) acceptor occurs with ultrafast rates such that the shortest fluorescence lifetime component (τ 1 ) is the measure of the fastest ET rate (τ 1 =τ ET fast =(k ET fast ) -1 ), assigned to the C151-amine contact pairs in which amine donors are properly oriented with respect to C151 to maximize the acceptor-donor electronic coupling (V el ). It is interestingly observed that as the amine solvents are diluted by suitable diluents (either keeping solvent dielectric constant similar or with increasing dielectric constant), the τ 1 remains almost in the similar range as long as the amine dilution does not cross a certain critical limit, which in terms of the amine mole fraction (x A ) is found to be ∼0.4 for aromatic amines and ∼0.8 for aliphatic amines. Beyond these dilutions in the two respective cases of the amine systems, the τ 1 values are seen to increase very sharply. The large difference in the critical x A values involving aromatic and aliphatic amine donors has been rationalized in terms of the largely different orientational restrictions for the ET reactions as imposed by the aliphatic (n-type) and aromatic (π-type) nature of the amine donors [A. K. Satpati et al., J. Mol. Struct. 878, 84 (2008)]. Since the highest occupied molecular orbital (HOMO) of the n-type aliphatic amines is mostly centralized at the amino nitrogen, only some specific orientations of these amines with respect to the close-contact acceptor dye [also of π-character; A. K. Satpati et al., J. Mol. Struct. 878, 84 (2008) and E. W. Castner et al., J. Phys. Chem. A 104, 2869 (2000)] can give suitable V el and thus ultrafast ET reaction. In contrary, the

Spectrally- and Time-Resolved Sum Frequency Generation (STiR-SFG): a new tool for ultrafast hydrogen bond dynamics at interfaces.

Science.gov (United States)

Benderskii, Alexander; Bordenyuk, Andrey; Weeraman, Champika

2006-03-01

The recently developed spectrally- and time-resolved Sum Frequency Generation (STiR-SFG) is a surface-selective 3-wave mixing (IR+visible) spectroscopic technique capable of measuring ultrafast spectral evolution of vibrational coherences. A detailed description of this measurement will be presented, and a noniterative method or deconvolving the laser pulses will be introduced to obtain the molecular response function. STiR-SFG, combined with the frequency-domain SFG spectroscopy, was applied to study hydrogen bonding dynamics at aqueous interfaces (D2O/CaF2). Spectral dynamics of the OD-stretch on the 50-150 fs time scale provides real-time observation of ultrafast H-bond rearrangement. Tuning the IR wavelength to the blue or red side of the OD-stretch transition, we selectively monitor the dynamics of different sub-ensembles in the distribution of the H-bond structures. The blue-side excitation (weaker H-bonding) shows monotonic red-shift of the OD-frequency. In contrast, the red-side excitation (stronger H-bonding structures) produces a blue-shift and a recursion, which may indicate the presence of an underdamped intermolecular mode of interfacial water. Effect of electrolyte concentration on the H-bond dynamics will be discussed.

Approximate critical surface of the bond-mixed square-lattice Ising model

International Nuclear Information System (INIS)

Levy, S.V.F.; Tsallis, C.; Curado, E.M.F.

1979-09-01

The critical surface of the quenched bond-mixed square-lattice spin-1/2 first-neighbour-interaction ferromagnetic Ising model (with exchange interactions J 1 and J 2 ) has been investigated. Through renormalization group and heuristical procedures, a very accurate (error inferior to 3x10 -4 in the variables t sub(i) = th (J sub(i)/k sub(b)T)) approximate numerical proposal for all points of this surface is presented. This proposal simultaneously satisfies all the available exact results concerning the surface, namely P sub(c) = 1/2, t sub(c) = √2 - 1, both limiting slopes in these points, and t 2 = (1-t 1 )/(1+t 1 ) for p = 1/2. Furthemore an analytic approximation (namely (1 - p) 1n(1 + t 1 ) + p 1n(1 + t 2 ) =(1/2)1n 2) is also proposed. In what concerns the available exact results, it only fails in reproducing one of the two limiting slopes, where there is an error of 1% in the derivative: these facts result in an estimated error less than 10 -3 (in the t-variables) for any points in the surface. (Author) [pt

SOCIAL BONDING: REGULATION BY NEUROPEPTIDES

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Claudia eLieberwirth

2014-06-01

Full Text Available Affiliative social relationships (e.g., among spouses, family members, and friends play an essential role in human society. These relationships affect psychological, physiological, and behavioral functions. As positive and enduring bonds are critical for the overall well-being of humans, it is not surprising that considerable effort has been made to study the neurobiological mechanisms that underlie social bonding behaviors. The present review details the involvement of the nonapeptides, oxytocin (OT and arginine vasopressin (AVP, in the regulation of social bonding in mammals including humans. In particular, we will discuss the role of OT and AVP in the formation of social bonds between partners of a mating pair as well as between parents and their offspring. Furthermore, the role of OT and AVP in the formation of interpersonal bonding involving trust is also discussed.

Gold-catalyzed intermolecular coupling of sulfonylacetylene with allyl ethers: [3,3]- and [1,3]-rearrangements

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Jungho Jun

2013-08-01

Full Text Available Gold-catalyzed intermolecular couplings of sulfonylacetylenes with allyl ethers are reported. A cooperative polarization of alkynes both by a gold catalyst and a sulfonyl substituent resulted in an efficient intermolecular tandem carboalkoxylation. Reactions of linear allyl ethers are consistent with the [3,3]-sigmatropic rearrangement mechanism, while those of branched allyl ethers provided [3,3]- and [1,3]-rearrangement products through the formation of a tight ion–dipole pair.

Cooperativity effect involving drug-DNA/RNA intermolecular interaction: A B3LYP-D3 and MP2 theoretical investigation on ketoprofen⋯cytosine⋯H2O system.

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Zhen, Jun-Ping; Wei, Xiao-Chun; Shi, Wen-Jing; Huang, Zhu-Yuan; Jin, Bo; Zhou, Yu-Kun

2017-11-14

In order to examine the origin of the drug action and design new DNA/RNA-targeted drugs, the cooperativity effect involving drug-DNA/RNA intermolecular interaction in ketoprofen⋯cytosine⋯H 2 O ternary system were investigated by the B3LYP, B3LYP-D3, and MP2 methods with the 6-311++G(2d,p) basis set. The thermodynamic cooperativity was also evaluated at 310.15 K. The N-H⋯O, O-H⋯O, O-H⋯N, C-H⋯N, and C-H⋯O H bonds coexist in ternary complexes. The intermolecular interactions obtained by B3LYP-D3 are close to those calculated by MP2. The steric effects and van der Waals interactions have little influence on the cooperativity effects. The anti-cooperativity effect in ket⋯cyt⋯H 2 O is far more notable than the cooperativity effect, and the stability of the cyclic structure with anti-cooperativity effect is higher than that of the linear structure with cooperativity effect, as is confirmed by the AIM (atoms in molecules) and RDG (reduced density gradient) analysis. Thus, it can be inferred that, in the presence of H 2 O, the anti-cooperativity effect plays a dominant role in the drug-DNA/RNA interaction, and the nature of the hydration in the binding of drugs to DNA/RNA bases is the H-bonding anti-cooperativity effect. Furthermore, the drug always links simultaneously with DNA/RNA base and H 2 O, and only in this way can the biological activity of drugs play a role. In most cases, the enthalpy change is the major factor driving the cooperativity, as is different from most of biomacromolecule complexes.

Unusual bond paths in organolithium compounds

International Nuclear Information System (INIS)

Bachrach, S.M.; Ritchie, J.P.

1986-01-01

We have applied the topological method to a number of organolithium compounds. The wavefunctions were determined with GAUSSIAN-82 using 3-21G basis set and fully optimized geometries. Gradient paths were obtained using the RHODER package and critical points were located using EXTREME. These results indicate the unusual nature of organolithium compounds. The strange bond paths arise mainly from the ionic nature of the C-Li interaction. We suggest that the term ''bond path'' may best be suited for covalent bonds. 4 figs., 1 tab

Conformational Effects through Hydrogen Bonding in a Constrained γ-Peptide Template: From Intraresidue Seven-Membered Rings to a Gel-Forming Sheet Structure.

Science.gov (United States)

Awada, Hawraà; Grison, Claire M; Charnay-Pouget, Florence; Baltaze, Jean-Pierre; Brisset, François; Guillot, Régis; Robin, Sylvie; Hachem, Ali; Jaber, Nada; Naoufal, Daoud; Yazbeck, Ogaritte; Aitken, David J

2017-05-05

A series of three short oligomers (di-, tri-, and tetramers) of cis-2-(aminomethyl)cyclobutane carboxylic acid, a γ-amino acid featuring a cyclobutane ring constraint, were prepared, and their conformational behavior was examined spectroscopically and by molecular modeling. In dilute solutions, these peptides showed a number of low-energy conformers, including ribbonlike structures pleated around a rarely observed series of intramolecular seven-membered hydrogen bonds. In more concentrated solutions, these interactions defer to an organized supramolecular assembly, leading to thermoreversible organogel formation notably for the tripeptide, which produced fibrillar xerogels. In the solid state, the dipeptide adopted a fully extended conformation featuring a one-dimensional network of intermolecularly H-bonded molecules stacked in an antiparallel sheet alignment. This work provides unique insight into the interplay between inter- and intramolecular H-bonded conformer topologies for the same peptide template.

Body of Knowledge (BOK) for Copper Wire Bonds

Science.gov (United States)

Rutkowski, E.; Sampson, M. J.

2015-01-01

Copper wire bonds have replaced gold wire bonds in the majority of commercial semiconductor devices for the latest technology nodes. Although economics has been the driving mechanism to lower semiconductor packaging costs for a savings of about 20% by replacing gold wire bonds with copper, copper also has materials property advantages over gold. When compared to gold, copper has approximately: 25% lower electrical resistivity, 30% higher thermal conductivity, 75% higher tensile strength and 45% higher modulus of elasticity. Copper wire bonds on aluminum bond pads are also more mechanically robust over time and elevated temperature due to the slower intermetallic formation rate - approximately 1/100th that of the gold to aluminum intermetallic formation rate. However, there are significant tradeoffs with copper wire bonding - copper has twice the hardness of gold which results in a narrower bonding manufacturing process window and requires that the semiconductor companies design more mechanically rigid bonding pads to prevent cratering to both the bond pad and underlying chip structure. Furthermore, copper is significantly more prone to corrosion issues. The semiconductor packaging industry has responded to this corrosion concern by creating a palladium coated copper bonding wire, which is more corrosion resistant than pure copper bonding wire. Also, the selection of the device molding compound is critical because use of environmentally friendly green compounds can result in internal CTE (Coefficient of Thermal Expansion) mismatches with the copper wire bonds that can eventually lead to device failures during thermal cycling. Despite the difficult problems associated with the changeover to copper bonding wire, there are billions of copper wire bonded devices delivered annually to customers. It is noteworthy that Texas Instruments announced in October of 2014 that they are shipping microcircuits containing copper wire bonds for safety critical automotive applications

Effects of intermolecular interactions on absorption intensities of the fundamental and the first, second, and third overtones of OH stretching vibrations of methanol and t-butanol‑d9 in n-hexane studied by visible/near-infrared/infrared spectroscopy

Science.gov (United States)

Morisawa, Yusuke; Suga, Arisa

2018-05-01

Visible (Vis), near-infrared (NIR) and IR spectra in the 15,600-2500 cm- 1 region were measured for methanol, methanol-d3, and t-butanol-d9 in n-hexane to investigate effects of intermolecular interaction on absorption intensities of the fundamental and the first, second, and third overtones of their OH stretching vibrations. The relative area intensities of OH stretching bands of free and hydrogen-bonded species were plotted versus the vibrational quantum number using logarithm plots (V = 1-4) for 0.5 M methanol, 0.5 M methanol‑d3, and 0.5 M t-butanol-d9 in n-hexane. In the logarithm plots the relative intensities of free species yield a linear dependence irrespective of the solutes while those of hydrogen-bonded species deviate significantly from the linearity. The observed results suggest that the modifications in dipole moment functions of the OH bond induced by the formation of the hydrogen bondings change transient dipole moment, leading to the deviations of the dependences of relative absorption intensities on the vibrational quantum number from the linearity.

The Role of Molecule Clustering by Hydrogen Bond in Hydrous Ethanol on Laminar Burning Velocity

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I Made Suarta

2016-01-01

Full Text Available The role of hydrogen bond molecule clustering in laminar burning velocities was observed. The water in hydrous ethanol can change the interaction between water-ethanol molecules. A certain amount of water can become oxygenated which increases the burning velocity. The hydrogen bond interaction pattern of ethanol and water molecules was modeled. Based on the molecular model, azeotropic behavior emerges from ethanol-water hydrogen bond, which is at a 95.1%v composition. The interaction with water molecule causes the ethanol molecule to be clustered with centered oxygenated compound. So, it supplies extra oxygen and provides intermolecular empty spaces that are easily infiltrated by the air. In the azeotropic composition, the molecular bond chain is the shortest, so hypothetically the burning velocity is anticipated to increase. The laminar burning velocity of ethanol fuel was tested in a cylindrical explosion bomb in lean, stoichiometric, and rich mixtures. The experimental result showed that the maximum burning velocity occurred at hydrous ethanol of 95.5%v composition. This discrepancy is the result of the addition of energy from 7.7% free ethanol molecules that are not clustered. At the rich mixture, the burning velocity of this composition is higher than that of anhydrous ethanol.

Aqueous heterogeneity at the air/water interface revealed by 2D-HD-SFG spectroscopy.

Science.gov (United States)

Hsieh, Cho-Shuen; Okuno, Masanari; Hunger, Johannes; Backus, Ellen H G; Nagata, Yuki; Bonn, Mischa

2014-07-28

Water molecules interact strongly with each other through hydrogen bonds. This efficient intermolecular coupling causes strong delocalization of molecular vibrations in bulk water. We study intermolecular coupling at the air/water interface and find intermolecular coupling 1) to be significantly reduced and 2) to vary strongly for different water molecules at the interface--whereas in bulk water the coupling is homogeneous. For strongly hydrogen-bonded OH groups, coupling is roughly half of that of bulk water, due to the lower density in the near-surface region. For weakly hydrogen-bonded OH groups that absorb around 3500 cm(-1), which are assigned to the outermost, yet hydrogen-bonded OH groups pointing towards the liquid, coupling is further reduced by an additional factor of 2. Remarkably, despite the reduced structural constraints imposed by the interfacial hydrogen-bond environment, the structural relaxation is slow and the intermolecular coupling of these water molecules is weak. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Methyl group dynamics in paracetamol and acetanilide: probing the static properties of intermolecular hydrogen bonds formed by peptide groups

Science.gov (United States)

Johnson, M. R.; Prager, M.; Grimm, H.; Neumann, M. A.; Kearley, G. J.; Wilson, C. C.

1999-06-01

Measurements of tunnelling and librational excitations for the methyl group in paracetamol and tunnelling excitations for the methyl group in acetanilide are reported. In both cases, results are compared with molecular mechanics calculations, based on the measured low temperature crystal structures, which follow an established recipe. Agreement between calculated and measured methyl group observables is not as good as expected and this is attributed to the presence of comprehensive hydrogen bond networks formed by the peptide groups. Good agreement is obtained with a periodic quantum chemistry calculation which uses density functional methods, these calculations confirming the validity of the one-dimensional rotational model used and the crystal structures. A correction to the Coulomb contribution to the rotational potential in the established recipe using semi-emipircal quantum chemistry methods, which accommodates the modified charge distribution due to the hydrogen bonds, is investigated.

Inversion symmetry and local vs. dispersive interactions in the nucleation of hydrogen bonded cyclic n-mer and tape of imidazolecarboxamidines

Directory of Open Access Journals (Sweden)

2008-07-01

Full Text Available Substitutional changes to imidazolecarboxamidine that preserved intermolecular hydrogen bonding in the solid state were used to study the relationship between packing and the hydrogen bond motif. Various motifs competed, but the most common imidazolecarboxamidine crystalline phase was a Ci symmetric dimer that established inversion centers by associating enantiomeric tautomers. Counter to intuition, the calculated gas-phase energies per molecule of the solid state atomic coordinates of the Ci dimer motifs were higher than those of the C1 dimer, trimer, tetramer and tape motifs, while the packing densities of Ci dimers were found to be higher. This result was interpreted as an enhanced ability of the Ci dimers to pack. If other motifs competed, the hydrogen bonds and conformations should be lower in energy than the Ci dimer. The results detail the effect of packing on the conformation in these molecules. The results are interpreted as a rough measure of the energetic compromise between packing and the energies related to the coordinates involving one dihedral angle and hydrogen bonding. The results establish a connection between solution and solid phase conformation.

Hydrogen-bonding behavior of various conformations of the HNO3…(CH3OH)2 ternary system.

Science.gov (United States)

Özsoy, Hasan; Uras-Aytemiz, Nevin; Balcı, F Mine

2017-12-21

Nine minima were found on the intermolecular potential energy surface for the ternary system HNO 3 (CH 3 OH) 2 at the MP2/aug-cc-pVDZ level of theory. The cooperative effect, which is a measure of the hydrogen-bonding strength, was probed in these nine conformations of HNO 3 …(CH 3 OH) 2 . The results are discussed here in terms of structures, energetics, infrared vibrational frequencies, and topological parameters. The cooperative effect was observed to be an important contributor to the total interaction energies of the cyclic conformers of HNO 3 …(CH 3 OH) 2 , meaning that it cannot be neglected in simulations in which the pair-additive potential is applied. Graphical abstract The H-bonding behavior of various conformations of the HNO 3 (CH 3 OH) 2 trimer was investigated.

Synthesis and spectroscopic exploration of carboxylic acid derivatives of 6-hydroxy-1-keto-1,2,3,4-tetrahydrocarbazole: Hydrogen bond sensitive fluorescent probes

International Nuclear Information System (INIS)

Krishna Mitra, Amrit; Ghosh, Sujay; Chakraborty, Suchandra; Basu, Samita; Saha, Chandan

2013-01-01

Two new fluorescent carboxylic acid derivatives having 6-hydroxy-1-keto-1,2,3,4-tetrahydrocarbazole moiety, 2-(1-oxo-2,3,4,9-tetrahydro-1H-carbazol-6-yloxy)acetic acid [OTHCA] and 2-(7-methoxy-1-oxo-2,3,4,9-tetrahydro-1H-carbazol-6-yloxy)acetic acid [MOTHCA] were synthesized by Japp–Klingemann reaction followed by Fischer indole cyclization. Extensive spectroscopic investigation has been carried out on the compounds in sixteen different aprotic and protic solvents as well as in binary solvent mixtures using absorption, steady-state and time-resolved fluorescence techniques. Fluorescence maxima of the compounds have shifted consistently to longer wavelength in mediums of higher polarity and hydrogen bonding ability. Dipole moment change of the molecules upon photoexcitation has been calculated using Lippert–Mataga theory of solvatochromic shifts. Kamlet–Taft solvatochromic comparison method has been used to determine the dependence of spectral shifts upon empirical solvent parameters. Formation of intermolecular hydrogen bonding of both OTHCA and MOTHCA with protic solvents has been proved by comparing their spectral responses in toluene–acetonitrile and toluene–methanol solvent mixtures. -- Highlights: • The compounds have similar electronic distribution in ground and excited state. • Emission maxima shift towards red with increase in the E T (30) value of the solvents. • Dipole moment change in the excited state is different in protic and aprotic solvents. • OTHCA and MOTHCA form intermolecular hydrogen bond with protic solvents. • Fluorescence lifetime decays are bi-exponential in long chain alcoholic solvents

Interplay between tetrel and triel bonds in RC6H4CN⋯MF3CN⋯BX3 complexes: A combined symmetry-adapted perturbation theory, Møller-Plesset, and quantum theory of atoms-in-molecules study.

Science.gov (United States)

Yourdkhani, Sirous; Korona, Tatiana; Hadipour, Nasser L

2015-12-15

Intermolecular ternary complexes composed of: (1) the centrally placed trifluoroacetonitrile or its higher analogs with central carbon exchanged by silicon or germanium (M = C, Si, Ge), (2) the benzonitrile molecule or its para derivatives on one side, and (3) the boron trifluoride of trichloride molecule (X = F, Cl) on the opposite side as well as the corresponding intermolecular tetrel- and triel-bonded binary complexes, were investigated by symmetry-adapted perturbation theory (SAPT) and the supermolecular Møller-Plesset method (MP2) at the complete basis set limit for optimized geometries. A character of interactions was studied by quantum theory of atoms-in-molecules (QTAIM). A comparison of interaction energies and QTAIM bond descriptors for dimers and trimers reveals that tetrel and triel bonds increase in their strength if present together in the trimer. For the triel-bonded complex, this growth leads to a change of the bond character from closed-shell to partly covalent for Si or Ge tetrel atoms, so the resulting bonding scheme corresponds to a preliminary stage of the SN2 reaction. Limitations of the Lewis theory of acids and bases were shown by its failure in predicting the stability order of the triel complexes. The necessity of including interaction energy terms beyond the electrostatic component for an elucidation of the nature of σ- and π-holes was presented by a SAPT energy decomposition and by a study of differences in monomer electrostatic potentials obtained either from isolated monomer densities, or from densities resulting from a perturbation with the effective field of another monomer. © 2015 Wiley Periodicals, Inc.

Photoinitiated reactions in weakly bonded complexes

International Nuclear Information System (INIS)

Wittig, C.

1993-01-01

This paper discusses photoinitiated reactions in weakly bonded binary complexes in which the constituents are only mildly perturbed by the intermolecular bond. Such complexes, with their large zero point excursions, set the stage for events that occur following electronic excitation of one of the constituents. This can take several forms, but in all cases, entrance channel specificity is imposed by the character of the complex as well as the nature of the photoinitiation process. This has enabled us to examine aspects of bimolecular processes: steric effects, chemical branching ratios, and inelastic scattering. Furthermore, monitoring reactions directly in the time domain can reveal mechanisms that cannot be inferred from measurements of nascent product excitations. Consequently, we examined several systems that had been studied previously by our group with product state resolution. With CO 2 /HI, in which reaction occurs via a HOCO intermediate, the rates agree with RRKM predictions. With N 2 O/HI, the gas phase single collision reaction yielding OH + N 2 has been shown to proceed mainly via an HNNO intermediate that undergoes a 1,3-hydrogen shift to the OH + N 2 channel. With complexes, ab initio calculations and high resolution spectroscopic studies of analogous systems suggest that the hydrogen, while highly delocalized, prefers the oxygen to the nitrogen. We observe that OH is produced with a fast risetime (< 250 fs) which can be attributed to either direct oxygen-side attack or rapid HNNO decomposition and/or a termolecular contribution involving the nearby iodine

Dilemmas in zirconia bonding: A review

Directory of Open Access Journals (Sweden)

Obradović-Đuričić Kosovka

2013-01-01

Full Text Available This article presents a literature review on the resin bond to zirconia ceramic. Modern esthetic dentistry has highly recognized zirconia, among other ceramic materials. Biocompatibility of zirconia, chemical and dimensional stability, excellent mechanical properties, all together could guarantee optimal therapeutical results in complex prosthodontic reconstruction. On the other hand, low thermal degradation, aging of zirconia as well as problematic bonding of zirconia framework to dental luting cements and tooth structures, opened the room for discussion concerning their clinical durability. The well known methods of mechanical and chemical bonding used on glass-ceramics are not applicable for use with zirconia. Therefore, under critical clinical situations, selection of the bonding mechanism should be focused on two important points: high initial bond strength value and long term bond strength between zirconia-resin interface. Also, this paper emphases the use of phosphate monomer luting cements on freshly air-abraded zirconia as the simplest and most effective way for zirconia cementation procedure today.

Generalized bond percolation and statistical mechanics

International Nuclear Information System (INIS)

Tsallis, C.

1978-05-01

A generalization of traditional bond percolation is performed, in the sens that bonds have now the possibility of partially transmitting the information (a fact which leads to the concept of 'fidelity' of the bond), and also in the sens that, besides the normal tendency to equiprobability, the bonds are allowed to substantially change the information. Furthermore the fidelity is allowed, to become an aleatory variable, and the operational rules concerning the associated distribution laws are determined. Thermally quenched random bonds and the whole body of Statistical Mechanics become particular cases of this formalism, which is in general adapted to the treatment of all problems whose main characteristic is to preserve a part of the information through a long path or array (critical phenomena, regime changements, thermal random models, etc). Operationally it provides a quick method for the calculation of the equivalent probability of complex clusters within the traditional bond percolation problem [pt

Comparison of shear bond strength of stainless steel brackets bonded with three light- cured adhesives

Directory of Open Access Journals (Sweden)

Zahra Minaei Basharik

2015-09-01

Full Text Available Introduction: The bonding process of the brackets to enamel has been a critical issue in orthodontic research. The purpose of this study was to evaluate the shear bond strength of 3 light-cured adhesives (transbond XT, Z250, light bond. Materials &Methods: In this study sixty extracted human premolars were collected and randomly divided into 3 test groups. All teeth were etched by 37% phosphoric acid. In first group brackets were bonded by Transbond XT adhesive, in group two brackets were bonded by Light bond adhesive and in third group were bonded by filtek Z250 composite. All of them were cured with Ortholux xt for 40 seconds.24 hours after thermocycling, Shear Bond Strength (SBS values of these brackets were recorded using a Universal Testing Machine. Adhesive Remnant Index (ARI scores were determined after the failure of the brackets, using Stereo Microscope the data were analyzed using ANOVA and Chi-square tests. Results: Mean shear bond strength of Transbond XT, light bond and Z250 were 28.9±2.25 MPa, 25.06±1.98 MPa and 26.8±2.57 MPa, respectively. No significant difference was observed in the SBS among the groups and a clinically acceptable SBS was found for the three adhesives. ARI scores were not significantly different between the various groups (P>0.05. Conclusion: This study showed that the Z250 can be used as light bond and transbond xt to bond orthodontic brackets and ARI and SBS scores were not significantly different.

Stability and Reactivity of Cyclometallated Naphthylamine Complexes in Pd-C Bond Insertion Reactions with Coordinated Alkynylphosphanes

KAUST Repository

Chen, Shuli

2013-09-17

Phenylbis(phenylethynyl)phosphane PhP(C≡CPh)2 coordinates regiospecifically to the α-methyl-chiral ortho-platinated and -palladated naphthylamine units at the positions trans to the nitrogen donors. The P→Pt coordination bond is kinetically inert, whereas the P→Pd bond is labile. Upon heating of these phosphane complexes at 70 °C, one of the C≡C bonds in the coordinated PhP(C≡CPh)2 was activated towards an intermolecular Pd-C bond insertion reaction with an external ortho-palladated naphthylamine ring. No intramolecular insertion reaction occurred. In contrast to its palladium analogue, the ortho-platinated ring is not reactive towards coordinated PhP(C≡CPh)2, although it can promote the Pd-C bond insertion reaction. However, despite the high kinetic stability of the P→Pt coordination, the organoplatinum unit is a noticeably weaker activator than its organopalladium counterpart. The chirality of the reacting ortho-metallated naphthylamine ligand exhibited high stereochemical influence on the formation of the new stereogenic phosphorus center during the course of these C-C bond-formation reactions. The coordination chemistry and the absolute stereochemistry of the dimetallic products were determined by single-crystal X-ray crystallographic analysis. The asymmetric monoinsertion of PhP(C≡CPh)2 coordinated to a cyclometallated N,N-dimethyl naphthyl/benzylamine template into the Pd-C bonds of N,N-dimethylnaphthylamine palladacycles has been demonstrated for the synthesis of a variety of new P-stereogenic homo- or heterodimetallic complexes. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Can hydrogen bonds improve the hole-mobility in amorphous organic semiconductors? Experimental and theoretical insights

KAUST Repository

Mimaite, Viktorija; Grazulevicius, Juozas Vidas; Laurinaviciute, Rasa; Volyniuk, Dmytro; Jankauskas, Vygintas; Sini, Gjergji

2015-01-01

© The Royal Society of Chemistry 2015. Five hole-transporting triphenylamine derivatives containing methoxy and methyl groups are synthesized and investigated. The hole-mobility increases in the presence of methyl and methoxy substituents, exceeding 10-2 cm2 V-1 s-1 in the case of methyl groups. Quantum mechanical calculations on these compounds indicate very different dipole moments and intermolecular interaction strengths, with intriguing correlations with the trend in hole-mobility. Temperature dependent hole-mobility measurements indicate disorder dominated hole transport. The values of the energetic disorder parameter (σ) decrease upon methyl and methoxy substitutions despite the increase in dipole moments. This trend is discussed as a function of the interaction energy between adjacent molecules, the dipole moment, the molecular polarizability, and the conformational degree of freedom. Our results indicate that the global decrease of σ upon methyl and methoxy substitutions is dominated by the larger decrease in the geometrical randomness component of the energetic disorder. A direct correlation is established between the decrease in geometrical randomness and the increase in intermolecular interaction energies, mainly stemming from the additional C-H⋯π, O, N hydrogen bonds induced by methyl and methoxy groups.

Crystal structure, vibrational spectra and DFT studies of hydrogen bonded 1,2,4-triazolium hydrogenselenate

Science.gov (United States)

Arjunan, V.; Thirunarayanan, S.; Marchewka, M. K.; Mohan, S.

2017-10-01

The new hydrogen bonded molecular complex 1,2,4-triazolium hydrogenselenate (THS) is prepared by the reaction of 1H-1,2,4-triazole and selenic acid. This complex is stabilised by N-H⋯O and C-H⋯O hydrogen bonding and electrostatic attractive forces between 1H and 1,2,4-triazolium cations and hydrogen selenate anions. The XRD studies revealed that intermolecular proton transfer occur from selenic acid to 1H-1,2,4-triazole molecule, results in the formation of 1,2,4-triazolium hydrogenselenate which contains 1,2,4-triazolium cations and hydrogenselenate anions. The molecular structure of THS crystal has also been optimised by using Density Functional Theory (DFT) using B3LYP/cc-pVTZ and B3LYP/6-311++G** methods in order to find the whole characteristics of the molecular complex. The theoretical structural parameters such as bond length, bond angle and dihedral angle determined by DFT methods are well agreed with the XRD parameters. The atomic charges and thermodynamic properties are also calculated and analysed. The energies of frontier molecular orbitals HOMO, LUMO, HOMO-1, LUMO+1 and LUMO-HUMO energy gap are calculated to understand the kinetic stability and chemical reactivity of the molecular complex. The natural bond orbital analysis (NBO) has been performed in order to study the intramolecular bonding interactions and delocalisation of electrons. These intra molecular charge transfer may induce biological activities such as antimicrobials, antiinflammatory, antifungal etc. The complete vibrational assignments of THS have been performed by using FT-IR and FT-Raman spectra.

Catalytic Intermolecular Cross-Couplings of Azides and LUMO-Activated Unsaturated Acyl Azoliums

KAUST Repository

Li, Wenjun; Ajitha, Manjaly John; Lang, Ming; Huang, Kuo-Wei; Wang, Jian

2017-01-01

An example for the catalytic synthesis of densely functionalized 1,2,3-triazoles through a LUMO activation mode has been developed. The protocol is enabled by intermolecular cross coupling reactions of azides with in situ-generated alpha

Development of ab initio techniques critical for future science-based explosives R&D

Energy Technology Data Exchange (ETDEWEB)

Wixom, Ryan R. [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Mattsson, Ann Elisabet [Sandia National Lab. (SNL-CA), Livermore, CA (United States)

2013-10-01

Density Functional Theory (DFT) has emerged as an indispensable tool in materials research, since it can accurately predict properties of a wide variety of materials at both equilibrium and extreme conditions. However, for organic molecular crystal explosives, successful application of DFT has largely failed due to the inability of current exchange-correlation functionals to correctly describe intermolecular van der Waals (vdWs) forces. Despite this, we have discovered that even with no treatment of vdWs bonding, the AM05 functional and DFT based molecular dynamics (MD) could be used to study the properties of molecular crystals under compression. We have used DFT-MD to predict the unreacted Hugoniots for PETN and HNS and validated the results by comparison with crystalline and porous experimental data. Since we are also interested in applying DFT methods to study the equilibrium volume properties of explosives, we studied the nature of the vdWs bonding in pursuit of creating a new DFT functional capable of accurately describing equilibrium bonding of molecular crystals. In this report we discuss our results for computing shock Hugoniots of molecular crystals and also what was learned about the nature of bonding in these materials.

Relationship between thin-film bond strength as measured by a scratch test, and indentation hardness for bonding agents.

Science.gov (United States)

Kusakabe, Shusuke; Rawls, H Ralph; Hotta, Masato

2016-03-01

To evaluate thin-film bond strength between a bonding agent and human dentin, using a scratch test, and the characteristics and accuracy of measurement. One-step bonding agents (BeautiBond; Bond Force; Adper Easy Bond; Clearfil tri-S Bond) and two-step bonding agents (Cleafil SE Bond; FL-Bond II) were investigated in this study. Flat dentin surfaces were prepared for extracted human molars. The dentin surfaces were ground and bonding agents were applied and light cured. The thin-film bond strength test of the specimens was evaluated by the critical load at which the coated bonding agent failed and dentin appeared. The scratch mark sections were then observed under a scanning electron microscope. Indentation hardness was evaluated by the variation in depth under an applied load of 10gf. Data were compared by one-way ANOVA with the Scheffé's post hoc multiple comparison test (pstrength and indentation hardness were analyzed using analysis of correlation and covariance. The thin-film bond strength of two-step bonding agents were found to be significantly higher than that of one-step bonding agents with small standard deviations. Scratch marks consistently showed adhesive failure in the vicinity of the bonding agent/dentin interface. The indentation hardness showed a trend that two-step bonding agents have greater hardness than one-step bonding agents. A moderately significant correlation (r(2)=0.31) was found between thin-film bond strength and indentation hardness. Thin-film bond strength test is a valid and reliable means of evaluating bond strength in the vicinity of the adhesive interface and is more accurate than other methods currently in use. Further, the thin-film bond strength is influenced by the hardness of the cued bonding agent. Copyright © 2015 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Superconducting joint of Bi-2223/Ag superconducting tapes by diffusion bonding

International Nuclear Information System (INIS)

Guo Wei; Zou Guisheng; Wu Aiping; Wang Yanjun; Bai Hailin; Ren Jialie

2009-01-01

61-Filaments Bi-2223/Ag superconducting tapes have been joined by diffusion bonding. The critical currents (I C s) of the joints are obtained by using standard four probe method under no magnetic field in the liquid nitrogen. The microstructures of the joints are evaluated by the electron microscope in electron backscatter diffraction mode and the phase compositions of the superconducting cores of the joint and the original tape are determined by X-ray diffraction (XRD). The results show diffusion bonding is effective bonding technique for HTS tapes, and the bonding time is reduced greatly from hundreds of hours to a few hours, and the bonding pressure also changes from 140-4000 MPa to 3 MPa. Furthermore, the diffusion bonding joints sustain superconducting properties, and the critical current ratios (CCR O ) of the joints are in the range of 35%-80%. Microstructures of the typical joint display a good bonding and some defects existed in traditional method are avoided. XRD results show that the phase compositions of the superconducting cores have no obvious changes before and after diffusion bonding, which offers physical and material bases for high superconducting property of the joints.

