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Sample records for intermolecular heck coupling

  1. Intermolecular Photocatalyzed Heck-like Coupling of Unactivated Alkyl Bromides by a Dinuclear Gold Complex.

    PubMed

    Xie, Jin; Li, Jian; Weingand, Vanessa; Rudolph, Matthias; Hashmi, A Stephen K

    2016-08-26

    A practical protocol for a photocatalyzed alkyl-Heck-like reaction of unactivated alkyl bromides and different alkenes promoted by dinuclear gold photoredox catalysis in the presence of an inorganic base is reported. Primary, secondary, and tertiary unactivated alkyl bromides with β-hydrogen can be applied. Esters, aldehydes, ketones, nitriles, alcohols, heterocycles, alkynes, alkenes, ethers, and halogen moieties are all well tolerated. In addition to 1,1-diarylalkenes, silylenolethers and enamides can also be applied, which further increases the synthetic potential of the reaction. The mild reaction conditions, broad substrate scope, and an excellent functional-group tolerance deliver an ideal tool for synthetic chemists that can even be used for challenging late-stage modifications of complex natural products. PMID:27348503

  2. Enantioselective oxidative boron Heck reactions.

    PubMed

    Lee, A-L

    2016-06-28

    This review highlights the use of the oxidative boron Heck reaction in enantioselective Heck-type couplings. The enantioselective oxidative boron Heck reaction overcomes several limitations of the traditional Pd(0)-catalysed Heck coupling and has subsequently allowed for intermolecular couplings of challenging systems such as cyclic enones, acyclic alkenes, and even site selectively on remote alkenes. PMID:26529247

  3. Synthesis of substituted quinolines via allylic amination and intramolecular Heck-coupling.

    PubMed

    Murru, Siva; McGough, Brandon; Srivastava, Radhey S

    2014-12-01

    A new catalytic approach for the synthesis of substituted quinolines via C-N and C-C bond formation using 2-haloaryl hydroxylamines and allylic C-H substrates is described. Fe-catalyzed allylic C-H amination followed by Pd-catalyzed intramolecular Heck-coupling and aerobic dehydrogenation deliver the valuable quinoline and naphthyridine heterocycles in good to excellent overall yields. In this process, Pd(OAc)2 plays a dual role in catalyzing Heck coupling as well as aerobic dehydrogenation of dihydroquinolines. PMID:25247637

  4. Olefins from biomass feedstocks: catalytic ester decarbonylation and tandem Heck-type coupling.

    PubMed

    John, Alex; Hogan, Levi T; Hillmyer, Marc A; Tolman, William B

    2015-02-14

    With the goal of avoiding the need for anhydride additives, the catalytic decarbonylation of p-nitrophenylesters of aliphatic carboxylic acids to their corresponding olefins, including commodity monomers like styrene and acrylates, has been developed. The reaction is catalyzed by palladium complexes in the absence of added ligands and is promoted by alkali/alkaline-earth metal halides. Combination of catalytic decarbonylation and Heck-type coupling with aryl esters in a single pot process demonstrates the viability of employing a carboxylic acid as a "masked olefin" in synthetic processes. PMID:25579879

  5. Reactions of nitroxides 15. Cinnamates bearing a nitroxyl moiety synthesized using a Mizoroki–Heck cross-coupling reaction

    PubMed Central

    Huras, Bogumiła

    2015-01-01

    Summary Cinnamic acid derivatives bearing a nitroxyl moiety (2,2,6,6-tetramethyl-1-oxyl-4-piperidyl 3-E-aryl acrylates) were synthesized in 30–100% yield using a Mizoroki–Heck cross-coupling reaction between 4-acryloyloxy-2,2,6,6-tetramethylpiperidine-1-oxyl and iodobenzene derivatives in the presence of palladium(II) acetate coordinated with a tri(o-tolyl)phosphine ligand immobilized in a polyurea matrix. PMID:26199672

  6. Reactions of nitroxides 15. Cinnamates bearing a nitroxyl moiety synthesized using a Mizoroki-Heck cross-coupling reaction.

    PubMed

    Zakrzewski, Jerzy; Huras, Bogumiła

    2015-01-01

    Cinnamic acid derivatives bearing a nitroxyl moiety (2,2,6,6-tetramethyl-1-oxyl-4-piperidyl 3-E-aryl acrylates) were synthesized in 30-100% yield using a Mizoroki-Heck cross-coupling reaction between 4-acryloyloxy-2,2,6,6-tetramethylpiperidine-1-oxyl and iodobenzene derivatives in the presence of palladium(II) acetate coordinated with a tri(o-tolyl)phosphine ligand immobilized in a polyurea matrix. PMID:26199672

  7. Pd loaded amphiphilic COF as catalyst for multi-fold Heck reactions, C-C couplings and CO oxidation

    PubMed Central

    Mullangi, Dinesh; Nandi, Shyamapada; Shalini, Sorout; Sreedhala, Sheshadri; Vinod, Chathakudath P.; Vaidhyanathan, Ramanathan

    2015-01-01

    COFs represent a class of polymers with designable crystalline structures capable of interacting with active metal nanoparticles to form excellent heterogeneous catalysts. Many valuable ligands/monomers employed in making coordination/organic polymers are prepared via Heck and C-C couplings. Here, we report an amphiphilic triazine COF and the facile single-step loading of Pd0 nanoparticles into it. An 18–20% nano-Pd loading gives highly active composite working in open air at low concentrations (Conc. Pd(0) <0.05 mol%, average TON 1500) catalyzing simultaneous multiple site Heck couplings and C-C couplings using ‘non-boronic acid’ substrates, and exhibits good recyclability with no sign of catalyst leaching. As an oxidation catalyst, it shows 100% conversion of CO to CO2 at 150 °C with no loss of activity with time and between cycles. Both vapor sorptions and contact angle measurements confirm the amphiphilic character of the COF. DFT-TB studies showed the presence of Pd-triazine and Pd-Schiff bond interactions as being favorable. PMID:26057044

  8. Synthesis of tricyclic heterocycles via a tandem aryl alkylation/heck coupling sequence.

    PubMed

    Alberico, Dino; Rudolph, Alena; Lautens, Mark

    2007-02-01

    A norbornene-mediated palladium-catalyzed sequence is described in which two alkyl-aryl bonds and one alkenyl-aryl bond are formed in one pot with use of microwave irradiation. A variety of symmetrical and unsymmetrical oxygen-, nitrogen-, silicon-, and sulfur-containing tricyclic heterocycles were synthesized from a Heck acceptor and an aryl iodide containing two tethered alkyl halides. This approach was further applied to the synthesis of a tricyclic mescaline analogue. PMID:17253794

  9. A versatile approach to flavones via a one-pot Pd(II)-catalyzed dehydrogenation/oxidative boron-Heck coupling sequence of chromanones.

    PubMed

    Lee, Jun; Yu, Jihyun; Son, Seung Hwan; Heo, Jinyuk; Kim, Taelim; An, Ji-Young; Inn, Kyung-Soo; Kim, Nam-Jung

    2016-01-14

    A variety of flavones were expediently synthesized from readily accessible chromanones via a one-pot sequence involving Pd(II)-catalyzed dehydrogenation and oxidative boron-Heck coupling with arylboronic acid pinacol esters. In particular, the use of arylboronic acid pinacol esters was found to significantly improve the yield of the reaction. PMID:26592753

  10. Visualizing coherent intermolecular dipole-dipole coupling in real space.

    PubMed

    Zhang, Yang; Luo, Yang; Zhang, Yao; Yu, Yun-Jie; Kuang, Yan-Min; Zhang, Li; Meng, Qiu-Shi; Luo, Yi; Yang, Jin-Long; Dong, Zhen-Chao; Hou, J G