Noncovalent Intermolecular Interactions in Organic Electronic Materials: Implications for the Molecular Packing vs Electronic Properties of Acenes

KAUST Repository

Sutton, Christopher

2015-10-30

Noncovalent intermolecular interactions, which can be tuned through the toolbox of synthetic chemistry, determine not only the molecular packing but also the resulting electronic, optical, and mechanical properties of materials derived from π-conjugated molecules, oligomers, and polymers. Here, we provide an overview of the theoretical underpinnings of noncovalent intermolecular interactions and briefly discuss the computational chemistry approaches used to understand the magnitude of these interactions. These methodologies are then exploited to illustrate how noncovalent intermolecular interactions impact important electronic properties-such as the electronic coupling between adjacent molecules, a key parameter for charge-carrier transport-through a comparison between the prototype organic semiconductor pentacene with a series of N-substituted heteropentacenes. Incorporating an understanding of these interactions into the design of organic semiconductors can assist in developing novel materials systems from this fascinating molecular class. © 2015 American Chemical Society.

Electrochemistry of transition metal complex catalysts Part 10. Intra- and intermolecular electrochemically activated C-H addition to the central metal atom of a P-C-P-pincer iridium complex

International Nuclear Information System (INIS)

Novak, Filip; Speiser, Bernd; Mohammad, Hani A.Y.; Mayer, Hermann A.

2004-01-01

The electrochemical properties of a promising catalyst for C-H bond activation are investigated. This P-C-P-pincer complex of iridium exhibits an intramolecular C-H oxidative addition at room temperature, which becomes enhanced upon oxidation. The reaction product is detected by cyclic voltammetry. Mechanistic, kinetic, and thermodynamic information is extracted from experiments in combination with digital simulation. Multicycle voltammograms and voltammograms of mixtures consistently suggest an extended square scheme as the electrode reaction mechanism. The unsubstituted parent compound shows a more complex redox behavior including a coupled ECE sequence. Intermolecular C-H activation by reaction of the complex in the presence of cyclooctane is indicated by characteristic changes in the cyclic voltammograms

The social life of bonding theory.

Science.gov (United States)

Crouch, M; Manderson, L

1995-09-01

'Bonding' as a crucial factor of the early post-partum entered obstetric and paediatric practice after the publication of Maternal and Infant Bonding in 1976 by Klaus and Kennell. The concept has held its place since, as witnessed by medical textbook accounts of it, and the perception of 'instantaneous bonding' as a vital component of the ideal birth experience has dominated media representations of childbirth and, until very recently, feminist writing. Only during the last few years has this literature taken into account research findings concerning the guilt and anxiety experienced by women whose expectations regarding 'bonding' are not realised. While it is now generally acknowledged that maternal attachment develops over an extended period of time, 'bonding' as used extensively in both popular and scientific literature conflates a wide range of meanings and blurs the boundaries between process and outcome. This facilitates the entry of ideological elements into a field which is, by its very nature, deeply significant for human experience. We therefore argue for a continuing critical appraisal of the role of 'bonding' in both general and scientific research.

Critical parameters of hard-core Yukawa fluids within the structural theory

Science.gov (United States)

Bahaa Khedr, M.; Osman, S. M.

2012-10-01

A purely statistical mechanical approach is proposed to account for the liquid-vapor critical point based on the mean density approximation (MDA) of the direct correlation function. The application to hard-core Yukawa (HCY) fluids facilitates the use of the series mean spherical approximation (SMSA). The location of the critical parameters for HCY fluid with variable intermolecular range is accurately calculated. Good agreement is observed with computer simulation results and with the inverse temperature expansion (ITE) predictions. The influence of the potential range on the critical parameters is demonstrated and the universality of the critical compressibility ratio is discussed. The behavior of the isochoric and isobaric heat capacities along the equilibrium line and the near vicinity of the critical point is discussed in details.

Effective Fragment Potential Method for H-Bonding: How To Obtain Parameters for Nonrigid Fragments.

Science.gov (United States)

Dubinets, Nikita; Slipchenko, Lyudmila V

2017-07-20

Accuracy of the effective fragment potential (EFP) method was explored for describing intermolecular interaction energies in three dimers with strong H-bonded interactions, formic acid, formamide, and formamidine dimers, which are a part of HBC6 database of noncovalent interactions. Monomer geometries in these dimers change significantly as a function of intermonomer separation. Several EFP schemes were considered, in which fragment parameters were prepared for a fragment in its gas-phase geometry or recomputed for each unique fragment geometry. Additionally, a scheme in which gas-phase fragment parameters are shifted according to relaxed fragment geometries is introduced and tested. EFP data are compared against the coupled cluster with single, double, and perturbative triple excitations (CCSD(T)) method in a complete basis set (CBS) and the symmetry adapted perturbation theory (SAPT). All considered EFP schemes provide a good agreement with CCSD(T)/CBS for binding energies at equilibrium separations, with discrepancies not exceeding 2 kcal/mol. However, only the schemes that utilize relaxed fragment geometries remain qualitatively correct at shorter than equilibrium intermolecular distances. The EFP scheme with shifted parameters behaves quantitatively similar to the scheme in which parameters are recomputed for each monomer geometry and thus is recommended as a computationally efficient approach for large-scale EFP simulations of flexible systems.

Low-temperature wafer-level gold thermocompression bonding: modeling of flatness deviations and associated process optimization for high yield and tough bonds

Science.gov (United States)

Stamoulis, Konstantinos; Tsau, Christine H.; Spearing, S. Mark

2005-01-01

Wafer-level, thermocompression bonding is a promising technique for MEMS packaging. The quality of the bond is critically dependent on the interaction between flatness deviations, the gold film properties and the process parameters and tooling used to achieve the bonds. The effect of flatness deviations on the resulting bond is investigated in the current work. The strain energy release rate associated with the elastic deformation required to overcome wafer bow is calculated. A contact yield criterion is used to examine the pressure and temperature conditions required to flatten surface roughness asperities in order to achieve bonding over the full apparent area. The results are compared to experimental data of bond yield and toughness obtained from four-point bend delamination testing and microscopic observations of the fractured surfaces. Conclusions from the modeling and experiments indicate that wafer bow has negligible effect on determining the variability of bond quality and that the well-bonded area is increased with increasing bonding pressure. The enhanced understanding of the underlying deformation mechanisms allows for a better controlled trade-off between the bonding pressure and temperature.

Highly Stereoselective Intermolecular Haloetherification and Haloesterification of Allyl Amides

Science.gov (United States)

Soltanzadeh, Bardia; Jaganathan, Arvind; Staples, Richard J.

2016-01-01

An organocatalytic and highly regio-, diastereo-, and enantioselective intermolecular haloetherification and haloesterification reaction of allyl amides is reported. A variety of alkene substituents and substitution patterns are compatible with this chemistry. Notably, electronically unbiased alkene substrates exhibit exquisite regio- and diastereoselectivity for the title transformation. We also demonstrate that the same catalytic system can be used in both chlorination and bromination reactions of allyl amides with a variety of nucleophiles with little or no modification. PMID:26110812

On the representation of the electric charge distribution in ethane for calculations of the molecular quadrupole moment and intermolecular electrostatic energy

DEFF Research Database (Denmark)

Hansen, Flemming Yssing; Alldredge, G. P.; Bruch, L. W.

1985-01-01

and gives a repulsive rather than an attractive electrostatic interaction at typical intermolecular distances. In the local multipole model, the atom-site dipoles give the largest contribution to both the molecular quadrupole moment and the intermolecular interaction. The Journal of Chemical Physics...

Solvation study of the non-specific lipid transfer protein from wheat by intermolecular NOEs with water and small organic molecules

International Nuclear Information System (INIS)

Liepinsh, Edvards; Sodano, Patrick; Tassin, Severine; Marion, Didier; Vovelle, Francoise; Otting, Gottfried

1999-01-01

Intermolecular nuclear Overhauser effects (NOEs) were measured between the protons of various small solvent or gas molecules and the non-specific lipid transfer protein (ns-LTP) from wheat. Intermolecular NOEs were observed with the hydrophobic pocket in the interior of wheat ns-LTP, which grew in intensity in the order cyclopropane (saturated solution) < methane (140 bar) < ethane (40 bar) < acetonitrile (5% in water) < cyclohexane (saturated solution) < benzene (saturated solution). No intermolecular NOEs were observed with dioxane (5% in water). The intermolecular NOEs were negative for all of the organic molecules tested. Intermolecular NOEs between wheat ns-LTP and water were weak or could not be distinguished from exchange-relayed NOEs. As illustrated by the NOEs with cyclohexane versus dioxane, the hydrophobic pocket in wheat ns-LTP preferably binds non-polar molecules. Yet, polar molecules like acetonitrile can also be accommodated. The pressure dependence of the NOEs between methane and wheat ns-LTP indicated incomplete occupancy, even at 190 bar methane pressure. In general, NOE intensities increased with the size of the ligand molecule and its vapor pressure. NMR of the vapor phase showed excellent resolution between the signals from the gas phase and those from the liquid phase. The vapor concentration of cyclohexane was fivefold higher than that of the dioxane solution, supporting the binding of cyclohexane versus uptake of dioxane

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

Science.gov (United States)

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

2016-05-01

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

Role of interatomic bonding in the mechanical anisotropy and interlayer cohesion of CSH crystals

Energy Technology Data Exchange (ETDEWEB)

Dharmawardhana, C.C. [Department of Physics and Astronomy, University of Missouri—Kansas City, Kansas City, MO 64110 (United States); Misra, A. [Department of Civil, Environmental, and Architectural Engineering, University of Kansas, Lawrence, KS 66045 (United States); Aryal, S.; Rulis, P. [Department of Physics and Astronomy, University of Missouri—Kansas City, Kansas City, MO 64110 (United States); Ching, W.Y., E-mail: ccdxz8@mail.umkc.edu [Department of Physics and Astronomy, University of Missouri—Kansas City, Kansas City, MO 64110 (United States)

2013-10-15

Atomic scale properties of calcium silicate hydrate (CSH), the main binding phase of hardened Portland cement, are not well understood. Over a century of intense research has identified almost 50 different crystalline CSH minerals which are mainly categorized by their Ca/Si ratio. The electronic structure and interatomic bonding in four major CSH crystalline phases with structures close to those found in hardened cement are investigated via ab initio methods. Our result reveals the critical role of hydrogen bonding and importance of specifying precise locations for water molecules. Quantitative analysis of contributions from different bond types to the overall cohesion shows that while the Si-O covalent bonds dominate, the hydrogen bonding and Ca-O bonding are also very significant. Calculated results reveal the correlation between bond topology and interlayer cohesion. The overall bond order density (BOD) is found to be a more critical measure than the Ca/Si ratio in classifying different CSH crystals.

Intermolecular crosslinks mediate aggregation of phospholipid vesicles by pulmonary surfactant-associated protein SAP-35

International Nuclear Information System (INIS)

Ross, G.R.; Sawyer, J.; Whitsett, J.

1987-01-01

Pulmonary surfactant-associated protein, Mr=35,000 (SAP-35) is known to bind phospholipids and is hypothesized to function in the organization of surfactant lipid membranes. SAP-35 has been observed to accelerate the calcium-induced aggregation of phospholipid vesicles. In order to define the molecular domains of SAP-35 which function in phospholipid aggregation, they have measured the light scattering properties (400nm) of purified canine SAP-35-phospholipid vesicle suspensions. Accelerated aggregation of unilamellar vesicles, requires SAP-35 and at least 2mM free calcium. The initial rate of A 400 change is proportional to the amount of native SAP-35 added over lipid:protein molar ratios ranging from 100:1 to 5000:1. Removal of the SAP-35 collagen-like domain and a specific cysteine residue involved in intermolecular disulfide bonding by bacterial collagenase digestion destroys the protein's lipid aggregation activity. Pre-incubation of SAP-35 with dithiothreitol (DTT) under nondenaturing conditions also results in a time-dependent loss of aggregation activity. Sucrose density gradient floatation of SAP-35 with 14 C dipalmitoyl phosphatidycholine labelled vesicles in the absence or presence of DTT suggests retention of SAP-35 lipid binding capacity. These data demonstrate the importance of SAP-35 triple helix and disulfide crosslinking integrity for the aggregation of unilamellar phospholipid vesicles

Dual hydrogen-bonding motifs in complexes formed between tropolone and formic acid

Science.gov (United States)

Nemchick, Deacon J.; Cohen, Michael K.; Vaccaro, Patrick H.

2016-11-01

The near-ultraviolet π*←π absorption system of weakly bound complexes formed between tropolone (TrOH) and formic acid (FA) under cryogenic free-jet expansion conditions has been interrogated by exploiting a variety of fluorescence-based laser-spectroscopic probes, with synergistic quantum-chemical calculations built upon diverse model chemistries being enlisted to unravel the structural and dynamical properties of the pertinent ground [X˜ 1A'] and excited [A˜ 1A'(" separators="π*π )] electronic states. For binary TrOH ṡ FA adducts, the presence of dual hydrogen-bond linkages gives rise to three low-lying isomers designated (in relative energy order) as INT, EXT1, and EXT2 depending on whether docking of the FA ligand to the TrOH substrate takes place internal or external to the five-membered reaction cleft of tropolone. While the symmetric double-minimum topography predicted for the INT potential surface mediates an intermolecular double proton-transfer event, the EXT1 and EXT2 structures are interconverted by an asymmetric single proton-transfer process that is TrOH-centric in nature. The A ˜ -X ˜ origin of TrOH ṡ FA at ν˜ 00=27 484 .45 cm-1 is displaced by δ ν˜ 00=+466 .76 cm-1 with respect to the analogous feature for bare tropolone and displays a hybrid type - a/b rotational contour that reflects the configuration of binding. A comprehensive analysis of vibrational landscapes supported by the optically connected X˜ 1A' and A˜ 1A'(" separators="π*π ) manifolds, including the characteristic isotopic shifts incurred by partial deuteration of the labile TrOH and FA protons, has been performed leading to the uniform assignment of numerous intermolecular (viz., modulating hydrogen-bond linkages) and intramolecular (viz., localized on monomer subunits) degrees of freedom. The holistic interpretation of all experimental and computational findings affords compelling evidence that an external-binding motif (attributed to EXT1), rather than the

The influence of adherent surface preparation on bond durability

International Nuclear Information System (INIS)

Rider, A.N.; Arnott, D.R.; Olsson-Jacques, C.L.

1999-01-01

Full text: One of the major factors limiting the use of adhesive bonding is the problem associated with the production of adhesive joints that can maintain their initial strength over long periods of time in hostile environments. It is well known that the adherent surface preparation method is critical to the formation of a durable adhesive bond. Work presented in this paper focuses on the critical aspects of the surface preparation of aluminium employed for the manufacture of aluminium-epoxy joints. The surface preparation procedure examined is currently employed by the RAAF for repairs requiring metal to adhesive bonding. The influence of each step in the surface preparation on the ultimate bond durability performance of the adhesive joint is examined by a combination of methods. Double cantilever wedge style adhesive joints are loaded in mode 1 opening and then exposed to a humid environment. X-ray photoelectron spectroscopy (XPS) and contact angle measurements of the aluminium adherent before bonding provides information about the adherent surface chemistry. XPS is also employed to analyse the surfaces of the bonded specimens post failure to establish the locus of fracture. This approach provides important information regarding the properties influencing bond durability as well as the bond failure mechanisms. A two step bond degradation model was developed to qualitatively describe the observed bond durability performance and fracture data. The first step involves controlled moisture ingress by stress induced microporosity of the adhesive in the interfacial region. The second step determines the locus of fracture through the relative dominance of one of three competitive processes, viz: oxide degradation, polymer desorption, or polymer degradation. A key element of the model is the control exercised over the interfacial microporosity by the combined interaction of stress and the relative densities of strong and weak linkages at the metal to adhesive interface

N-(N-[2-(3,5-Difluorophenyl)acetyl]-(S)-alanyl)-(S)-phenylglycine tert-butyl ester (DAPT): an inhibitor of γ-secretase, revealing fine electronic and hydrogen-bonding features

Energy Technology Data Exchange (ETDEWEB)

Czerwinski, Andrzej; Valenzuela, Francisco [Peptides International Inc., 11621 Electron Drive, Louisville, KY 40299 (United States); Afonine, Pavel [Lawrence Berkeley National Laboratory, One Cyclotron Road, Building 64R0121, Berkeley, CA 94720 (United States); Dauter, Miroslawa, E-mail: dauter@anl.gov [Basic Research Program, SAIC-Frederick Inc., Synchrotron Radiation Research Section, MCL, NCI, Argonne National Laboratory, Biosciences Division, Building 202, Argonne, IL 60439 (United States); Dauter, Zbigniew [Synchrotron Radiation Research Section, MCL, NCI, Argonne National Laboratory, Biosciences Division, Building 202, Argonne, IL 60439 (United States); Peptides International Inc., 11621 Electron Drive, Louisville, KY 40299 (United States)

2010-12-01

The title compound, C{sub 23}H{sub 26}F{sub 2}N{sub 2}O{sub 4}, is a dipeptidic inhibitor of γ-secretase, one of the enzymes involved in Alzheimer’s dis@@ease. The mol@@ecule adopts a compact conformation, without intra@@molecular hydrogen bonds. In the crystal structure, one of the amide N atoms forms the only inter@@molecular N—H⋯O hydrogen bond; the second amide N atom does not form hydrogen bonds. High-resolution synchrotron diffraction data permitted the unequivocal location and refinement without restraints of all H atoms, and the identification of the characteristic shift of the amide H atom engaged in the hydrogen bond from its ideal position, resulting in a more linear hydrogen bond. Significant residual densities for bonding electrons were revealed after the usual SHELXL refinement, and modeling of these features as additional inter@@atomic scatterers (IAS) using the program PHENIX led to a significant decrease in the R factor from 0.0411 to 0.0325 and diminished the r.m.s. deviation level of noise in the final difference Fourier map from 0.063 to 0.037 e Å{sup −3}.

Pharmaceutical cocrystals, salts and multicomponent systems; intermolecular interactions and property based design.

Science.gov (United States)

Berry, David J; Steed, Jonathan W

2017-08-01

As small molecule drugs become harder to develop and less cost effective for patient use, efficient strategies for their property improvement become increasingly important to global health initiatives. Improvements in the physical properties of Active Pharmaceutical Ingredients (APIs), without changes in the covalent chemistry, have long been possible through the application of binary component solids. This was first achieved through the use of pharmaceutical salts, within the last 10-15years with cocrystals and more recently coamorphous systems have also been consciously applied to this problem. In order to rationally discover the best multicomponent phase for drug development, intermolecular interactions need to be considered at all stages of the process. This review highlights the current thinking in this area and the state of the art in: pharmaceutical multicomponent phase design, the intermolecular interactions in these phases, the implications of these interactions on the material properties and the pharmacokinetics in a patient. Copyright © 2017 Elsevier B.V. All rights reserved.

Optimizing Noncovalent Interactions Between Lignin and Synthetic Polymers to Develop Effective Compatibilizers

Energy Technology Data Exchange (ETDEWEB)

Henry, Nathan [University of Tennessee, Knoxville (UTK); Harper, David [University of Tennessee, Knoxville (UTK), Center for Renewable Carbon; Dadmun, Mark D [ORNL

2012-01-01

Experiments are designed and completed to identify an effective polymeric compatibilizer for lignin polystyrene blends. Copolymers of styrene and vinylphenol are chosen as the structure of the compatibilizer as the VPh unit can readily form intermolecular hydrogen bonds with the lignin molecule. Electron microscopy, thermal analysis, and neutron refl ectivity results demonstrate that among these compatibilizers, a copolymer of styrene and VPh with 20% 30% VPh most readily forms intermolecular interactions with the lignin molecule and results in the most well-dispersed blends with lignin. This behavior is explained by invoking the competition of intra- and intermolecular hydrogen bonding and functional group accessibility in forming intermolecular interactions.

Catalyst-Controlled and Tunable, Chemoselective Silver-Catalyzed Intermolecular Nitrene Transfer: Experimental and Computational Studies.

Science.gov (United States)

Dolan, Nicholas S; Scamp, Ryan J; Yang, Tzuhsiung; Berry, John F; Schomaker, Jennifer M

2016-11-09

The development of new catalysts for selective nitrene transfer is a continuing area of interest. In particular, the ability to control the chemoselectivity of intermolecular reactions in the presence of multiple reactive sites has been a long-standing challenge in the field. In this paper, we demonstrate examples of silver-catalyzed, nondirected, intermolecular nitrene transfer reactions that are both chemoselective and flexible for aziridination or C-H insertion, depending on the choice of ligand. Experimental probes present a puzzling picture of the mechanistic details of the pathways mediated by [( t Bu 3 tpy)AgOTf] 2 and (tpa)AgOTf. Computational studies elucidate these subtleties and provide guidance for the future development of new catalysts exhibiting improved tunability in group transfer reactions.

Molecular simulation of fluids with non-identical intermolecular potentials: Thermodynamic properties of 10-5 + 12-6 Mie potential binary mixtures

International Nuclear Information System (INIS)

Stiegler, Thomas; Sadus, Richard J.

2015-01-01

General methods for combining interactions between particles characterised by non-identical intermolecular potentials are investigated. The combination methods are tested by performing molecular dynamics simulations to determine the pressure, energy, isochoric and isobaric heat capacities, thermal expansion coefficient, isothermal compressibility, Joule-Thomson coefficient, and speed of sound of 10-5 + 12-6 Mie potential binary mixtures. In addition to the two non-identical Mie potentials, mixtures are also studied with non-identical intermolecular parameters. The combination methods are compared with results obtained by simply averaging the Mie exponents. When either the energy or size parameters are non-identical, very significant differences emerge in the thermodynamic properties predicted by the alternative combination methods. The isobaric heat capacity is the thermodynamic property that is most affected by the relative magnitude of the intermolecular potential parameters and the method for combining non-identical potentials. Either the arithmetic or geometric combination of potentials provides a simple and effective way of performing simulations involving mixtures of components characterised by non-identical intermolecular potentials, which is independent of their functional form

Mechanism of intermolecular hydroacylation of vinylsilanes catalyzed by a rhodium(I) olefin complex: a DFT study.

Science.gov (United States)

Meng, Qingxi; Shen, Wei; Li, Ming

2012-03-01

Density functional theory (DFT) was used to investigate the Rh(I)-catalyzed intermolecular hydroacylation of vinylsilane with benzaldehyde. All intermediates and transition states were optimized completely at the B3LYP/6-31G(d,p) level (LANL2DZ(f) for Rh). Calculations indicated that Rh(I)-catalyzed intermolecular hydroacylation is exergonic, and the total free energy released is -110 kJ mol(-1). Rh(I)-catalyzed intermolecular hydroacylation mainly involves the active catalyst CA2, rhodium-alkene-benzaldehyde complex M1, rhodium-alkene-hydrogen-acyl complex M2, rhodium-alkyl-acyl complex M3, rhodium-alkyl-carbonyl-phenyl complex M4, rhodium-acyl-phenyl complex M5, and rhodium-ketone complex M6. The reaction pathway CA2 + R2 → M1b → T1b → M2b → T2b1 → M3b1 → T4b → M4b → T5b → M5b → T6b → M6b → P2 is the most favorable among all reaction channels of Rh(I)-catalyzed intermolecular hydroacylation. The reductive elimination reaction is the rate-determining step for this pathway, and the dominant product predicted theoretically is the linear ketone, which is consistent with Brookhart's experiments. Solvation has a significant effect, and it greatly decreases the free energies of all species. The use of the ligand Cp' (Cp' = C(5)Me(4)CF(3)) decreased the free energies in general, and in this case the rate-determining step was again the reductive elimination reaction.

Dispersion-corrected first-principles calculation of terahertz vibration, and evidence for weak hydrogen bond formation

Science.gov (United States)

Takahashi, Masae; Ishikawa, Yoichi; Ito, Hiromasa

2013-03-01

A weak hydrogen bond (WHB) such as CH-O is very important for the structure, function, and dynamics in a chemical and biological system WHB stretching vibration is in a terahertz (THz) frequency region Very recently, the reasonable performance of dispersion-corrected first-principles to WHB has been proven. In this lecture, we report dispersion-corrected first-principles calculation of the vibrational absorption of some organic crystals, and low-temperature THz spectral measurement, in order to clarify WHB stretching vibration. The THz frequency calculation of a WHB crystal has extremely improved by dispersion correction. Moreover, the discrepancy in frequency between an experiment and calculation and is 10 1/cm or less. Dispersion correction is especially effective for intermolecular mode. The very sharp peak appearing at 4 K is assigned to the intermolecular translational mode that corresponds to WHB stretching vibration. It is difficult to detect and control the WHB formation in a crystal because the binding energy is very small. With the help of the latest intense development of experimental and theoretical technique and its careful use, we reveal solid-state WHB stretching vibration as evidence for the WHB formation that differs in respective WHB networks The research was supported by the Ministry of Education, Culture, Sports, Science and Technology of Japan (Grant No. 22550003).

Self-Organization of +-Crown Ether Derivatives into Double-Columnar Arrays Controlled by Supramolecular Isomers of Hydrogen-Bonded Anionic Biimidazolate Ni Complexes

Directory of Open Access Journals (Sweden)

Makoto Tadokoro

2012-01-01

Full Text Available Anionic tris (biimidazolate nickelate (II ([Ni(Hbim3]−, which is a hydrogen-bonding (H-bonding molecular building block, undergoes self-organization into honeycomb-sheet superstructures connected by complementary intermolecular H-bonds. The crystal obtained from the stacking of these sheets is assembled into channel frameworks, approximately 2 nm wide, that clathrate two cationic K+-crown ether derivatives organised into one-dimensional (1D double-columnar arrays. In this study, we have shown that all five cationic guest-included crystals form nanochannel structures that clathrate the 1-D double-columnar arrays of one of the four types of K+-crown ether derivatives, one of which induces a polymorph. This is accomplished by adaptably fitting two types of anionic [Ni(Hbim3]− host arrays. One is a ΔΛ−ΔΛ−ΔΛ⋯ network with H-bonded linkages alternating between the two different optical isomers of the Δ and Λ types with flexible H-bonded [Ni(Hbim3]−. The other is a ΔΔΔ−ΛΛΛ⋯ network of a racemate with 1-D H-bonded arrays of the same optical isomer for each type. Thus, [Ni(Hbim3]− can assemble large cations such as K+ crown-ether derivatives into double-columnar arrays by highly recognizing flexible H-bonding arrangements with two host networks of ΔΛ−ΔΛ−ΔΛ⋯ and ΔΔΔ−ΛΛΛ⋯.

Studying Intermolecular Forces with a Dual Gas Chromatography and Boiling Point Investigation

Science.gov (United States)

Cunningham, William Patrick; Xia, Ian; Wickline, Kaitlyn; Huitron, Eric Ivan Garcia; Heo, Jun

2018-01-01

A procedure for the study of structural differences and intermolecular attraction between ethanol and 1-butanol based in laboratory work is described. This study provides comparisons of data retrieved from both a determination of boiling point and gas chromatography traces for the mixture. The methodology reported here should provide instructors…

Bond financing for renewable energy in Asia

International Nuclear Information System (INIS)

Ng, Thiam Hee; Tao, Jacqueline Yujia

2016-01-01

Addressing the financing gap for renewable energy (RE) projects in Asia is critical to ensure that the rapidly increasing energy needs could be met sustainably. This paper explores the cause of the financing gap in Asia and proposes the use of bond financing to address the financing gap. Specifically, three fixed income instruments, namely local currency denominated (LCY) corporate bonds, asset backed project bonds and financial green bonds, will be assessed. Whilst the potential for these three instruments to mobilize large flows of private sector financing is great, key supportive policies aimed at reducing the capital market bias for conventional power generation technologies and supportive RE policies are required. Another key aspect would be the necessary deepening of local and regional fixed income markets before such capital market instruments are able to play a big role. - Highlights: •This study looks at the current financing gap and RE financing landscape in developing Asia. •LCY corporate bonds, asset backed projects bonds and financial green bonds could help to address the financing gap for RE in the region. •Policy recommendations for building the fixed income market for RE projects are provided.

Contrasting intermolecular and intramolecular exciplex formation of a 1,4-dicyano-2-methylnaphthalene-N,N-dimethyl-p-toluidine dyad.

Science.gov (United States)

Imoto, Mitsutaka; Ikeda, Hiroshi; Fujii, Takayuki; Taniguchi, Hisaji; Tamaki, Akihiro; Takeda, Motonori; Mizuno, Kazuhiko

2010-05-07

An intramolecular exciplex is formed upon excitation of the cyclohexane solution of the 1,4-dicyano-2-methylnaphthalene-N,N-dimethyl-p-toluidine dyad, but little if any intramolecular CT complex exists in the ground state of this substance in solution. In contrast, in the crystalline state, the dyad forms an intermolecular mixed-stack CT complex in the ground state and an intermolecular exciplex when it is photoexcited.

A covalent attraction between two molecular cation TTF·~+

Institute of Scientific and Technical Information of China (English)

WANG FangFang; WANG Yi; WANG BingQiang; WANG YinFeng; MA Fang; Li ZhiRu

2009-01-01

The optimized structure of the tetrathiafulvalence radical-cation dimer (TTF·~+-TTF·~+) with all-real frequencies is obtained at MP2/6-311G level,which exhibits the attraction between two molecular cation TTF·~+.The new attraction interaction is a 20-center-2-electron intermolecular covalent π/π bonding with a telescope shape.The covalent π/π bonding has the bonding energy of about-21 kcal·mol~(-1) and is concealed by the Coulombic repulsion between two TTF·~+ cations.This intermolecular covalent attraction also influences the structure of the TTF·~+ subunit,I.e.,its molecular plane is bent by an angle θ=5.6°.This work provides new knowledge on intermolecular interaction.

A covalent attraction between two molecular cation TTF·~+

Institute of Scientific and Technical Information of China (English)

无

2009-01-01

The optimized structure of the tetrathiafulvalence radical-cation dimer(TTF·+-TTF·+) with all-real frequencies is obtained at MP2/6-311G level,which exhibits the attraction between two molecular cation TTF·+.The new attraction interaction is a 20-center-2-electron intermolecular covalent π /π bonding with a telescope shape.The covalent π /π bonding has the bonding energy of about -21 kcal·mol-1 and is concealed by the Coulombic repulsion between two TTF·+ cations.This intermolecular covalent attraction also influences the structure of the TTF·+ subunit,i.e.,its molecular plane is bent by an angle θ=5.6°.This work provides new knowledge on intermolecular interaction.

Refined ab initio intermolecular ground-state potential energy surface for the He-C2H2 van der Waals complex

DEFF Research Database (Denmark)

Fernández, Berta; Henriksen, Christian; Farrelly, David

2013-01-01

A refined CCSD(T) intermolecular potential energy surface is developed for the He-C2H2 van der Waals complex. For this, 206 points on the intermolecular potential energy surface, evaluated using the CCSD(T) method and the aug-cc-pVQZ basis set extended with a set of 3s3p2d1f1g midbond functions...

Salting Effects as an Illustration of the Relative Strength of Intermolecular Forces

Science.gov (United States)

Person, Eric C.; Golden, Donnie R.; Royce, Brenda R.

2010-01-01

This quick and inexpensive demonstration of the salting of an alcohol out of an aqueous solution illustrates the impact of intermolecular forces on solubility using materials familiar to many students. Ammonium sulfate (fertilizer) is added to an aqueous 35% solution of isopropyl alcohol (rubbing alcohol and water) containing food coloring as a…

Factors correlating with significant differences between X-ray structures of myoglobin

International Nuclear Information System (INIS)

Rashin, Alexander A.; Domagalski, Marcin J.; Zimmermann, Michael T.; Minor, Wladek; Chruszcz, Maksymilian; Jernigan, Robert L.

2014-01-01

Conformational differences between myoglobin structures are studied. Most structural differences in whale myoglobin beyond the uncertainty threshold can be correlated with a few specific structural factors. There are always exceptions and a search for additional factors is needed. The results might have serious implications for biological insights from conformational differences. Validation of general ideas about the origins of conformational differences in proteins is critical in order to arrive at meaningful functional insights. Here, principal component analysis (PCA) and distance difference matrices are used to validate some such ideas about the conformational differences between 291 myoglobin structures from sperm whale, horse and pig. Almost all of the horse and pig structures form compact PCA clusters with only minor coordinate differences and outliers that are easily explained. The 222 whale structures form a few dense clusters with multiple outliers. A few whale outliers with a prominent distortion of the GH loop are very similar to the cluster of horse structures, which all have a similar GH-loop distortion apparently owing to intermolecular crystal lattice hydrogen bonds to the GH loop from residues near the distal histidine His64. The variations of the GH-loop coordinates in the whale structures are likely to be owing to the observed alternative intermolecular crystal lattice bond, with the change to the GH loop distorting bonds correlated with the binding of specific ‘unusual’ ligands. Such an alternative intermolecular bond is not observed in horse myoglobins, obliterating any correlation with the ligands. Intermolecular bonds do not usually cause significant coordinate differences and cannot be validated as their universal cause. Most of the native-like whale myoglobin structure outliers can be correlated with a few specific factors. However, these factors do not always lead to coordinate differences beyond the previously determined uncertainty

Factors correlating with significant differences between X-ray structures of myoglobin

Energy Technology Data Exchange (ETDEWEB)

Rashin, Alexander A., E-mail: alexander-rashin@hotmail.com [BioChemComp Inc., 543 Sagamore Avenue, Teaneck, NJ 07666 (United States); Iowa State University, 112 Office and Lab Bldg, Ames, IA 50011-3020 (United States); Domagalski, Marcin J. [University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA 22908 (United States); Zimmermann, Michael T. [Iowa State University, 112 Office and Lab Bldg, Ames, IA 50011-3020 (United States); Minor, Wladek [University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA 22908 (United States); Chruszcz, Maksymilian [University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA 22908 (United States); University of South Carolina, 631 Sumter Street, Columbia, SC 29208 (United States); Jernigan, Robert L. [Iowa State University, 112 Office and Lab Bldg, Ames, IA 50011-3020 (United States); BioChemComp Inc., 543 Sagamore Avenue, Teaneck, NJ 07666 (United States)

2014-02-01

Conformational differences between myoglobin structures are studied. Most structural differences in whale myoglobin beyond the uncertainty threshold can be correlated with a few specific structural factors. There are always exceptions and a search for additional factors is needed. The results might have serious implications for biological insights from conformational differences. Validation of general ideas about the origins of conformational differences in proteins is critical in order to arrive at meaningful functional insights. Here, principal component analysis (PCA) and distance difference matrices are used to validate some such ideas about the conformational differences between 291 myoglobin structures from sperm whale, horse and pig. Almost all of the horse and pig structures form compact PCA clusters with only minor coordinate differences and outliers that are easily explained. The 222 whale structures form a few dense clusters with multiple outliers. A few whale outliers with a prominent distortion of the GH loop are very similar to the cluster of horse structures, which all have a similar GH-loop distortion apparently owing to intermolecular crystal lattice hydrogen bonds to the GH loop from residues near the distal histidine His64. The variations of the GH-loop coordinates in the whale structures are likely to be owing to the observed alternative intermolecular crystal lattice bond, with the change to the GH loop distorting bonds correlated with the binding of specific ‘unusual’ ligands. Such an alternative intermolecular bond is not observed in horse myoglobins, obliterating any correlation with the ligands. Intermolecular bonds do not usually cause significant coordinate differences and cannot be validated as their universal cause. Most of the native-like whale myoglobin structure outliers can be correlated with a few specific factors. However, these factors do not always lead to coordinate differences beyond the previously determined uncertainty

Strong Intermolecular Exciton Couplings in Solid-State Circular Dichroism of Aryl Benzyl Sulfoxides

Czech Academy of Sciences Publication Activity Database

Padula, Daniele; Di Pietro, S.; Capozzi, M. A. M.; Cardellicchio, C.; Pescitelli, G.