    2016-03-31

    Many important energy-transfer and optical processes, in both biological and artificial systems, depend crucially on excitonic coupling that spans several chromophores. Such coupling can in principle be described in a straightforward manner by considering the coherent intermolecular dipole-dipole interactions involved. However, in practice, it is challenging to directly observe in real space the coherent dipole coupling and the related exciton delocalizations, owing to the diffraction limit in conventional optics. Here we demonstrate that the highly localized excitations that are produced by electrons tunnelling from the tip of a scanning tunnelling microscope, in conjunction with imaging of the resultant luminescence, can be used to map the spatial distribution of the excitonic coupling in well-defined arrangements of a few zinc-phthalocyanine molecules. The luminescence patterns obtained for excitons in a dimer, which are recorded for different energy states and found to resemble σ and π molecular orbitals, reveal the local optical response of the system and the dependence of the local optical response on the relative orientation and phase of the transition dipoles of the individual molecules in the dimer. We generate an in-line arrangement up to four zinc-phthalocyanine molecules, with a larger total transition dipole, and show that this results in enhanced 'single-molecule' superradiance from the oligomer upon site-selective excitation. These findings demonstrate that our experimental approach provides detailed spatial information about coherent dipole-dipole coupling in molecular systems, which should enable a greater understanding and rational engineering of light-harvesting structures and quantum light sources. PMID:27029277

  11. Visualizing coherent intermolecular dipole–dipole coupling in real space

    NASA Astrophysics Data System (ADS)

    Zhang, Yang; Luo, Yang; Zhang, Yao; Yu, Yun-Jie; Kuang, Yan-Min; Zhang, Li; Meng, Qiu-Shi; Luo, Yi; Yang, Jin-Long; Dong, Zhen-Chao; Hou, J. G.

    2016-03-01

    Many important energy-transfer and optical processes, in both biological and artificial systems, depend crucially on excitonic coupling that spans several chromophores. Such coupling can in principle be described in a straightforward manner by considering the coherent intermolecular dipole–dipole interactions involved. However, in practice, it is challenging to directly observe in real space the coherent dipole coupling and the related exciton delocalizations, owing to the diffraction limit in conventional optics. Here we demonstrate that the highly localized excitations that are produced by electrons tunnelling from the tip of a scanning tunnelling microscope, in conjunction with imaging of the resultant luminescence, can be used to map the spatial distribution of the excitonic coupling in well-defined arrangements of a few zinc-phthalocyanine molecules. The luminescence patterns obtained for excitons in a dimer, which are recorded for different energy states and found to resemble σ and π molecular orbitals, reveal the local optical response of the system and the dependence of the local optical response on the relative orientation and phase of the transition dipoles of the individual molecules in the dimer. We generate an in-line arrangement up to four zinc-phthalocyanine molecules, with a larger total transition dipole, and show that this results in enhanced ‘single-molecule’ superradiance from the oligomer upon site-selective excitation. These findings demonstrate that our experimental approach provides detailed spatial information about coherent dipole–dipole coupling in molecular systems, which should enable a greater understanding and rational engineering of light-harvesting structures and quantum light sources.

  12. Scalable synthesis of oxazolones from propargylic alcohols through multistep palladium(II) catalysis: β-selective oxidative Heck coupling of cyclic sulfonyl enamides and aryl boroxines.

    PubMed

    Alamsetti, Santosh Kumar; Persson, Andreas K Å; Jiang, Tuo; Bäckvall, Jan-E

    2013-12-16

    A whale of a scale: The title oxidative Heck coupling proceeded with unusual β selectivity to generate a variety of branched substituted oxazolones (see scheme; Ts=p-toluenesulfonyl). The three-step synthesis from readily available starting materials with a simple palladium catalyst and inexpensive reagents could be carried out in a single reaction vessel or scaled up for the preparation of large amounts of these amino acid precursors. PMID:24174347

  13. NIR bacteriochlorin chromophores accessed by Heck and Sonogashira cross-coupling reactions on a tetrabromobacteriochlorin derivative.

    PubMed

    de Assis, Francisco F; Ferreira, Marco A B; Brocksom, Timothy J; de Oliveira, Kleber T

    2016-01-28

    The synthesis of a new tetrabromobacteriochlorin BCBr4 is reported having the 3,4-dibromo-1H-pyrrole-2-carbaldehyde (10) as the major precursor. The BCBr4 was successfully employed in Pd cross-coupling reactions with methyl acrylate, phenyl acetylene and 4-ethynylanisole. In all three cases, the desired tetra-coupled products were obtained in good to excellent yields, and present a significant red shift in the UV-Vis bands above 800 nm. DFT and TD-DFT theoretical analyses of the NIR bacteriochlorin chromophores were performed in order to evaluate the effect of β substitution on their electronic structures. PMID:26676846

  14. Probing intermolecular couplings in liquid water with two-dimensional infrared photon echo spectroscopy

    NASA Astrophysics Data System (ADS)

    Paarmann, A.; Hayashi, T.; Mukamel, S.; Miller, R. J. D.

    2008-05-01

    Two-dimensional infrared photon echo and pump probe studies of the OH stretch vibration provide a sensitive probe of the correlations and couplings in the hydrogen bond network of liquid water. The nonlinear response is simulated using numerical integration of the Schrödinger equation with a Hamiltonian constructed to explicitly treat intermolecular coupling and nonadiabatic effects in the highly disordered singly and doubly excited vibrational exciton manifolds. The simulated two-dimensional spectra are in close agreement with our recent experimental results. The high sensitivity of the OH stretch vibration to the bath dynamics is found to arise from intramolecular mixing between states in the two-dimensional anharmonic OH stretch potential. Surprisingly small intermolecular couplings reproduce the experimentally observed intermolecular energy transfer times.

  15. Selenium-ligated palladium(II) complexes as highly active catalysts for carbon-carbon coupling reactions: the Heck reaction.

    PubMed

    Yao, Qingwei; Kinney, Elizabeth P; Zheng, Chong

    2004-08-19

    Three selenium-ligated Pd(II) complexes were readily synthesized and shown to be extremely active catalysts for the Heck reaction of various aryl bromides, including deactivated and heterocyclic ones. The catalytic activity of the selenide-based Pd(II) complexes not only rivals but vastly outperforms that of the corresponding phosphorus and sulfur analogues. Practical advantages of the selenium-based catalysts include their straightforward synthesis and high activity in the absence of any additives as well as the enhanced stability of the selenide ligands toward air oxidation. PMID:15330667

  16. Optical Activity Enhanced by Strong Inter-molecular Coupling in Planar Chiral Metamaterials

    PubMed Central

    Kim, Teun-Teun; Oh, Sang Soon; Park, Hyun-Sung; Zhao, Rongkuo; Kim, Seong-Han; Choi, Wonjune; Min, Bumki; Hess, Ortwin

    2014-01-01

    The polarization of light can be rotated in materials with an absence of molecular or structural mirror symmetry. While this rotating ability is normally rather weak in naturally occurring chiral materials, artificial chiral metamaterials have demonstrated extraordinary rotational ability by engineering intra-molecular couplings. However, while in general, chiral metamaterials can exhibit strong rotatory power at or around resonances, they convert linearly polarized waves into elliptically polarized ones. Here, we demonstrate that strong inter-molecular coupling through a small gap between adjacent chiral metamolecules can lead to a broadband enhanced rotating ability with pure rotation of linearly polarized electromagnetic waves. Strong inter-molecular coupling leads to nearly identical behaviour in magnitude, but engenders substantial difference in phase between transmitted left and right-handed waves. PMID:25209452

  17. Design and Synthesis of Antitumor Heck-Coupled Sclareol Analogues: Modulation of BH3 Family Members by SS-12 in Autophagy and Apoptotic Cell Death.