2014-01-01

Roč. 26, č. 9 (2014), s. 462-470 ISSN 0899-0042 Institutional support: RVO:61388963 Keywords : organic crystals * TDDFT CD calculations * pairwise additive approximation * two-body effects * intermolecular forces in crystal lattices Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.886, year: 2014

Intermolecular interaction of fosinopril with bovine serum albumin (BSA): The multi-spectroscopic and computational investigation.

Science.gov (United States)

Zhou, Kai-Li; Pan, Dong-Qi; Lou, Yan-Yue; Shi, Jie-Hua

2018-04-16

The intermolecular interaction of fosinopril, an angiotensin converting enzyme inhibitor with bovine serum albumin (BSA), has been investigated in physiological buffer (pH 7.4) by multi-spectroscopic methods and molecular docking technique. The results obtained from fluorescence and UV absorption spectroscopy revealed that the fluorescence quenching mechanism of BSA induced by fosinopril was mediated by the combined dynamic and static quenching, and the static quenching was dominant in this system. The binding constant, K b , value was found to lie between 2.69 × 10 3 and 9.55 × 10 3  M -1 at experimental temperatures (293, 298, 303, and 308 K), implying the low or intermediate binding affinity between fosinopril and BSA. Competitive binding experiments with site markers (phenylbutazone and diazepam) suggested that fosinopril preferentially bound to the site I in sub-domain IIA on BSA, as evidenced by molecular docking analysis. The negative sign for enthalpy change (ΔH 0 ) and entropy change (ΔS 0 ) indicated that van der Waals force and hydrogen bonds played important roles in the fosinopril-BSA interaction, and 8-anilino-1-naphthalenesulfonate binding assay experiments offered evidence of the involvements of hydrophobic interactions. Moreover, spectroscopic results (synchronous fluorescence, 3-dimensional fluorescence, and Fourier transform infrared spectroscopy) indicated a slight conformational change in BSA upon fosinopril interaction. Copyright © 2018 John Wiley & Sons, Ltd.

Morse-Morse-Spline-Van der Waals intermolecular potential suitable for hexafluoride gases

International Nuclear Information System (INIS)

Coroiu, Ilioara

2004-01-01

Several effective isotopic pair potential functions have been proposed to characterize the bulk properties of quasispherical molecules, in particular the hexafluorides, but none got a success. Unfortunately, these potentials have repulsive walls steeper than those which describe the hexafluorides. That these intermolecular potentials are not quite adequate is shown by the lack of complete agreement between theory and experiment even for the rare gases. Not long ago, R. A. Aziz et al. have constructed a Morse-Morse-Spline-Van der Waals (MMSV) potential. The MMSV potential incorporates the determination of C 6 dispersion coefficient and it reasonably correlates second virial coefficients and viscosity data of sulphur hexafluoride at the same time. None of the potential functions previously proposed in literature could predict these properties simultaneously. We calculated the second virial coefficients and a large number of Chapman-Cowling collision integrals for this improved intermolecular potential, the MMSV potential. The results were tabulated for a large reduced temperature range, kT/ε from 0.1 to 100. The treatment was entirely classical and no corrections for quantum effects were made. The higher approximations to the transport coefficients and the isotopic thermal diffusion factor were also calculated and tabulated for the same range. In this paper we present the evaluation of the uranium hexafluoride potential parameters for the MMSV intermolecular potential. To find a single set of potential parameters which could predict all the transport properties (viscosity, thermal conductivity, self diffusion, etc.), as well as the second virial coefficients, simultaneously, the method suggested by Morizot and a large assortment of literature data were used. Our results emphasized that the Morse-Morse-Spline-Van der Waals potential have the best overall predictive ability for gaseous hexafluoride data, certain for uranium hexafluoride. (author)

Diffusion bonding of IN 718 to VM 350 grade maraging steel

Science.gov (United States)

Crosby, S. R.; Biederman, R. R.; Reynolds, C. C.

1972-01-01

Diffusion bonding studies have been conducted on IN 718, VM 350 and the dissimilar alloy couple, IN 718 to maraging steel. The experimental processing parameters critical to obtaining consistently good diffusion bonds between IN 718 and VM 350 were determined. Interrelationships between temperature, pressure and surface preparation were explored for short bending intervals under vacuum conditions. Successful joining was achieved for a range of bonding cycle temperatures, pressures and surface preparations. The strength of the weaker parent material was used as a criterion for a successful tensile test of the heat treated bond. Studies of VM-350/VM-350 couples in the as-bonded condition showed a greater yielding and failure outside the bond region.

Modeling the effect of intermolecular force on the size-dependent pull-in behavior of beam-type NEMS using modified couple stress theory

Energy Technology Data Exchange (ETDEWEB)

Beni, Yaghoub Tadi; Karimipour, Iman [Shahrekord University, Shahrekord (Iran, Islamic Republic of); Abadyan, Mohamadreza [Islamic Azad University, Shahrekord (Iran, Islamic Republic of)

2014-09-15

Experimental observations reveal that the physical response of nano structures is size-dependent. Herein, modified couple stress theory has been used to study the effect of intermolecular van der Waals force on the size dependent pull-in of nano bridges and nano cantilevers. Three approaches including using differential transformation method, applying numerical method and developing a simple lumped parameter model have been employed to solve the governing equation of the systems. The pull-in parameters i.e. critical tip deflection and instability voltage of the nano structures have been determined. Effect of the van der Waals attraction and the size dependency and the importance of coupling between them on the pull-in performance have been discussed.

Modeling the effect of intermolecular force on the size-dependent pull-in behavior of beam-type NEMS using modified couple stress theory

International Nuclear Information System (INIS)

Beni, Yaghoub Tadi; Karimipour, Iman; Abadyan, Mohamadreza

2014-01-01

Experimental observations reveal that the physical response of nano structures is size-dependent. Herein, modified couple stress theory has been used to study the effect of intermolecular van der Waals force on the size dependent pull-in of nano bridges and nano cantilevers. Three approaches including using differential transformation method, applying numerical method and developing a simple lumped parameter model have been employed to solve the governing equation of the systems. The pull-in parameters i.e. critical tip deflection and instability voltage of the nano structures have been determined. Effect of the van der Waals attraction and the size dependency and the importance of coupling between them on the pull-in performance have been discussed.

A quantum mechanical study of water adsorption on the (110) surfaces of rutile SnO₂ and TiO₂: investigating the effects of intermolecular interactions using hybrid-exchange density functional theory.

Science.gov (United States)

Patel, M; Sanches, F F; Mallia, G; Harrison, N M

2014-10-21

Periodic hybrid-exchange density functional theory calculations are used to explore the first layer of water at model oxide surfaces, which is an important step for understanding the photocatalytic reactions involved in solar water splitting. By comparing the structure and properties of SnO2(110) and TiO2(110) surfaces in contact with water, the effects of structural and electronic differences on the water chemistry are examined. The dissociative adsorption mode at low coverage (1/7 ML) up to monolayer coverage (1 ML) on both SnO2 and TiO2(110) surfaces is analysed. To investigate further the intermolecular interactions between adjacent adsorbates, monolayer adsorption on each surface is explored in terms of binding energies and bond lengths. Analysis of the water adsorption geometry and energetics shows that the relative stability of water adsorption on SnO2(110) is governed largely by the strength of the chemisorption and hydrogen bonds at the surface of the adsorbate-substrate system. However on TiO2(110), a more complicated scenario of the first layer of water on its surface arises in which there is an interplay between chemisorption, hydrogen bonding and adsorbate-induced atomic displacements in the surface. Furthermore the projected density of states of each surface in contact with a mixture of adsorbed water molecules and adsorbed hydroxyls is presented and sheds some light on the nature of the crystalline chemical bonds as well as on why adsorbed water has often been reported to be unstable on rutile SnO2(110).

Investigation of Anisotropic Bonded Magnets in Permanent Magnet Machine Applications

Science.gov (United States)

Khazdozian, H. A.; McCall, S. K.; Kramer, M. J.; Paranthaman, M. P.; Nlebedim, I. C.

Rare earth elements (REE) provide the high energy product necessary for permanent magnets, such as sintered Nd2Fe14B, in many applications like wind energy generators. However, REEs are considered critical materials due to risk in their supply. To reduce the use of critical materials in permanent magnet machines, the performance of anisotropic bonded NdFeB magnets, aligned under varying magnetic field strength, was simulated using 3D finite element analysis in a 3MW direct-drive permanent magnet generator (DDPMG), with sintered N42 magnets used as a baseline for comparison. For direct substitution of the anisotropic bonded magnets, approximately 85% of the efficiency of the baseline model was achieved, irrespective of the alignment field. The torque and power generation of the DDPMG was not found to vary significantly with increase in the alignment field. Finally, design changes were studied to allow for the achievement of rated torque and power with the use of anisotropic bonded magnets, demonstrating the potential for reduction of critical materials in permanent magnets for renewable energy applications. This work was supported by the Critical Materials Institute, an Energy Innovation Hub funded by the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Advanced Manufacturing Office.

Ab initio ground state phenylacetylene-argon intermolecular potential energy surface and rovibrational spectrum

DEFF Research Database (Denmark)

Cybulski, Hubert; Fernandez, Berta; Henriksen, Christian

2012-01-01

to the axis perpendicular to the phenylacetylene plane and containing the center of mass. The calculated interaction energy is -418.9 cm(-1). To check further the potential, we obtain the rovibrational spectrum of the complex and the results are compared to the available experimental data. (C) 2012 American......We evaluate the phenylacetylene-argon intermolecular potential energy surface by fitting a representative number of ab initio interaction energies to an analytic function. These energies are calculated at a grid of intermolecular geometries, using the CCSD(T) method and the aug-cc-pVDZ basis set...... extended with a series of 3s3p2d1flg midbond functions. The potential is characterized by two equivalent global minima where the Ar atom is located above and below the phenylacetylene plane at a distance of 3.5781 angstrom from the molecular center of mass and at an angle of 9.08 degrees with respect...

Catalytic Intermolecular Cross-Couplings of Azides and LUMO-Activated Unsaturated Acyl Azoliums

KAUST Repository

Li, Wenjun

2017-02-15

An example for the catalytic synthesis of densely functionalized 1,2,3-triazoles through a LUMO activation mode has been developed. The protocol is enabled by intermolecular cross coupling reactions of azides with in situ-generated alpha,beta-unsaturated acyl azoliums. High yields and broad scope as well as the investigation of reaction mechanism are reported.

Laser-heating wire bonding on MEMS packaging

Directory of Open Access Journals (Sweden)

Yuetao Liu

2014-02-01

Full Text Available Making connections is critical in fabrication of MEMS (Micro-Electro-Mechanical Systems. It is also complicated, because the temperature during joining affects both the bond produced and the structure and mechanical properties of the moving parts of the device. Specifications for MEMS packaging require that the temperature not exceed 240 °C. However, usually, temperatures can reach up to 300 °C during conventional thermosonic wire bonding. Such a temperature will change the distribution of dopants in CMOS (Complementary Metal Oxide Semiconductor circuits. In this paper we propose a new heating process. A semiconductor laser (wavelength 808 nm is suggested as the thermal source for wire bonding. The thermal field of this setup was analyzed, and specific mathematical models of the field were built. Experimental results show that the heating can be focused on the bonding pad, and that much lower heat conduction occurs, compared with that during the normal heating method. The bond strength increases with increasing laser power. The bond strengths obtained with laser heating are slightly lower than those obtained with the normal heating method, but can still meet the strength requirements for MEMS.

Fluorescence Correlation Spectroscopy to Study Diffusion of Polymer Chains within Layered Hydrogen-Bonded Polymer Films

Science.gov (United States)

Pristinski, Denis; Kharlampieva, Evguenia; Sukhishvili, Svetlana

2002-03-01

Fluorescence Correlation Spectroscopy (FCS) has been used to probe molecular motions within polymer multilayers formed by hydrogen-bonding sequential self-assembly. Polyethylene glycol (PEG) molecules were end-labeled with the fluorescent tags, and self-assembled with polymethacrylic acid (PMAA) using layer-by-layer deposition. We have found that molecules included in the top adsorbed layer have significant mobility at the millisecond time scale, probably due to translational diffusion. However, their dynamics deviate from classical Brownian motion with a single diffusion time. Possible reasons for the deviation are discussed. We found that motions were significantly slowed with increasing depth within the PEG/PMAA multilayer. This phenomena occured in a narrow pH range around 4.0 in which intermolecular interactions were relatively weak.

Programmable display of DNA-protein chimeras for controlling cell-hydrogel interactions via reversible intermolecular hybridization.

Science.gov (United States)

Zhang, Zhaoyang; Li, Shihui; Chen, Niancao; Yang, Cheng; Wang, Yong

2013-04-08

Extensive studies have been recently carried out to achieve dynamic control of cell-material interactions primarily through physicochemical stimulation. The purpose of this study was to apply reversible intermolecular hybridization to program cell-hydrogel interactions in physiological conditions based on DNA-antibody chimeras and complementary oligonucleotides. The results showed that DNA oligonucleotides could be captured to and released from the immobilizing DNA-functionalized hydrogels with high specificity via DNA hybridization. Accordingly, DNA-antibody chimeras were captured to the hydrogels, successfully inducing specific cell attachment. The cell attachment to the hydrogels reached the plateau at approximately half an hour after the functionalized hydrogels and the cells were incubated together. The attached cells were rapidly released from the bound hydrogels when triggering complementary oligonucleotides were introduced to the system. However, the capability of the triggering complementary oligonucleotides in releasing cells was affected by the length of intermolecular hybridization. The length needed to be at least more than 20 base pairs in the current experimental setting. Notably, because the procedure of intermolecular hybridization did not involve any harsh condition, the released cells maintained the same viability as that of the cultured cells. The functionalized hydrogels also exhibited the potential to catch and release cells repeatedly. Therefore, this study demonstrates that it is promising to regulate cell-material interactions dynamically through the DNA-programmed display of DNA-protein chimeras.

Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining

Science.gov (United States)

Kukshal, Vandna; Kim, In-Kwon; Hura, Gregory L.; Tomkinson, Alan E.; Tainer, John A.; Ellenberger, Tom

2015-01-01

Mammalian DNA ligase III (LigIII) functions in both nuclear and mitochondrial DNA metabolism. In the nucleus, LigIII has functional redundancy with DNA ligase I whereas LigIII is the only mitochondrial DNA ligase and is essential for the survival of cells dependent upon oxidative respiration. The unique LigIII zinc finger (ZnF) domain is not required for catalytic activity but senses DNA strand breaks and stimulates intermolecular ligation of two DNAs by an unknown mechanism. Consistent with this activity, LigIII acts in an alternative pathway of DNA double strand break repair that buttresses canonical non-homologous end joining (NHEJ) and is manifest in NHEJ-defective cancer cells, but how LigIII acts in joining intermolecular DNA ends versus nick ligation is unclear. To investigate how LigIII efficiently joins two DNAs, we developed a real-time, fluorescence-based assay of DNA bridging suitable for high-throughput screening. On a nicked duplex DNA substrate, the results reveal binding competition between the ZnF and the oligonucleotide/oligosaccharide-binding domain, one of three domains constituting the LigIII catalytic core. In contrast, these domains collaborate and are essential for formation of a DNA-bridging intermediate by adenylated LigIII that positions a pair of blunt-ended duplex DNAs for efficient and specific intermolecular ligation. PMID:26130724

3-[(R-3,3-Dichloro-2-hydroxypropyl]-8-hydroxy-6-methoxy-1H-isochromen-1-one

Directory of Open Access Journals (Sweden)

Yong-Cheng Lin

2008-09-01

Full Text Available The title compound, C13H12Cl2O5, is an isocoumarin compound which has been isolated from the ethyl acetate extract of the fermentation broth of actinomycete Streptomyces sp. (V4 from the South China Sea. There are intra- and intermolecular hydrogen bonds and halogen bonds [Cl...Cl = 3.434 (2 Å; C—Cl...Cl = 121.6°]. The intermolecular O—H...O hydrogen bonds link molecules into chains along the b axis.

Modulation of intermolecular interactions in single-molecule magnets

Science.gov (United States)

Heroux, Katie Jeanne

Polynuclear manganese clusters exhibiting interesting magnetic and quantum properties have been an area of intense research since the discovery of the first single-molecule magnet (SMM) in 1993. These molecules, below their blocking temperature, function as single-domain magnetic particles which exhibit classical macroscale magnetic properties as well as quantum mechanical phenomena such as quantum tunnelling of magnetization (QTM) and quantum phase interference. The union of classical and quantum behavior in these nanomaterials makes SMMs ideal candidates for high-density information storage and quantum computing. However, environmental coupling factors (nuclear spins, phonons, neighboring molecules) must be minimized if such applications are ever to be fully realized. The focus of this work is making small structural changes in well-known manganese SMMs in order to drastically enhance the overall magnetic and quantum properties of the system. Well-isolated molecules of high crystalline quality should lead to well-defined energetic and spectral properties as well. An advantage of SMMs over bulk magnetic materials is that they can be chemically altered from a "bottom-up" approach providing a synthetic tool for tuning magnetic properties. This systematic approach is utilized in the work presented herein by incorporating bulky ligands and/or counterions to "isolate" the magnetic core of [Mn4] dicubane SMMs. Reducing intermolecular interactions in the crystal lattice (neighboring molecules, solvate molecules, dipolar interactions) is an important step toward developing viable quantum computing devices. Detailed bulk magnetic studies as well as single crystal magnetization hysteresis and high-frequency EPR studies on these sterically-isolated complexes show enhanced, and sometimes even unexpected, quantum dynamics. The importance of intra- and intermolecular interactions remains a common theme throughout this work, extending to other SMMs of various topology including

An approach to the intermolecular energy in pure liquids

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GAbriel Hernández de la Torre

2010-07-01

Full Text Available Se propone un método para: estimar la energía potencial de repulsión de cualquier molécula central como una función de las densidades ortobáricas en líquidos puros no auto asociados; estimar los parámetros necesarios para calcular la energía de dispersión de London; calcular los números de coordinación promedio, distancias intermoleculares de interacción, diámetros moleculares y de grupos; en moléculas globulares, moléculas planas y parafinas normales.

Hydrogen bond dynamics and water structure in glucose-water solutions by depolarized Rayleigh scattering and low-frequency Raman spectroscopy

Science.gov (United States)

Paolantoni, Marco; Sassi, Paola; Morresi, Assunta; Santini, Sergio

2007-07-01

The effect of glucose on the relaxation process of water at picosecond time scales has been investigated by depolarized Rayleigh scattering (DRS) experiments. The process is assigned to the fast hydrogen bonding dynamics of the water network. In DRS spectra this contribution can be safely separated from the slower relaxation process due to the sugar. The detected relaxation time is studied at different glucose concentrations and modeled considering bulk and hydrating water contributions. As a result, it is found that in diluted conditions the hydrogen bond lifetime of proximal water molecules becomes about three times slower than that of the bulk. The effect of the sugar on the hydrogen bond water structure is investigated by analyzing the low-frequency Raman (LFR) spectrum sensitive to intermolecular modes. The addition of glucose strongly reduces the intensity of the band at 170cm-1 assigned to a collective stretching mode of water molecules arranged in cooperative tetrahedral domains. These findings indicate that proximal water molecules partially lose the tetrahedral ordering typical of the bulk leading to the formation of high density environments around the sugar. Thus the glucose imposes a new local order among water molecules localized in its hydration shell in which the hydrogen bond breaking dynamics is sensitively retarded. This work provides new experimental evidences that support recent molecular dynamics simulation and thermodynamics results.

Recent mass spectrometry-based techniques and considerations for disulfide bond characterization in proteins.

Science.gov (United States)

Lakbub, Jude C; Shipman, Joshua T; Desaire, Heather

2018-04-01

Disulfide bonds are important structural moieties of proteins: they ensure proper folding, provide stability, and ensure proper function. With the increasing use of proteins for biotherapeutics, particularly monoclonal antibodies, which are highly disulfide bonded, it is now important to confirm the correct disulfide bond connectivity and to verify the presence, or absence, of disulfide bond variants in the protein therapeutics. These studies help to ensure safety and efficacy. Hence, disulfide bonds are among the critical quality attributes of proteins that have to be monitored closely during the development of biotherapeutics. However, disulfide bond analysis is challenging because of the complexity of the biomolecules. Mass spectrometry (MS) has been the go-to analytical tool for the characterization of such complex biomolecules, and several methods have been reported to meet the challenging task of mapping disulfide bonds in proteins. In this review, we describe the relevant, recent MS-based techniques and provide important considerations needed for efficient disulfide bond analysis in proteins. The review focuses on methods for proper sample preparation, fragmentation techniques for disulfide bond analysis, recent disulfide bond mapping methods based on the fragmentation techniques, and automated algorithms designed for rapid analysis of disulfide bonds from liquid chromatography-MS/MS data. Researchers involved in method development for protein characterization can use the information herein to facilitate development of new MS-based methods for protein disulfide bond analysis. In addition, individuals characterizing biotherapeutics, especially by disulfide bond mapping in antibodies, can use this review to choose the best strategies for disulfide bond assignment of their biologic products. Graphical Abstract This review, describing characterization methods for disulfide bonds in proteins, focuses on three critical components: sample preparation, mass

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

Science.gov (United States)

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...

A general intermolecular force field based on tight-binding quantum chemical calculations

Science.gov (United States)

Grimme, Stefan; Bannwarth, Christoph; Caldeweyher, Eike; Pisarek, Jana; Hansen, Andreas

2017-10-01

A black-box type procedure is presented for the generation of a molecule-specific, intermolecular potential energy function. The method uses quantum chemical (QC) information from our recently published extended tight-binding semi-empirical scheme (GFN-xTB) and can treat non-covalently bound complexes and aggregates with almost arbitrary chemical structure. The necessary QC information consists of the equilibrium structure, Mulliken atomic charges, charge centers of localized molecular orbitals, and also of frontier orbitals and orbital energies. The molecular pair potential includes model density dependent Pauli repulsion, penetration, as well as point charge electrostatics, the newly developed D4 dispersion energy model, Drude oscillators for polarization, and a charge-transfer term. Only one element-specific and about 20 global empirical parameters are needed to cover systems with nuclear charges up to radon (Z = 86). The method is tested for standard small molecule interaction energy benchmark sets where it provides accurate intermolecular energies and equilibrium distances. Examples for structures with a few hundred atoms including charged systems demonstrate the versatility of the approach. The method is implemented in a stand-alone computer code which enables rigid-body, global minimum energy searches for molecular aggregation or alignment.

THz absorption spectrum of the CO2–H2O complex: Observation and assignment of intermolecular van der Waals vibrations

DEFF Research Database (Denmark)

Andersen, Jonas; Heimdal, J.; Wallin Mahler Andersen, Denise

2014-01-01

have been assigned and provide crucial observables for benchmark theoretical descriptions of this systems’ flat intermolecular potential energy surface. A (semi)-empirical value for the zero-point energy of 273 ± 15 cm−1 from the class of intermolecular van der Waals vibrations is proposed...... and the combination with high-level quantum chemical calculations provides a value of 726 ± 15 cm−1 for the dissociation energy D0...

Estimation of the thermodynamic parameters of hydrogen bonding in alcohol solutions by the method of infrared spectroscopy

Science.gov (United States)

Vedernikova, E. V.; Gafurov, M. M.; Ataev, M. B.

2011-01-01

Hydrogen bonding (H-bonding) is a specific type of intermolecular interaction being formed for favorable mutual orientations of the interacting molecules. One of the authors had developed a model concept relating the H-bonding energy with the change of stretching vibrations Δν = νOH - νOH-NC of the alcohol OH-group in acetonitrile and acetone solutions: Δ H = 89.24Δν/ν0. The calculated H-bond energy was 10.45 kJ/mole for acetonitrile and Δ H = 12.12 kJ/mole for acetone. The results obtained are compared with the data calculated using the equilibrium constant of H-bonding reaction; they can also be used to calculate all other thermodynamic H-bond parameters by measuring the equilibrium constant K c in a certain temperature interval. The equilibrium constant is calculated from the Lambert-Bouguer-Beer law: {K_c} = {{C_{{text{OH}} \\cdots {text{NC}}}}}/{{C_{text{OH}} \\cdot {C_{text{NC}}}}} , ∆ F = - RT ṡ ln K c , ∆ H = RT 2 ṡ d(ln K c )/ dT, and Δ S = {Δ H - Δ F}/T . For the methanol solution in acetonitrile, Δν = 115 cm-1, Δ H = 10.87 kJ/mole, and K c = 42 L/mole. For the ethanol solution in acetonitrile, Δν = 118 cm-1, Δ H = 10.01 kJ/mole, and K c = 34 L/mole. For the propanol solution in acetonitrile, Δν = 110 cm-1, Δ H = 8.36 kJ/mole, and K c = 13 L/mole. All calculations are performed using the developed programs. The spectra are recorded on Perkin-Elmer-180 and Specord-84 IR-spectrometers. The values of the thermodynamic parameters calculated and estimated from K c - f( T) are in good agreement with each other and with the available literature data.

Diamond-like nanoparticles influence on flavonoids transport: molecular modelling

Science.gov (United States)

Plastun, Inna L.; Agandeeva, Ksenia E.; Bokarev, Andrey N.; Zenkin, Nikita S.

2017-03-01

Intermolecular interaction of diamond-like nanoparticles and flavonoids is investigated by numerical simulation. Using molecular modelling by the density functional theory method, we analyze hydrogen bonds formation and their influence on IR - spectra and structure of molecular complex which is formed due to interaction between flavonoids and nanodiamonds surrounded with carboxylic groups. Enriched adamantane (1,3,5,7 - adamantanetetracarboxylic acid) is used as an example of diamond-like nanoparticles. Intermolecular forces and structure of hydrogen bonds are investigated. IR - spectra and structure parameters of quercetin - adamantanetetracarboxylic acid molecular complex are obtained by numerical simulation using the Gaussian software complex. Received data coincide well with experimental results. Intermolecular interactions and hydrogen bonding structure in the obtained molecular complex are examined. Possibilities of flavonoids interaction with DNA at the molecular level are also considered.

Hydrogen Bonding Interaction between Atmospheric Gaseous Amides and Methanol

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Hailiang Zhao

2016-12-01

Full Text Available Amides are important atmospheric organic–nitrogen compounds. Hydrogen bonded complexes of methanol (MeOH with amides (formamide, N-methylformamide, N,N-dimethylformamide, acetamide, N-methylacetamide and N,N-dimethylacetamide have been investigated. The carbonyl oxygen of the amides behaves as a hydrogen bond acceptor and the NH group of the amides acts as a hydrogen bond donor. The dominant hydrogen bonding interaction occurs between the carbonyl oxygen and the OH group of methanol as well as the interaction between the NH group of amides and the oxygen of methanol. However, the hydrogen bonds between the CH group and the carbonyl oxygen or the oxygen of methanol are also important for the overall stability of the complexes. Comparable red shifts of the C=O, NH- and OH-stretching transitions were found in these MeOH–amide complexes with considerable intensity enhancement. Topological analysis shows that the electron density at the bond critical points of the complexes fall in the range of hydrogen bonding criteria, and the Laplacian of charge density of the O–H∙∙∙O hydrogen bond slightly exceeds the upper value of the Laplacian criteria. The energy decomposition analysis further suggests that the hydrogen bonding interaction energies can be mainly attributed to the electrostatic, exchange and dispersion components.

Hydrogen Bonding Interaction between Atmospheric Gaseous Amides and Methanol.

Science.gov (United States)

Zhao, Hailiang; Tang, Shanshan; Xu, Xiang; Du, Lin

2016-12-30

Amides are important atmospheric organic-nitrogen compounds. Hydrogen bonded complexes of methanol (MeOH) with amides (formamide, N -methylformamide, N , N -dimethylformamide, acetamide, N -methylacetamide and N , N -dimethylacetamide) have been investigated. The carbonyl oxygen of the amides behaves as a hydrogen bond acceptor and the NH group of the amides acts as a hydrogen bond donor. The dominant hydrogen bonding interaction occurs between the carbonyl oxygen and the OH group of methanol as well as the interaction between the NH group of amides and the oxygen of methanol. However, the hydrogen bonds between the CH group and the carbonyl oxygen or the oxygen of methanol are also important for the overall stability of the complexes. Comparable red shifts of the C=O, NH- and OH-stretching transitions were found in these MeOH-amide complexes with considerable intensity enhancement. Topological analysis shows that the electron density at the bond critical points of the complexes fall in the range of hydrogen bonding criteria, and the Laplacian of charge density of the O-H∙∙∙O hydrogen bond slightly exceeds the upper value of the Laplacian criteria. The energy decomposition analysis further suggests that the hydrogen bonding interaction energies can be mainly attributed to the electrostatic, exchange and dispersion components.

Hydrogen bonded supra-molecular framework in inorganic-organic hybrid compounds: Syntheses, structures, and photoluminescent properties

Science.gov (United States)

Yan, Li; Liu, Wei; Li, Chuanbi; Wang, Yifei; Ma, Li; Dong, Qinqin

2013-03-01

Two novel compounds constructed from aromatic acid and N-Heterocyclic ligands have been synthesized by hydrothermal reaction: [Cd(mip)(1,8-NDC)(H2O)]2 (1) [mip = 2-(3-methoxyphenyl)-1H-imidazo[4,5-f][1,10]phenanthroline, 1,8-NDC = naphthalene-1,8-dicarboxylic acid] and Cd(mip)2(NTC)2 (2) [NTC = nicotinic acid]. Compounds 1 and 2 are characterized by elemental analysis, IR, single crystal X-ray diffraction and thermogravimetric analysis (TGA). Single-crystal X-ray investigation reveals that compounds 1-2 are 0 dimensional (0D) structures, and the existence of hydrogen bonds and π-π interactions lead the 0D to 2D novel framework. Hydrogen bonds and π-π interactions are powerful non-covalent intermolecular interactions for directing supra-molecular architectures. TG analysis shows clear courses of weight loss, which corresponds to the decomposition of different ligands. At room temperature, compound 1 exhibits emission at 449 nm upon excitation at 325 nm, and compound 2 shows a strong emission at 656 nm upon excitation at 350 nm. Fluorescent spectrum displays that compounds 1 and 2 are potential luminescent materials.

A conserved hydrogen-bond network in the catalytic centre of animal glutaminyl cyclases is critical for catalysis.

Science.gov (United States)

Huang, Kai-Fa; Wang, Yu-Ruei; Chang, En-Cheng; Chou, Tsung-Lin; Wang, Andrew H-J

2008-04-01

QCs (glutaminyl cyclases; glutaminyl-peptide cyclotransferases, EC 2.3.2.5) catalyse N-terminal pyroglutamate formation in numerous bioactive peptides and proteins. The enzymes were reported to be involved in several pathological conditions such as amyloidotic disease, osteoporosis, rheumatoid arthritis and melanoma. The crystal structure of human QC revealed an unusual H-bond (hydrogen-bond) network in the active site, formed by several highly conserved residues (Ser(160), Glu(201), Asp(248), Asp(305) and His(319)), within which Glu(201) and Asp(248) were found to bind to substrate. In the present study we combined steady-state enzyme kinetic and X-ray structural analyses of 11 single-mutation human QCs to investigate the roles of the H-bond network in catalysis. Our results showed that disrupting one or both of the central H-bonds, i.e., Glu(201)...Asp(305) and Asp(248)...Asp(305), reduced the steady-state catalysis dramatically. The roles of these two COOH...COOH bonds on catalysis could be partly replaced by COOH...water bonds, but not by COOH...CONH(2) bonds, reminiscent of the low-barrier Asp...Asp H-bond in the active site of pepsin-like aspartic peptidases. Mutations on Asp(305), a residue located at the centre of the H-bond network, raised the K(m) value of the enzyme by 4.4-19-fold, but decreased the k(cat) value by 79-2842-fold, indicating that Asp(305) primarily plays a catalytic role. In addition, results from mutational studies on Ser(160) and His(319) suggest that these two residues might help to stabilize the conformations of Asp(248) and Asp(305) respectively. These data allow us to propose an essential proton transfer between Glu(201), Asp(305) and Asp(248) during the catalysis by animal QCs.

H/D Isotope Effects in Hydrogen Bonded Systems

Directory of Open Access Journals (Sweden)

Aleksander Filarowski

2013-04-01

Full Text Available An extremely strong H/D isotope effect observed in hydrogen bonded A-H…B systems is connected with a reach diversity of the potential shape for the proton/deuteron motion. It is connected with the anharmonicity of the proton/deuteron vibrations and of the tunneling effect, particularly in cases of short bridges with low barrier for protonic and deuteronic jumping. Six extreme shapes of the proton motion are presented starting from the state without possibility of the proton transfer up to the state with a full ionization. The manifestations of the H/D isotope effect are best reflected in the infra-red absorption spectra. A most characteristic is the run of the relationship between the isotopic ratio nH/nD and position of the absorption band shown by using the example of NHN hydrogen bonds. One can distinguish a critical range of correlation when the isotopic ratio reaches the value of ca. 1 and then increases up to unusual values higher than . The critical range of the isotope effect is also visible in NQR and NMR spectra. In the critical region one observes a stepwise change of the NQR frequency reaching 1.1 MHz. In the case of NMR, the maximal isotope effect is reflected on the curve presenting the dependence of Δd (1H,2H on d (1H. This effect corresponds to the range of maximum on the correlation curve between dH and ΔpKa that is observed in various systems. There is a lack in the literature of quantitative information about the influence of isotopic substitution on the dielectric properties of hydrogen bond except the isotope effect on the ferroelectric phase transition in some hydrogen bonded crystals.

Intermolecular effects on the radiogenic formation of electron-capture phosphorus-centered radicals. A single-crystal ESR study of diastereoisomeric precursors

Energy Technology Data Exchange (ETDEWEB)

Aagaard, O.M.; Janssen, R.A.J.; de Waal, B.F.M.; Buck, H.M. (Eindhoven Univ. of Technology (Netherlands))

1990-01-31

ESR experiments on X-irradiated single crystals of the 2R,4S,5R and 2S,4S,5R diastereoisomers of 2-chloro-3,4-dimethyl-5-phenyl-1,3,2-oxazaphospholidine 2-sulfide reveal that the yield of radiogenic electron-capture reactions in the solid state strongly depends on intermolecular interactions in the crystal. In the present case a high yield of P-Cl three-electron-bond phosphoranyl radical anions is found in crystals of the 2R,4S,5R isomer, whereas no radical formation can be detected for the 2S,4S,5R isomer. An analysis of nonbonded interactions with neighboring molecules reveals that the geometry relaxation necessary for the radical stabilization is easily accommodated in crystals of the 2R,4S,SR isomer but not in the 2S,4S,5R isomer, explaining the observed difference in electron-capture efficiency. Experiments on radical formation in a MeTHF host matrix give further insight into the importance of the environment on radiogenic radical formation. The possible concurrent effect of the matrix on the electronic configuration and spin density distribution of the resulting phosphoranyl radical is discussed.

Intermolecular effects on the radiogenic formation of electron-capture phosphorus-centered radicals. A single-crystal ESR study of diastereoisomeric precursors

International Nuclear Information System (INIS)

Aagaard, O.M.; Janssen, R.A.J.; de Waal, B.F.M.; Buck, H.M.

1990-01-01

ESR experiments on X-irradiated single crystals of the 2R,4S,5R and 2S,4S,5R diastereoisomers of 2-chloro-3,4-dimethyl-5-phenyl-1,3,2-oxazaphospholidine 2-sulfide reveal that the yield of radiogenic electron-capture reactions in the solid state strongly depends on intermolecular interactions in the crystal. In the present case a high yield of P-Cl three-electron-bond phosphoranyl radical anions is found in crystals of the 2R,4S,5R isomer, whereas no radical formation can be detected for the 2S,4S,5R isomer. An analysis of nonbonded interactions with neighboring molecules reveals that the geometry relaxation necessary for the radical stabilization is easily accommodated in crystals of the 2R,4S,SR isomer but not in the 2S,4S,5R isomer, explaining the observed difference in electron-capture efficiency. Experiments on radical formation in a MeTHF host matrix give further insight into the importance of the environment on radiogenic radical formation. The possible concurrent effect of the matrix on the electronic configuration and spin density distribution of the resulting phosphoranyl radical is discussed

Testing intermolecular potential functions using transport property data

International Nuclear Information System (INIS)

Clifford, A.A.; Dickinson, E.; Gray, P.; Scott, A.C.

1975-01-01

The viscosity of hydrogen has been measured at eight temperatures from 273 to 1060K, using a capillary-flow viscometer. The results have been used to test the repulsive part of a recently formulated H 2 /H 2 intermolecular potential function, obtained from molecular-beam measurements. Agreement between the experimental and predicted values for viscosity is within 3.5%, which corresponds approximately to the combined quoted uncertainties in the two sets of data. However, if the value of the distance parameter of the potential is reduced by about 1.5%, the agreement obtained is within 0.75% over the whole temperature range. This modified potential function gives better agreement with the available higher temperature viscosities and second virial coefficients. (author)

Recognition of a novel type X═N-Hal···Hal (X = C, S, P; Hal = F, Cl, Br, I) halogen bonding.

Science.gov (United States)

Gushchin, Pavel V; Kuznetsov, Maxim L; Haukka, Matti; Kukushkin, Vadim Yu

2013-04-04

The chlorination of the eight-membered platinum(II) chelates [PtCl2{NH═C(NR2)N(Ph)C(═NH)N(Ph)C(NR2)═NH}] (R = Me (1); R2 = (CH2)5 (2)) with uncomplexed imino group with Cl2 gives complexes bearing the ═N-Cl moiety [PtCl4{NH═C(NR2)N(Ph)C(═NCl)N(Ph)C(NR2)═NH}] (R = Me (3); R2 = (CH2)5 (4)). X-ray study for 3 revealed a novel type intermolecular halogen bonding ═N-Cl···Cl(-), formed between the Cl atom of the chlorinated imine and the chloride bound to the platinum(IV) center. The processing relevant structural data retrieved from the Cambridge Structural Database (CSDB) shows that this type of halogen bonding is realized in 18 more molecular species having X═N-Hal moieties (X = C, P, S, V, W; Hal = Cl, Br, I), but this weak ═N-Hal···Hal(-) bonding was totally neglected in the previous works. The presence of the halogen bonding in 3 was confirmed by theoretical calculations at the density functional theory (DFT, M06-2X) level, and its nature was analyzed.

Intermolecular detergent-membrane protein noes for the characterization of the dynamics of membrane protein-detergent complexes.

Science.gov (United States)

Eichmann, Cédric; Orts, Julien; Tzitzilonis, Christos; Vögeli, Beat; Smrt, Sean; Lorieau, Justin; Riek, Roland

2014-12-11

The interaction between membrane proteins and lipids or lipid mimetics such as detergents is key for the three-dimensional structure and dynamics of membrane proteins. In NMR-based structural studies of membrane proteins, qualitative analysis of intermolecular nuclear Overhauser enhancements (NOEs) or paramagnetic resonance enhancement are used in general to identify the transmembrane segments of a membrane protein. Here, we employed a quantitative characterization of intermolecular NOEs between (1)H of the detergent and (1)H(N) of (2)H-perdeuterated, (15)N-labeled α-helical membrane protein-detergent complexes following the exact NOE (eNOE) approach. Structural considerations suggest that these intermolecular NOEs should show a helical-wheel-type behavior along a transmembrane helix or a membrane-attached helix within a membrane protein as experimentally demonstrated for the complete influenza hemagglutinin fusion domain HAfp23. The partial absence of such a NOE pattern along the amino acid sequence as shown for a truncated variant of HAfp23 and for the Escherichia coli inner membrane protein YidH indicates the presence of large tertiary structure fluctuations such as an opening between helices or the presence of large rotational dynamics of the helices. Detergent-protein NOEs thus appear to be a straightforward probe for a qualitative characterization of structural and dynamical properties of membrane proteins embedded in detergent micelles.

Intermolecular RNA Recombination Occurs at Different Frequencies in Alternate Forms of Brome Mosaic Virus RNA Replication Compartments

Directory of Open Access Journals (Sweden)

Hernan Garcia-Ruiz

2018-03-01

Full Text Available Positive-strand RNA viruses replicate their genomes in membrane-bound replication compartments. Brome mosaic virus (BMV replicates in vesicular invaginations of the endoplasmic reticulum membrane. BMV has served as a productive model system to study processes like virus-host interactions, RNA replication and recombination. Here we present multiple lines of evidence showing that the structure of the viral RNA replication compartments plays a fundamental role and that recruitment of parental RNAs to a common replication compartment is a limiting step in intermolecular RNA recombination. We show that a previously defined requirement for an RNA recruitment element on both parental RNAs is not to function as a preferred crossover site, but in order for individual RNAs to be recruited into the replication compartments. Moreover, modulating the form of the replication compartments from spherular vesicles (spherules to more expansive membrane layers increased intermolecular RNA recombination frequency by 200- to 1000-fold. We propose that intermolecular RNA recombination requires parental RNAs to be recruited into replication compartments as monomers, and that recruitment of multiple RNAs into a contiguous space is much more common for layers than for spherules. These results could explain differences in recombination frequencies between viruses that replicate in association with smaller spherules versus larger double-membrane vesicles and convoluted membranes.

2-{[4-(1,3-Benzothiazol-2-ylphenyl](methylamino}acetic acid

Directory of Open Access Journals (Sweden)

Yong Zhang

2009-11-01

Full Text Available In the title compound, C16H14N2O2S, the dihedral angle between the benzothiazole ring system and benzene ring is 3.11 (2°. In the crystal structure, intermolecular O—H...N hydrogen bonds link molecules into chains along [100] and these chains are, in turn, linked into a three-dimensional network via weak intermolecular C—H...O hydrogen bonds.

Study of intermolecular interactions in binary mixtures of 2-(dimethylamino)ethanol with methanol and ethanol at various temperatures

International Nuclear Information System (INIS)

Pandey, Puneet Kumar; Pandey, Vrijesh Kumar; Awasthi, Anjali; Nain, Anil Kumar; Awasthi, Aashees

2014-01-01

Graphical abstract: The densities and ultrasonic speeds of the binary mixtures over the entire composition range were measured at various temperatures at atmospheric pressure. The excess molar volumes, isentropic compressibilities, and molar isentropic compressions have been calculated. The variations of these parameters with composition and temperature are discussed. The IR spectra were recorded they further supported the conclusion drawn from excess parameters, which indicates the presence of intermolecular hydrogen bonding between the oxygen atom of DMAE molecules and hydrogen atom of methanol and ethanol molecules in these mixtures.. - Highlights: • The study reports density and ultrasonic velocity data of 2-(dimethylamino)ethanol + methanol/ethanol mixtures. • To elucidate the interactions in 2-(dimethylamino)ethanol + methanol/ethanol binary mixtures. • Provides information on nature and relative strength of interactions in these mixtures. • Correlates physicochemical properties with interactions in these mixtures. - Abstract: The densities, ρ and ultrasonic speeds, u of the binary mixtures of 2-(dimethylamino)ethanol (DMAE) with methanol/ethanol, including those of pure liquids, over the entire composition range were measured at 298.15, 308.15 and 318.15 K. From the experimental data, the excess molar volumes, V m E and excess isentropic compressibilities, κ s E have been calculated. The excess partial molar volumes, V ¯ m,1 E and V ¯ m,2 E and excess partial molar isentropic compressions, K ¯ s,m,1 E and K ¯ s,m,2 E over the whole composition range; and partial molar volumes, V ¯ m,1 ° and V ¯ m,2 ° , partial molar isentropic compressions, K ¯ s,m,1 ° and K ¯ s,m,2 ° , excess partial molar volumes, V ¯ m,1 °E and V ¯ m,2 °E , and excess partial molar isentropic compressions, K ¯ s,m,1 °E and K ¯ s,m,2 °E at infinite dilution have also been calculated. The variations of these parameters with composition and temperature are

Resonance energy transfer (RET)-Induced intermolecular pairing force: a tunable weak interaction and its application in SWNT separation.

Science.gov (United States)

Pan, Xiaoyong; Chen, Hui; Wang, Wei Zhi; Ng, Siu Choon; Chan-Park, Mary B

2011-07-21

This paper explores evidence of an optically mediated interaction that is active in the separation mechanism of certain selective agents through consideration of the contrasting selective behaviors of two conjugated polymers with distinct optical properties. The involvement of a RET-induced intermolecular pairing force is implied by the different illumination response behaviors. The magnitude of this interaction scales with the external stimulus parameter, the illumination irradiance (I), and thus is tunable. This suggests a facile technique to modify the selectivity of polymers toward specific SWNT species by altering the polymer structure to adjust the corresponding intermolecular interaction. This is the first experimental verification and application of a RET-induced intermolecular pairing force to SWNT separation. With this kind of interaction taken into account, reasonable interpretation of some conflicting data, especially PLE maps, can be easily made. The above conclusion can be applied to other substances as long as they are electrically neutral and there is photon-induced RET between them. The significant magnitude of this interaction makes direct manipulation of molecules/particles possible and is expected to have applications in molecular engineering. © 2011 American Chemical Society

INTERACTIONS: DESIGN, IMPLEMENTATION AND EVALUATION OF A COMPUTATIONAL TOOL FOR TEACHING INTERMOLECULAR FORCES IN HIGHER EDUCATION

Directory of Open Access Journals (Sweden)

Francisco Geraldo Barbosa

2015-12-01

Full Text Available Intermolecular forces are a useful concept that can explain the attraction between particulate matter as well as numerous phenomena in our lives such as viscosity, solubility, drug interactions, and dyeing of fibers. However, studies show that students have difficulty understanding this important concept, which has led us to develop a free educational software in English and Portuguese. The software can be used interactively by teachers and students, thus facilitating better understanding. Professors and students, both graduate and undergraduate, were questioned about the software quality and its intuitiveness of use, facility of navigation, and pedagogical application using a Likert scale. The results led to the conclusion that the developed computer application can be characterized as an auxiliary tool to assist teachers in their lectures and students in their learning process of intermolecular forces.

Physical mechanisms of Cu-Cu wafer bonding

International Nuclear Information System (INIS)

Rebhan, B.

2014-01-01

Modern manufacturing processes of complex integrated semiconductor devices are based on wafer-level manufacturing of components which are subsequently interconnected. When compared with classical monolithic bi-dimensional integrated circuits (2D ICs), the new approach of three-dimensional integrated circuits (3D ICs) exhibits significant benefits in terms of signal propagation delay and power consumption due to the reduced metal interconnection length and allows high integration levels with reduced form factor. Metal thermo-compression bonding is a process suitable for 3D interconnects applications at wafer level, which facilitates the electrical and mechanical connection of two wafers even processed in different technologies, such as complementary metal oxide semiconductor (CMOS) and microelectromechanical systems (MEMS). Due to its high electrical conductivity, copper is a very attractive material for electrical interconnects. For Cu-Cu wafer bonding the process requires typically bonding for around 1 h at 400°C and high contact pressure applied during bonding. Temperature reduction below such values is required in order to solve issues regarding (i) throughput in the wafer bonder, (ii) wafer-to-wafer misalignment after bonding and (iii) to minimise thermo-mechanical stresses or device degradation. The aim of this work was to study the physical mechanisms of Cu-Cu bonding and based on this study to further optimise the bonding process for low temperatures. The critical sample parameters (roughness, oxide, crystallinity) were identified using selected analytical techniques and correlated with the characteristics of the bonded Cu-Cu interfaces. Based on the results of this study the impact of several materials and process specifications on the bonding result were theoretically defined and experimentally proven. These fundamental findings subsequently facilitated low temperature (LT) metal thermo-compression Cu-Cu wafer bonding and even room temperature direct

Characterization of the hydrogen bond in molecular systems of biological interest by neutron scattering; Caracterisation de la liaison hydrogene dans des systemes moleculaires d'interet biologique par diffusion de neutrons

Energy Technology Data Exchange (ETDEWEB)

Cavillon, F

2004-10-15

This work presents a methodology for the analysis of the scattering spectra of neutrons on molecular liquids. This method is based on the adjustment of the molecular form factor concerning great momentum transfer. The subtraction of the intra-molecular contributions gives access to information on inter-molecular interactions such as the hydrogen bond. 3 systems with increasing levels of difficulty have been studied: the ammonia molecule, the N-methyl-formamide (NMF) and the N-methyl-acetamide (NMA). The value we get for the N-D intermolecular distance of the liquid ammonia molecule is 1.7 angstrom, this value is different from the value generally admitted (2.3 angstrom) but we have validated it by studying the isotopic substitution N{sup 14}/N{sup 15}. The adjustment to the NMF is obtained with a good accuracy but the characterization of the hydrogen bound is more delicate to infer. A preliminary study of the NMA molecule shows that this method can give relevant results on complex molecules.

Visualized Bond Scission in Mechanically Activated Polymers

Institute of Scientific and Technical Information of China (English)

Yuan Yuan; Yu-lan Chen

2017-01-01

Visualization and quantitative evaluation of covalent bond scission in polymeric materials are critical in understanding their failure mechanisms and improving the toughness and reliability of the materials.Mechano-responsive polymers with the ability of molecular-level transduction of force into chromism and luminescence have evoked major interest and experienced significant progress.In the current review,we highlight the recent achievements in covalent mechanochromic and mechanoluminescent polymers,leading to a bridge between macroscopic mechanical properties and microscopic bond scission events.After a general introduction concerning polymer mechanochemistry,various examples that illustrate the strategies of design and incorporation of functional and weak covalent bonds in polymers were presented,the mechanisms underlying the optical phenomenon were introduced and their potential applications as stress sensors were discussed.This review concludes with a comment on the opportunities and challenges of the field.

Interface Fracture in Adhesively Bonded Shell Structures

DEFF Research Database (Denmark)

Jensen, Henrik Myhre

2008-01-01

Two methods for the prediction of crack propagation through the interface of adhesively bonded shells are discussed. One is based on a fracture mechanics approach; the other is based on a cohesive zone approach. Attention is focussed on predicting the shape of the crack front and the critical...

4-(4-Chlorophenyl-6-hydroxy-5-(2-thienylcarbonyl-6-(trifluoromethyl-3,4,5,6-tetrahydropyrimidin-2(1H-one monohydrate

Directory of Open Access Journals (Sweden)

Mohammad Hossein Mosslemin

2009-06-01

Full Text Available The asymmetric unit of the title compound, C16H12ClF3N2O3S·H2O, contains two crystallographically independent organic molecules and two water molecules. The organic species are linked by an intermolecular O—H...O hydrogen bond, while the water molecules are connected to them through intermolecular O—H...N hydrogen bonds. The thiophene and phenyl rings are oriented at dihedral angles of 62.35 (4 in the first independent molecule and 60.74 (5° in the second, while the pyrimidine rings adopt twisted conformations in both molecules. Intramolecular N—H...F interactions result in the formation of two five-membered rings having envelope conformations. In the crystal structure, further intermolecular O—H...O and N—H...O hydrogen bonds link the molecules into chains.

Ethyl 2-{3-[(2-chloro-1,3-thiazol-5-ylmethyl]-4-nitroimino-1,3,5-triazinan-1-yl}acetate

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Chuan-wen Sun

2010-06-01

Full Text Available In the title compound, C11H15ClN6O4S, which belongs to the neonicotinoid class of insecticidally active heterocyclic compounds, the six-membered triazine ring adopts an opened envolope conformation. The planar nitro imine group [dihedral angle between nitro and imine groups = 1.07 (7°] and the thiazole ring are oriented at a dihedral angle of 69.62 (8°. A classical intramolecular N—H...O hydrogen bond is found in the molecular structure. Moreover, one classical intermolecular N—H...N and four non-classical C—H...O and C—H...N hydrogen bonds are also present in the crystal structure. Besides intermolecular hydrogen bonds, the Cl atom forms an intermolecular short contact [3.020 (2 Å] with one of the nitro O atoms.

Prediction of fracture toughness and durability of adhesively bonded composite joints with undesirable bonding conditions

Science.gov (United States)

Musaramthota, Vishal

Advanced composite materials have enabled the conventional aircraft structures to reduce weight, improve fuel efficiency and offer superior mechanical properties. In the past, materials such as aluminum, steel or titanium have been used to manufacture aircraft structures for support of heavy loads. Within the last decade or so, demand for advanced composite materials have been emerging that offer significant advantages over the traditional metallic materials. Of particular interest in the recent years, there has been an upsurge in scientific significance in the usage of adhesively bonded composite joints (ABCJ's). ABCJ's negate the introduction of stress risers that are associated with riveting or other classical techniques. In today's aircraft transportation market, there is a push to increase structural efficiency by promoting adhesive bonding to primary joining of aircraft structures. This research is focused on the issues associated with the durability and related failures in bonded composite joints that continue to be a critical hindrance to the universal acceptance of ABCJ's. Of particular interest are the short term strength, contamination and long term durability of ABCJ's. One of the factors that influence bond performance is contamination and in this study the influence of contamination on composite-adhesive bond quality was investigated through the development of a repeatable and scalable surface contamination procedure. Results showed an increase in the contaminant coverage area decreases the overall bond strength significantly. A direct correlation between the contaminant coverage area and the fracture toughness of the bonded joint was established. Another factor that influences bond performance during an aircraft's service life is its long term strength upon exposure to harsh environmental conditions or when subjected to severe mechanical loading. A test procedure was successfully developed in order to evaluate durability of ABCJ's comprising severe

First-principle study on bonding mechanism of ZnO by LDA+U method

International Nuclear Information System (INIS)

Zhou, G.C.; Sun, L.Z.; Zhong, X.L.; Chen Xiaoshuang; Wei Lu; Wang, J.B.

2007-01-01

The electronic structure and the bonding mechanism of ZnO have been studied by using the Full-Potential Linear Augmented Plane Wave (FP-LAPW) method within the density-functional theory (DFT) based on LDA+U exchange correlation potential. The valence and the bonding charge density are calculated and compared with those derived from LDA and GGA to describe the bonding mechanism. The charge transfer along with the bonding process is analyzed by using the theory of Atoms in Molecules (AIM). The bonding, the topological characteristics and the p-d coupling effects on the bonding mechanism of ZnO are shown quantitatively with the critical points (CPs) along the bonding trajectory and the charge in the atomic basins. Meanwhile, the bonding characteristics for wurtzite, zinc blende and rocksalt phase of ZnO are discussed systematically in the present paper

N,N′-Bis(2-hydroxy-3-ethoxybenzylidenebutane-1,4-diamine

Directory of Open Access Journals (Sweden)

Hoong-Kun Fun

2009-04-01

Full Text Available The title Schiff base compound, C22H28N2O4, lies across a crystallographic inversion centre and adopts an E configuration with respect to the C=N bond. Pairs of weak intermolecular C—H...O interactions link neighbouring molecules into dimers with an R22(28 ring motif. The crystal structure is stabilized by intermolecular C—H...π interactions. An intramolecular O—H...N hydrogen bond occurs.

Identification of parameters of cohesive elements for modeling of adhesively bonded joints of epoxy composites

Directory of Open Access Journals (Sweden)

Kottner R.

2013-12-01

Full Text Available Adhesively bonded joints can be numerically simulated using the cohesive crack model. The critical strain energy release rate and the critical opening displacement are the parameters which must be known when cohesive elements in MSC.Marc software are used. In this work, the parameters of two industrial adhesives Hunstman Araldite 2021 and Gurit Spabond 345 for bonding of epoxy composites are identified. Double Cantilever Beam (DCB and End Notched Flexure (ENF test data were used for the identification. The critical opening displacements were identified using an optimization algorithm where the tests and their numerical simulations were compared.

The study of intermolecular interactions in NLO crystal melaminium chloride hemihydrate using DFT simulation and Hirshfeld surface analysis

Science.gov (United States)

Sangeetha, K.; Kumar, V. R. Suresh; Marchewka, M. K.; Binoy, J.

2018-05-01

Since, the intermolecular interactions play a crucial role in the formation of crystalline network, its analysis throws light on structure dependent crystalline properties. In the present study, DFT based vibrational spectral investigation has been performed in the stretching region (3500 cm-1 - 2800 cm-1) of IR and Raman spectra of melaminium chloride hemihydrates. The intermolecular interaction has been investigated by analyzing the half width of the OH and NH stretching profile of the deconvoluted spectra. Correlation of vibrational spectra with Hirshfeld surface analysis and finger print plot has been contemplated and molecular docking studies has been performed on melaminium chloride hemihydrate to assess its role in the drug transport mechanism and toxicity to human body.

Unconventional Quantum Critical Points

OpenAIRE

Xu, Cenke

2012-01-01

In this paper we review the theory of unconventional quantum critical points that are beyond the Landau's paradigm. Three types of unconventional quantum critical points will be discussed: (1). The transition between topological order and semiclassical spin ordered phase; (2). The transition between topological order and valence bond solid phase; (3). The direct second order transition between different competing orders. We focus on the field theory and universality class of these unconventio...

Noncovalent Intermolecular Interactions in Organic Electronic Materials: Implications for the Molecular Packing vs Electronic Properties of Acenes

KAUST Repository

Sutton, Christopher; Risko, Chad; Bredas, Jean-Luc

2015-01-01

Noncovalent intermolecular interactions, which can be tuned through the toolbox of synthetic chemistry, determine not only the molecular packing but also the resulting electronic, optical, and mechanical properties of materials derived from π

Rubrene: The interplay between intramolecular and intermolecular interactions determines the planarization of its tetracene core in the solid state

KAUST Repository

Sutton, Christopher

2015-06-15

Rubrene is one of the most studied molecular semiconductors; its chemical structure consists of a tetracene backbone with four phenyl rings appended to the two central fused rings. Derivatization of these phenyl rings can lead to two very different solid-state molecular conformations and packings: One in which the tetracene core is planar and there exists substantive overlap among neighboring π-conjugated backbones; and another where the tetracene core is twisted and the overlap of neighboring π-conjugated backbones is completely disrupted. State-of-the-art electronic-structure calculations show for all isolated rubrene derivatives that the twisted conformation is more favorable (by -1.7 to -4.1 kcal mol-1), which is a consequence of energetically unfavorable exchange-repulsion interactions among the phenyl side groups. Calculations based on available crystallographic structures reveal that planar conformations of the tetracene core in the solid state result from intermolecular interactions that can be tuned through well-chosen functionalization of the phenyl side groups, and lead to improved intermolecular electronic couplings. Understanding the interplay of these intramolecular and intermolecular interactions provides insight into how to chemically modify rubrene and similar molecular semiconductors to improve the intrinsic materials electronic properties.

2-(2-Hydroxy-3-methoxyphenyl-1H-benzimidazol-3-ium perchlorate

Directory of Open Access Journals (Sweden)

Chuan Chen

2012-06-01

Full Text Available In the title molecular salt, C14H13N2O2+·ClO4−, the ring systems in the cation are almost coplanar [dihedral angle = 5.53 (13°]. Intramolecular N—H...O and O—H...O hydrogen bonds generate S(6 and S(5 rings, respectively. In the crystal, the two H atoms involved in the intramolecular hydrogen bonds also participate in intermolecular links to acceptor O atoms of the perchlorate anions. A simple intermolecular N—H...O bond also occurs. Together, these form a double-chain structure along [101].

Pressure effect on the amide I frequency of the solvated α-helical structure in water

International Nuclear Information System (INIS)

Takekiyo, T; Yoshimura, Y; Shimizu, A; Koizumi, T; Kato, M; Taniguchi, Y

2007-01-01

As a model system of the pressure dependence of the amide I mode of the solvated α-helical structure in a helical peptide, we have calculated the frequency shifts of the amide I modes as a function of the distance between trans-N-methylacetamide (t-NMA) dimer and a water molecule (d C=O···H-O ) by the density-functional theory (DFT) method at the B3LYP/6-31G++(d,p) level. Two amide I frequencies at 1652 and 1700 cm -1 were observed under this calculation. The former is ascribed to the amide I mode forming the intermolecular hydrogen bond (H-bond) between t-NMA and H 2 O in addition to the intermolecular H-bond in the t-NMA dimer. The latter is due to the amide I mode forming only the intermolecular H-bond in the t-NMA dimer. We have found that the amide I frequency at 1652 cm -1 shifts to a lower frequency with decreasing d C=O···H-O ) (i.e., increasing pressure), whereas that at 1700 cm -1 shifts to a higher frequency. The amide I frequency shift of 1652 cm -1 is larger than that of 1700 cm -1 by the intermolecular H-bond. Thus, our results clearly indicate that the pressure-induced amide I frequency shift of the solvated α-helical structure correlates with the change in d C=O···H-O )

ReaxFF molecular dynamics simulation of intermolecular structure formation in acetic acid-water mixtures at elevated temperatures and pressures

Science.gov (United States)

Sengul, Mert Y.; Randall, Clive A.; van Duin, Adri C. T.

2018-04-01

The intermolecular structure formation in liquid and supercritical acetic acid-water mixtures was investigated using ReaxFF-based molecular dynamics simulations. The microscopic structures of acetic acid-water mixtures with different acetic acid mole fractions (1.0 ≥ xHAc ≥ 0.2) at ambient and critical conditions were examined. The potential energy surface associated with the dissociation of acetic acid molecules was calculated using a metadynamics procedure to optimize the dissociation energy of ReaxFF potential. At ambient conditions, depending on the acetic acid concentration, either acetic acid clusters or water clusters are dominant in the liquid mixture. When acetic acid is dominant (0.4 ≤ xHAc), cyclic dimers and chain structures between acetic acid molecules are present in the mixture. Both structures disappear at increased water content of the mixture. It was found by simulations that the acetic acid molecules released from these dimer and chain structures tend to stay in a dipole-dipole interaction. These structural changes are in agreement with the experimental results. When switched to critical conditions, the long-range interactions (e.g., second or fourth neighbor) disappear and the water-water and acetic acid-acetic acid structural formations become disordered. The simulated radial distribution function for water-water interactions is in agreement with experimental and computational studies. The first neighbor interactions between acetic acid and water molecules are preserved at relatively lower temperatures of the critical region. As higher temperatures are reached in the critical region, these interactions were observed to weaken. These simulations indicate that ReaxFF molecular dynamics simulations are an appropriate tool for studying supercritical water/organic acid mixtures.

Bonding in ZnSb

DEFF Research Database (Denmark)

Bjerg, Lasse; Madsen, Georg K. H.; Iversen, Bo Brummerstedt

Thermoelectric materials are capable of converting waste heat into usable electric energy. The conversion efficiency depends critically on the electronic band structure. Theoretical calculations predict the semiconducting ZnSb to have a promising efficiency if it is n-doped. The details of the lo......Thermoelectric materials are capable of converting waste heat into usable electric energy. The conversion efficiency depends critically on the electronic band structure. Theoretical calculations predict the semiconducting ZnSb to have a promising efficiency if it is n-doped. The details...... of the lowest conduction band have therefore been investigated. Electrons placed in the lowest conduction band are predicted to increase the bonding between second nearest neighbour atoms. This causes a lowering of the energy at special points in the first Brillouin zone. Thereby, the dispersion of the lowest...

Template Syntheses, Crystal Structures and Supramolecular Assembly of Hexaaza Macrocyclic Copper(II) Complexes

International Nuclear Information System (INIS)

Kim, Taehyung; Kim, Ju Chang; Lough, Alan J.

2013-01-01

Two new hexaaza macrocyclic copper(II) complexes were prepared by a template method and structurally characterized. In the solid state, they were self-assembled by intermolecular interactions to form the corresponding supramolecules 1 and 2, respectively. In the structure of 1, the copper(II) macrocycles are bridged by a tp ligand to form a macrocyclic copper(II) dimer. The dimer extends its structure by intermolecular forces such as hydrogen bonds and C-H···π interactions, resulting in the formation of a double stranded 1D supramolecule. In 2, the basic structure is a monomeric copper(II) macrocycle with deprotonated imidazole pendants. An undulated 1D hydrogen bonded array is achieved through hydrogen bonds between imidazole pendants and secondary amines, where the imidazole pendants act as a hydrogen bond acceptor. The 1D hydrogen bonded supramolecular chain is supported by C-H···π interactions between the methyl groups of acetonitrile ligands and imidazole pendants of the copper(II) macrocycles. In both complexes, the introduction of imidazoles to the macrocycle as a pendant plays an important role for the formation of supramolecules, where they act as intermolecular hydrogen bond donors and/or acceptors, C-H···π and π-π interactions

Catching the role of anisotropic electronic distribution and charge transfer in halogen bonded complexes of noble gases

Energy Technology Data Exchange (ETDEWEB)

Bartocci, Alessio; Cappelletti, David; Pirani, Fernando [Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia 06123 (Italy); Belpassi, Leonardo [Istituto di Scienze e Tecnologie Molecolari del CNR, Perugia 06123 (Italy); Falcinelli, Stefano [Dipartimento di Ingegneria Civile ed Ambientale, Università degli Studi di Perugia, 06125 Perugia (Italy); Grandinetti, Felice [Dipartimento per la Innovazione nei sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università della Tuscia, 01100 Viterbo (Italy); Tarantelli, Francesco [Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia 06123 (Italy); Istituto di Scienze e Tecnologie Molecolari del CNR, Perugia 06123 (Italy)

2015-05-14

The systems studied in this work are gas-phase weakly bound adducts of the noble-gas (Ng) atoms with CCl{sub 4} and CF{sub 4}. Their investigation was motivated by the widespread current interest for the intermolecular halogen bonding (XB), a structural motif recognized to play a role in fields ranging from elementary processes to biochemistry. The simulation of the static and dynamic behaviors of complex systems featuring XB requires the formulation of reliable and accurate model potentials, whose development relies on the detailed characterization of strength and nature of the interactions occurring in simple exemplary halogenated systems. We thus selected the prototypical Ng-CCl{sub 4} and Ng-CF{sub 4} and performed high-resolution molecular beam scattering experiments to measure the absolute scale of their intermolecular potentials, with high sensitivity. In general, we expected to probe typical van der Waals interactions, consisting of a combination of size (exchange) repulsion with dispersion/induction attraction. For the He/Ne-CF{sub 4}, the analysis of the glory quantum interference pattern, observable in the velocity dependence of the integral cross section, confirmed indeed this expectation. On the other hand, for the He/Ne/Ar-CCl{sub 4}, the scattering data unravelled much deeper potential wells, particularly for certain configurations of the interacting partners. The experimental data can be properly reproduced only including a shifting of the repulsive wall at shorter distances, accompanied by an increased role of the dispersion attraction, and an additional short-range stabilization component. To put these findings on a firmer ground, we performed, for selected geometries of the interacting complexes, accurate theoretical calculations aimed to evaluate the intermolecular interaction and the effects of the complex formation on the electron charge density of the constituting moieties. It was thus ascertained that the adjustments of the potential

Insights into the Electronic Structure of Ozone and Sulfur Dioxide from Generalized Valence Bond Theory: Bonding in O3 and SO2.

Science.gov (United States)

Takeshita, Tyler Y; Lindquist, Beth A; Dunning, Thom H

2015-07-16

There are many well-known differences in the physical and chemical properties of ozone (O3) and sulfur dioxide (SO2). O3 has longer and weaker bonds than O2, whereas SO2 has shorter and stronger bonds than SO. The O-O2 bond is dramatically weaker than the O-SO bond, and the singlet-triplet gap in SO2 is more than double that in O3. In addition, O3 is a very reactive species, while SO2 is far less so. These disparities have been attributed to variations in the amount of diradical character in the two molecules. In this work, we use generalized valence bond (GVB) theory to characterize the electronic structure of ozone and sulfur dioxide, showing O3 does indeed possess significant diradical character, whereas SO2 is effectively a closed shell molecule. The GVB results provide critical insights into the genesis of the observed difference in these two isoelectronic species. SO2 possesses a recoupled pair bond dyad in the a"(π) system, resulting in SO double bonds. The π system of O3, on the other hand, has a lone pair on the central oxygen atom plus a pair of electrons in orbitals on the terminal oxygen atoms that give rise to a relatively weak π interaction.

Coiodação de alquenos com nucleófilos oxigenados: reações intermoleculares

Directory of Open Access Journals (Sweden)

Sanseverino Antonio Manzolillo

2001-01-01

Full Text Available A review on the electrophilic addition of iodine to alkenes in the presence of oxygen containing nucleophiles (cohalogenation reaction is presented. The intermolecular reactions are discussed with emphasis in methods of reaction and synthetic applications of the resulting vicinal iodo-functionalized products (iodohydrins, beta-iodoethers and beta-iodocarboxylates.

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

Science.gov (United States)

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. :...

Comparison of shear bond strength of the stainless steel metallic brackets bonded by three bonding systems

Directory of Open Access Journals (Sweden)

Mehdi Ravadgar

2013-09-01

Full Text Available Introduction: In orthodontic treatment, it is essential to establish a satisfactory bond between enamel and bracket. After the self-etch primers (SEPs were introduced for the facilitation of bracket bonding in comparison to the conventional etch-and-bond system, multiple studies have been carried out on their shear bond strengths which have yielded different results. This study was aimed at comparing shear bond strengths of the stainless steel metallic brackets bonded by three bonding systems. Methods: In this experimental in vitro study, 60 extracted human maxillary premolar teeth were randomly divided into three equal groups: in the first group, Transbond XT (TBXT light cured composite was bonded with Transbond plus self-etching primer (TPSEP in the second group, TBXT composite was bonded with the conventional method of acid etching and in the third group, the self cured composite Unite TM bonding adhesive was bonded with the conventional method of acid etching. In all the groups, Standard edgewise-022 metallic brackets (American Orthodontics, Sheboygan, USA were used. Twenty-four hours after the completion of thermocycling, shear bond strength of brackets was measured by Universal Testing Machine (Zwick. In order to compare the shear bond strengths of the groups, the variance analysis test (ANOVA was adopted and p≤0.05 was considered as a significant level. Results: Based on megapascal, the average shear bond strength for the first, second, and third groups was 8.27±1.9, 9.78±2, and 8.92±2.5, respectively. There was no significant difference in the shear bond strength of the groups. Conclusions: Since TPSEP shear bond strength is approximately at the level of the conventional method of acid etching and within the desirable range for orthodontic brackets shear bond strength, applying TPSEP can serve as a substitute for the conventional method of etch and bond, particularly in orthodontic operations.