    PubMed

    Shakeel-u-Rehman; Rah, Bilal; Lone, Shabir H; Rasool, Reyaz Ur; Farooq, Saleem; Nayak, Debasis; Chikan, Naveed Anjum; Chakraborty, Souneek; Behl, Akanksha; Mondhe, Dilip Manikaro; Goswami, Anindya; Bhat, Khursheed Ahmad

    2015-04-23

    Sclareol, a promising anticancer labdane diterpene, was isolated from Salvia sclarea. Keeping the basic stereochemistry-rich framework of the molecule intact, a method for the synthesis of novel sclareol analogues was designed using palladium(II)-catalyzed oxidative Heck coupling reaction in order to study their structure-activity relationship. Both sclareol and its derivatives showed an interesting cytotoxicity profile, with 15-(4-fluorophenyl)sclareol (SS-12) as the most potent analogue, having IC50 = 0.082 μM against PC-3 cells. It was found that SS-12 commonly interacts with Bcl-2 and Beclin 1 BH3 domain proteins and enhances autophagic flux by modulating autophagy-related proteins. Moreover, inhibition of autophagy by autophagy inhibitors protected against SS-12-induced apoptosis. Finally, SS-12 effectively suppressed tumor growth in vivo in Ehrlich's ascitic and solid Sarcoma-180 mouse models. PMID:25825934

  18. Intermolecular electronic coupling in organic molecular thin films measured by temperature modulation spectroscopy

    SciTech Connect

    Yadav, Abhishek; Jin, Y; Chan, P. K. L.; Shtein, Max; Pipe, Kevin P.

    2010-01-01

    Temperature modulation spectroscopy is used to obtain the temperature dependences of oscillator strength, exciton transition energy, and line width for a copper phthalocyanine thin film. With increasing temperature, the oscillator strength exhibits a pronounced decrease for charge transfer (CT) excitons, making this technique suitable for differentiating exciton types. From the measured magnitude and temperature dependence of the CT oscillator strength, we obtain estimates for the intermolecular electronic coupling and its exponential decay coefficient.

  19. Density Analysis of Intra- and Intermolecular Vibronic Couplings toward Bath Engineering for Singlet Fission.

    PubMed

    Ito, Soichi; Nagami, Takanori; Nakano, Masayoshi

    2015-12-17

    Vibronic coupling plays a crucial role in singlet fission whereby a singlet exciton splits into two triplet excitons. In order to reveal the physicochemical origin of the vibronic coupling associated with singlet fission as well as to clarify its relationship with chemical structure, we evaluate relevant vibronic couplings from the viewpoint of their spatial contributions described by vibronic coupling density. From the analysis using a model tetracene dimer, a typical singlet fission system, the frequency dependence of vibronic couplings in each electronic state is found to be significantly different from that of another depending on the nature of the electronic structure (intra/intermolecular excitation) and the related vibrational motion. These findings contribute not only to the fundamental understanding of the singlet fission mechanism from the viewpoint of vibronic couplings but also to opening a new path to designing highly efficient singlet fission materials through phonon-bath engineering. PMID:26673196

  20. Property (RD) for Hecke Pairs

    NASA Astrophysics Data System (ADS)

    Shirbisheh, Vahid

    2012-06-01

    As the first step towards developing noncommutative geometry over Hecke C ∗-algebras, we study property (RD) (Rapid Decay) for Hecke pairs. When the subgroup H in a Hecke pair ( G, H) is finite, we show that the Hecke pair ( G, H) has (RD) if and only if G has (RD). This provides us with a family of examples of Hecke pairs with property (RD). We also adapt Paul Jolissant's works in Jolissaint (J K-Theory 2:723-735, 1989; Trans Amer Math Soc 317(1):167-196, 1990) to the setting of Hecke C ∗-algebras and show that when a Hecke pair ( G, H) has property (RD), the algebra of rapidly decreasing functions on the set of double cosets is closed under holomorphic functional calculus of the associated (reduced) Hecke C ∗-algebra. Hence they have the same K 0-groups.

  1. Green synthesis of Pd/CuO nanoparticles by Theobroma cacao L. seeds extract and their catalytic performance for the reduction of 4-nitrophenol and phosphine-free Heck coupling reaction under aerobic conditions.

    PubMed

    Nasrollahzadeh, Mahmoud; Sajadi, S Mohammad; Rostami-Vartooni, Akbar; Bagherzadeh, Mojtaba

    2015-06-15

    We report the green synthesis of palladium/CuO nanoparticles (Pd/CuO NPs) using Theobroma cacao L. seeds extract and their catalytic activity for the reduction of 4-nitrophenol and Heck coupling reaction under aerobic conditions. The catalyst was characterized using the powder XRD, TEM, EDS, UV-vis and FT-IR. This method has the advantages of high yields, elimination of surfactant, ligand and homogeneous catalysts, simple methodology and easy work up. The catalyst can be recovered from the reaction mixture and reused several times without any significant loss of catalytic activity. PMID:25721860

  2. Functionalized β-cyclodextrin as supramolecular ligand and their Pd(OAc)2 complex: highly efficient and reusable catalyst for Mizoroki-Heck cross-coupling reactions in aqueous medium.

    PubMed

    Dindulkar, Someshwar D; Jeong, Daham; Kim, Hwanhee; Jung, Seunho

    2016-07-22

    A novel class of water soluble palladium complexes with recognition abilities based on functionalized β-cyclodextrin has been synthesized. The complex demonstrated high catalytic activity and a supramolecular platform for phosphine-free Mizoroki-Heck cross-coupling reactions in water. The efficient arylation of alkenes was carried out using different iodo- and bromo-arenes with good to excellent yields (up to 96%). The advantages, like recyclability of catalysts, operational simplicity and accessibility in aqueous medium, make this protocol eco-friendly. PMID:27208891

  3. Cross-dehydrogenative coupling for the intermolecular C–O bond formation

    PubMed Central

    Krylov, Igor B; Vil’, Vera A

    2015-01-01

    Summary The present review summarizes primary publications on the cross-dehydrogenative C–O coupling, with special emphasis on the studies published after 2000. The starting compound, which donates a carbon atom for the formation of a new C–O bond, is called the CH-reagent or the C-reagent, and the compound, an oxygen atom of which is involved in the new bond, is called the OH-reagent or the O-reagent. Alcohols and carboxylic acids are most commonly used as O-reagents; hydroxylamine derivatives, hydroperoxides, and sulfonic acids are employed less often. The cross-dehydrogenative C–O coupling reactions are carried out using different C-reagents, such as compounds containing directing functional groups (amide, heteroaromatic, oxime, and so on) and compounds with activated C–H bonds (aldehydes, alcohols, ketones, ethers, amines, amides, compounds containing the benzyl, allyl, or propargyl moiety). An analysis of the published data showed that the principles at the basis of a particular cross-dehydrogenative C–O coupling reaction are dictated mainly by the nature of the C-reagent. Hence, in the present review the data are classified according to the structures of C-reagents, and, in the second place, according to the type of oxidative systems. Besides the typical cross-dehydrogenative coupling reactions of CH- and OH-reagents, closely related C–H activation processes involving intermolecular C–O bond formation are discussed: acyloxylation reactions with ArI(O2CR)2 reagents and generation of O-reagents in situ from C-reagents (methylarenes, aldehydes, etc.). PMID:25670997

  4. Cross-dehydrogenative coupling for the intermolecular C-O bond formation.

    PubMed

    Krylov, Igor B; Vil', Vera A; Terent'ev, Alexander O

    2015-01-01

    The present review summarizes primary publications on the cross-dehydrogenative C-O coupling, with special emphasis on the studies published after 2000. The starting compound, which donates a carbon atom for the formation of a new C-O bond, is called the CH-reagent or the C-reagent, and the compound, an oxygen atom of which is involved in the new bond, is called the OH-reagent or the O-reagent. Alcohols and carboxylic acids are most commonly used as O-reagents; hydroxylamine derivatives, hydroperoxides, and sulfonic acids are employed less often. The cross-dehydrogenative C-O coupling reactions are carried out using different C-reagents, such as compounds containing directing functional groups (amide, heteroaromatic, oxime, and so on) and compounds with activated C-H bonds (aldehydes, alcohols, ketones, ethers, amines, amides, compounds containing the benzyl, allyl, or propargyl moiety). An analysis of the published data showed that the principles at the basis of a particular cross-dehydrogenative C-O coupling reaction are dictated mainly by the nature of the C-reagent. Hence, in the present review the data are classified according to the structures of C-reagents, and, in the second place, according to the type of oxidative systems. Besides the typical cross-dehydrogenative coupling reactions of CH- and OH-reagents, closely related C-H activation processes involving intermolecular C-O bond formation are discussed: acyloxylation reactions with ArI(O2CR)2 reagents and generation of O-reagents in situ from C-reagents (methylarenes, aldehydes, etc.). PMID:25670997

  5. Similarity-transformed perturbation theory on top of truncated local coupled cluster solutions: Theory and applications to intermolecular interactions

    SciTech Connect

    Azar, Richard Julian Head-Gordon, Martin

    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.