Comparison of shear bond strength of the stainless steel metallic brackets bonded by three bonding systems

Directory of Open Access Journals (Sweden)

Mehdi Ravadgar

2013-09-01

Full Text Available Introduction: In orthodontic treatment, it is essential to establish a satisfactory bond between enamel and bracket. After the self-etch primers (SEPs were introduced for the facilitation of bracket bonding in comparison to the conventional etch-and-bond system, multiple studies have been carried out on their shear bond strengths which have yielded different results. This study was aimed at comparing shear bond strengths of the stainless steel metallic brackets bonded by three bonding systems. Methods: In this experimental in vitro study, 60 extracted human maxillary premolar teeth were randomly divided into three equal groups: in the first group, Transbond XT (TBXT light cured composite was bonded with Transbond plus self-etching primer (TPSEP; in the second group, TBXT composite was bonded with the conventional method of acid etching; and in the third group, the self cured composite Unite TM bonding adhesive was bonded with the conventional method of acid etching. In all the groups, Standard edgewise-022 metallic brackets (American Orthodontics, Sheboygan, USA were used. Twenty-four hours after the completion of thermocycling, shear bond strength of brackets was measured by Universal Testing Machine (Zwick. In order to compare the shear bond strengths of the groups, the variance analysis test (ANOVA was adopted and p≤0.05 was considered as a significant level. Results: Based on megapascal, the average shear bond strength for the first, second, and third groups was 8.27±1.9, 9.78±2, and 8.92±2.5, respectively. There was no significant difference in the shear bond strength of the groups. Conclusions: Since TPSEP shear bond strength is approximately at the level of the conventional method of acid etching and within the desirable range for orthodontic brackets shear bond strength, applying TPSEP can serve as a substitute for the conventional method of etch and bond, particularly in orthodontic operations.

Condensation in a capped capillary is a continuous critical phenomenon.

Science.gov (United States)

Parry, A O; Rascón, C; Wilding, N B; Evans, R

2007-06-01

We show that condensation in a capped capillary slit is a continuous interfacial critical phenomenon, related intimately to several other surface phase transitions. In three dimensions, the adsorption and desorption branches correspond to the unbinding of the meniscus from the cap and opening, respectively, and are equivalent to 2D-like complete-wetting transitions. For dispersion forces, the singularities on the two branches are distinct, owing to the different interplay of geometry and intermolecular forces. In two dimensions we establish precise connection, or covariance, with 2D critical-wetting and wedge-filling transitions: i.e., we establish that certain interfacial properties in very different geometries are identical. Our predictions of universal scaling and covariance in finite capillaries are supported by extensive Ising model simulation studies in two and three dimensions.

Supramolecular interactions in the solid state

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Giuseppe Resnati

2015-11-01

Full Text Available In the last few decades, supramolecular chemistry has been at the forefront of chemical research, with the aim of understanding chemistry beyond the covalent bond. Since the long-range periodicity in crystals is a product of the directionally specific short-range intermolecular interactions that are responsible for molecular assembly, analysis of crystalline solids provides a primary means to investigate intermolecular interactions and recognition phenomena. This article discusses some areas of contemporary research involving supramolecular interactions in the solid state. The topics covered are: (1 an overview and historical review of halogen bonding; (2 exploring non-ambient conditions to investigate intermolecular interactions in crystals; (3 the role of intermolecular interactions in morphotropy, being the link between isostructurality and polymorphism; (4 strategic realisation of kinetic coordination polymers by exploiting multi-interactive linker molecules. The discussion touches upon many of the prerequisites for controlled preparation and characterization of crystalline materials.

Application of terahertz spectroscopy and theoretical calculation in dimethylurea isomers investigation

Science.gov (United States)

Zhao, Yonghong; Li, Zhi; Liu, Jianjun; Chen, Tao; Zhang, Huo; Qin, Binyi; Wu, Yifang

2018-03-01

The characteristic absorption spectra of two structural isomers of dimethylurea(DMU) in 0.6-1.8 THz region have been measured using terahertz time-domain spectroscopy (THZ-TDS) at room temperature. Significant differences have been found between their terahertz spectra and implied that the THZ-TDS is an effective means of identifying structural isomers. To simulate their spectra, calculations on single molecule and cluster of 1,1-DMU and 1,3-DMU were performed, and we found that the cluster calculations using DFT-D3 method are better to predict the experimental spectra. Using the normal mode as displacements in redundant internal coordinates and the GaussView program, most observed THz vibrational modes are assigned to bending and rocking modes related to the intermolecular hydrogen bonding interactions, and twisting mode of ethyl groups. The different spectral features of two isomers mainly arise from different intermolecular hydrogen bonds resulting from different atom arrangements in molecules and different molecule arrangements in crystals. Using the reduced-density-gradient (RDG) analysis, the positions and types of intermolecular hydrogen bonding interactions in 1,1-DMU and 1,3-DMU crystals are visualized. Therefore, we can confirm that THz-TDS can be used as an effective means for the recognition of structural isomers and detection of intermolecular hydrogen bonding interactions in these crystals.

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

Science.gov (United States)

Sassi, Michel; Carter, Damien J; Uberuaga, Blas P; Stanek, Christopher R; Mancera, Ricardo L; Marks, Nigel A

2014-09-04

Recent ab initio molecular dynamics simulations have shown that radioactive carbon does not normally fragment DNA bases when it decays. Motivated by this finding, density functional theory and Bader analysis have been used to quantify the effect of C → N transmutation on hydrogen bonding in DNA base pairs. We find that (14)C decay has the potential to significantly alter hydrogen bonds in a variety of ways including direct proton shuttling (thymine and cytosine), thermally activated proton shuttling (guanine), and hydrogen bond breaking (cytosine). Transmutation substantially modifies both the absolute and relative strengths of the hydrogen bonding pattern, and in two instances (adenine and cytosine), the density at the critical point indicates development of mild covalent character. Since hydrogen bonding is an important component of Watson-Crick pairing, these (14)C-induced modifications, while infrequent, may trigger errors in DNA transcription and replication.

Binding Cellulose and Chitosan via Intermolecular Inclusion Interaction: Synthesis and Characterisation of Gel

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Jiufang Duan

2015-01-01

Full Text Available A novel cellulose-chitosan gel was successfully prepared in three steps: (1 ferrocene- (Fc- cellulose with degrees of substitution (DS of 0.5 wt% was synthesised by ferrocenecarboxylic acid and cellulose within dimethylacetamide/lithium chloride (DMAc/LiCl; (2 the β-cyclodextrin (β-CD groups were introduced onto the chitosan chains by reacting chitosan with epichlorohydrin in dimethyl sulphoxide and a DS of 0.35 wt%; (3 thus, the cellulose-chitosan gel was obtained via an intermolecular inclusion interaction of Fc-cellulose and β-CD-chitosan in DMA/LiCl, that is, by an intermolecular inclusion interaction, between the Fc groups of cellulose and the β-CD groups on the chitosan backbone at room temperature. The successful synthesis of Fc-cellulose and β-CD-chitosan was characterised by 13C-NMR spectroscopy. The gel based on β-CD-chitosan and Fc-cellulose was formed under mild conditions which can engender autonomous healing between cut surfaces after 24 hours: the gel cannot self-heal while the cut surfaces were coated with a solution of a competitive guest (adamantane acid. The cellulose-chitosan complex made by this method underwent self-healing. Therefore, this study provided a novel method of expanding the application of chitosan by binding it with another polymer.

Intermolecular rhodium-catalyzed [2 + 2 + 2] carbocyclization reactions of 1,6-enynes with symmetrical and unsymmetrical alkynes†

Science.gov (United States)

Andrew Evans, P.; Sawyer, James R.; Lai, Kwong Wah; Huffman, John C.

2006-01-01

The crossed intermolecular rhodium-catalyzed [2 + 2 + 2] carbocyclization of carbon and heteroatom tethered 1,6-enynes can be accomplished with symmetrical and unsymmetrical alkynes, to afford the corresponding bicyclohexadienes in an efficient and highly selective manner. PMID:16075089

1-(4-Fluorophenyl-2-(1H-1,2,4-triazol-1-ylethanone hemihydrate

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Dong-liang Liu

2011-12-01

Full Text Available In the title compound, C10H8FN3O·0.5H2O, the dihedral angle between the mean planes of the rings is 99.80 (4°. The water molecule lies on a twofold axis. Weak intermolecular O—H...N and C—H...O hydrogen bonds link one water molecule with four phenylethanone molecules, while intermolecular C—H...O hydrogen bonds involving the ketone group link phenylethanone molecules into layers parallel to (100.

Intermolecular interaction studies of glyphosate with water

Science.gov (United States)

Manon, Priti; Juglan, K. C.; Kaur, Kirandeep; Sethi, Nidhi; Kaur, J. P.

2017-07-01

The density (ρ), viscosity (η) and ultrasonic velocity (U) of glyphosate with water have been measured on different ultrasonic frequency ranges from 1MHz, 2MHz, 3MHz & 5MHz by varying concentrations (0.05%, 0.10%, 0.15%, 0.20%, 0.25%, 0.30%, 0.35%, & 0.40%) at 30°C. The specific gravity bottle, Ostwald's viscometer and quartz crystal interferometer were used to determine density (ρ), viscosity (η) and ultrasonic velocity (U). These three factors contribute in evaluating the other parameters as acoustic impedance (Z), adiabatic compressibility (β), relaxation time (τ), intermolecular free length (Lf), free volume (Vf), ultrasonic attenuation (α/f2), Rao's constant (R), Wada's constant (W) and relative strength (R). Solute-solvent interaction is confirmed by ultrasonic velocity and viscosity values, which increases with increase in concentration indicates stronger association between solute and solvent molecules. With rise in ultrasonic frequency the interaction between the solute and solvent particles decreases. The linear variations in Rao's constant and Wada's constant suggest the absence of complex formation.

The cation-controlled and hydrogen bond-mediated shear-thickening behaviour of a tree-fern isolated polysaccharide.

Science.gov (United States)

Wee, May S M; Matia-Merino, Lara; Goh, Kelvin K T

2015-10-05

The shear-thickening rheological behaviour (between 5 and 20s(-1)) of a 5% (w/w) viscoelastic gum extracted from the fronds of the native New Zealand black tree fern or mamaku in Māori was further explored by manipulating the salt content. The freeze-dried mamaku gum contained a high mineral content and sugars which upon removal via dialysis, resulted in the loss of shear thickening. However, this loss was reversible by the addition of salts to the dialysed dispersion. The mechanism of shear-thickening behaviour was therefore hypothesised to be due to shear-induced transition of intra- to intermolecular hydrogen bonding, promoted by the screening effect of cations. Mono-, di- and trivalent salts, i.e. Na(+), K(+), N(CH3)4(+), Ca(2+), Mg(2+), Al(3+) and La(3+) at concentrations between 0.001 and 1.0M were tested to support the hypothesis as well as to demonstrate the sensitivity of the biopolymer to cation valency and concentrations. The cation valency and concentration were crucial factors in determining: (i) zero-shear viscosity, (ii) critical shear rate, γ˙c (or shear rate at the onset of shear-thickening) and (iii) the extent of shear-thickening of the solution. For mono- and divalent cations these parameters were similar at equivalent ionic strengths and fairly independent of the cation type. Trivalent cations (La(3+)) however caused precipitation of the gum in the concentration range of 0.005-0.05 M but clear dispersions were obtained above 0.05 M. Copyright © 2015 Elsevier Ltd. All rights reserved.

New strategies for the chemical separation of actinides and lanthanides

International Nuclear Information System (INIS)

Hudson, M.J.; Iveson, P.B.

2002-01-01

A general model is proposed for the effective design of ligands for partitioning. There is no doubt that the correct design of a molecule is required for the effective separation by separation of metal ions such as lanthanides(III) and actinides(III). Heterocyclic ligands with aromatic rings systems have a rich chemistry, which is only now becoming sufficiently well understood, in relation to the partitioning process. The synthesis, characterisation and structures of some chosen molecules will be introduced in order to illustrate some important features. For example, the molecule N-butyl-2-amino-4,6-di (2-pyridyl)-1,3,5-triazine (BADPTZ), which is an effective solvent extraction reagent for actinides and lanthanides, has been synthesised, characterised and its interaction with metal ions studied. The interesting and important features of this molecule will be compared with those of other heterocyclic molecules such as 2,6-bis(5-butyl-1,2,4-triazol-3-yl) pyridine (DBTZP), which is a candidate molecule for the commercial separation of actinides and lanthanide elements. Primary Coordination Sphere. One of the most critical features concerning whether a molecule is a suitable extraction reagent is the nature of the binding and co-ordination in the primary co-ordination sphere. This effect will be considered in depth for the selected heterocylic molecules. It will be shown how the bonding of the heterocyclic and nitrate ligands changes as the complete lanthanide series is traversed from lanthanum to lutetium. For effective solvent extraction, the ligand(s) should be able completely to occupy the primary co-ordination sphere of the metal ion to be extracted. Interactions in the secondary co-ordination sphere are of less importance. Inter-complex Hydrogen Bonding Interactions. Another feature that will be considered is the intermolecular binding between ligands when bound to the metal ion. Thus the intermolecular structures between complex molecules will be considered

Fuel pellets from biomass - Processing, bonding, raw materials

Energy Technology Data Exchange (ETDEWEB)

Stelte, W.

2011-12-15

The present study investigates several important aspects of biomass pelletization. Seven individual studies have been conducted and linked together, in order to push forward the research frontier of biomass pelletization processes. The first study was to investigate influence of the different processing parameters on the pressure built up in the press channel of a pellet mill. It showed that the major factor was the press channel length as well as temperature, moisture content, particle size and extractive content. Furthermore, extractive migration to the pellet surface at an elevated temperature played an important role. The second study presented a method of how key processing parameters can be estimated, based on a pellet model and a small number of fast and simple laboratory trials using a single pellet press. The third study investigated the bonding mechanisms within a biomass pellet, which indicate that different mechanisms are involved depending on biomass type and pelletizing conditions. Interpenetration of polymer chains and close intermolecular distance resulting in better secondary bonding were assumed to be the key factors for high mechanical properties of the formed pellets. The outcome of this study resulted in study four and five investigating the role of lignin glass transition for biomass pelletization. It was demonstrated that the softening temperature of lignin was dependent on species and moisture content. In typical processing conditions and at 8% (wt) moisture content, transitions were identified to be at approximately 53-63 deg. C for wheat straw and about 91 deg. C for spruce lignin. Furthermore, the effects of wheat straw extractives on the pelletizing properties and pellet stability were investigated. The sixth and seventh study applied the developed methodology to test the pelletizing properties of thermally pre-treated (torrefied) biomass from spruce and wheat straw. The results indicated that high torrefaction temperatures above 275 deg

Nonacarbonyl-1κ3C,2κ3C,3κ3C-μ-bis(diphenylarsinomethane-1:2κ2As:As'-[tris(2-chloroethyl phosphite-3κP]-triangulo-triruthenium(0

Directory of Open Access Journals (Sweden)

Omar bin Shawkataly

2010-08-01

Full Text Available In the title triangulo-triruthenium(0 compound, [Ru3(C25H22As2(C6H12Cl3O3P(CO9], the bis(diphenylarsinomethane ligand bridges an Ru—Ru bond and the monodentate phosphine ligand bonds to the third Ru atom. Both the arsine and phosphine ligands are equatorial with respect to the Ru3 triangle. In addition, each Ru atom carries one equatorial and two axial terminal carbonyl ligands. In the crystal packing, the molecules are linked by intermolecular C—H...O hydrogen bonds into a three-dimensional framework. Weak intermolecular C—H...π interactions further stabilize the crystal structure.

Synthesis of benzimidazoles by potassium tert-butoxide-promoted intermolecular cyclization reaction of 2-iodoanilines with nitriles.

Science.gov (United States)

Xiang, Shi-Kai; Tan, Wen; Zhang, Dong-Xue; Tian, Xian-Li; Feng, Chun; Wang, Bi-Qin; Zhao, Ke-Qing; Hu, Ping; Yang, Hua

2013-11-14

The synthesis of benzimidazoles by intermolecular cyclization reaction of 2-iodoanilines with nitriles has been developed. These reactions proceeded without the aid of any transition metals or ligands and just using KOBu(t) as the base. A variety of substituted benzimidazole derivatives can be synthesized by the approach.

Asymmetric fluid criticality. I. Scaling with pressure mixing.

Science.gov (United States)

Kim, Young C; Fisher, Michael E; Orkoulas, G

2003-06-01

The thermodynamic behavior of a fluid near a vapor-liquid and, hence, asymmetric critical point is discussed within a general "complete" scaling theory incorporating pressure mixing in the nonlinear scaling fields as well as corrections to scaling. This theory allows for a Yang-Yang anomaly in which mu(")(sigma)(T), the second temperature derivative of the chemical potential along the phase boundary, diverges like the specific heat when T-->T(c); it also generates a leading singular term, /t/(2beta), in the coexistence curve diameter, where t[triple bond](T-T(c))/T(c). The behavior of various special loci, such as the critical isochore, the critical isotherm, the k-inflection loci, on which chi((k))[triple bond]chi(rho,T)/rho(k) (with chi=rho(2)k(B)TK(T)) and C((k))(V)[triple bond]C(V)(rho,T)/rho(k) are maximal at fixed T, is carefully elucidated. These results are useful for analyzing simulations and experiments, since particular, nonuniversal values of k specify loci that approach the critical density most rapidly and reflect the pressure-mixing coefficient. Concrete illustrations are presented for the hard-core square-well fluid and for the restricted primitive model electrolyte. For comparison, a discussion of the classical (or Landau) theory is presented briefly and various interesting loci are determined explicitly and illustrated quantitatively for a van der Waals fluid.

Structure, vibrations and quantum chemical investigations of hydrogen bonded complex of bis(1-hydroxy-2-methylpropan-2-aminium)selenate

Science.gov (United States)

Thirunarayanan, S.; Arjunan, V.; Marchewka, M. K.; Mohan, S.

2017-04-01

The hydrogen bonded molecular complex bis(1-hydroxy-2-methylpropan-2-aminium)selenate (C8H24N2O6Se) has been prepared by the reaction of 2-amino-2-methyl propanol and selenic acid. The X-ray diffraction analysis revealed that the intermolecular proton transfer from selenic acid (SeO4H2) to 2-amino-2-methylpropanol results in the formation of bis(1-hydroxy-2-methylpropan-2-aminium)selenate (HMPAS) salt and the fragments are connected through H-bonding and ion pairing. The N-H⋯O and O-H⋯O interactions between 2-amino-2-methylpropanol and selenic acid determine the supramolecular arrangement in three-dimensional space. The salt crystallises in the space group P121/n1 of monoclinic system. The complete vibrational assignments of HMPAS have been performed by FTIR and FT-Raman spectroscopy. The experimental data are correlated with the structural properties namely the energy, thermodynamic parameters, atomic charges, hybridization concepts and vibrational frequencies determined by quantum chemical studies performed with B3LYP method using 6-311++G*, 6-31+G* and 6-31G** basis sets.

Eight supramolecular assemblies constructed from bis(benzimidazole) and organic acids through strong classical hydrogen bonding and weak noncovalent interactions

Science.gov (United States)

Jin, Shouwen; Wang, Daqi

2014-05-01

Eight crystalline organic acid-base adducts derived from alkane bridged bis(N-benzimidazole) and organic acids (2,4,6-trinitrophenol, p-nitrobenzoic acid, m-nitrobenzoic acid, 3,5-dinitrobenzoic acid, 5-sulfosalicylic acid and oxalic acid) were prepared and characterized by X-ray diffraction analysis, IR, mp, and elemental analysis. Of the eight compounds five are organic salts (1, 4, 6, 7 and 8) and the other three (2, 3, and 5) are cocrystals. In all of the adducts except 1 and 8, the ratio of the acid and the base is 2:1. All eight supramolecular assemblies involve extensive intermolecular classical hydrogen bonds as well as other noncovalent interactions. The role of weak and strong noncovalent interactions in the crystal packing is ascertained. These weak interactions combined, all the complexes displayed 3D framework structure. The results presented herein indicate that the strength and directionality of the classical N+-H⋯O-, O-H⋯O, and O-H⋯N hydrogen bonds (ionic or neutral) and other nonbonding associations between acids and ditopic benzimidazoles are sufficient to bring about the formation of cocrystals or organic salts.

Structure/property relationships in non-linear optical materials

Energy Technology Data Exchange (ETDEWEB)

Cole, J M [Institut Max von Laue - Paul Langevin (ILL), 38 - Grenoble (France); [Durham Univ. (United Kingdom); Howard, J A.K. [Durham Univ. (United Kingdom); McIntyre, G J [Institut Max von Laue - Paul Langevin (ILL), 38 - Grenoble (France)

1997-04-01

The application of neutrons to the study of structure/property relationships in organic non-linear optical materials (NLOs) is described. In particular, charge-transfer effects and intermolecular interactions are investigated. Charge-transfer effects are studied by charge-density analysis and an example of one such investigation is given. The study of intermolecular interactions concentrates on the effects of hydrogen-bonding and an example is given of two structurally similar molecules with very disparate NLO properties, as a result of different types of hydrogen-bonding. (author). 3 refs.

Thiobarbiturate and barbiturate salts of pefloxacin drug: Growth, structure, thermal stability and IR-spectra

Science.gov (United States)

Golovnev, Nicolay N.; Molokeev, Maxim S.; Lesnikov, Maxim K.; Sterkhova, Irina V.; Atuchin, Victor V.

2017-12-01

Three new salts of pefloxacin (PefH) with thiobarbituric (H2tba) and barbituric (H2ba) acids, pefloxacinium 2-thiobarbiturate trihydrate, PefH2(Htba)·3H2O (1), pefloxacinium 2-thiobarbiturate, PefH2(Htba) (2) and bis(pefloxacinium barbiturate) hydrate, (PefH2)2(Hba)2·2.56H2O (3) are synthesized and structurally characterized by the X-ray single-crystal diffraction. The structures of 1-3 contain intramolecular hydrogen bonds Csbnd H⋯F, Osbnd H⋯O. Intermolecular hydrogen bonds Nsbnd H⋯O and Osbnd H⋯O form a 2D plane network in 1. In 2 and 3, intermolecular hydrogen bonds Nsbnd H⋯O form the infinite chains. In 1-3, the Htba- and Hba- ions are connected with PefH2+ only by one intermolecular hydrogen bond Nsbnd H⋯O. In 2 and 3, two Htba- and Hba- ions are connected by two hydrogen bonds Nsbnd H⋯O. These pairs form infinite chains. All three structures are stabilized by the π-π interactions of the head-to-tail type between PefH2+ ions. Compounds 2 and 3 are characterized by powder XRD, TG-DSC and FT-IR.

Intermolecular Interactions between Eosin Y and Caffeine Using 1H-NMR Spectroscopy

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Macduff O. Okuom

2013-01-01

Full Text Available DETECHIP has been used in testing analytes including caffeine, cocaine, and tetrahydrocannabinol (THC from marijuana, as well as date rape and club drugs such as flunitrazepam, gamma-hydroxybutyric acid (GHB, and methamphetamine. This study investigates the intermolecular interaction between DETECHIP sensor eosin Y (DC1 and the analyte (caffeine that is responsible for the fluorescence and color changes observed in the actual array. Using 1H-NMR, 1H-COSY, and 1H-DOSY NMR methods, a proton exchange from C-8 of caffeine to eosin Y is proposed.

The same number of optimized parameters scheme for determining intermolecular interaction energies

DEFF Research Database (Denmark)

Kristensen, Kasper; Ettenhuber, Patrick; Eriksen, Janus Juul

2015-01-01

We propose the Same Number Of Optimized Parameters (SNOOP) scheme as an alternative to the counterpoise method for treating basis set superposition errors in calculations of intermolecular interaction energies. The key point of the SNOOP scheme is to enforce that the number of optimized wave...... as numerically. Numerical results for second-order Møller-Plesset perturbation theory (MP2) and coupled-cluster with single, double, and approximate triple excitations (CCSD(T)) show that the SNOOP scheme in general outperforms the uncorrected and counterpoise approaches. Furthermore, we show that SNOOP...

Symmetry in the polarization expansion for intermolecular forces

International Nuclear Information System (INIS)

Chipman, D.M.; Hirschfelder, J.O.

1980-01-01

In the usual polarization expansion for intermolecular forces, exchange effects that determine the separations of energy levels within the manifold of interacting states are ignored. Previous low order calculations on simple physical systems have indicated that these exchange terms can be described reasonably well by an appropriate ad hoc symmetrization of the polarization wave function (the SYM-P method). But theoretical considerations suggest that the SYM-P method should be good for only one of the interacting states and not for the others in the manifold. Here this long standing apparent conflict between theoretical expectations and actual results is explained by consideration of a simple model system in which the relevant equations can be solved exactly. It is concluded that while the SYM-P method is potentially exact for only one of the interacting states, it may provide good approximations to the other states of the manifold in the case of large separations of the interacting subsystems

Effect of ethanol-wet-bonding technique on resin–enamel bonds

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Muhammet Kerim Ayar

2014-03-01

Conclusion: The ethanol-wet-bonding technique may increase the bond strength of commercial adhesives to enamel. The chemical composition of the adhesives can affect the bond strength of adhesives when bonding to acid-etched enamel, using the ethanol-wet-bonding technique. Some adhesive systems used in the present study may simultaneously be applied to enamel and dentin using ethanol-wet-bonding. Furthermore, deploying ethanol-wet-bonding for the tested commercial adhesives to enamel can increase the adhesion abilities of these adhesives to enamel.

Parental Bonding

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T. Paul de Cock

2014-08-01

Full Text Available Estimating the early parent–child bonding relationship can be valuable in research and practice. Retrospective dimensional measures of parental bonding provide a means for assessing the experience of the early parent–child relationship. However, combinations of dimensional scores may provide information that is not readily captured with a dimensional approach. This study was designed to assess the presence of homogeneous groups in the population with similar profiles on parental bonding dimensions. Using a short version of the Parental Bonding Instrument (PBI, three parental bonding dimensions (care, authoritarianism, and overprotection were used to assess the presence of unobserved groups in the population using latent profile analysis. The class solutions were regressed on 23 covariates (demographics, parental psychopathology, loss events, and childhood contextual factors to assess the validity of the class solution. The results indicated four distinct profiles of parental bonding for fathers as well as mothers. Parental bonding profiles were significantly associated with a broad range of covariates. This person-centered approach to parental bonding has broad utility in future research which takes into account the effect of parent–child bonding, especially with regard to “affectionless control” style parenting.

Trimeric Hydrogen Bond in Geometrically Frustrated Hydroxyl Cobalt Halogenides

International Nuclear Information System (INIS)

Xiao-Dong, Liu; Masato, Hagihala; Xu-Guang, Zheng; Dong-Dong, Meng; Wan-Jun, Tao; Sen-Lin, Zhang; Qi-Xin, Guo

2011-01-01

The mid-infrared absorption spectra of geometrically frustrated hydroxyl cobalt halogenides Co 2 (OH) 3 Cl and Co 2 (OH) 3 Br are measured by FTIR spectrometers, and the stretching vibrational modes of hydroxyl groups are found to be 3549cm −1 and 3524cm −1 respectively. Through finding their true terminal O-H group stretching vibration frequencies, we obtain 107cm −1 and 99cm −1 red shift caused by the corresponding O-H···Cl and O-H···Br hydrogen bonds. Rarely reported trimeric hydrogen bonds (Co 3 ≡O-H) 3 ···Cl/Br are pointed out to demonstrate the relative weakness of this kind of hydrogen bond which may have a critical effect on the lattice symmetry and magnetic structures. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

Highly Convergent Total Synthesis of (+)-Lithospermic Acid via a Late-Stage Intermolecular C–H Olefination

Science.gov (United States)

Wang, Dong-Hui; Yu, Jin-Quan

2011-01-01

The total synthesis of (+)-lithospermic acid is reported, which exploits two successive C–H activation reactions as the key steps. Rh-catalyzed carbene C–H insertion reaction using Davies’ catalyst built the dihydrobenzofuran core, and a late-stage intermolecular C–H olefination coupled the olefin unit with the dihydrobenzofuran core to construct the molecule in a highly convergent manner. PMID:21443224

An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method

Science.gov (United States)

Asada, Naoya; Fedorov, Dmitri G.; Kitaura, Kazuo; Nakanishi, Isao; Merz, Kenneth M.

2012-01-01

We propose an approach based on the overlapping multicenter ONIOM to evaluate intermolecular interaction energies in large systems and demonstrate its accuracy on several representative systems in the complete basis set limit at the MP2 and CCSD(T) level of theory. In the application to the intermolecular interaction energy between insulin dimer and 4′-hydroxyacetanilide at the MP2/CBS level, we use the fragment molecular orbital method for the calculation of the entire complex assigned to the lowest layer in three-layer ONIOM. The developed method is shown to be efficient and accurate in the evaluation of the protein-ligand interaction energies. PMID:23050059

H-shaped supra-amphiphiles based on a dynamic covalent bond.

Science.gov (United States)

Wang, Guangtong; Wang, Chao; Wang, Zhiqiang; Zhang, Xi

2012-10-16

The imine bond, a kind of dynamic covalent bond, is used to bind two bolaform amphiphiles together with spacers, yielding H-shaped supra-amphiphiles. Micellar aggregates formed by the self-assembly of the H-shaped supra-amphiphiles are observed. When pH is tuned down from basic to slightly acidic, the benzoic imine bond can be hydrolyzed, leading to the dissociation of H-shaped supra-amphiphiles. Moreover, H-shaped supra-amphiphiles have a lower critical micelle concentration than their building blocks, which is very helpful in enhancing the stability of the benzoic imine bond being hydrolyzed by acid. The surface tension isotherms of the H-shaped supra-amphiphiles with different spacers indicate their twisty conformation at a gas-water interface. The study of H-shaped supra-amphiphiles can enrich the family of amphiphiles, and moreover, the pH-responsiveness may make them apply to controlled or targetable drug delivery in a biological environment.

Heteroleptic and Homoleptic Iron(III Spin-Crossover Complexes; Effects of Ligand Substituents and Intermolecular Interactions between Co-Cation/Anion and the Complex

Directory of Open Access Journals (Sweden)

Wasinee Phonsri

2017-08-01

Full Text Available The structural and magnetic properties of a range of new iron(III bis-tridentate Schiff base complexes are described with emphasis on how intermolecular structural interactions influence spin states and spin crossover (SCO in these d5 materials. Three pairs of complexes were investigated. The first pair are the neutral, heteroleptic complexes [Fe(3-OMe-SalEen(thsa] 1 and [Fe(3-MeOSalEen(3-EtOthsa] 2, where 3-R-HSalEen = (E-2-(((2-(ethylaminoethyliminomethyl-6-R-phenol and 3-R-H2thsa = thiosemicarbazone-3-R-salicylaldimine. They display spin transitions above room temperature. However, 2 shows incomplete and gradual change, while SCO in 1 is complete and more abrupt. Lower cooperativity in 2 is ascribed to the lack of π–π interactions, compared to 1. The second pair, cationic species [Fe(3-EtOSalEen2]NO3 3 and [Fe(3-EtOSalEen2]Cl 4 differ only in the counter-anion. They show partial SCO above room temperature with 3 displaying a sharp transition at 343 K. Weak hydrogen bonds from cation to Cl− probably lead to weaker cooperativity in 4. The last pair, CsH2O[Fe(3-MeO-thsa2] 5 and Cs(H2O2[Fe(5-NO2-thsa2] 6, are anionic homoleptic chelates that have different substituents on the salicylaldiminate rings of thsa2−. The Cs cations bond to O atoms of water and the ligands, in unusual ways thus forming attractive 1D and 3D networks in 5 and 6, respectively, and 5 remains HS (high spin at all temperatures while 6 remains LS (low spin. Comparisons are made to other literature examples of Cs salts of [Fe(5-R-thsa2]− (R = H and Br.

Non-Covalent Interactions in Hydrogen Storage Materials LiN(CH32BH3 and KN(CH32BH3

Directory of Open Access Journals (Sweden)

Filip Sagan

2016-03-01

Full Text Available In the present work, an in-depth, qualitative and quantitative description of non-covalent interactions in the hydrogen storage materials LiN(CH32BH3 and KN(CH32BH3 was performed by means of the charge and energy decomposition method (ETS-NOCV as well as the Interacting Quantum Atoms (IQA approach. It was determined that both crystals are stabilized by electrostatically dominated intra- and intermolecular M∙∙∙H–B interactions (M = Li, K. For LiN(CH32BH3 the intramolecular charge transfer appeared (B–H→Li to be more pronounced compared with the corresponding intermolecular contribution. We clarified for the first time, based on the ETS-NOCV and IQA methods, that homopolar BH∙∙∙HB interactions in LiN(CH32BH3 can be considered as destabilizing (due to the dominance of repulsion caused by negatively charged borane units, despite the fact that some charge delocalization within BH∙∙∙HB contacts is enforced (which explains H∙∙∙H bond critical points found from the QTAIM method. Interestingly, quite similar (to BH∙∙∙HB intermolecular homopolar dihydrogen bonds CH∙∙∙HC appared to significantly stabilize both crystals—the ETS-NOCV scheme allowed us to conclude that CH∙∙∙HC interactions are dispersion dominated, however, the electrostatic and σ/σ*(C–H charge transfer contributions are also important. These interactions appeared to be more pronounced in KN(CH32BH3 compared with LiN(CH32BH3.

Rubrene: The interplay between intramolecular and intermolecular interactions determines the planarization of its tetracene core in the solid state

KAUST Repository

Sutton, Christopher; Marshall, Michael S.; Sherrill, C. David; Risko, Chad; Bredas, Jean-Luc

2015-01-01

exchange-repulsion interactions among the phenyl side groups. Calculations based on available crystallographic structures reveal that planar conformations of the tetracene core in the solid state result from intermolecular interactions that can be tuned

Metal-Catalyzed Intra- and Intermolecular Addition of Carboxylic Acids to Alkynes in Aqueous Media: A Review

Directory of Open Access Journals (Sweden)

Javier Francos

2017-11-01

Full Text Available The metal-catalyzed addition of carboxylic acids to alkynes is a very effective tool for the synthesis of carboxylate-functionalized olefinic compounds in an atom-economical manner. Thus, a large variety of synthetically useful lactones and enol-esters can be accessed through the intra- or intermolecular versions of this process. In order to reduce the environmental impact of these reactions, considerable efforts have been devoted in recent years to the development of catalytic systems able to operate in aqueous media, which represent a real challenge taking into account the tendency of alkynes to undergo hydration in the presence of transition metals. Despite this, different Pd, Pt, Au, Cu and Ru catalysts capable of promoting the intra- and intermolecular addition of carboxylic acids to alkynes in a selective manner in aqueous environments have appeared in the literature. In this review article, an overview of this chemistry is provided. The synthesis of β-oxo esters by catalytic addition of carboxylic acids to terminal propargylic alcohols in water is also discussed.

Structural changes and intermolecular interactions of filled ice Ic structure for hydrogen hydrate under high pressure

International Nuclear Information System (INIS)

Machida, S; Hirai, H; Kawamura, T; Yamamoto, Y; Yagi, T

2010-01-01

High-pressure experiments of hydrogen hydrate were performed using a diamond anvil cell under conditions of 0.1-44.2 GPa and at room temperature. Also, high pressure Raman studies of solid hydrogen were performed in the pressure range of 0.1-43.7 GPa. X-ray diffractometry (XRD) for hydrogen hydrate revealed that a known high-pressure structure, filled ice Ic structure, of hydrogen hydrate transformed to a new high-pressure structure at approximately 35-40 GPa. A comparison of the Raman spectroscopy of a vibron for hydrogen molecules between hydrogen hydrate and solid hydrogen revealed that the extraction of hydrogen molecules from hydrogen hydrate occurred above 20 GPa. Also, the Raman spectra of a roton revealed that the rotation of hydrogen molecules in hydrogen hydrate was suppressed at around 20 GPa and that the rotation recovered under higher pressure. These results indicated that remarkable intermolecular interactions in hydrogen hydrate between neighboring hydrogen molecules and between guest hydrogen molecules and host water molecules might occur. These intermolecular interactions could produce the stability of hydrogen hydrate.

Organophotocatalysis: Insights into the Mechanistic Aspects of Thiourea-Mediated Intermolecular [2+2] Photocycloadditions.