  6. Magnetically Separable Fe3O4@DOPA-Pd: A Heterogeneous Catalyst for Aqueous Heck Reaction

    EPA Science Inventory

    Magnetically separable Fe3O4@DOPA-Pd catalyst has been synthesized via anchoring of palladium over dopamine-coated magnetite via non-covalent interaction and the catalyst is utilized for expeditious Heck coupling in aqueous media.

  7. Effect of a weak magnetic field on the Mizoroki-Heck coupling reaction in the presence of wicker-like palladium-poly(N-vinylpyrrolidone)-iron nanocatalyst

    NASA Astrophysics Data System (ADS)

    Rafiee, Ezzat; Joshaghani, Mohammad; Abadi, Parvaneh Ghaderi-Shekhi

    2016-06-01

    The wicker-like Pd-PVP-Fe (palladium-poly(N-vinylpyrrolidone)-iron) was synthesized by the external magnetic field (EMF). The Pd-based catalyst with nano and the face-centered cubic (fcc) structure was obtained at room temperature without using any additive. The resulting composite was characterized. The results show that EMF has a great influence on morphology, particle size, and crystalline structure of the Pd-PVP-Fe composite. The resulting composite (Pd-PVP-Fe), was found to be an effective catalyst for the Mizoroki-Heck reaction while is exposed to EMF with the intensity at 486 μT. The reused catalyst for at least five repeating cycles, shows excellent activity.

  8. Vibrational nano-spectroscopic imaging correlating structure with intermolecular coupling and dynamics

    PubMed Central

    Pollard, Benjamin; Muller, Eric A.; Hinrichs, Karsten; Raschke, Markus B.

    2014-01-01

    Molecular self-assembly, the function of biomembranes and the performance of organic solar cells rely on nanoscale molecular interactions. Understanding and control of such materials have been impeded by difficulties in imaging their properties with the desired nanometre spatial resolution, attomolar sensitivity and intermolecular spectroscopic specificity. Here we implement vibrational scattering-scanning near-field optical microscopy with high spectral precision to investigate the structure–function relationship in nano-phase separated block copolymers. A vibrational resonance is used as a sensitive reporter of the local chemical environment and we image, with few nanometre spatial resolution and 0.2 cm−1 spectral precision, solvatochromic Stark shifts and line broadening correlated with molecular-scale morphologies. We discriminate local variations in electric fields between nano-domains with quantitative agreement with dielectric continuum models. This ability to directly resolve nanoscale morphology and associated intermolecular interactions can form a basis for the systematic control of functionality in multicomponent soft matter systems. PMID:24721995

  9. Glycosaminoglycan and DNA Binding Induced Intra- and Intermolecular Exciton Coupling of the bis-4-Aminoquinoline Surfen.

    PubMed

    Zsila, Ferenc

    2015-09-01

    Despite the diverse biological activities of the glycosaminoglycan (GAG) antagonist surfen, the molecular details of its interaction with biomacromolecules remain poorly understood. Therefore, heparin and DNA binding properties of surfen were studied by circular dichroism (CD) and UV absorption spectroscopy methods. High-affinity (Ka  ~ 10(7)  M(-1)) association of surfen to the chiral heparin chain gives rise to a characteristic biphasic CD pattern due to the conformational twist of the aminoquinoline moieties around the central urea bridge. At higher drug loading, intermolecular stacking of surfen molecules alters the induced CD profile and also provokes strong UV hypochromism. In contrast to the right-handed heparin template, binding of surfen to the left-helicity chondroitin sulfate chains produces inverted CD pattern. Large UV hypochromism as well as polyphasic induced ellipticity bands indicate that surfen intercalates between the base pairs of calf-thymus DNA. Extensive CD spectroscopic changes observed at higher drug binding ratios refer to cooperative binding interactions between the intercalated drug molecules. The inherent conformational flexibility of surfen demonstrated here for the first time is important in its binding to distinct macromolecular targets and should be considered for rational drug design of novel GAG antagonists. PMID:26096963

  10. Cobalt-catalyzed intermolecular C(sp(2))-O cross-coupling.

    PubMed

    Kundu, Debasish; Tripathy, Manisha; Maity, Pintu; Ranu, Brindaban C

    2015-06-01

    Cobalt(II)-catalyzed C(sp(2) )O cross-coupling between aryl/heteroaryl alcohols and vinyl/aryl halides in the presence of Cu(I) has been achieved under ligand-free conditions. In this reaction, copper plays a significant role in transmetalation rather than being directly involved in the CO coupling. This unique Co/Cu-dual catalyst system provides an easy access to a library of aryl-vinyl, heteroaryl-styryl, aryl-aryl, and heteroaryl-heteroaryl ethers in the absence of any ligand or additive. PMID:25926040

  11. Computational IR spectroscopy of water: OH stretch frequencies, transition dipoles, and intermolecular vibrational coupling constants

    NASA Astrophysics Data System (ADS)

    Choi, Jun-Ho; Cho, Minhaeng

    2013-05-01

    The Hessian matrix reconstruction method initially developed to extract the basis mode frequencies, vibrational coupling constants, and transition dipoles of the delocalized amide I, II, and III vibrations of polypeptides and proteins from quantum chemistry calculation results is used to obtain those properties of delocalized O-H stretch modes in liquid water. Considering the water symmetric and asymmetric O-H stretch modes as basis modes, we here develop theoretical models relating vibrational frequencies, transition dipoles, and coupling constants of basis modes to local water configuration and solvent electric potential. Molecular dynamics simulation was performed to generate an ensemble of water configurations that was in turn used to construct vibrational Hamiltonian matrices. Obtaining the eigenvalues and eigenvectors of the matrices and using the time-averaging approximation method, which was developed by the Skinner group, to calculating the vibrational spectra of coupled oscillator systems, we could numerically simulate the O-H stretch IR spectrum of liquid water. The asymmetric line shape and weak shoulder bands were quantitatively reproduced by the present computational procedure based on vibrational exciton model, where the polarization effects on basis mode transition dipoles and inter-mode coupling constants were found to be crucial in quantitatively simulating the vibrational spectra of hydrogen-bond networking liquid water.

  12. Intermolecular (119)Sn,(31)P Through-Space Spin-Spin Coupling in a Solid Bivalent Tin Phosphido Complex.

    PubMed

    Arras, Janet; Eichele, Klaus; Maryasin, Boris; Schubert, Hartmut; Ochsenfeld, Christian; Wesemann, Lars

    2016-05-01

    A bivalent tin complex [Sn(NP)2] (NP = [(2-Me2NC6H4)P(C6H5)](-)) was prepared and characterized by X-ray diffraction and solution and solid-state nuclear magnetic resonance (NMR) spectroscopy. In agreement with the X-ray structures of two polymorphs of the molecule, (31)P and (119)Sn CP/MAS NMR spectra revealed one crystallographic phosphorus and tin site with through-bond (1)J((117/119)Sn,(31)P) and through-space (TS)J((117/119)Sn,(31)P) spin-spin couplings. Density functional theory (DFT) calculations of the NMR parameters confirm the experimental data. The observation of through-space (TS)J((117/119)Sn,(31)P) couplings was unexpected, as the distances of the phosphorus atoms of one molecule and the tin atom of the neighboring molecule (>4.6 Å) are outside the sum of the van der Waals radii of the atoms P and Sn (4.32 Å). The intermolecular Sn···P separations are clearly too large for bonding interactions, as supported by a natural bond orbital (NBO) analysis. PMID:27071033

  13. Catalysis in the Service of Green Chemistry: Nobel Prize-Winning Palladium-Catalysed Cross-Couplings, Run in Water at Room Temperature: Heck, Suzuki-Miyaura and Negishi reactions carried out in the absence of organic solvents, enabled by micellar catalysis.