Science.gov (United States)

Vallavoju, Nandini; Selvakumar, Sermadurai; Pemberton, Barry C; Jockusch, Steffen; Sibi, Mukund P; Sivaguru, Jayaraman

2016-04-25

Mechanistic investigations of the intermolecular [2+2] photocycloaddition of coumarin with tetramethylethylene mediated by thiourea catalysts reveal that the reaction is enabled by a combination of minimized aggregation, enhanced intersystem crossing, and altered excited-state lifetime(s). These results clarify how the excited-state reactivity can be manipulated through catalyst-substrate interactions and reveal a third mechanistic pathway for thiourea-mediated organo-photocatalysis. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

ON THE DURABILITY OF RESIN-DENTIN BONDS: IDENTIFYING THE WEAKEST LINKS

Science.gov (United States)

Zhang, Zihou; Beitzel, Dylan; Mutluay, Mustafa; Tay, Franklin R.; Pashley, David H.; Arola, Dwayne

2015-01-01

Fatigue of resin-dentin adhesive bonds is critical to the longevity of resin composite restorations. Objectives The objectives were to characterize the fatigue and fatigue crack growth resistance of resin-dentin bonds achieved using two different commercial adhesives and to identify apparent “weak-links”. Methods Bonded interface specimens were prepared using Adper Single Bond Plus (SB) or Adper Scotchbond Multi-Purpose (SBMP) adhesives and 3M Z100 resin composite according to the manufacturers instructions. The stress-life fatigue behavior was evaluated using the twin bonded interface approach and the fatigue crack growth resistance was examined using bonded interface Compact Tension (CT) specimens. Fatigue properties of the interfaces were compared to those of the resin-adhesive, resin composite and coronal dentin. Results The fatigue strength of the SBMP interface was significantly greater than that achieved by SB (p≤0.01). Both bonded interfaces exhibited significantly lower fatigue strength than that of the Z100 and dentin. Regarding the fatigue crack growth resistance, the stress intensity threshold (ΔKth) of the SB interface was significantly greater (p≤0.01) than that of the SBMP, whereas the ΔKth of the interfaces was more than twice that of the parent adhesives. Significance Collagen fibril reinforcement of the resin adhesive is essential to the fatigue crack growth resistance of resin-dentin bonds. Resin tags that are not well hybridized into the surrounding intertubular dentin and/or poor collagen integrity are detrimental to the bonded interface durability. PMID:26169318

The extended variant of the bond valence-bond length correlation curve for boron(III)-oxygen bonds

International Nuclear Information System (INIS)

Sidey, Vasyl

2015-01-01

The extended variant of the bond valence (s)-bond length (r) correlation curve for boron(III)-oxygen bonds has been closely approximated using the three-parameter function s = [k/(r - l)] - m, where s is measured in valence units (vu), r is measured in Aa, k = 0.53 Aa.vu, l = 0.975(1) Aa and m = 0.32 vu. The function s = exp[(r 0 - r)/b] traditionally used in the modern bond valence model requires the separate set of the bond valence parameters (r 0 = 1.362 Aa; b = 0.23 Aa) in order to approximate the above s-r curve for the bonds shorter than ∝1.3 Aa.

Controlled Self-Assembly of Low-Dimensional Alq3 Nanostructures from 1D Nanowires to 2D Plates via Intermolecular Interactions

Science.gov (United States)

Gu, Jianmin; Yin, Baipeng; Fu, Shaoyan; Jin, Cuihong; Liu, Xin; Bian, Zhenpan; Li, Jianjun; Wang, Lu; Li, Xiaoyu

2018-03-01

Due to the intense influence of the shape and size of the photon building blocks on the limitation and guidance of optical waves, an important strategy is the fabrication of different structures. Herein, organic semiconductor tris-(8-hydroxyquinoline)aluminium (Alq3) nanostructures with controllable morphology, ranging from one-dimensional nanowires to two-dimensional plates, have been prepared through altering intermolecular interactions with employing the anti-solvent diffusion cooperate with solvent-volatilization induced self-assembly method. The morphologies of the formed nanostructures, which are closely related to the stacking modes of the molecules, can be exactly controlled by altering the polarity of anti-solvents that can influence various intermolecular interactions. The synthesis strategy reported here can potentially be extended to other functional organic nanomaterials.

Understanding Bonds - Denmark

DEFF Research Database (Denmark)

Rimmer, Nina Røhr

2016-01-01

Undervisningsmateriale. A bond is a debt security, similar to an ”I Owe You document” (IOU). When you purchase a bond, you are lending money to a government, municipality, corporation, federal agency or other entity known as the issuer. In return for the loan, the issuer promises to pay you...... a specified rate of interest during the life of the bond and to repay the face value of the bond (the principal) when it “matures,” or comes due. Among the types of bonds you can choose from are: Government securities, municipal bonds, corporate bonds, mortgage and asset-backed securities, federal agency...... securities and foreign government bonds....

Similarity-transformed perturbation theory on top of truncated local coupled cluster solutions: Theory and applications to intermolecular interactions

Energy Technology Data Exchange (ETDEWEB)

Azar, Richard Julian, E-mail: julianazar2323@berkeley.edu; Head-Gordon, Martin, E-mail: mhg@cchem.berkeley.edu [Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

2015-05-28

Your correspondents develop and apply fully nonorthogonal, local-reference perturbation theories describing non-covalent interactions. Our formulations are based on a Löwdin partitioning of the similarity-transformed Hamiltonian into a zeroth-order intramonomer piece (taking local CCSD solutions as its zeroth-order eigenfunction) plus a first-order piece coupling the fragments. If considerations are limited to a single molecule, the proposed intermolecular similarity-transformed perturbation theory represents a frozen-orbital variant of the “(2)”-type theories shown to be competitive with CCSD(T) and of similar cost if all terms are retained. Different restrictions on the zeroth- and first-order amplitudes are explored in the context of large-computation tractability and elucidation of non-local effects in the space of singles and doubles. To accurately approximate CCSD intermolecular interaction energies, a quadratically growing number of variables must be included at zeroth-order.

Reliability Criteria for Thick Bonding Wire.

Science.gov (United States)

Dagdelen, Turker; Abdel-Rahman, Eihab; Yavuz, Mustafa

2018-04-17

Bonding wire is one of the main interconnection techniques. Thick bonding wire is widely used in power modules and other high power applications. This study examined the case for extending the use of traditional thin wire reliability criteria, namely wire flexure and aspect ratio, to thick wires. Eleven aluminum (Al) and aluminum coated copper (CucorAl) wire samples with diameter 300 μm were tested experimentally. The wire response was measured using a novel non-contact method. High fidelity FEM models of the wire were developed and validated. We found that wire flexure is not correlated to its stress state or fatigue life. On the other hand, aspect ratio is a consistent criterion of thick wire fatigue life. Increasing the wire aspect ratio lowers its critical stress and increases its fatigue life. Moreover, we found that CucorAl wire has superior performance and longer fatigue life than Al wire.

Reliability Criteria for Thick Bonding Wire

Science.gov (United States)

Yavuz, Mustafa

2018-01-01

Bonding wire is one of the main interconnection techniques. Thick bonding wire is widely used in power modules and other high power applications. This study examined the case for extending the use of traditional thin wire reliability criteria, namely wire flexure and aspect ratio, to thick wires. Eleven aluminum (Al) and aluminum coated copper (CucorAl) wire samples with diameter 300 μm were tested experimentally. The wire response was measured using a novel non-contact method. High fidelity FEM models of the wire were developed and validated. We found that wire flexure is not correlated to its stress state or fatigue life. On the other hand, aspect ratio is a consistent criterion of thick wire fatigue life. Increasing the wire aspect ratio lowers its critical stress and increases its fatigue life. Moreover, we found that CucorAl wire has superior performance and longer fatigue life than Al wire. PMID:29673194

The chemical bond in inorganic chemistry the bond valence model

CERN Document Server

Brown, I David

2016-01-01

The bond valence model is a version of the ionic model in which the chemical constraints are expressed in terms of localized chemical bonds formed by the valence charge of the atoms. Theorems derived from the properties of the electrostatic flux predict the rules obeyed by both ionic and covalent bonds. They make quantitative predictions of coordination number, crystal structure, bond lengths and bond angles. Bond stability depends on the matching of the bonding strengths of the atoms, while the conflicting requirements of chemistry and space lead to the structural instabilities responsible for the unusual physical properties displayed by some materials. The model has applications in many fields ranging from mineralogy to molecular biology.

Probing intermolecular protein-protein interactions in the calcium-sensing receptor homodimer using bioluminescence resonance energy transfer (BRET)

DEFF Research Database (Denmark)

Jensen, Anders A.; Hansen, Jakob L; Sheikh, Søren P

2002-01-01

-induced intermolecular movements in the CaR homodimer using the new bioluminescence resonance energy transfer technique, BRET2, which is based on the transference of energy from Renilla luciferase (Rluc) to the green fluorescent protein mutant GFP2. We tagged CaR with Rluc and GFP2 at different intracellular locations...

Critical behavior of the two-dimensional first passage time

International Nuclear Information System (INIS)

Chayes, J.T.; Chayes, L.; Durrett, R.

1986-01-01

We study the two-dimensional first passage problem in which bonds have zero and unit passage times with probability p and 1-p, respectively. We provide that as the zero-time bonds approach the percolation threshold p/sub c/, the first passage time exhibits the same critical behavior as the correlation function of the underlying percolation problem. In particular, if the correlation length obeys ξ(p)--chemical bondp-p/sub c/chemical bond/sup -//sup v/, then the first passage time constant satisfies μ(p)--chemical bondp-p/sub c/chemical bond/sup v/. At p/sub c/, where it has been asserted that the first passage time from 0 to x scales as chemical bondxchemical bond to a power psi with 0< psi<1, we show that the passage times grow like log chemical bondxchemical bond, i.e., the fluid spreads exponentially rapidly

Amalgam shear bond strength to dentin using different bonding agents.

Science.gov (United States)

Vargas, M A; Denehy, G E; Ratananakin, T

1994-01-01

This study evaluated the shear bond strength of amalgam to dentin using five different bonding agents: Amalgambond Plus, Optibond, Imperva Dual, All-Bond 2, and Clearfil Liner Bond. Flat dentin surfaces obtained by grinding the occlusal portion of 50 human third molars were used for this study. To contain the amalgam on the tooth surface, cylindrical plastic molds were placed on the dentin and secured with sticky wax. The bonding agents were then applied according to the manufacturers' instructions or light activated and Tytin amalgam was condensed into the plastic molds. The samples were thermocycled and shear bond strengths were determined using an Instron Universal Testing Machine. Analysis by one-way ANOVA indicated significant difference between the five groups (P < 0.05). The bond strength of amalgam to dentin was significantly higher with Amalgambond Plus using the High-Performance Additive than with the other four bonding agents.

Elucidation of the relationships between H-bonding patterns and excited state dynamics in cyclovalone.

Science.gov (United States)

Lamperti, Marco; Maspero, Angelo; Tønnesen, Hanne H; Bondani, Maria; Nardo, Luca

2014-08-28

Cyclovalone is a synthetic curcumin derivative in which the keto-enolic system is replaced by a cyclohexanone ring. This modification of the chemical structure might in principle result in an excited state that is more stable than that of curcumin, which in turn should produce an enhanced phototoxicity. Indeed, although curcumin exhibits photosensitized antibacterial activity, this compound is characterized by very fast excited-state dynamics which limit its efficacy as a photosensitizer. In previous works we showed that the main non-radiative decay pathway of keto-enolic curcuminoids is through excited-state transfer of the enolic proton to the keto-oxygen. Another effective deactivation pathway involves an intermolecular charge transfer mechanism occurring at the phenyl rings, made possible by intramolecular H-bonding between the methoxy and the hydroxyl substituent. In this paper we present UV-Vis and IR absorption spectra data with the aim of elucidating the intramolecular charge distribution of this compound and its solvation patterns in different environments, with particular focus on solute-solvent H-bonding features. Moreover, we discuss steady state and time-resolved fluorescence data that aim at characterizing the excited-state dynamics of cyclovalone, and we compare its decay photophysics to that of curcumin. Finally, because during the characterization procedures we found evidence of very fast photodegradation of cyclovalone, its photostability in four organic solvents was studied by HPLC and the corresponding relative degradation rates were calculated.

Elucidation of the Relationships between H-Bonding Patterns and Excited State Dynamics in Cyclovalone

Directory of Open Access Journals (Sweden)

Marco Lamperti

2014-08-01

Full Text Available Cyclovalone is a synthetic curcumin derivative in which the keto-enolic system is replaced by a cyclohexanone ring. This modification of the chemical structure might in principle result in an excited state that is more stable than that of curcumin, which in turn should produce an enhanced phototoxicity. Indeed, although curcumin exhibits photosensitized antibacterial activity, this compound is characterized by very fast excited-state dynamics which limit its efficacy as a photosensitizer. In previous works we showed that the main non-radiative decay pathway of keto-enolic curcuminoids is through excited-state transfer of the enolic proton to the keto-oxygen. Another effective deactivation pathway involves an intermolecular charge transfer mechanism occurring at the phenyl rings, made possible by intramolecular H-bonding between the methoxy and the hydroxyl substituent. In this paper we present UV-Vis and IR absorption spectra data with the aim of elucidating the intramolecular charge distribution of this compound and its solvation patterns in different environments, with particular focus on solute-solvent H-bonding features. Moreover, we discuss steady state and time-resolved fluorescence data that aim at characterizing the excited-state dynamics of cyclovalone, and we compare its decay photophysics to that of curcumin. Finally, because during the characterization procedures we found evidence of very fast photodegradation of cyclovalone, its photostability in four organic solvents was studied by HPLC and the corresponding relative degradation rates were calculated.

Convertible bond valuation focusing on Chinese convertible bond market

OpenAIRE

Yang, Ke

2010-01-01

This paper mainly discusses the methods of valuation of convertible bonds in Chinese market. Different from common convertible bonds in European market, considering the complicate features of Chinese convertible bond, this paper represents specific pricing approaches for pricing convertible bonds with different provisions along with the increment of complexity of these provisions. More specifically, this paper represents the decomposing method and binomial tree method for pricing both of Non-...

Introducing a Hydrogen-Bond Donor into a Weakly Nucleophilic Brønsted Base: Alkali Metal Hexamethyldisilazides (MHMDS, M=Li, Na, K, Rb and Cs) with Ammonia.

Science.gov (United States)

Neufeld, Roman; Michel, Reent; Herbst-Irmer, Regine; Schöne, Ralf; Stalke, Dietmar

2016-08-22

Alkali metal 1,1,1,3,3,3-hexamethyldisilazide (MHMDSs) are one of the most utilised weakly nucleophilic Brønsted bases in synthetic chemistry and especially in natural product synthesis. Like lithium organics, they aggregate depending on the employed donor solvents. Thus, they show different reactivity and selectivity as a function of their aggregation and solvation state. To date, monomeric LiHMDS with monodentate donor bases was only characterised in solution. Since the first preparation of LiHMDS in 1959 by Wannagat and Niederprüm, all efforts to crystallise monomeric LiHMDS in the absence of chelating ligands failed. Herein, we present ammonia adducts of LiHMDS, NaHMDS, KHMDS, RbHMDS and CsHMDS with unprecedented aggregation motifs: 1) The hitherto missing monomeric key compound in the LiHMDS aggregation architectures. Monomeric crystal structures of trisolvated LiHMDS (1) and NaHMDS (2), showing unique intermolecular hydrogen bonds, 2) the unprecedented tetrasolvated KHMDS (3) and RbHMDS (4) dimers and 3) the disolvated CsHMDS (5) dimer with very close intermolecular Si-CH3 ⋅⋅⋅Cs s-block "agostic" interactions have been prepared and characterised by single-crystal X-ray structure analysis. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effects of intermolecular interactions on the stability of carbon nanotube–gold nanoparticle conjugates in solution

Directory of Open Access Journals (Sweden)

Konczak L

2016-11-01

Full Text Available Lukasz Konczak,1 Jolanta Narkiewicz-Michalek,2 Giorgia Pastorin,3 Tomasz Panczyk1 1Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Cracow, 2Department of Chemistry, Maria Curie-Sklodowska University, Lublin, Poland; 3Department of Pharmacy, National University of Singapore, Singapore Abstract: This work deals with the role of intermolecular interactions in the stability of a carbon nanotube (CNT capped by functionalized gold nanoparticles (AuNPs. The importance of such a system is due to its potential application as a pH-controlled drug carrier. Our preliminary experimental studies showed that fabrication of such a nanobottle/nanocontainer is feasible and it is possible to encapsulate the anticancer drug cisplatin inside the inner space of a CNT and seal its ends by functionalized AuNPs. The expected behavior, that is, detachment of AuNPs at acidic pH and the release of cisplatin, was, however, not observed. On the other hand, our theoretical studies of chemically identical system led to the conclusion that the release of cisplatin at acidic pH should be observed. Therefore, in this work, a deeper theoretical analysis of various factors that could be responsible for the disagreement between experimental and theoretical results were performed. The study found that the major factor is a large dispersion interaction component acting between CNT and AuNP in solution in the case of the experimental system. This factor can be controlled to some extent by tuning the system size or the ratio between AuNP diameter and CNT diameter. Thus, such kind of a pH-sensitive drug carrier is still of great interest, but its structural parameters need to be properly adjusted. Keywords: hydrazone bond, drug delivery, dispersion interactions, cisplatin, acidic pH

A general transformation to canonical form for potentials in pairwise interatomic interactions.

Science.gov (United States)

Walton, Jay R; Rivera-Rivera, Luis A; Lucchese, Robert R; Bevan, John W

2015-06-14

A generalized formulation of explicit force-based transformations is introduced to investigate the concept of a canonical potential in both fundamental chemical and intermolecular bonding. Different classes of representative ground electronic state pairwise interatomic interactions are referenced to a chosen canonical potential illustrating application of such transformations. Specifically, accurately determined potentials of the diatomic molecules H2, H2(+), HF, LiH, argon dimer, and one-dimensional dissociative coordinates in Ar-HBr, OC-HF, and OC-Cl2 are investigated throughout their bound potentials. Advantages of the current formulation for accurately evaluating equilibrium dissociation energies and a fundamentally different unified perspective on nature of intermolecular interactions will be emphasized. In particular, this canonical approach has significance to previous assertions that there is no very fundamental distinction between van der Waals bonding and covalent bonding or for that matter hydrogen and halogen bonds.

Photophysical and computational investigation of the intermolecular interactions of pyrene with phenothiazine and promazine

Energy Technology Data Exchange (ETDEWEB)

Güloğlu, Pınar; Acar, Nursel, E-mail: nursel.acar@ege.edu.tr

2016-10-20

Highlights: • Intermolecular interactions of pyrene with phenothiazine/promazine were investigated. • All investigated systems were optimized at ωB97XD/6-31G(d,p) level in gas phase. • The electronic transitions were determined using frontier orbitals. • Both Py–Pheno and Py–Prom are potential candidates for charge transfer systems. - Abstract: The intermolecular interactions between the pyrene (Py) (as acceptor) and phenothiazine (Pheno), promazine (Prom) (as donors) were investigated using UV/Vis absorption and fluorescence spectroscopy. Fluorescence quenching rate constants for Py–Pheno and Py–Prom systems have been calculated approximately 10{sup 10} M{sup −1} s{sup −1}, indicating diffusion controlled processes. A computational investigation has also been carried out in gas phase at ωB97XD/6-31G(d,p) level. Time-dependent density functional theory (TDDFT) was used to calculate the electronic transitions of molecules at B3LYP/6-311++G(d,p) level. Total electronic energies, complexation energies, free energy differences, excitation wavelengths, and HOMO–LUMO energy gaps are discussed in gas phase. Analyses of first excited singlet states have indicated charge transfers transitions between Py and Pheno, Prom through π–π stacking in gas phase at 433 nm and 466 nm, respectively. Due to its charge transfer character, Py–Pheno and Py–Prom systems seem to be appropriate models to investigate and design photosensitive materials.

Thermodynamics of hydrogen bonding and van der Waals interactions of organic solutes in solutions of imidazolium based ionic liquids: “Structure-property” relationships

International Nuclear Information System (INIS)

Varfolomeev, Mikhail A.; Khachatrian, Artashes A.; Akhmadeev, Bulat S.; Solomonov, Boris N.

2016-01-01

Highlights: • Solution enthalpies of organic solutes in imidazolium based ionic liquids were measured. • van der Waals interactions scale of imidazolium based ionic liquids was proposed. • Enthalpies of solvation of organic solutes in ionic liquids were determined. • Hydrogen bond enthalpies of organic solutes with ionic liquids were calculated. • Relationships between structure of ionic liquids and thermochemical data were obtained. - Abstract: In the present work thermochemistry of intermolecular interactions of organic compounds in solutions of imidazolium based ionic liquids (ILs) has been studied using solution calorimetry method. Enthalpies of solution at infinite dilution of non-polar (alkanes, aromatic hydrocarbons) and polar (alcohols, amides, and etc.) organic solutes in two ionic liquids 1-butyl-3-methylimidazolium tetrafluoroborate and 1-butyl-3-methylimidazolium trifluoromethanesulfonate were measured at 298.15 K. The scale of van der Waals interactions of imidazolium based ILs has been proposed on the basis of solution enthalpies of n-alkanes in their media. The effect of the cation and anion structure of ILs on the enthalpies of solvation was analyzed. Enthalpies of hydrogen bonding of organic solutes with imidazolium based ILs were determined. It has been shown that these values are close to zero for proton acceptor solutes. At the same time, enthalpies of hydrogen bonding of proton donor solutes with ionic liquids are increased depending the anion: tetrafluoroborate ≈ bis(trifluoromethylsulfonyl)imide < 2-(2-methoxyethoxy)ethyl sulfate < trifluoromethanesulfonate. Enthalpies of van der Waals interactions and hydrogen bonding in the solutions of imidazolium based ionic liquids were compared with the same data for molecular solvents.

Thermodynamics of hydrogen bonding and van der Waals interactions of organic solutes in solutions of imidazolium based ionic liquids: “Structure-property” relationships

Energy Technology Data Exchange (ETDEWEB)

Varfolomeev, Mikhail A., E-mail: vma.ksu@gmail.com; Khachatrian, Artashes A.; Akhmadeev, Bulat S.; Solomonov, Boris N.

2016-06-10

Highlights: • Solution enthalpies of organic solutes in imidazolium based ionic liquids were measured. • van der Waals interactions scale of imidazolium based ionic liquids was proposed. • Enthalpies of solvation of organic solutes in ionic liquids were determined. • Hydrogen bond enthalpies of organic solutes with ionic liquids were calculated. • Relationships between structure of ionic liquids and thermochemical data were obtained. - Abstract: In the present work thermochemistry of intermolecular interactions of organic compounds in solutions of imidazolium based ionic liquids (ILs) has been studied using solution calorimetry method. Enthalpies of solution at infinite dilution of non-polar (alkanes, aromatic hydrocarbons) and polar (alcohols, amides, and etc.) organic solutes in two ionic liquids 1-butyl-3-methylimidazolium tetrafluoroborate and 1-butyl-3-methylimidazolium trifluoromethanesulfonate were measured at 298.15 K. The scale of van der Waals interactions of imidazolium based ILs has been proposed on the basis of solution enthalpies of n-alkanes in their media. The effect of the cation and anion structure of ILs on the enthalpies of solvation was analyzed. Enthalpies of hydrogen bonding of organic solutes with imidazolium based ILs were determined. It has been shown that these values are close to zero for proton acceptor solutes. At the same time, enthalpies of hydrogen bonding of proton donor solutes with ionic liquids are increased depending the anion: tetrafluoroborate ≈ bis(trifluoromethylsulfonyl)imide < 2-(2-methoxyethoxy)ethyl sulfate < trifluoromethanesulfonate. Enthalpies of van der Waals interactions and hydrogen bonding in the solutions of imidazolium based ionic liquids were compared with the same data for molecular solvents.

Reliability Criteria for Thick Bonding Wire

Directory of Open Access Journals (Sweden)

Turker Dagdelen

2018-04-01

Full Text Available Bonding wire is one of the main interconnection techniques. Thick bonding wire is widely used in power modules and other high power applications. This study examined the case for extending the use of traditional thin wire reliability criteria, namely wire flexure and aspect ratio, to thick wires. Eleven aluminum (Al and aluminum coated copper (CucorAl wire samples with diameter 300 μm were tested experimentally. The wire response was measured using a novel non-contact method. High fidelity FEM models of the wire were developed and validated. We found that wire flexure is not correlated to its stress state or fatigue life. On the other hand, aspect ratio is a consistent criterion of thick wire fatigue life. Increasing the wire aspect ratio lowers its critical stress and increases its fatigue life. Moreover, we found that CucorAl wire has superior performance and longer fatigue life than Al wire.

Photoinduced intermolecular electron transfer and off-resonance Raman characteristics of Rhodamine 101/N,N-diethylaniline

International Nuclear Information System (INIS)

Jiang, Li-lin; Liu, Wei-long; Song, Yun-fei; He, Xing; Wang, Yang; Wang, Chang; Wu, Hong-lin; Yang, Fang; Yang, Yan-qiang

2014-01-01

Highlights: • Mechanism of PIET reaction process for the Rh101 + /DEA system is investigated. • The significant geometrical changes of the charge–transfer complex are explained. • Forward Electron transfer from DEA to Rh101 +∗ occurs with lifetime of 425–560 fs. • Backward electron transfer occurs with a time constant of 46.16–51.40 ps. • Intramolecular vibrational relaxation occurs with lifetime of 2.77–5.39 ps. - Abstract: The ultrafast photoinduced intermolecular electron transfer (PIET) reaction of Rhodamine 101 (Rh101 + ) in N,N-diethylaniline (DEA) was investigated using off-resonance Raman, femtosecond time-resolved multiplex transient grating (TG) and transient absorption (TA) spectroscopies. The Raman spectra indicate that the C=C stretching vibration of the chromophore aromatic ring is more sensitive to ET compared with the C-C stretching mode. The ultrafast photoinduced intermolecular forward ET (FET) from DEA to Rh101 +∗ occurs on a time scale of τ FET = 425–560 fs. The backward ET (BET) occurs in the inverted region with a time constant of τ BET = 46.16–51.40 ps. The intramolecular vibrational relaxation (IVR) process occurs on the excited state potential energy surface with the time constant of τ IVR = 2.77–5.39 ps

N-(3-Nitrophenylmaleamic acid

Directory of Open Access Journals (Sweden)

B. Thimme Gowda

2010-07-01

Full Text Available In the title compound, C10H8N2O5, the molecule is slightly distorted from planarity. The molecular structure is stabilized by two intramolecular hydrogen bonds. The first is a short O—H...O hydrogen bond (H...O distance = 1.57 Å within the maleamic acid unit and the second is a C—H...O hydrogen bond (H...O distance = 2.24 Å which connects the amide group with the benzene ring. The nitro group is twisted by 6.2 (2° out of the plane of the benzene ring. The crystal structure manifests a variety of hydrogen bonding. The packing is dominated by a strong intermolecular N—H...O interaction which links the molecules into chains running along the b axis. The chains within a plane are further assembled by three additional types of intermolecular C—H...O hydrogen bonds to form a sheet parallel to the (overline{1}01 plane.

2,2′-Dihydroxybiphenyl-3,3′-dicarbaldehyde dioxime

Directory of Open Access Journals (Sweden)

Ekaterina Golovnia

2009-08-01

Full Text Available The molecule of the title compound, C14H12N2O4, lies across a crystallographic inversion centre situated at the mid-point of the C—C intra-annular bond. The molecule is not planar, the dihedral angle between the aromatic rings being 50.1 (1°. The oxime group is in an E position with respect to the –OH group and forms an intramolecular O—H...N hydrogen bond. In the crystal structure, intermolecular O—H...O hydrogen bonds link molecules into chains propagating along [001]. The crystal structure is further stabilized by intermolecular stacking interactions between the rings [centroid-to-centroid distance = 3.93 (1 Å], resulting in layers parallel to the bc plane.

Effect of Bonding Pressure and Bonding Time on the Tensile Properties of Cu-Foam / Cu-Plate Diffusion Bonded Joint

International Nuclear Information System (INIS)

Kim, Sang-Ho; Heo, Hoe-Jun; Kang, Chung-Yun; Yoon, Tae-Jin

2016-01-01

Open cell Cu foam, which has been widely utilized in various industries because of its high thermal conductivity, lightweight and large surface area, was successfully joined with Cu plate by diffusion bonding. To prevent excessive deformation of the Cu foam during bonding process, the bonding pressure should be lower than 500 kPa at 800 ℃ for 60 min and bonding pressure should be lowered with increasing holding time. The bonding strength was evaluated by tensile tests. The tensile load of joints increased with the bonding pressure and holding time. In the case of higher bonding pressure or time, the bonded length at the interface was usually longer than the cross-sectional length of the foam, so fracture occurred at the foam. For the same reason, base metal (foam) fracture mainly occurred at the node-plate junction rather than in the strut-plate junction because the bonded surface area of the node was relatively larger than that of the strut.

Intermolecular Interactions in Ternary Glycerol–Sample–H2O

DEFF Research Database (Denmark)

Westh, Peter; Rasmussen, Erik Lumby; Koga, Yoshikata

2011-01-01

We studied the intermolecular interactions in ternary glycerol (Gly)–sample (S)–H2O systems at 25 °C. By measuring the excess partial molar enthalpy of Gly, HGlyEHEGly, we evaluated the Gly–Gly enthalpic interaction, HGly-GlyEHEGly--Gly, in the presence of various samples (S). For S, tert...... little effect on HGly-GlyEHEGly--Gly. This contrasts with our earlier studies on 1P–S–H2O in that Na+, F− and Cl− are found as hydration centers from the induced changes on HIP-IPEHEIP--IP in the presence of S, while Br−, I−, and SCN− are found to act as hydrophiles. In comparison with the Hofmeister...... ranking of these ions, the kosmotropes are hydration centers and the more kosmotropic the higher the hydration number, consistent with the original Hofmeister’s concept of “H2O withdrawing power.” Br−, I− and SCN−, on the other hand, acted as hydrophiles and the more chaotropic they are the more...

Self-healing polymer gels based on dynamic covalent bonds%基于动态共价键的可自愈合聚合物凝胶

Institute of Scientific and Technical Information of China (English)

张云飞; 邓国华

2012-01-01

简要介绍了动态共价键既具有普通共价键的高强度和稳定性,又能像分子间作用力（如氢键）那样可逆地断裂和重组的特点,以及基于动态共价键构筑智能凝胶材料的优势。综述了多种动态共价键,如芳香基苯并呋喃酮二聚体（diarylbibenzo furanone,DABBF）、三硫酯（trithiocarbonate,TTC）、芳基硼酸酯、酰腙键（acylhydrazone bond）、双硫键（disulfide bond）等的结构及其动态化学,以及应用它们合成聚合物凝胶的方法、凝胶的自愈合机理和性能。提出了发现和采用多种动态共价键构筑可自愈合聚合物凝胶的趋势,为此须解决多种动态共价键的相容性、凝胶自愈合机理与性能的光谱表征等问题,并加强应用研究。%Dynamic covalent bonds have high mechanical strength and stability like ordinary covalent bonds and can reversibly break and rebuild like intermolecular forces(such as hydrogen bonding).The properties of dynamic covalent bonds are introduced.The advantages of building smart gels based on dynamic covalent bonds are described.Specifically,the structure and dynamic chemistry of diarylbibenzo furanone(DABBF),trithiocarbonate(TTC),phenylboronic aciddiol ester bond,acylhydrazone bond and disulfide bond are reviewed.The methods of utilizing those dynamic covalent bonds to construct dynamic gels with self-healing properties,including the healing mechanisms,are presented.Combining two or more covalent bonds to construct dynamic gels with more complex responsiveness are proposed.Problems,such as compatibility of the dynamic covalent bonds,spectroscopic methods for characterizing self-healing mechanisms and capabilities,and application-oriented systems need to be further investigated.

Bond Issues.

Science.gov (United States)

Pollack, Rachel H.

2000-01-01

Notes trends toward increased borrowing by colleges and universities and offers guidelines for institutions that are considering issuing bonds to raise money for capital projects. Discussion covers advantages of using bond financing, how use of bonds impacts on traditional fund raising, other cautions and concerns, and some troubling aspects of…

A simple and reliable approach to docking protein-protein complexes from very sparse NOE-derived intermolecular distance restraints

International Nuclear Information System (INIS)

Tang, Chun; Clore, G. Marius

2006-01-01

A simple and reliable approach for docking protein-protein complexes from very sparse NOE-derived intermolecular distance restraints (as few as three from a single point) in combination with a novel representation for an attractive potential between mapped interaction surfaces is described. Unambiguous assignments of very sparse intermolecular NOEs are obtained using a reverse labeling strategy in which one the components is fully deuterated with the exception of selective protonation of the δ-methyl groups of isoleucine, while the other component is uniformly 13 C-labeled. This labeling strategy can be readily extended to selective protonation of Ala, Leu, Val or Met. The attractive potential is described by a 'reduced' radius of gyration potential applied specifically to a subset of interfacial residues (those with an accessible surface area ≥ 50% in the free proteins) that have been delineated by chemical shift perturbation. Docking is achieved by rigid body minimization on the basis of a target function comprising the sparse NOE distance restraints, a van der Waals repulsion potential and the 'reduced' radius of gyration potential. The method is demonstrated for two protein-protein complexes (EIN-HPr and IIA Glc -HPr) from the bacterial phosphotransferase system. In both cases, starting from 100 different random orientations of the X-ray structures of the free proteins, 100% convergence is achieved to a single cluster (with near identical atomic positions) with an overall backbone accuracy of ∼2 A. The approach described is not limited to NMR, since interfaces can also be mapped by alanine scanning mutagenesis, and sparse intermolecular distance restraints can be derived from double cycle mutagenesis, cross-linking combined with mass spectrometry, or fluorescence energy transfer

Room temperature Cu-Cu direct bonding using surface activated bonding method

International Nuclear Information System (INIS)

Kim, T.H.; Howlader, M.M.R.; Itoh, T.; Suga, T.

2003-01-01

Thin copper (Cu) films of 80 nm thickness deposited on a diffusion barrier layered 8 in. silicon wafers were directly bonded at room temperature using the surface activated bonding method. A low energy Ar ion beam of 40-100 eV was used to activate the Cu surface prior to bonding. Contacting two surface-activated wafers enables successful Cu-Cu direct bonding. The bonding process was carried out under an ultrahigh vacuum condition. No thermal annealing was required to increase the bonding strength since the bonded interface was strong enough at room temperature. The chemical constitution of the Cu surface was examined by Auger electron spectroscope. It was observed that carbon-based contaminations and native oxides on copper surface were effectively removed by Ar ion beam irradiation for 60 s without any wet cleaning processes. An atomic force microscope study shows that the Ar ion beam process causes no surface roughness degradation. Tensile test results show that high bonding strength equivalent to bulk material is achieved at room temperature. The cross-sectional transmission electron microscope observations reveal the presence of void-free bonding interface without intermediate layer at the bonded Cu surfaces

Multicomponent hydrogen-bonding organic solids constructed from 6-hydroxy-2-naphthoic acid and N-heterocycles: Synthesis, structural characterization and synthon discussion

Science.gov (United States)

Zong, Yingxia; Shao, Hui; Pang, Yanyan; Wang, Debao; Liu, Kang; Wang, Lei

2016-07-01

Seven novel multicomponent crystals involving various substituted organic amine molecules and 6-hydroxy-2-naphthoic acid were prepared and characterized by using single crystal X-ray diffraction, infrared and thermogravimetric analyses (TGA). Crystal structures with 1,4-bis(imidazol) butane (L1) 1, 1,4-bis(imidazol-1-ylmethyl)benzene (L2) 2, 1-phenyl piperazine 3, 2-amino-4-hydroxy-6-methyl pyrimidine 4, 4,4'-bipyridine 5, 5,5'-dimethyl-2,2'-dipyridine 6, 2-amino-4,6-dimethyl pyrimidine 7 were determined. Among the seven molecular complexes, total proton transfer from 6-hydroxy-2-naphthoic acid to coformer has occurred in crystals 1-4, while the remaining were cocrystals. X-ray single-crystal structures of these complexes reveal that strong hydrogen bonding O-H···O/N-H···O/O-H···N and weak C-H···O/C-H···π/π···π intermolecular interactions direct the packing modes of molecular crystals together. The analysis of supramolecular synthons in the present structures shows that some classical supramolecular synthons like pyridine-carboxylic acid heterosynthon R22 (7) and aminopyridine-carboxylic acid heterosynthon R22 (8), are again observed in constructing the hydrogen-bonding networks in this paper. Besides, we noticed that water molecules act as a significant hydrogen-bonding connector in constructing supramolecular architectures of 3, 4, 6, and 7.