    PubMed

    Lipshutz, Bruce H; Taft, Benjamin R; Abela, Alexander R; Ghorai, Subir; Krasovskiy, Arkady; Duplais, Christophe

    2012-04-01

    Palladium-catalysed cross-couplings, in particular Heck, Suzuki-Miyaura and Negishi reactions developed over three decades ago, are routinely carried out in organic solvents. However, alternative media are currently of considerable interest given an increasing emphasis on making organic processes 'greener'; for example, by minimising organic waste in the form of organic solvents. Water is the obvious leading candidate in this regard. Hence, this review focuses on the application of micellar catalysis, in which a 'designer' surfactant enables these award-winning coupling reactions to be run in water at room temperature. PMID:23555153

  14. The origins of intra- and inter-molecular vibrational couplings: A case study of H2O-Ar on full and reduced-dimensional potential energy surface

    NASA Astrophysics Data System (ADS)

    Hou, Dan; Ma, Yong-Tao; Zhang, Xiao-Long; Li, Hui

    2016-01-01

    The origin and strength of intra- and inter-molecular vibrational coupling is difficult to probe by direct experimental observations. However, explicitly including or not including some specific intramolecular vibrational modes to study intermolecular interaction provides a precise theoretical way to examine the effects of anharmonic coupling between modes. In this work, a full-dimension intra- and inter-molecular ab initio potential energy surface (PES) for H2O-Ar, which explicitly incorporates interdependence on the intramolecular (Q1, Q2, Q3) normal-mode coordinates of the H2O monomer, has been calculated. In addition, four analytic vibrational-quantum-state-specific PESs are obtained by least-squares fitting vibrationally averaged interaction energies for the (v1, v2, v3) = (0, 0, 0), (0, 0, 1), (1, 0, 0), (0, 1, 0) states of H2O to the three-dimensional Morse/long-range potential function. Each vibrationally averaged PES fitted to 442 points has root-mean-square (rms) deviation smaller than 0.15 cm-1, and required only 58 parameters. With the 3D PESs of H2O-Ar dimer system, we employed the combined radial discrete variable representation/angular finite basis representation method and Lanczos algorithm to calculate rovibrational energy levels. This showed that the resulting vibrationally averaged PESs provide good representations of the experimental infrared data, with rms discrepancies smaller than 0.02 cm-1 for all three rotational branches of the asymmetric stretch fundamental transitions. The infrared band origin shifts associated with three fundamental bands of H2O in H2O-Ar complex are predicted for the first time and are found to be in good agreement with the (extrapolated) experimental values. Upon introduction of additional intramolecular degrees of freedom into the intermolecular potential energy surface, there is clear spectroscopic evidence of intra- and intermolecular vibrational couplings.

  15. Intermolecular Transposition of Is10 Causes Coupled Homologous Recombination at the Transposition Site

    PubMed Central

    Eichenbaum, Z.; Livneh, Z.

    1995-01-01

    Interplasmid and chromosome to plasmid transposition of IS10 were studied by assaying inactivation of the phage 434 cI gene, carried on a low copy number plasmid. This was detected by the activity of the tet gene expressed from the phage 434 P(R) promoter. Each interplasmid transposition resulted in the fusion of the donor and acceptor plasmids into cointegrate structure, with a 9-bp duplication of the target DNA at the insertion site. Cointegrate formation was abolished in δrecA strains, although simple insertions of IS10 were observed. This suggests a two-stage mechanism involving IS10 conservative transposition, followed by homologous recombination between the donor and the acceptor. Two plasmids carrying inactive IS10 sequences were fused to cointegrates at a 100-fold lower frequency, suggesting that homologous recombination is coupled to and stimulated by the transposition event. Each IS10 transposition from the chromosome to the acceptor plasmid involved replicon fusion, providing a mechanism for IS10-mediated integration of extrachromosomal elements into the chromosome. This was accompanied by the formation of an additional copy of IS10 in the chromosome. Thus, like replicative transposition, conservative transposition of IS10 is accompanied by cointegrate formation and results in duplication of the IS10. PMID:7672587

  16. Branched Arylalkenes from Cinnamates: Selectivity Inversion in Heck Reactions by Carboxylates as Deciduous Directing Groups.

    PubMed

    Tang, Jie; Hackenberger, Dagmar; Goossen, Lukas J

    2016-09-01

    A decarboxylative Mizoroki-Heck coupling of aryl halides with cinnamic acids has been developed in which the carboxylate group directs the arylation into its β-position before being tracelessly removed through protodecarboxylation. In the presence of a copper/palladium catalyst, both electron-rich and electron-deficient aryl bromides and chlorides bearing numerous functionalities were successfully coupled with broadly available cinnamates, with selective formation of 1,1-disubstituted alkenes. This reaction concept, in which the carboxylate acts as a deciduous directing group, ideally complements traditional 1,2-selective Heck reactions of styrenes. PMID:27485163

  17. The origins of intra- and inter-molecular vibrational couplings: A case study of H2O-Ar on full and reduced-dimensional potential energy surface.

    PubMed

    Hou, Dan; Ma, Yong-Tao; Zhang, Xiao-Long; Li, Hui

    2016-01-01

    The origin and strength of intra- and inter-molecular vibrational coupling is difficult to probe by direct experimental observations. However, explicitly including or not including some specific intramolecular vibrational modes to study intermolecular interaction provides a precise theoretical way to examine the effects of anharmonic coupling between modes. In this work, a full-dimension intra- and inter-molecular ab initio potential energy surface (PES) for H2O-Ar, which explicitly incorporates interdependence on the intramolecular (Q1,  Q2,  Q3) normal-mode coordinates of the H2O monomer, has been calculated. In addition, four analytic vibrational-quantum-state-specific PESs are obtained by least-squares fitting vibrationally averaged interaction energies for the (v1,  v2,  v3) =  (0,  0,  0), (0,  0,  1), (1,  0,  0), (0,  1,  0) states of H2O to the three-dimensional Morse/long-range potential function. Each vibrationally averaged PES fitted to 442 points has root-mean-square (rms) deviation smaller than 0.15 cm(-1), and required only 58 parameters. With the 3D PESs of H2O-Ar dimer system, we employed the combined radial discrete variable representation/angular finite basis representation method and Lanczos algorithm to calculate rovibrational energy levels. This showed that the resulting vibrationally averaged PESs provide good representations of the experimental infrared data, with rms discrepancies smaller than 0.02 cm(-1) for all three rotational branches of the asymmetric stretch fundamental transitions. The infrared band origin shifts associated with three fundamental bands of H2O in H2O-Ar complex are predicted for the first time and are found to be in good agreement with the (extrapolated) experimental values. Upon introduction of additional intramolecular degrees of freedom into the intermolecular potential energy surface, there is clear spectroscopic evidence of intra- and intermolecular vibrational couplings. PMID:26747800

  18. An energy decomposition analysis for intermolecular interactions from an absolutely localized molecular orbital reference at the coupled-cluster singles and doubles level

    SciTech Connect

    Azar, R. Julian; Head-Gordon, Martin

    2012-01-14

    We propose a wave function-based method for the decomposition of intermolecular interaction energies into chemically-intuitive components, isolating both mean-field- and explicit correlation-level contributions. We begin by solving the locally-projected self-consistent field for molecular interactions equations for a molecular complex, obtaining an intramolecularly polarized reference of self-consistently optimized, absolutely-localized molecular orbitals (ALMOs), determined with the constraint that each fragment MO be composed only of atomic basis functions belonging to its own fragment. As explicit inter-electronic correlation is integral to an accurate description of weak forces underlying intermolecular interaction potentials, namely, coordinated fluctuations in weakly interacting electronic densities, we add dynamical correlation to the ALMO polarized reference at the coupled-cluster singles and doubles level, accounting for explicit dispersion and charge-transfer effects, which map naturally onto the cluster operator. We demonstrate the stability of energy components with basis set extension, follow the hydrogen bond-breaking coordinate in the C{sub s}-symmetry water dimer, decompose the interaction energies of dispersion-bound rare gas dimers and other van der Waals complexes, and examine charge transfer-dominated donor-acceptor interactions in borane adducts. We compare our results with high-level calculations and experiment when possible.

  19. H2 and (H2)2 molecules with an ab initio optimization of wave functions in correlated state: electron-proton couplings and intermolecular microscopic parameters

    NASA Astrophysics Data System (ADS)

    Kądzielawa, Andrzej P.; Bielas, Agata; Acquarone, Marcello; Biborski, Andrzej; Maśka, Maciej M.; Spałek, Józef

    2014-12-01

    The hydrogen molecules H2 and {{≤ft( {{H}2} \\right)}2} are analyzed with electronic correlations taken into account between the 1s electrons in an exact manner. The optimal single-particle Slater orbitals are evaluated in the correlated state of H2 by combining their variational determination with the diagonalization of the full Hamiltonian in the second-quantization language. All electron-ion coupling constants are determined explicitly and their relative importance is discussed. Sizable zero-point motion amplitude and the corresponding energy are then evaluated by taking into account the anharmonic contributions up to the ninth order in the relative displacement of the ions from their static equilibrium value. The applicability of the model to solid molecular hydrogen is briefly analyzed by calculating intermolecular microscopic parameters for the 2× {{H}2} rectangular configuration, as well its ground state energy.

  20. Intra- and Intermolecular Nickel-Catalyzed Reductive Cross-Electrophile Coupling Reactions of Benzylic Esters with Aryl Halides.

    PubMed

    Konev, Mikhail O; Hanna, Luke E; Jarvo, Elizabeth R

    2016-06-01

    Nickel-catalyzed cross-electrophile coupling reactions of benzylic esters and aryl halides have been developed. Both inter- and intramolecular variants proceed under mild reaction conditions. A range of heterocycles and functional groups are tolerated under the reaction conditions. Additionally, the first example of a stereospecific cross-electrophile coupling of a secondary benzylic ester is described. PMID:27099968

  1. Driving Forces for Covalent Assembly of Porphyrins by Selective C-H Bond Activation and Intermolecular Coupling on a Copper Surface.

    PubMed

    Floris, Andrea; Haq, Sam; In't Veld, Mendel; Amabilino, David B; Raval, Rasmita; Kantorovich, Lev

    2016-05-11

    Recent synthesis of covalent organic assemblies at surfaces has opened the promise of producing robust nanostructures for functional interfaces. To uncover how this new chemistry works at surfaces and understand the underlying mechanisms that control bond-breaking and bond-making processes at specific positions of the participating molecules, we study here the coupling reaction of tetra(mesityl)porphyrin molecules, which creates covalently connected networks on the Cu(110) surface by utilizing the 4-methyl groups as unique connection points. Using scanning tunneling microscopy (STM), state-of-the-art density functional theory (DFT), and Nudged Elastic Band (NEB) calculations, we show that the unique directionality of the covalent bonding is found to stem from a chain of highly selective C-H activation and dehydrogenation processes, followed by specific intermolecular C-C coupling reactions that are facilitated by the surface, by steric constraints, and by anisotropic molecular diffusion. These insights provide the first steps toward developing synthetic rules for complex two-dimensional covalent organic chemistry that can be enacted directly at a surface to deliver specific macromolecular structures designed for specific functions. PMID:27097295

  2. Intermolecular reductive coupling of esters with benzophenones by low-valent titanium: synthesis of diarylmethyl ketones revisited.

    PubMed

    Kise, Naoki; Sakurai, Toshihiko

    2015-04-01

    The reductive coupling of aliphatic esters with benzophenones by Zn-TiCl4 in THF gave two- and four-electron reduced products, diaryl(hydroxy)methyl ketones, and diarylmethyl ketones selectively by controlling the reaction conditions. In the reaction of aromatic esters with benzophenones, diarylmethyl ketones were obtained as the sole products. N-(Alkoxycarbonyl)-(S)-α-amino acid methyl esters gave optically active diphenylmethyl ketones by reduction with benzophenone. The obtained diphenylmethyl ketones were transformed to 4,5-cis-disubstituted oxazolidin-2-ones stereoselectively. PMID:25748528

  3. Control of the intermolecular coupling of dibromotetracene on Cu(110) by the sequential activation of C-Br and C-H bonds.

    PubMed

    Ferrighi, Lara; Píš, Igor; Nguyen, Thanh Hai; Cattelan, Mattia; Nappini, Silvia; Basagni, Andrea; Parravicini, Matteo; Papagni, Antonio; Sedona, Francesco; Magnano, Elena; Bondino, Federica; Di Valentin, Cristiana; Agnoli, Stefano

    2015-04-01

    Dibromotetracene molecules are deposited on the Cu(110) surface at room temperature. The complex evolution of this system has been monitored at different temperatures (i.e., 298, 523, 673, and 723 K) by means of a variety of complementary techniques that range from STM and temperature-programmed desorption (TPD) to high-resolution X-ray spectroscopy (XPS) and near-edge X-ray absorption fine structure spectroscopy (NEXAFS). State-of-the-art density-functional calculations were used to determine the chemical processes that take place on the surface. After deposition at room temperature, the organic molecules are transformed into organometallic monomers through debromination and carbon-radical binding to copper adatoms. Organometallic dimers, trimers, or small oligomers, which present copper-bridged molecules, are formed by increasing the temperature. Surprisingly, further heating to 673 K causes the formation of elongated chains along the Cu(110) close-packed rows as a consequence of radical-site migration to the thermodynamically more stable molecule heads. Finally, massive dehydrogenation occurs at the highest temperature followed by ring condensation to nanographenic patches. This study is a paradigmatic example of how intermolecular coupling can be modulated by the stepwise control of a simple parameter, such as temperature, through a sequence of domino reactions. PMID:25711882

  4. Copper-Catalyzed Oxidative Heck Reactions between Alkyltrifluoroborates and Vinylarenes

    PubMed Central

    Liwosz, Timothy W.; Chemler, Sherry R.

    2013-01-01

    We report herein that potassium alkyltrifluoroborates can be utilized in oxidative Heck-type reactions with vinyl arenes. The reaction is catalyzed by a Cu(OTf)2/1,10-phenanthroline with MnO2 as the stoichiometric oxidant. In addition to the alkyl Heck, amination, esterification and dimerization reactions of alkyltrifluoroborates are demonstrated under analogous reaction conditions. Evidence for an alkyl radical intermediate is presented. PMID:23734764

  5. Hecke-Clifford Algebras and Spin Hecke Algebras IV: Odd Double Affine Type

    NASA Astrophysics Data System (ADS)

    Khongsap, Ta; Wang, Weiqiang

    2009-01-01

    We introduce an odd double affine Hecke algebra (DaHa) generated by a classical Weyl group W and two skew-polynomial subalgebras of anticommuting generators. This algebra is shown to be Morita equivalent to another new DaHa which are generated by W and two polynomial-Clifford subalgebras. There is yet a third algebra containing a spin Weyl group algebra which is Morita (super)equivalent to the above two algebras. We establish the PBW properties and construct Verma-type representations via Dunkl operators for these algebras.

  6. Synthesis of Pd-N-heterocyclic carbene Pd-catalyst and its application in MW-assisted Heck and Suzuki reaction

    EPA Science Inventory

    The first Pd-N-heterocyclic carbene (NHC) complex in the form of organic silica is prepared using sol-gel method and its application in Heck and Suzuki reactions are demonstrated. These C-C coupling reactions proceeded efficiently under the influence of microwave irradiation, wit...