Tert-butyl 3-oxo-2,3,4,5,6,7-hexahydro-1H-pyrazolo[4,3-c]pyridine-5-carboxylate

Directory of Open Access Journals (Sweden)

Tara Shahani

2010-01-01

Full Text Available In the title compound, C11H17N3O3, the pyrazole ring is approximately planar, with a maximum deviation of 0.005 (2 Å, and forms a dihedral angle of 5.69 (13° with the plane through the six atoms of the piperidine ring. In the crystal, pairs of intermolecular N—H...O hydrogen bonds form dimers with neighbouring molecules, generating R22(8 ring motifs. These dimers are further linked into two-dimensional arrays parallel to the bc plane by intermolecular N—H...O and C—H...O hydrogen bonds.

Sulfur dioxide induced aggregation of wine thaumatin-like proteins: Role of disulfide bonds.

Science.gov (United States)

Chagas, Ricardo; Laia, César A T; Ferreira, Ricardo B; Ferreira, Luísa M

2018-09-01

Aggregation of heat unstable wine proteins is responsible for the economically and technologically detrimental problem called wine protein haze. This is caused by the aggregation of thermally unfolded proteins that can precipitate in bottled wine. To study the influence of SO 2 in this phenomenon, wine proteins were isolated and thaumatins were identified has the most prone to aggregate in the presence of this compound. Isolated wine thaumatins aggregation was followed by dynamic light scattering (DLS), circular dichroism (CD), fluorescence spectroscopy and size exclusion chromatography (SEC). Our experimental results demonstrate that protein thermal unfolding after exposure of the protein to 70 °C does not present differences whether SO 2 is present or not. Conversely, when the protein solution is cooled to 15 °C (after heat stress) significant analytical changes can be observed between samples with and without SO 2 . A remarkable change of circular dichroism spectra in the region 220-230 nm is observed (which can be related to S-S torsion angles), as well as an increase in tryptophan fluorescence intensity (absence of fluorescence quenching by S-S bonds). Formation of covalently-linked dimeric and tetrameric protein species were also detected by SEC. The ability to dissolve the aggregates with 8 M urea seems to indicate that hydrophobic interactions are prevalent in the formed aggregates. Also, the reduction of these aggregates with tris (2-carboxyethyl) phosphine (TCEP) to only monomeric species reveals the presence of intermolecular S-S bonds. Copyright © 2018 Elsevier Ltd. All rights reserved.

Pressure bonding molybdenum alloy (TZM) to reaction-bonded silicon nitride

International Nuclear Information System (INIS)

Huffsmith, S.A.; Landingham, R.L.

1978-01-01

Topping cycles could boost the energy efficiencies of a variety of systems by using what is now waste heat. One such topping cycle uses a ceramic helical expander and would require that a reaction-bonded silicon nitride (RBSN) rotor be bonded to a shaft of TZM (Mo-0.5 wt % Ti-0.08 wt % Zr). Coupon studies show that TZM can be bonded to RBSN at 1300 0 C and 69 MPa if there is an interlayer of MoSi 2 . A layer of finely ground (10 μm) MoSi 2 facilitates bond formation and provides a thicker bond interface. The hardness and grain structure of the TZM and RBSN were not affected by the temperature and pressure required to bond the coupons

Deconfined Quantum Critical Points: Symmetries and Dualities

Directory of Open Access Journals (Sweden)

Chong Wang

2017-09-01

Full Text Available The deconfined quantum critical point (QCP, separating the Néel and valence bond solid phases in a 2D antiferromagnet, was proposed as an example of (2+1D criticality fundamentally different from standard Landau-Ginzburg-Wilson-Fisher criticality. In this work, we present multiple equivalent descriptions of deconfined QCPs, and use these to address the possibility of enlarged emergent symmetries in the low-energy limit. The easy-plane deconfined QCP, besides its previously discussed self-duality, is dual to N_{f}=2 fermionic quantum electrodynamics, which has its own self-duality and hence may have an O(4×Z_{2}^{T} symmetry. We propose several dualities for the deconfined QCP with SU(2 spin symmetry which together make natural the emergence of a previously suggested SO(5 symmetry rotating the Néel and valence bond solid orders. These emergent symmetries are implemented anomalously. The associated infrared theories can also be viewed as surface descriptions of (3+1D topological paramagnets, giving further insight into the dualities. We describe a number of numerical tests of these dualities. We also discuss the possibility of “pseudocritical” behavior for deconfined critical points, and the meaning of the dualities and emergent symmetries in such a scenario.

Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design.

Science.gov (United States)

Maguire, Jack B; Boyken, Scott E; Baker, David; Kuhlman, Brian

2018-05-08

Hydrogen bond networks play a critical role in determining the stability and specificity of biomolecular complexes, and the ability to design such networks is important for engineering novel structures, interactions, and enzymes. One key feature of hydrogen bond networks that makes them difficult to rationally engineer is that they are highly cooperative and are not energetically favorable until the hydrogen bonding potential has been satisfied for all buried polar groups in the network. Existing computational methods for protein design are ill-equipped for creating these highly cooperative networks because they rely on energy functions and sampling strategies that are focused on pairwise interactions. To enable the design of complex hydrogen bond networks, we have developed a new sampling protocol in the molecular modeling program Rosetta that explicitly searches for sets of amino acid mutations that can form self-contained hydrogen bond networks. For a given set of designable residues, the protocol often identifies many alternative sets of mutations/networks, and we show that it can readily be applied to large sets of residues at protein-protein interfaces or in the interior of proteins. The protocol builds on a recently developed method in Rosetta for designing hydrogen bond networks that has been experimentally validated for small symmetric systems but was not extensible to many larger protein structures and complexes. The sampling protocol we describe here not only recapitulates previously validated designs with performance improvements but also yields viable hydrogen bond networks for cases where the previous method fails, such as the design of large, asymmetric interfaces relevant to engineering protein-based therapeutics.

Chemical bond fundamental aspects of chemical bonding

CERN Document Server

Frenking, Gernot

2014-01-01

This is the perfect complement to ""Chemical Bonding - Across the Periodic Table"" by the same editors, who are two of the top scientists working on this topic, each with extensive experience and important connections within the community. The resulting book is a unique overview of the different approaches used for describing a chemical bond, including molecular-orbital based, valence-bond based, ELF, AIM and density-functional based methods. It takes into account the many developments that have taken place in the field over the past few decades due to the rapid advances in quantum chemica

Intermolecular symmetry-adapted perturbation theory study of large organic complexes

International Nuclear Information System (INIS)

Heßelmann, Andreas; Korona, Tatiana

2014-01-01

Binding energies for the complexes of the S12L database by Grimme [Chem. Eur. J. 18, 9955 (2012)] were calculated using intermolecular symmetry-adapted perturbation theory combined with a density-functional theory description of the interacting molecules. The individual interaction energy decompositions revealed no particular change in the stabilisation pattern as compared to smaller dimer systems at equilibrium structures. This demonstrates that, to some extent, the qualitative description of the interaction of small dimer systems may be extrapolated to larger systems, a method that is widely used in force-fields in which the total interaction energy is decomposed into atom-atom contributions. A comparison of the binding energies with accurate experimental reference values from Grimme, the latter including thermodynamic corrections from semiempirical calculations, has shown a fairly good agreement to within the error range of the reference binding energies

INS study of intermolecular interaction at the silicone-fumed silica interface

International Nuclear Information System (INIS)

Sheka, E.F.; Natkaniec, I.

1999-01-01

Complete text of publication follows. The paper presents results related to the interface formed between finned silica particles and polydimethylsiloxane polymers, presented in the study by a five-member cyclic oligomer SiS. The substrate surface is terminated by either hydroxyl units or by trimethylsiloxy ones. When the interface is formed, methyl units are the main constituents providing neutron scattering. Protium/deuterium exchange has been used to distinguish the latter belonging to either adsorbate or substrate. A detailed analysis of the intermolecular interaction impact on both adsorbed molecule and substrate has been performed. The observed features are supported by the vibrational spectra calculations performed on the basis of a modem quantum-chemical approach and supplemented by the solution of the inverse spectral problem. (author)

2,2,2-Trichloro-N-(3,4-dimethylphenylacetamide

Directory of Open Access Journals (Sweden)

Hartmut Fuess

2009-05-01

Full Text Available The conformation of the N—H bond in the title compound, C10H10Cl3NO, is anti to the C=O bond. The amide H atom exhibits both intramolecular N—H...Cl and intermolecular N—H...O hydrogen bonding. The latter interactions link the molecules into infinite chains.

Wire bonding in microelectronics

CERN Document Server

Harman, George G

2010-01-01

Wire Bonding in Microelectronics, Third Edition, has been thoroughly revised to help you meet the challenges of today's small-scale and fine-pitch microelectronics. This authoritative guide covers every aspect of designing, manufacturing, and evaluating wire bonds engineered with cutting-edge techniques. In addition to gaining a full grasp of bonding technology, you'll learn how to create reliable bonds at exceedingly high yields, test wire bonds, solve common bonding problems, implement molecular cleaning methods, and much more. Coverage includes: Ultrasonic bonding systems and technologies, including high-frequency systems Bonding wire metallurgy and characteristics, including copper wire Wire bond testing Gold-aluminum intermetallic compounds and other interface reactions Gold and nickel-based bond pad plating materials and problems Cleaning to improve bondability and reliability Mechanical problems in wire bonding High-yield, fine-pitch, specialized-looping, soft-substrate, and extreme-temperature wire bo...

A critical analysis of Islamic bond: A case study on Sunway Treasury Sukuk

OpenAIRE

Uddin, Md Akther; Sultan, Yousuf; Hosen, Mosharrof; Ullah, Nazim

2015-01-01

Sukuk has been playing a significant role in developing Islamic finance, more specifically, Islamic capital market. Islamic financial institutions have very limited number of liquid investments other than hard cash to hold as conventional short-term bonds, commercial papers and notes are interest based and prohibited in Shari’ah. The rapid growth in Sukuk market not only in Malaysia but also internationally indicates huge potential of this innovative financial instrument. In this paper, an at...

Thermodynamic and mechanical effects of disulfide bonds in CXCLl7 chemokine

Science.gov (United States)

Singer, Christopher

Chemokines are a family of signaling proteins mainly responsible for the chemotaxis of leukocytes, where their biological activity is modulated by their oligomerization state. Here, the dynamics and thermodynamic stability are characterized in monomer and homodimer structures of CXCL7, one of the most abundant platelet chemokines. The effects of dimerization and disulfide bond formation are investigated using computational methods that include molecular dynamics (MD) simulations and the Distance Constraint Model (DCM). A consistent picture emerges for the effect of dimerization and role of the Cys5-Cys31 and Cys7- Cys47 disulfide bonds. Surprisingly, neither disulfide bond is critical for maintaining structural stability in the monomer or dimer, although the monomer is destabilized more than the dimer upon removal of disulfide bonds. Instead, it is found that disulfide bonds influence the native state dynamics as well as modulates the relative stability between monomer and dimer. The combined analysis elucidates how CXCL7 is mechanically stable as a monomer, and how upon dimerization flexibly correlated motions are induced between the 30s and 50s loop within each monomer and across the dimer interface. Interestingly, the greatest gain in flexibility upon dimerization occurs when both disulfide bonds are present in each domain, and the homodimer is least stable relative to its two monomers. These results suggest the highly conserved disulfide bonds in chemokines facilitate a structural mechanism for distinguishing functional characteristics between monomer and dimer.

Distinguishing the Effects of Bond-Length Alternation versus Bond-Order Alternation on the Nonlinear Optical Properties of π-Conjugated Chromophores

KAUST Repository

Gieseking, Rebecca L.; Risko, Chad; Bredas, Jean-Luc

2015-01-01

Understanding the relationships between the molecular nonlinear optical (NLO) properties and the bond-length alternation (BLA) or π-bond-order alternation (BOA) along the molecular backbone of linear π-conjugated systems has proven widely useful in the development of NLO organic chromophores and materials. Here, we examine model polymethines to elucidate the reliability of these relationships. While BLA is solely a measure of molecular geometric structure, BOA includes information pertaining to the electronic structure. As a result, BLA is found to be a good predictor of NLO properties only when optimized geometries are considered, whereas BOA is more broadly applicable. Proper understanding of the distinction between BLA and BOA is critical when designing computational studies of NLO properties, especially for molecules in complex environments or in nonequilibrium geometries. © 2015 American Chemical Society.

Distinguishing the Effects of Bond-Length Alternation versus Bond-Order Alternation on the Nonlinear Optical Properties of π-Conjugated Chromophores

KAUST Repository

Gieseking, Rebecca L.

2015-06-18

Understanding the relationships between the molecular nonlinear optical (NLO) properties and the bond-length alternation (BLA) or π-bond-order alternation (BOA) along the molecular backbone of linear π-conjugated systems has proven widely useful in the development of NLO organic chromophores and materials. Here, we examine model polymethines to elucidate the reliability of these relationships. While BLA is solely a measure of molecular geometric structure, BOA includes information pertaining to the electronic structure. As a result, BLA is found to be a good predictor of NLO properties only when optimized geometries are considered, whereas BOA is more broadly applicable. Proper understanding of the distinction between BLA and BOA is critical when designing computational studies of NLO properties, especially for molecules in complex environments or in nonequilibrium geometries. © 2015 American Chemical Society.

Formation of an intermolecular charge-transfer compound in UHV codeposited tetramethoxypyrene and tetracyanoquinodimethane

DEFF Research Database (Denmark)

Medjanik, K.; Perkert, S.; Naghavi, S.

2010-01-01

Ultrahigh vacuum (UHV)-deposited films of the mixed phase of tetramethoxypyrene and tetracyanoquinodimethane (TMP -TCNQ ) on gold have been studied using ultraviolet photoelectron spectroscopy (UPS), x-ray diffraction (XRD), infrared (IR) spectroscopy, and scanning tunneling spectroscopy (STS......). The formation of an intermolecular charge-transfer (CT) compound is evident from the appearance of new reflexes in XRD (d =0.894nm and d =0.677nm). A softening of the CN stretching vibration (redshift by 7 cm⊃-1) of TCNQ is visible in the IR spectra, being indicative of a CT on the order of 0.3e from TMP...

Analysis of factors influencing the bond strength in roll bonding processes

Science.gov (United States)

Khaledi, Kavan; Wulfinghoff, Stephan; Reese, Stefanie

2018-05-01

Cold Roll Bonding (CRB) is recognized as an industrial technique in which the metal sheets are joined together in order to produce laminate metal composites. In this technique, a metallurgical bond resulting from severe plastic deformation is formed between the rolled metallic layers. The main objective of this paper is to analyse different factors which may affect the bond formation in rolling processes. To achieve this goal, first, an interface model is employed which describes both the bonding and debonding. In this model, the bond strength evolution between the metallic layers is calculated based on the film theory of bonding. On the other hand, the debonding process is modelled by means of a bilinear cohesive zone model. In the numerical section, different scenarios are taken into account to model the roll bonding process of metal sheets. The numerical simulation includes the modelling of joining during the roll bonding process followed by debonding in a Double Cantilever Beam (DCB) peeling test. In all simulations, the metallic layers are regarded as elastoplastic materials subjected to large plastic deformations. Finally, the effects of some important factors on the bond formation are numerically investigated.

Polarized IR spectra of resonance assisted hydrogen bond (RAHB) in 2-hydroxyazobenzenes

International Nuclear Information System (INIS)

Rospenk, Maria; Majewska, Paulina; Czarnik-Matusewicz, Boguslawa; Sobczyk, Lucjan

2006-01-01

The polarized IR spectra in the region 4000-400 cm -1 over the temperature range 298-370 K of liquid crystalline (LC) 4-chloro-2'-hydroxy-4'-pentyloxyazobenzene (CHPAB) containing strong O-H...N RAHBs were studied. It has been established that molecules of this compound undergoes a spontaneous ordering in thin layers (10-20 μm) between the KRS-5 plates. The order degree expressed by the S parameter exceeds 0.6 for the Smectic A and crystalline phases. The best indicator of orientation is the mode at 1084 cm -1 as its transition dipole moment is oriented parallel to the long axis of the molecule. A good marker is also the γ(OH) band with the transition dipole moment nearly perpendicular to the long axis. The intramolecular O-H...N hydrogen bonding shows features characteristic of RAHB. The transition dipole moment of the ν(OH) vibrations forms with the long axis of the molecule the angle equal to 43 ± 3 deg. (the OH bond is oriented to this axis at the angle of 9 deg.) that convincingly speaks in favour of a coupling between the proton and π-electron motions. Similar behaviour is manifested by a broad absorption in the finger print region that can be interpreted in terms of the modification of the potential energy shape due to the plane-to-plane intermolecular interaction and appearance of the second minimum. A marked ordering of molecules in the isotropic phase is also observed evidencing some alignment of molecules extended far beyond the monomolecular layers on the surfaces of the KRS-5 windows

A four-armed Schiff base: 6,6′,6′′,6′′′-tetramethoxy-2,2′,2′′,2′′′-[methanetetrayltetrakis(methylenenitrilomethylidyne]tetraphenol

Directory of Open Access Journals (Sweden)

Guang-Qi Jiang

2008-08-01

Full Text Available In the structure of the title compound, C37H40N4O8, pentaerythrityltetramine is bonded to four o-vanillin molecules, forming a four-armed Schiff base molecule. These molecules are connected by intermolecular C—H...O hydrogen bonds. Intramolecular C—H...N and O—H...N hydrogen bonds are also present.

Simultaneous bond degradation and bond formation during phenol-formaldehyde curing with wood

Science.gov (United States)

Daniel J. Yelle; John Ralph

2016-01-01

Bonding of wood using phenol–formaldehyde adhesive develops highly durable bonds. Phenol– formaldehyde is believed to form primary bonds with wood cell wall polymers (e.g., lignin). However, it is unclear how this adhesive interacts and bonds to lignin. Through wood solubilisation methodologies, earlywood and latewood bonded assemblies were characterized using two-...

Importance of the Donor:Fullerene intermolecular arrangement for high-efficiency organic photovoltaics

KAUST Repository

Graham, Kenneth; Cabanetos, Clement; Jahnke, Justin P.; Idso, Matthew N.; El Labban, Abdulrahman; Ngongang Ndjawa, Guy Olivier; Heumueller, Thomas; Vandewal, Koen; Salleo, Alberto; Chmelka, Bradley F.; Amassian, Aram; Beaujuge, Pierre; McGehee, Michael D.

2014-01-01

The performance of organic photovoltaic (OPV) material systems are hypothesized to depend strongly on the intermolecular arrangements at the donor:fullerene interfaces. A review of some of the most efficient polymers utilized in polymer:fullerene PV devices, combined with an analysis of reported polymer donor materials wherein the same conjugated backbone was used with varying alkyl substituents, supports this hypothesis. Specifically, the literature shows that higher-performing donor-acceptor type polymers generally have acceptor moieties that are sterically accessible for interactions with the fullerene derivative, whereas the corresponding donor moieties tend to have branched alkyl substituents that sterically hinder interactions with the fullerene. To further explore the idea that the most beneficial polymer:fullerene arrangement involves the fullerene docking with the acceptor moiety, a family of benzo[1,2-b:4,5-b]dithiophene-thieno[3,4-c]pyrrole-4,6-dione polymers (PBDTTPD derivatives) was synthesized and tested in a variety of PV device types with vastly different aggregation states of the polymer. In agreement with our hypothesis, the PBDTTPD derivative with a more sterically accessible acceptor moiety and a more sterically hindered donor moiety shows the highest performance in bulk-heterojunction, bilayer, and low-polymer concentration PV devices where fullerene derivatives serve as the electron-accepting materials. Furthermore, external quantum efficiency measurements of the charge-transfer state and solid-state two-dimensional (2D) 13C{1H} heteronuclear correlation (HETCOR) NMR analyses support that a specific polymer:fullerene arrangement is present for the highest performing PBDTTPD derivative, in which the fullerene is in closer proximity to the acceptor moiety of the polymer. This work demonstrates that the polymer:fullerene arrangement and resulting intermolecular interactions may be key factors in determining the performance of OPV material systems

Importance of the Donor:Fullerene intermolecular arrangement for high-efficiency organic photovoltaics

KAUST Repository

Graham, Kenneth

2014-07-09

The performance of organic photovoltaic (OPV) material systems are hypothesized to depend strongly on the intermolecular arrangements at the donor:fullerene interfaces. A review of some of the most efficient polymers utilized in polymer:fullerene PV devices, combined with an analysis of reported polymer donor materials wherein the same conjugated backbone was used with varying alkyl substituents, supports this hypothesis. Specifically, the literature shows that higher-performing donor-acceptor type polymers generally have acceptor moieties that are sterically accessible for interactions with the fullerene derivative, whereas the corresponding donor moieties tend to have branched alkyl substituents that sterically hinder interactions with the fullerene. To further explore the idea that the most beneficial polymer:fullerene arrangement involves the fullerene docking with the acceptor moiety, a family of benzo[1,2-b:4,5-b]dithiophene-thieno[3,4-c]pyrrole-4,6-dione polymers (PBDTTPD derivatives) was synthesized and tested in a variety of PV device types with vastly different aggregation states of the polymer. In agreement with our hypothesis, the PBDTTPD derivative with a more sterically accessible acceptor moiety and a more sterically hindered donor moiety shows the highest performance in bulk-heterojunction, bilayer, and low-polymer concentration PV devices where fullerene derivatives serve as the electron-accepting materials. Furthermore, external quantum efficiency measurements of the charge-transfer state and solid-state two-dimensional (2D) 13C{1H} heteronuclear correlation (HETCOR) NMR analyses support that a specific polymer:fullerene arrangement is present for the highest performing PBDTTPD derivative, in which the fullerene is in closer proximity to the acceptor moiety of the polymer. This work demonstrates that the polymer:fullerene arrangement and resulting intermolecular interactions may be key factors in determining the performance of OPV material systems

Effect of aromatization of the ring on intramolecular H-bond in 3-hydroxy-4-formylo derivatives of fulvene

Science.gov (United States)

Oziminski, Wojciech P.; Krygowski, Tadeusz M.

2011-06-01

DFT optimization of H-bonded 3-hydroxy-4-formylo derivatives of fulvene aromatized by amino substitution at C6 or by complexation with Li atom was performed using the B3LYP functional together with 6-311+G(d,p) basis set. Several aromaticity indicators (HOMA, NICS, pEDA and Shannon aromaticity) confirm an increase of aromaticity in the sequence: fulvene, 6-aminofulvene, Li-complex with fulvene and in the case of H-bonded 3-hydroxy-4-formylo derivatives, exhibited in the same sequence an increase of H-bond strength estimated by direct comparison of energy for H-bonded and open conformations, as well as by using AIM based electron densities at bond critical point.

Bond strength of masonry

NARCIS (Netherlands)

Pluijm, van der R.; Vermeltfoort, A.Th.

1992-01-01

Bond strength is not a well defined property of masonry. Normally three types of bond strength can be distinguished: - tensile bond strength, - shear (and torsional) bond strength, - flexural bond strength. In this contribution the behaviour and strength of masonry in deformation controlled uniaxial

Comparative evaluation of shear bond strength of metallic brackets bonded with two different bonding agents under dry conditions and with saliva contamination

Directory of Open Access Journals (Sweden)

Mashallah Khanehmasjedi

2017-02-01

Conclusion: Application of Single Bond and Assure bonding agents resulted in adequate bond strength of brackets to tooth structures. Contamination with saliva significantly decreased the bond strength of Assure bonding agent compared with dry conditions.

A simple and reliable approach to docking protein-protein complexes from very sparse NOE-derived intermolecular distance restraints

Energy Technology Data Exchange (ETDEWEB)

Tang, Chun; Clore, G. Marius [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: mariusc@intra.niddk.nih.gov

2006-09-15

A simple and reliable approach for docking protein-protein complexes from very sparse NOE-derived intermolecular distance restraints (as few as three from a single point) in combination with a novel representation for an attractive potential between mapped interaction surfaces is described. Unambiguous assignments of very sparse intermolecular NOEs are obtained using a reverse labeling strategy in which one the components is fully deuterated with the exception of selective protonation of the {delta}-methyl groups of isoleucine, while the other component is uniformly {sup 13}C-labeled. This labeling strategy can be readily extended to selective protonation of Ala, Leu, Val or Met. The attractive potential is described by a 'reduced' radius of gyration potential applied specifically to a subset of interfacial residues (those with an accessible surface area {>=} 50% in the free proteins) that have been delineated by chemical shift perturbation. Docking is achieved by rigid body minimization on the basis of a target function comprising the sparse NOE distance restraints, a van der Waals repulsion potential and the 'reduced' radius of gyration potential. The method is demonstrated for two protein-protein complexes (EIN-HPr and IIA{sup Glc}-HPr) from the bacterial phosphotransferase system. In both cases, starting from 100 different random orientations of the X-ray structures of the free proteins, 100% convergence is achieved to a single cluster (with near identical atomic positions) with an overall backbone accuracy of {approx}2 A. The approach described is not limited to NMR, since interfaces can also be mapped by alanine scanning mutagenesis, and sparse intermolecular distance restraints can be derived from double cycle mutagenesis, cross-linking combined with mass spectrometry, or fluorescence energy transfer.

Recent Advances in Adhesive Bonding - The Role of Biomolecules, Nanocompounds, and Bonding Strategies in Enhancing Resin Bonding to Dental Substrates.

Science.gov (United States)

Münchow, Eliseu A; Bottino, Marco C

2017-09-01

To present an overview on the main agents (i.e., biomolecules and nanocompounds) and/or strategies currently available to amplify or stabilize resin-dentin bonding. According to studies retrieved for full text reading (2014-2017), there are currently six major strategies available to overcome resin-dentin bond degradation: (i) use of collagen crosslinking agents, which may form stable covalent bonds with collagen fibrils, thus strengthening the hybrid layer; (ii) use of antioxidants, which may allow further polymerization reactions over time; (iii) use of protease inhibitors, which may inhibit or inactivate metalloproteinases; (iv) modification of the bonding procedure, which may be performed by using the ethanol wet-bonding technique or by applying an additional adhesive (hydrophobic) coating, thereby strengthening the hybrid layer; (v) laser treatment of the substrate prior to bonding, which may cause specific topographic changes in the surface of dental substrates, increasing bonding efficacy; and (vi) reinforcement of the resin matrix with inorganic fillers and/or remineralizing agents, which may positively enhance physico-mechanical properties of the hybrid layer. With the present review, we contributed to the better understanding of adhesion concepts and mechanisms of resin-dentin bond degradation, showing the current prospects available to solve that problematic. Also, adhesively-bonded restorations may be benefited by the use of some biomolecules, nanocompounds or alternative bonding strategies in order to minimize bond strength degradation.

Photoinduced intermolecular electron transfer and off-resonance Raman characteristics of Rhodamine 101/N,N-diethylaniline

Energy Technology Data Exchange (ETDEWEB)

Jiang, Li-lin [Department of Physics, Harbin Institute of Technology, Harbin 150001 (China); School of Mechanical and Electronic Engineering, Hezhou University, Hezhou 542800 (China); Liu, Wei-long; Song, Yun-fei; He, Xing; Wang, Yang; Wang, Chang; Wu, Hong-lin [Department of Physics, Harbin Institute of Technology, Harbin 150001 (China); Yang, Fang [National Key Laboratory of Science and Technology on Tunable Laser, Department of Optoelectronics Information Science Technology, Harbin Institute of Technology, Harbin 150001 (China); Yang, Yan-qiang, E-mail: yqyang@hit.edu.cn [Department of Physics, Harbin Institute of Technology, Harbin 150001 (China); National Key Laboratory of Shock Wave and Detonation Physics, Institute of Fluid Physics, China Academy of Engineering Physics, Mianyang 621900, Sichuan (China)

2014-01-31

Highlights: • Mechanism of PIET reaction process for the Rh101{sup +}/DEA system is investigated. • The significant geometrical changes of the charge–transfer complex are explained. • Forward Electron transfer from DEA to Rh101{sup +∗} occurs with lifetime of 425–560 fs. • Backward electron transfer occurs with a time constant of 46.16–51.40 ps. • Intramolecular vibrational relaxation occurs with lifetime of 2.77–5.39 ps. - Abstract: The ultrafast photoinduced intermolecular electron transfer (PIET) reaction of Rhodamine 101 (Rh101{sup +}) in N,N-diethylaniline (DEA) was investigated using off-resonance Raman, femtosecond time-resolved multiplex transient grating (TG) and transient absorption (TA) spectroscopies. The Raman spectra indicate that the C=C stretching vibration of the chromophore aromatic ring is more sensitive to ET compared with the C-C stretching mode. The ultrafast photoinduced intermolecular forward ET (FET) from DEA to Rh101{sup +∗} occurs on a time scale of τ{sub FET} = 425–560 fs. The backward ET (BET) occurs in the inverted region with a time constant of τ{sub BET} = 46.16–51.40 ps. The intramolecular vibrational relaxation (IVR) process occurs on the excited state potential energy surface with the time constant of τ{sub IVR} = 2.77–5.39 ps.

Criticality of the bond-diluted Ising ferromagnet in a semi-infinite simple cubic lattice

International Nuclear Information System (INIS)

Silva, L.R. da; Tsallis, C.; Sarmento, E.F.

1987-01-01

We study the phase diagram and universality classes of the quenched bond-diluted spin 1/2 Ising ferromagnetic in a semi-infinite simple cubic lattice with a (0,0,1) free surface. We observe that surface ferromagnetism persists below the d=2 percolation threshold p c 2D = 1/2, in fact down to pc∼0,42. (M.W.O.) [pt

Study of variation in thermal width of nematic and induced smectic ordering phase of citric acid (CA) and 4-heptyloxybenzoic acid (7OBA) hydrogen bonded liquid crystal complexes

Science.gov (United States)

Sundaram, S.; Jayaprakasam, R.; Praveena, R.; Rajasekaran, T. R.; Senthil, T. S.; Vijayakumar, V. N.

2018-01-01

Hydrogen-bonded liquid crystals (HBLCs) have been derived from nonmesogenic citric acid (CA) and mesogenic 4-heptyloxybenzoic acid (7OBA) yielding a highly ordered smectic C (Sm C) phase along with the new smectic X (Sm X) phase which has been identified as fingerprint-type texture. Optical (polarizing optical microscopy), thermal (differential scanning calorimetry) and structural (Fourier transform infrared spectroscopy and nuclear magnetic resonance spectroscopy) properties are studied. A noteworthy observation is that the intermolecular H-bond (between CA and 7OBA) influences on its melting point and clearing temperature of the HBLCs which exhibits lower value than those of the individual compounds. A typical extended mesophase region has been observed in the present complex while varying the mixture ratio (1:1 to 1:3) than those of individual compounds. The change in the ratio of the mesogenic compound in the mixture alters thermal properties such as enthalpy value and thermal span width in nematic (N) region of HBLC complex. Optical tilt angle measurement of CA+7OBA in Sm C phase has been discussed to identify the molecular position in the mesophase.

Synthesis, spectral characterization and structural studies of a novel O, N, O donor semicarbazone and its binuclear copper complex with hydrogen bond stabilized lattice

Science.gov (United States)

Layana, S. R.; Saritha, S. R.; Anitha, L.; Sithambaresan, M.; Sudarsanakumar, M. R.; Suma, S.

2018-04-01

A novel O,N,O donor salicylaldehyde-N4-phenylsemicarbazone, (H2L) has been synthesized and physicochemically characterized. Detailed structural studies of H2L using single crystal X-ray diffraction technique reveals the existence of intra and inter molecular hydrogen bonding interactions, which provide extra stability to the molecule. We have successfully synthesized a binuclear copper(II) complex, [Cu2(HL)2(NO3)(H2O)2]NO3 with phenoxy bridging between the two copper centers. The complex was characterized by elemental analysis, magnetic susceptibility and conductivity measurements, FT-IR, UV-Visible, mass and EPR spectral methods. The grown crystals of the copper complex were employed for the single crystal X-ray diffraction studies. The complex possesses geometrically different metal centers, in which the ligand coordinates through ketoamide oxygen, azomethine nitrogen and deprotonated phenoxy oxygen. The extensive intermolecular hydrogen bonding interactions of the coordinated and the lattice nitrate groups interconnect the complex units to form a 2D supramolecular assembly. The ESI mass spectrum substantiates the existence of 1:1 complex. The g values obtained from the EPR spectrum in frozen DMF suggest dx2 -y2 ground state for the unpaired electron.

Comparative evaluation of shear bond strength of metallic brackets bonded with two different bonding agents under dry conditions and with saliva contamination.

Science.gov (United States)

Khanehmasjedi, Mashallah; Naseri, Mohammad Ali; Khanehmasjedi, Samaneh; Basir, Leila

2017-02-01

This study compared the shear bond strength of metallic brackets bonded with Single Bond and Assure bonding agents under dry and saliva-contamination conditions. Sixty sound premolar teeth were selected, and stainless-steel brackets were bonded on enamel surfaces with Single Bond and Assure bonding agents under dry condition or with saliva contamination. Shear bond strength values of brackets were measured in a universal testing machine. The adhesive remnant index scores were determined after debonding of the brackets under a stereomicroscope. One-way analysis of variance (ANOVA) was used to analyze bond strength. Two-by-two comparisons were made with post hoc Tukey tests (pbrackets to tooth structure were 9.29±8.56 MPa and 21.25±8.93 MPa with the use of Assure resin bonding agent under saliva-contamination and dry conditions, respectively. These values were 10.13±6.69 MPa and 14.09±6.6 MPa, respectively, under the same conditions with the use of Single Bond adhesive. Contamination with saliva resulted in a significant decrease in the bond strength of brackets to tooth structure with the application of Assure adhesive resin (pbrackets to tooth structures. Contamination with saliva significantly decreased the bond strength of Assure bonding agent compared with dry conditions. Copyright © 2016. Published by Elsevier Taiwan LLC.

Biological Activity Predictions and Hydrogen Bonding Analysis in Quinolines

Science.gov (United States)

Gupta, Palvi; Kamni

The paper has been designed to make a comprehensive review of a particular series of organic molecular assembly in the form of compendium. An overview of general description of fifteen quinoline derivatives has been given. The biological activity spectra of quinoline derivatives have been correlated on structure activity relationships base which provides the different Pa (possibility of activity) and Pi (possibility of inactivity) values. Expositions of the role of intermolecular interactions in the identified derivatives have been discussed with the standard distance and angle cut-off criteria criteria as proposed by Desiraju and Steiner (1999) in an International monogram on crystallography. Distance-angle scatter plots for intermolecular interactions are presented for a better understanding of the packing interactions which exist in quinoline derivatives.