  7. The Differential Graded Odd NilHecke Algebra

    NASA Astrophysics Data System (ADS)

    Ellis, Alexander P.; Qi, You

    2016-05-01

    We equip the odd nilHecke algebra and its associated thick calculus category with diagrammatically local differentials. The resulting differential graded Grothendieck groups are isomorphic to two different forms of the positive part of quantum {{{sl}_2}} at a fourth root of unity.

  8. Kinetic Study of the Heck Reaction: An Interdisciplinary Experiment

    ERIC Educational Resources Information Center

    Gozzi, Christel; Bouzidi, Naoual

    2008-01-01

    The aim of this experiment is to study and calculate the kinetic constant of a Heck reaction: the arylation of but-3-en-2-ol by iodobenzene catalyzed by palladium acetate in presence of triethylamine in DMF. The reaction leads to a mixture of two ketones. Students use GC analysis to quantify reagents and products of reaction. They control the…

  9. Matsuda-Heck reaction with arenediazonium tosylates in water.

    PubMed

    Kutonova, Ksenia V; Trusova, Marina E; Stankevich, Andrey V; Postnikov, Pavel S; Filimonov, Victor D

    2015-01-01

    An environmentally friendly Matsuda-Heck reaction with arenediazonium tosylates has been developed for the first time. A range of alkenes was arylated in good to quantitative yields in water. The reaction is significantly accelerated when carried out under microwave heating. The arylation of haloalkylacrylates with diazonium salts has been implemented for the first time. PMID:25977709

  10. Hecke Groups, Dessins d'Enfants and the Archimedean Solids

    NASA Astrophysics Data System (ADS)

    He, Yang-Hui; Read, James

    2015-12-01

    Grothendieck's dessins d'enfants arise with ever-increasing frequency in many areas of 21st century mathematical physics. In this paper, we review the connections between dessins and the theory of Hecke groups. Focussing on the restricted class of highly symmetric dessins corresponding to the so-called Archimedean solids, we apply this theory in order to provide a means of computing representatives of the associated conjugacy classes of Hecke subgroups in each case. The aim of this paper is to demonstrate that dessins arising in mathematical physics can point to new and hitherto unexpected directions for further research. In addition, given the particular ubiquity of many of the dessins corresponding to the Archimedean solids, the hope is that the computational results of this paper will prove useful in the further study of these objects in mathematical physics contexts.

  11. Diverse N-Heterocyclic Ring Systems via Aza-Heck Cyclizations of N-(Pentafluorobenzoyloxy)sulfonamides.

    PubMed

    Hazelden, Ian R; Ma, Xiaofeng; Langer, Thomas; Bower, John F

    2016-09-01

    Aza-Heck cyclizations initiated by oxidative addition of Pd(0) -catalysts into the N-O bond of N-(pentafluoro-benzoyloxy)sulfonamides are described. These studies, which encompass only the second class of aza-Heck reaction developed to date, provide direct access to diverse N-heterocyclic ring systems. PMID:27460965

  12. Intermolecular perturbation theory

    NASA Astrophysics Data System (ADS)

    Hayes, I. C.; Hurst, G. J. B.; Stone, A. J.

    The new intermolecular perturbation theory described in the preceding papers is applied to some van der Waals molecules. HeBe is used as a test case, and the perturbation method converges well at interatomic distances down to about 4 a0, giving results in excellent agreement with supermolecule calculations. ArHF and ArHCl have been studied using large basis sets, and the results agree well with experimental data. The ArHX configuration is favoured over the ArXH configuration mainly because of larger polarization and charge-transfer contributions. In NeH2 the equilibrium geometry is determined by a delicate balance between opposing effects; with a double-zeta-polarization basis the correct configuration is predicted.

  13. Desensitization of metastable intermolecular composites

    DOEpatents

    Busse, James R.; Dye, Robert C.; Foley, Timothy J.; Higa, Kelvin T.; Jorgensen, Betty S.; Sanders, Victor E.; Son, Steven F.

    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.

  14. Aqueous Oxidative Heck Reaction as a Protein-Labeling Strategy

    PubMed Central

    Ourailidou, Maria Eleni; van der Meer, Jan-Ytzen; Baas, Bert-Jan; Jeronimus-Stratingh, Margot; Gottumukkala, Aditya L; Poelarends, Gerrit J; Minnaard, Adriaan J; Dekker, Frank J

    2014-01-01

    An increasing number of chemical reactions are being employed for bio-orthogonal ligation of detection labels to protein-bound functional groups. Several of these strategies, however, are limited in their application to pure proteins and are ineffective in complex biological samples such as cell lysates. Here we present the palladium-catalyzed oxidative Heck reaction as a new and robust bio-orthogonal strategy for linking functionalized arylboronic acids to protein-bound alkenes in high yields and with excellent chemoselectivity even in the presence of complex protein mixtures from living cells. Advantageously, this reaction proceeds under aerobic conditions, whereas most other metal-catalyzed reactions require inert atmosphere. PMID:24376051

  15. Bounds for Hecke eigenforms and their allied L-functions

    NASA Astrophysics Data System (ADS)

    Zhang, Qing

    We consider Hecke eigenforms and their allied L-functions from three aspects in this thesis. First we generalize the Iwaniec's spectral large sieve estimates of Maass cusp form to the local version for all congruence groups of level q. Our approach is based on an inequality for a general bilinear form involving Kloosterman sums and Bessel functions. The exceptional eigenvalues emerge in the course of the proof. In the second part, we extend Luo's result to prove a general optimal bound for L4-norms of the dihedral Maass forms associated to Hecke's grossencharacters of a fixed real quadratic field. Given a fixed quadratic field with discriminant D, we remove the condition that the narrow class number of K is 1. The key ingredients are Watson and Ichino's formula and the local spectral large sieve inequality established in the first part. Finally we obtain a long equation intended to establish an upper bound for the second moment of symmetric square L-functions. Petersson trace formula plays an important role and we study thoroughly an analogue of Estermann series using Hurwitz zeta function and establish its meromorphic extension and functional equation. This work provides a useful approach to the further study for the central value of the symmetric square L-functions.

  16. Stereospecific Synthesis of Tri- and Tetrasubstituted α-Fluoroacrylates by Mizoroki-Heck Reaction.

    PubMed

    Rousée, Kevin; Bouillon, Jean-Philippe; Couve-Bonnaire, Samuel; Pannecoucke, Xavier

    2016-02-01

    Ligand-free, efficient, palladium-catalyzed Mizoroki-Heck reaction between methyl α-fluoroacrylate and arene or hetarene iodides is reported for the first time. The reaction is stereospecific and provides fair to quantitative yields of fluoroalkenes. The Mizoroki-Heck reaction starting from more hindered and usually reluctant trisubstituted acrylate, to access tetrasubstituted fluoroalkenes, is also reported. Finally, the use of a three-step synthesis sequence, including Mizoroki-Heck reaction, allows the synthesis of fluorinated analogues of therapeutic agents with high yield. PMID:26809942

  17. Single-molecule magnets ``without'' intermolecular interactions

    NASA Astrophysics Data System (ADS)

    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).

  18. All exactly solvable U(1)-invariant quantum spin 1 chains from Hecke algebra

    SciTech Connect

    Alcarez, F.C. ); Koberle, R. ); Lima-Santos, A. )

    1992-12-10

    In this paper, the authors obtain all exactly integrable spin 1 quantum chains, which are U(1) invariant and satisfy the Hecke algebra. The authors present various generalizations for arbitrary spin S and discuss their solution via Bethe ansatz methods.