29 CFR 2580.412-19 - Term of the bond, discovery period, other bond clauses.

Science.gov (United States)

2010-07-01

... SECURITY ACT OF 1974 TEMPORARY BONDING RULES General Bond Rules § 2580.412-19 Term of the bond, discovery... 29 Labor 9 2010-07-01 2010-07-01 false Term of the bond, discovery period, other bond clauses... new bond must be obtained each year. There is nothing in the Act that prohibits a bond for a term...

Investigation of ball bond integrity for 0.8 mil (20 microns) diameter gold bonding wire on low k die in wire bonding technology

Science.gov (United States)

Kudtarkar, Santosh Anil

Microelectronics technology has been undergoing continuous scaling to accommodate customer driven demand for smaller, faster and cheaper products. This demand has been satisfied by using novel materials, design techniques and processes. This results in challenges for the chip connection technology and also the package technology. The focus of this research endeavor was restricted to wire bond interconnect technology using gold bonding wires. Wire bond technology is often regarded as a simple first level interconnection technique. In reality, however, this is a complex process that requires a thorough understanding of the interactions between the design, material and process variables, and their impact on the reliability of the bond formed during this process. This research endeavor primarily focused on low diameter, 0.8 mil thick (20 mum) diameter gold bonding wire. Within the scope of this research, the integrity of the ball bond formed by 1.0 mil (25 mum) and 0.8 mil (20 mum) diameter wires was compared. This was followed by the evaluation of bonds formed on bond pads having doped SiO2 (low k) as underlying structures. In addition, the effect of varying the percentage of the wire dopant, palladium and bonding process parameters (bonding force, bond time, ultrasonic energy) for 0.8 mil (20 mum) bonding wire was also evaluated. Finally, a degradation empirical model was developed to understand the decrease in the wire strength. This research effort helped to develop a fundamental understanding of the various factors affecting the reliability of a ball bond from a design (low diameter bonding wire), material (low k and bonding wire dopants), and process (wire bonding process parameters) perspective for a first level interconnection technique, namely wire bonding. The significance of this research endeavor was the systematic investigation of the ball bonds formed using 0.8 mil (20 microm) gold bonding wire within the wire bonding arena. This research addressed low k

Electronic structure, hydrogen bonding and spectroscopic profile of a new 1,2,4-triazole-5(4H)-thione derivative: A combined experimental and theoretical (DFT) analysis

Science.gov (United States)

Al-Tamimi, Abdul-Malek S.

2016-09-01

Density functional theory has been implemented to study the electronic structure, molecular properties and vibrational spectra of 3-(adamantan-1-yl)-4-(4-chlorophenyl)-1H-1,2,4-triazole-5(4H)-thione, a novel 1,2,4-triazole-5(4H)-thione derivative. Hydrogen bonded dimer of the title molecule has been studied using B3LYP, M06-2X and X3LYP functionals at 6-311++ G(d,p) level of theory. The intermolecular hydrogen bonding has been studied using NBO analysis of the dimer. Bader's AIM theory was also used to evaluate the strength as well as the hydrogen bonding characteristics. Experimental FT-IR and FT-Raman spectra of the title molecule were related with the spectral data obtained with DFT/B3LYP method. The 1H NMR chemical shifts of the title molecule were calculated by the GIAO method and compared with experimental results. Dipole moment, polarizability (α), first order static hyperpolarizability (β) along with molecular electrostatic potential surface have been calculated. Frequency-dependent first hyperpolarizabilities, β(-2ω;ω,ω) and β(-ω;ω,0) have also been evaluated to study the non-linear optical behavior of the title compound. UV-Vis spectrum of the title molecule was recorded and TD-DFT method has been used to calculate six lowest excited states and the corresponding excitation energies.

Structure phenomena in the bond zone of explosively bonded plates

International Nuclear Information System (INIS)

Livne, Z.

1979-12-01

In the bond areas of couples of explosively bonded plates, there are often zones, generally designated as ''molten pockets'', which have undergone melting and solidification. The object of the present study was to investigate molten pockets, which have a decisive effect on bond quality. The experimental samples for the study were chosen in consideration of the mutual behaviour of the plates constituting the couples, according to their equilibrium phase diagrams. To facilitate the investigation, large plates were bonded under conditions that enabled to to obtain wavy bond zones that included relatively large molten pockets. To clarify the complex nature of molten pockets and their surroundings, a wide variety of methods were employed. It was found that the shape and composition of molten pockets largely depend upon the mechanism of formation of both the bond wave and the molten pockets. It was also found that the composition of molten pockets is not homogeneous, which is manifest in the modification of the composition of the pockets, the solidification morphology, the phases, which have been identified by X-ray diffraction, and the bond strenght and hardness. Moreover, the different solidification morphologies revealed by metallography were found to depend upon the types of plates bonded, the bonding conditions and the location of pockets in the wavy interface. For molten pockets, cooling rates of 10 4 to 10 5 (degC/sec) have been deduced from interdendritic spacing, and found to be in good agreement with calculations after a mathematical model. It seems that the fast cooling rates and the steep temperature gradients are at the origin of the particular solidification phenomena observed in molten pockets

Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization

Energy Technology Data Exchange (ETDEWEB)

Christensen, Anders S., E-mail: andersx@chem.wisc.edu, E-mail: cui@chem.wisc.edu; Cui, Qiang, E-mail: andersx@chem.wisc.edu, E-mail: cui@chem.wisc.edu [Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706 (United States); Elstner, Marcus [Theoretische Chemische Biologie, Universität Karlsruhe, Kaiserstr. 12, 76131 Karlsruhe (Germany)

2015-08-28

Semi-empirical quantum mechanical methods traditionally expand the electron density in a minimal, valence-only electron basis set. The minimal-basis approximation causes molecular polarization to be underestimated, and hence intermolecular interaction energies are also underestimated, especially for intermolecular interactions involving charged species. In this work, the third-order self-consistent charge density functional tight-binding method (DFTB3) is augmented with an auxiliary response density using the chemical-potential equalization (CPE) method and an empirical dispersion correction (D3). The parameters in the CPE and D3 models are fitted to high-level CCSD(T) reference interaction energies for a broad range of chemical species, as well as dipole moments calculated at the DFT level; the impact of including polarizabilities of molecules in the parameterization is also considered. Parameters for the elements H, C, N, O, and S are presented. The Root Mean Square Deviation (RMSD) interaction energy is improved from 6.07 kcal/mol to 1.49 kcal/mol for interactions with one charged species, whereas the RMSD is improved from 5.60 kcal/mol to 1.73 for a set of 9 salt bridges, compared to uncorrected DFTB3. For large water clusters and complexes that are dominated by dispersion interactions, the already satisfactory performance of the DFTB3-D3 model is retained; polarizabilities of neutral molecules are also notably improved. Overall, the CPE extension of DFTB3-D3 provides a more balanced description of different types of non-covalent interactions than Neglect of Diatomic Differential Overlap type of semi-empirical methods (e.g., PM6-D3H4) and PBE-D3 with modest basis sets.

Intermolecular G-quadruplex structure-based fluorescent DNA detection system.

Science.gov (United States)

Zhou, Hui; Wu, Zai-Sheng; Shen, Guo-Li; Yu, Ru-Qin

2013-03-15

Adopting multi-donors to pair with one acceptor could improve the performance of fluorogenic detection probes. However, common dyes (e.g., fluorescein) in close proximity to each other would self-quench the fluorescence, and the fluorescence is difficult to restore. In this contribution, we constructed a novel "multi-donors-to-one acceptor" fluorescent DNA detection system by means of the intermolecular G-quadruplex (IGQ) structure-based fluorescence signal enhancement combined with the hairpin oligonucleotide. The novel IGQ-hairpin system was characterized using the p53 gene as the model target DNA. The proposed system showed an improved assay performance due to the introduction of IGQ-structure into fluorescent signaling probes, which could inhibit the background fluorescence and increase fluorescence restoration amplitude of fluoresceins upon target DNA hybridization. The proof-of-concept scheme is expected to provide new insight into the potential of G-quadruplex structure and promote the application of fluorescent oligonucleotide probes in fundamental research, diagnosis, and treatment of genetic diseases. Copyright © 2012 Elsevier B.V. All rights reserved.

Preparation of a 1:1 cocrystal of genistein with 4,4‧-bipyridine

Science.gov (United States)

Zhang, Yu-Nan; Yin, He-Mei; Zhang, Yu; Zhang, Da-Jun; Su, Xin; Kuang, Hai-Xue

2017-01-01

Based on analysing the relationship between the possible number of intermolecular O-H···N hydrogen bonds and the stoichiometric ratio, a 1:1 C15H10O5·C10H8N2 (genistein-4,4‧-bipyridine) cocrystal has been prepared by solution evaporation and characterized. This work successfully demonstrates that the stoichiometric ratio could be inferred by analysing the possible number of intermolecular hydrogen bonds between flavonoids and amines. The strategy provides a facile route for rational designing cocrystal of flavonoids with amines. Additionally, the title cocrystal shows advantages in terms of solubility and antibacterial properties in comparison to pure genistein.

Crystal structure of dichloridobis(N,N′-dimethylthiourea-κSmercury(II

Directory of Open Access Journals (Sweden)

Muhammad Ashraf Shaheen

2015-09-01

Full Text Available The molecular structure of the title compound, [HgCl2(C3H8N2S2], has point group symmetry 2, with the twofold rotation axis passing through the HgII atom. The latter is coordinated by two Cl atoms and two N,N′-dimethylthiourea (Dmtu ligands through their S atoms, defining a distorted tetrahedral coordination sphere with bond angles in the range 102.47 (4–118.32 (4°. Intra- and intermolecular hydrogen bonds of the type N—H...Cl with S(6 and R22(12 ring motifs are present. The intermolecular contacts make up polymeric chains extending parallel to [101].

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

Science.gov (United States)

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.

Cooperativity in Surface Bonding and Hydrogen Bonding of Water and Hydroxyl at Metal Surfaces

DEFF Research Database (Denmark)

Schiros, T.; Ogasawara, H.; Naslund, L. A.

2010-01-01

of the mixed phase at metal surfaces. The surface bonding can be considered to be similar to accepting a hydrogen bond, and we can thereby apply general cooperativity rules developed for hydrogen-bonded systems. This provides a simple understanding of why water molecules become more strongly bonded...... to the surface upon hydrogen bonding to OH and why the OH surface bonding is instead weakened through hydrogen bonding to water. We extend the application of this simple model to other observed cooperativity effects for pure water adsorption systems and H3O+ on metal surfaces.......We examine the balance of surface bonding and hydrogen bonding in the mixed OH + H2O overlayer on Pt(111), Cu(111), and Cu(110) via density functional theory calculations. We find that there is a cooperativity effect between surface bonding and hydrogen bonding that underlies the stability...

On the critical frontiers of Potts ferromagnets

International Nuclear Information System (INIS)

Magalhaes, A.C.N. de; Tsallis, C.

1981-01-01

A conjecture concerning the critical frontiers of q- state Potts ferromagnets on d- dimensional lattices (d > 1) which generalize a recent one stated for planar lattices is formulated. The present conjecture is verified within satisfactory accuracy (exactly in some cases) for all the lattices or arrays whose critical points are known. Its use leads to the prediction of: a) a considerable amount of new approximate critical points (26 on non-planar regular lattices, some others on Husimi trees and cacti); b) approximate critical frontiers for some 3- dimensional lattices; c) the possibly asymptotically exact critical point on regular lattices in the limit d→infinite for all q>=1; d) the possibly exact critical frontier for the pure Potts model on fully anisotropic Bethe lattices; e) the possibly exact critical frontier for the general quenched random-bond Potts ferromagnet (any P(J)) on isotropic Bethe lattices. (Author) [pt

X-ray diffraction study on the structure of concentrated aqueous solutions involving alanine molecules with different optical activities

International Nuclear Information System (INIS)

Kameda, Yasuo; Okuyama, Aya; Amo, Yuko; Usuki, Takeshi; Kohara, Shinji

2007-01-01

X-ray diffraction measurements on aqueous 2.5 mol% DL-, L-, and D-alanine solutions in D 2 O were carried out at 26±2degC in order to obtain information concerning the difference in the hydrogen-bonded structure between aqueous solutions involving amino acid molecules with different optical activities. The difference function, Δi inter (Q), between intermolecular interference term observed for DL- and L-alanine and between DL- and D-alanine solutions both exhibited a first peak at Q=1.6 A -1 , followed by oscillatory features extending to higher-Q region, implying that there is a difference in the intermolecular structure is present between these solutions. The difference distribution function, Δg inter (r), obtained from the Fourier transform of the Δi inter (Q) between DL- and L-, and between DL- and D-alanine solutions showed an obvious negative peak at r=2.8 A, which was attributed to the nearest neighbor hydrogen-bonded O...O interaction. The least squares fitting analysis of the observed Δi inter (Q) showed that the intermolecular O...O distance and the difference in the coordination number between DL- and L-, and between DL- and D-alanine solutions are 2.76(2) A and -0.18(1), and 2.81(3) A and -0.18(1), respectively. It was concluded that the intermolecular hydrogen-bonded network in aqueous L- and D-alanine solutions is stronger than that in the DL-alanine solution. (author)

Synthesis and Self-Assembly of Donor–Acceptor–Donor Based Oligothiophenes and Their Optoelectronic Properties

DEFF Research Database (Denmark)

Siram, Raja Bhaskar Kanth; Tandy, Kristen; Horecha, Marta

2011-01-01

In this work, the synthesis of an oligothiophene having a donor–acceptor–donor (D–A–D) chromophore with hydrogen bonding groups is described. The D–A–D molecule was demonstrated to self-organize via intermolecular H-bonding between barbituric acid units. Interactions between the oligothiophene su...

Crystal structure of catena-poly[[[triaquastrontium]-di-μ2-glycinato] dibromide

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Palanisamy Revathi

2015-07-01

Full Text Available In the title coordination polymer, {[Sr(C2H5NO22(H2O3]Br2}n, the Sr2+ ion and one of the water molecules are located on twofold rotation axes. The alkaline earth ion is nine-coordinated by three water O atoms and six O atoms of the carboxylate groups of four glycine ligands, two in a chelating mode and two in a monodentate mode. The glycine molecule exists in a zwitterionic form and bridges the cations into chains parallel to [001]. The Br− counter-anions are located between the chains. Intermolecular hydrogen bonds are formed between the amino and carboxylate groups of neighbouring glycine ligands, generating a head-to-tail sequence. Adjacent head-to-tail sequences are further interconnected by intermolecular N—H...Br hydrogen-bonding interactions into sheets parallel to (100. O—H...Br and O—H...O hydrogen bonds involving the coordinating water molecules are also present, consolidating the three-dimensional hydrogen-bonding network.

NMR Study on the Interaction of Trehalose with Lactose and Its Effect on the Hydrogen Bond Interaction in Lactose

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Eric Morssing Vilén

2013-08-01

Full Text Available Trehalose, a well-known stress-protector of biomolecules, has been investigated for its effect on the mobility, hydration and hydrogen bond interaction of lactose using diffusion-ordered NMR spectroscopy and NMR of hydroxy protons. In ternary mixtures of trehalose, lactose and water, the two sugars have the same rate of diffusion. The chemical shifts, temperature coefficients, vicinal coupling constants and ROE of the hydroxy protons in trehalose, lactose and sucrose were measured for the disaccharides alone in water/acetone-d6 solutions as well as in mixtures. The data indicated that addition of trehalose did not change significantly the strength of the hydrogen bond interaction between GlcOH3 and GalO5' in lactose. Small upfield shifts were however measured for all hydroxy protons when the sugar concentration was increased. The chemical shift of the GlcOH3 signal in lactose showed less change, attributed to the spatial proximity to GalO5'. Chemical exchange between hydroxy protons of lactose and trehalose was observed in the ROESY NMR spectra. Similar effects were observed with sucrose indicating no specific effect of trehalose at the concentrations investigated (73 to 763 mg/mL and suggesting that it is the concentration of hydroxy groups more than the type of sugars which is guiding intermolecular interactions.

Bond lengths and bond strengths in compounds of the 5f elements

International Nuclear Information System (INIS)

Zachariasen, W.H.

1975-01-01

The variation of bond length (D) with bond strength (S) in normal valence compounds of 3d, 4d, 5d-4f, and 6d-5f elements can be represented approximately as D(S)=D(0.5) F(S), where D(0.5) is a characteristic constant for a given bond and F(S) an empirical function which is the same for all bonds. A bond strength Ssub(ij)=ssub(ji) is assigned to the bond between atoms i and j such that Σsub(j) Ssub(ij)=vsub(i) and Σsub(i) Ssub(ij)=vsub(j), where vsub(i) and vsub(j) are the normal valences of the two atoms. The function F(S) decreases monotonically with increasing S, and is normalized to unity at S=0.5, so that the constant D(0.5) has the physical meaning of being the bond length adjusted to S=0.5. The method described above was used to interpret and systematize the experimental results on bond lengths in oxides, halides, and oxyhalides of the 5f elements. (U.S.)

Graphene-enhanced intermolecular interaction at interface between copper- and cobalt-phthalocyanines

Energy Technology Data Exchange (ETDEWEB)

Dou, Wei-Dong [Department of Physics, Shaoxing University, Shaoxing 312000 (China); Center of Super-Diamond and Advanced Films (COSDAF) and Department of Physics and Material Science, City University of Hong Kong, Hong Kong (China); Huang, Shu-Ping [Department of Chemistry, University of South Dakota, Vermillion, South Dakota 57069 (United States); Lee, Chun-Sing, E-mail: apcslee@cityu.edu.hk [Center of Super-Diamond and Advanced Films (COSDAF) and Department of Physics and Material Science, City University of Hong Kong, Hong Kong (China)

2015-10-07

Interfacial electronic structures of copper-phthalocyanine (CuPc), cobalt-phthalocyanine (CoPc), and graphene were investigated experimentally by using photoelectron spectroscopy. While the CuPc/graphene interface shows flat band structure and negligible interfacial dipole indicating quite weak molecule-substrate interaction, the CuPc/CoPc/graphene interface shows a large interfacial dipole and obvious energy level bending. Controlled experiments ruled out possible influences from the change in film structure of CuPc and pure π–π interaction between CoPc and CuPc. Analysis based on X-ray photoelectron spectroscopy and density functional theory reveals that the decrease in the work function for the CuPc/CoPc/graphene system is induced by the intermolecular interaction between CuPc and CoPc which is enhanced owning to the peculiar electronic properties at the CoPc-graphene interface.

Competition between weak OH···π and CH··O hydrogen bonds: THz spectroscopy of the C₂H₂—H₂O and C₂H₄—H₂O complexes

DEFF Research Database (Denmark)

Andersen, Jonas; Heimdal, Jimmy; Nelander, B.

2017-01-01

-bonded configuration with the H2O subunit acting as the hydrogen bond donor to the π-cloud of C2H4. A (semi)-empirical value for the change of vibrational zero-point energy of 4.0–4.1 kJ mol−1 is proposed and the combination with quantum chemical calculations at the CCSD(T)-F12b/aug-cc-pVQZ level provides a reliable....... The present findings demonstrate that the relative stability of the weak hydrogen bond motifs is not entirely rooted in differences of electronic energy but also to a large extent by differences in the vibrational zero-point energy contributions arising from the class of large-amplitude intermolecular modes....... estimate of 7.1 ± 0.3 kJ mol−1 for the dissociation energy D0 of the C2H4—H2O complex. In addition, tentative assignments for the two strongly infrared active OH librational modes of the ternary C2H4—HOH—C2H4 complex having H2O as a doubly OH⋯π hydrogen bond donor are proposed at 213.6 and 222.3 cm−1...

Voltage-assisted polymer wafer bonding

International Nuclear Information System (INIS)

Varsanik, J S; Bernstein, J J

2012-01-01

Polymer wafer bonding is a widely used process for fabrication of microfluidic devices. However, best practices for polymer bonds do not achieve sufficient bond strength for many applications. By applying a voltage to a polymer bond in a process called voltage-assisted bonding, bond strength is shown to improve dramatically for two polymers (Cytop™ and poly(methyl methacrylate)). Several experiments were performed to provide a starting point for further exploration of this technique. An optimal voltage range is experimentally observed with a reduction in bonding strength at higher voltages. Additionally, voltage-assisted bonding is shown to reduce void diameter due to bond defects. An electrostatic force model is proposed to explain the improved bond characteristics. This process can be used to improve bond strength for most polymers. (paper)

A molecular dynamics calculation of solid phase of malonic acid

Indian Academy of Sciences (India)

Recent studies suggest that hydrogen bonds, in particular, hydrogen bond chains play an important role in determining the properties of a substance.We report an investigation into the triclinic phase of crystalline malonic acid. One of two intermolecular interaction potentials proposed here is seen to predict the lattice ...

Neural Plasticity and Memory: Is Memory Encoded in Hydrogen Bonding Patterns?

Science.gov (United States)

Amtul, Zareen; Rahman, Atta-Ur

2016-02-01

Current models of memory storage recognize posttranslational modification vital for short-term and mRNA translation for long-lasting information storage. However, at the molecular level things are quite vague. A comprehensive review of the molecular basis of short and long-lasting synaptic plasticity literature leads us to propose that the hydrogen bonding pattern at the molecular level may be a permissive, vital step of memory storage. Therefore, we propose that the pattern of hydrogen bonding network of biomolecules (glycoproteins and/or DNA template, for instance) at the synapse is the critical edifying mechanism essential for short- and long-term memories. A novel aspect of this model is that nonrandom impulsive (or unplanned) synaptic activity functions as a synchronized positive-feedback rehearsal mechanism by revising the configurations of the hydrogen bonding network by tweaking the earlier tailored hydrogen bonds. This process may also maintain the elasticity of the related synapses involved in memory storage, a characteristic needed for such networks to alter intricacy and revise endlessly. The primary purpose of this review is to stimulate the efforts to elaborate the mechanism of neuronal connectivity both at molecular and chemical levels. © The Author(s) 2014.

Computational Study of Pincer Iridium Catalytic Systems: C-H, N-H, and C-C Bond Activation and C-C Coupling Reactions

Science.gov (United States)

Zhou, Tian

Computational chemistry has achieved vast progress in the last decades in the field, which was considered to be only experimental before. DFT (density functional theory) calculations have been proven to be able to be applied to large systems, while maintaining high accuracy. One of the most important achievements of DFT calculations is in exploring the mechanism of bond activation reactions catalyzed by organometallic complexes. In this dissertation, we discuss DFT studies of several catalytic systems explored in the lab of Professor Alan S. Goldman. Headlines in the work are: (1) (R4PCP)Ir alkane dehydrogenation catalysts are highly selective and different from ( R4POCOP)Ir catalysts, predicting different rate-/selectivity-determining steps; (2) The study of the mechanism for double C-H addition/cyclometalation of phenanthrene or biphenyl by (tBu4PCP)Ir(I) and ( iPr4PCP)Ir illustrates that neutral Ir(III) C-H addition products can undergo a very facile second C-H addition, particularly in the case of sterically less-crowded Ir(I) complexes; (3) (iPr4PCP)Ir pure solid phase catalyst is highly effective in producing high yields of alpha-olefin products, since the activation enthalpy for dehydrogenation is higher than that for isomerization via an allyl pathway; higher temperatures favor the dehydrogenation/isomerization ratio; (4) (PCP)Ir(H)2(N2H4) complex follows a hydrogen transfer mechanism to undergo both dehydrogenation to form N 2 and H2, as well as hydrogen transfer followed by N-N bond cleavage to form NH3, N2, and H2; (5) The key for the catalytic effect of solvent molecule in CO insertion reaction for RMn(CO)5 is hydrogen bond assisted interaction. The basicity of the solvent determines the strength of the hydrogen bond interaction during the catalytic path and determines the catalytic power of the solvent; and (6) Dehydrogenative coupling of unactivated C-H bonds (intermolecular vinyl-vinyl, intramolecular vinyl-benzyl) is catalyzed by precursors of the

30 CFR 281.33 - Bonds and bonding requirements.

Science.gov (United States)

2010-07-01

... 30 Mineral Resources 2 2010-07-01 2010-07-01 false Bonds and bonding requirements. 281.33 Section 281.33 Mineral Resources MINERALS MANAGEMENT SERVICE, DEPARTMENT OF THE INTERIOR OFFSHORE LEASING OF MINERALS OTHER THAN OIL, GAS, AND SULPHUR IN THE OUTER CONTINENTAL SHELF Financial Considerations § 281.33...

Are Bonding Agents being Effective on the Shear Bond Strength of Orthodontic Brackets Bonded to the Composite?

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Fahimeh Farzanegan

2014-06-01

Full Text Available Introduction: One of the clinical problems in orthodontics is the bonding of brackets tocomposite restorations. The aim of this study was to evaluate the shear bondstrength of brackets bonded to composite restorations using Excite. Methods:Forty brackets were bonded to composite surfaces, which were embedded inacrylic resin. One of the following four protocols was employed for surfacepreparation of the composite: group 1 37% phosphoric acid for 60 seconds, group2 roughening with a diamond bur plus 37% phosphoric acid for 60 seconds, group3 37% phosphoric acid for 60 seconds and the applying Excite®, group4 roughening with diamond bur plus 37% phosphoric acid for 60 seconds andapplying Excite®. Maxillary central brackets were bonded onto thecomposite prepared samples with Transbond XT. Shear Bond Strength (SBS wasmeasured by a universal testing machine. The ANOVA and Tukey test was utilizedfor data analysis. Results: There was a significant difference betweenthe four groups (P

Mechanism of Intermolecular Electron Transfer in Bionanostructures

Science.gov (United States)

Gruodis, A.; Galikova, N.; Šarka, K.; Saulė, R.; Batiuškaitė, D.; Saulis, G.

Hepatocellular carcinoma (HCC) is one of the most common malignant tumors worldwide. Most patients are inoperable and hepatoma cells are resistant to conventional chemotherapies. Thus, the development of novel therapies for HCC treatment is of paramount importance. Amongst different alimentary factors, vitamin C and vitamin K3 In the present work, it has been shown that the treatment of mouse hepatoma MH-22A cells by vitamin C and vitamin K3 at the ratio of 100:1 greatly enhanced their cytotoxicity. When cells were subjected to vitamin C at 200 μM or to vitamin K3 at 2 μM separately, their viability reduced by only about 10%. However, when vitamins C and K3 were combined at the same concentrations, they killed more than 90% of cells. To elucidate the mechanism of the synergistic cytotoxicity of the C&K3 mixture, theoretical quantum-chemical analysis of the dynamics of intermolecular electron transfer (IET) processes within the complexes containing C (five forms) and K3 (one form) has been carried out. Optimization of the ground state complex geometry has been provided by means of GAUSSIAN03 package. Simulation of the IET has been carried out using NUVOLA package, in the framework of molecular orbitals (MO). The rate of IET has been calculated using Fermi Golden rule. The results of simulations allow us to create the preliminary model of the reaction pathway.

Effects of pair correlation functions on intermolecular nuclear relaxation by translational and rotational diffusion in liquids

International Nuclear Information System (INIS)

Fries, P.

1978-01-01

In order to study the intermolecular relaxation due to magnetic dipolar interactions, we calculate the spectral densities resulting from random translational and rotational motions of spherical molecules carrying off-centre spins. The relative translational motion is treated in the frame-work of a general diffusion equation (the Smoluchowski equation) which takes into account the existence of effective forces between the molecules. This model implies a pair correlation function. i.e. a non unifom relative distribution of the molecules. The analytical calculations are carried out by taking correctly into account the hard sphere boundary conditions for the molecules. Explicit numerical calculations of the spectral densities are performed using finite difference methods and the pair correlation function of Verlet and Weiss obtained by computer experiments. The resulting calculations allow one to interpret the relaxation exhibited by benzene and some of its monohalogen derivatives which has been measured by Jonas et al. at various pressures. The effects of pair correlation and eccentricity contribute to a noticeable enhancement of the spectral densities, especially as the frequency increases. The translational correlation times calculated from the Stokes formula and those deduced from intermolecular relaxation studies are compared. It is shown that in order to distinguish which of the dynamical models is appropriate, measurements must be made as a function of frequency [fr

Insertion reactions into Pd[bond]O and Pd[bond]N bonds: preparation of alkoxycarbonyl, carbonato, carbamato, thiocarbamate, and thioureide complexes of palladium(II).

Science.gov (United States)

Ruiz, José; Martínez, M Teresa; Florenciano, Félix; Rodríguez, Venancio; López, Gregorio; Pérez, José; Chaloner, Penny A; Hitchcock, Peter B

2003-06-02

Mononuclear palladium hydroxo complexes of the type [Pd(N[bond]N)(C(6)F(5))(OH)] [(N[bond]N = 2,2'-bipyridine (bipy), 4,4'-dimethyl-2,2'-bipyridine (Me(2)bipy), 1,10-phenanthroline (phen), or N,N,N',N'-tetramethylethylenediamine (tmeda)] have been prepared by reaction of [Pd(N[bond]N)(C(6)F(5))(acetone)]ClO(4) with KOH in methanol. These hydroxo complexes react, in methanol, with CO (1 atm, room temperature) to yield the corresponding methoxycarbonyl complexes [Pd(N[bond]N)(C(6)F(5))(CO(2)Me)]. Similar alkoxycarbonyl complexes [Pd(N[bond]N)(C(6)F(5))(CO(2)R)] (N[bond]N = bis(3,5-dimethylpyrazol-1-yl)methane); R = Me, Et, or (i)Pr) are obtained when [Pd(N[bond]N)(C(6)F(5))Cl] is treated with KOH in the corresponding alcohol ROH and CO is bubbled through the solution. The reactions of [Pd(N[bond]N)(C(6)F(5))(OH)] (N[bond]N = bipy or Me(2)bipy) with CO(2), in tetrahydrofuran, lead to the formation of the binuclear carbonate complexes [(N[bond]N)(C(6)F(5))Pd(mu-eta(2)-CO(3))Pd(C(6)F(5))(N[bond]N)]. Complexes [Pd(N[bond]N)(C(6)F(5))(OH)] react in alcohol with PhNCS to yield the corresponding N-phenyl-O-alkylthiocarbamate complexes [Pd(N[bond]N)(C(6)F(5))[SC(OR)NPh

The Nature of the Hydrogen Bond Outline of a Comprehensive Hydrogen Bond Theory

CERN Document Server

Gilli, Gastone

2009-01-01

Hydrogen bond (H-bond) effects are known: it makes sea water liquid, joins cellulose microfibrils in trees, shapes DNA into genes and polypeptide chains into wool, hair, muscles or enzymes. Its true nature is less known and we may still wonder why O-H...O bond energies range from less than 1 to more than 30 kcal/mol without apparent reason. This H-bond puzzle is re-examined here from its very beginning and presented as an inclusive compilation of experimental H-bond energies andgeometries.New concepts emerge from this analysis: new classes of systematically strong H-bonds (CAHBs and RAHBs: cha

Lack of evidence for intermolecular epistatic interactions between adiponectin and resistin gene polymorphisms in Malaysian male subjects

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Cia-Hin Lau

2012-01-01

Full Text Available Epistasis (gene-gene interaction is a ubiquitous component of the genetic architecture of complex traits such as susceptibility to common human diseases. Given the strong negative correlation between circulating adiponectin and resistin levels, the potential intermolecular epistatic interactions between ADIPOQ (SNP+45T > G, SNP+276G > T, SNP+639T > C and SNP+1212A > G and RETN (SNP-420C > G and SNP+299G > A gene polymorphisms in the genetic risk underlying type 2 diabetes (T2DM and metabolic syndrome (MS were assessed. The potential mutual influence of the ADIPOQ and RETN genes on their adipokine levels was also examined. The rare homozygous genotype (risk alleles of SNP-420C > G at the RETN locus tended to be co-inherited together with the common homozygous genotypes (protective alleles of SNP+639T > C and SNP+1212A > G at the ADIPOQ locus. Despite the close structural relationship between the ADIPOQ and RETN genes, there was no evidence of an intermolecular epistatic interaction between these genes. There was also no reciprocal effect of the ADIPOQ and RETN genes on their adipokine levels, i.e., ADIPOQ did not affect resistin levels nor did RETN affect adiponectin levels. The possible influence of the ADIPOQ gene on RETN expression warrants further investigation.

Hydrogen bonding in ionic liquids.

Science.gov (United States)

Hunt, Patricia A; Ashworth, Claire R; Matthews, Richard P

2015-03-07

Ionic liquids (IL) and hydrogen bonding (H-bonding) are two diverse fields for which there is a developing recognition of significant overlap. Doubly ionic H-bonds occur when a H-bond forms between a cation and anion, and are a key feature of ILs. Doubly ionic H-bonds represent a wide area of H-bonding which has yet to be fully recognised, characterised or explored. H-bonds in ILs (both protic and aprotic) are bifurcated and chelating, and unlike many molecular liquids a significant variety of distinct H-bonds are formed between different types and numbers of donor and acceptor sites within a given IL. Traditional more neutral H-bonds can also be formed in functionalised ILs, adding a further level of complexity. Ab initio computed parameters; association energies, partial charges, density descriptors as encompassed by the QTAIM methodology (ρBCP), qualitative molecular orbital theory and NBO analysis provide established and robust mechanisms for understanding and interpreting traditional neutral and ionic H-bonds. In this review the applicability and extension of these parameters to describe and quantify the doubly ionic H-bond has been explored. Estimating the H-bonding energy is difficult because at a fundamental level the H-bond and ionic interaction are coupled. The NBO and QTAIM methodologies, unlike the total energy, are local descriptors and therefore can be used to directly compare neutral, ionic and doubly ionic H-bonds. The charged nature of the ions influences the ionic characteristics of the H-bond and vice versa, in addition the close association of the ions leads to enhanced orbital overlap and covalent contributions. The charge on the ions raises the energy of the Ylp and lowers the energy of the X-H σ* NBOs resulting in greater charge transfer, strengthening the H-bond. Using this range of parameters and comparing doubly ionic H-bonds to more traditional neutral and ionic H-bonds it is clear that doubly ionic H-bonds cover the full range of weak

Pair-bonding, romantic love, and evolution: the curious case of Homo sapiens.

Science.gov (United States)

Fletcher, Garth J O; Simpson, Jeffry A; Campbell, Lorne; Overall, Nickola C

2015-01-01

This article evaluates a thesis containing three interconnected propositions. First, romantic love is a "commitment device" for motivating pair-bonding in humans. Second, pair-bonding facilitated the idiosyncratic life history of hominins, helping to provide the massive investment required to rear children. Third, managing long-term pair bonds (along with family relationships) facilitated the evolution of social intelligence and cooperative skills. We evaluate this thesis by integrating evidence from a broad range of scientific disciplines. First, consistent with the claim that romantic love is an evolved commitment device, our review suggests that it is universal; suppresses mate-search mechanisms; has specific behavioral, hormonal, and neuropsychological signatures; and is linked to better health and survival. Second, we consider challenges to this thesis posed by the existence of arranged marriage, polygyny, divorce, and infidelity. Third, we show how the intimate relationship mind seems to be built to regulate and monitor relationships. Fourth, we review comparative evidence concerning links among mating systems, reproductive biology, and brain size. Finally, we discuss evidence regarding the evolutionary timing of shifts to pair-bonding in hominins. We conclude there is interdisciplinary support for the claim that romantic love and pair-bonding, along with alloparenting, played critical roles in the evolution of Homo sapiens. © The Author(s) 2014.

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