  19. On a generalization of a theorem of Erich Hecke.

    PubMed

    Lee, R; Weintraub, S H

    1982-12-01

    E. Hecke initiated the application of representation theory to the study of cusp forms. He showed that, for p a prime congruent to 3 mod 4, the difference of multiplicities of certain conjugate representations of SL(F(p)) on cusp forms of degree 1, level p, and weight >/=2 is given by the class number h(-p) of the field Q( radical-p). We apply the holomorphic Lefschetz theorem to actions on the Igusa compactification of the Siegel moduli space of degree 2 to compute the values of characters of the representations of Sp(4)(F(p)) on certain spaces of cusp forms of degree 2 and level p at parabolic elements of this group. Our results imply that here too, the difference in multiplicities of conjugate representations of Sp(4)(F(p)) is a multiple of h(-p). PMID:16593264

  20. Selection and identity rules for subductions of type A quantum Iwahori-Hecke algebras

    SciTech Connect

    Chilla, Vincenzo

    2007-11-15

    This paper is concerned with the subduction problem of type A quantum Iwahori-Hecke algebras CH(S{sub f},q{sup 2}) with a real deformation parameter q, i.e., the problem of decomposing irreducible representations of such algebras as direct sum of irreducible representations of the subalgebras CH(S{sub f{sub 1}},q{sup 2})xCH(S{sub f{sub 2}},q{sup 2}), with f{sub 1}+f{sub 2}=f. After giving a suitable combinatorial description for the subduction issue, we provide a selection rule, based on the Richardson-Littlewood criterion, which allows to determine the vanishing coupling coefficients between standard basis vectors for such representations, and we also present an equivariance condition for the subduction coefficients. Such results extend those ones corresponding to the subduction problem in symmetric group algebras CS{sub f}{down_arrow}CS{sub f{sub 1}}xCS{sub f{sub 2}} which are obtained by q approaching the value of 1.

  1. Direct observation of intermolecular interactions mediated by hydrogen bonding

    NASA Astrophysics Data System (ADS)

    De Marco, Luigi; Thämer, Martin; Reppert, Mike; Tokmakoff, Andrei

    2014-07-01

    Although intermolecular interactions are ubiquitous in physicochemical phenomena, their dynamics have proven difficult to observe directly, and most experiments rely on indirect measurements. Using broadband two-dimensional infrared spectroscopy (2DIR), we have measured the influence of hydrogen bonding on the intermolecular vibrational coupling between dimerized N-methylacetamide molecules. In addition to strong intramolecular coupling between N-H and C=O oscillators, cross-peaks in the broadband 2DIR spectrum appearing upon dimerization reveal strong intermolecular coupling that changes the character of the vibrations. In addition, dimerization changes the effects of intramolecular coupling, resulting in Fermi resonances between high and low-frequency modes. These results illustrate how hydrogen bonding influences the interplay of inter- and intramolecular vibrations, giving rise to correlated nuclear motions and significant changes in the vibrational structure of the amide group. These observations have direct impact on modeling and interpreting the IR spectra of proteins. In addition, they illustrate a general approach to direct molecular characterization of intermolecular interactions.

  2. Direct observation of intermolecular interactions mediated by hydrogen bonding

    SciTech Connect

    De Marco, Luigi; Reppert, Mike; Thämer, Martin; Tokmakoff, Andrei

    2014-07-21

    Although intermolecular interactions are ubiquitous in physicochemical phenomena, their dynamics have proven difficult to observe directly, and most experiments rely on indirect measurements. Using broadband two-dimensional infrared spectroscopy (2DIR), we have measured the influence of hydrogen bonding on the intermolecular vibrational coupling between dimerized N-methylacetamide molecules. In addition to strong intramolecular coupling between N–H and C=O oscillators, cross-peaks in the broadband 2DIR spectrum appearing upon dimerization reveal strong intermolecular coupling that changes the character of the vibrations. In addition, dimerization changes the effects of intramolecular coupling, resulting in Fermi resonances between high and low-frequency modes. These results illustrate how hydrogen bonding influences the interplay of inter- and intramolecular vibrations, giving rise to correlated nuclear motions and significant changes in the vibrational structure of the amide group. These observations have direct impact on modeling and interpreting the IR spectra of proteins. In addition, they illustrate a general approach to direct molecular characterization of intermolecular interactions.

  3. Quantitative Quantum Ergodicity and the Nodal Domains of Hecke-Maass Cusp Forms

    NASA Astrophysics Data System (ADS)

    Jung, Junehyuk

    2016-07-01

    We prove a quantitative statement of the quantum ergodicity for Hecke-Maass cusp forms on the modular surface. As an application of our result, along a density 1 subsequence of even Hecke-Maass cusp forms, we obtain a sharp lower bound for the L 2-norm of the restriction to a fixed compact geodesic segment of {η={iy : y > 0} subset H}. We also obtain an upper bound of {O_ɛ (t_φ^{3/8+ɛ} )} for the {L^∞} norm along a density 1 subsequence of Hecke-Maass cusp forms; for such forms, this is an improvement over the upper bound of {O_ɛ(t_φ^{5/12+ɛ} )} given by Iwaniec and Sarnak. In a recent work of Ghosh, Reznikov, and Sarnak, the authors proved for all even Hecke-Maass forms that the number of nodal domains, which intersect a geodesic segment of {η} , grows faster than {t_φ^{1/12-ɛ}} for any {ɛ > 0} , under the assumption that the Lindelöf Hypothesis is true and that the geodesic segment is long enough. Upon removing a density zero subset of even Hecke-Maass forms, we prove without making any assumptions that the number of nodal domains grows faster than {t_φ^{1/8-ɛ}} for any {ɛ > 0}.

  4. Characterization of human papillomavirus type 13 from focal epithelial hyperplasia Heck lesions.

    PubMed Central

    Pfister, H; Hettich, I; Runne, U; Gissmann, L; Chilf, G N

    1983-01-01

    Focal epithelial hyperplasia Heck lesions of a Turkish patient were shown to contain papillomavirus-specific DNA, which was molecularly cloned into bacteriophage lambda. It proved to be related to human papillomavirus (HPV) type 6 DNA and HPV type 11 DNA. Reassociation kinetics revealed a cross-hybridization of 4 and 3%, respectively. There was no cross-reactivity with HPV type 1, 2, 3, 4, 5, 8, or 10. This papillomavirus type will be referred to as HPV type 13. The DNA was characterized by cleavage with several restriction enzymes, and the cleavage sites were physically mapped. Papules from two additional cases of Morbus Heck contained HPV type 13 DNA as shown by Southern blot hybridization and by the characteristic cleavage patterns. This may indicate that HPV type 13 is more frequently associated with focal epithelial hyperplasia Heck than are other HPV types. Images PMID:6312071

  5. The local Hurwitz constant and Diophantine approximation on Hecke groups

    NASA Astrophysics Data System (ADS)

    Lehner, J.

    1990-10-01

    Define the Hecke group by {G_q} = < {( {begin{array}{*{20}{c}} 1 & {{⪉mb... ...{array}{*{20}{c}} 0 & { - 1} 1 & 0 } )} rangle , {λ _q} = 2cos π /q , q = 3,4, ldots . We call {G_q}(∞ ) the {G_q} -rationals, and R - {G_q}(∞ ) the {G_q} -irrationals. The problem we treat here is the approximation of {G_q} -irrationals by {G_q} -rationals. Let M(α ) be the upper bound of numbers c for which \\vertα - k/m\\vert < 1/c{m^2} for all {G_q} -irrationals and infinitely many k/m in {G_q}(∞ ) . Set h_q'= {inf _α }M(α ) . We call h_q' the Hurwitz constant for {G_q} . It is known that h_q'= 2 , q even; h_q'= 2{(1 + {(1 - {λ _q}/2)^2})^{1/2}} , q odd. In this paper we prove this result by using {λ _q} -continued fractions, as developed previously by D. Rosen. Write α - frac{{{P_{n - 1}}}}{{{Q_{n - 1}}}} = frac{{{{( - 1)}^{... ...}{\\varepsilon _2} \\cdots {\\varepsilon _n}}}{{{m_{n - 1}}(α )Q_{n - 1}^2}}, where {\\varepsilon _i} = ± 1 and {P_i}/{Q_i} are the convergents of the {λ _q} -continued fraction for α . Then M(α ) = {overline {lim } _n}{m_n}(α ) . We call {m_n}(α ) the local Hurwitz constant. In the final section we prove some results on the local Hurwitz constant. For example (Theorem 4), it is shown that if q is odd and {\\varepsilon _{n + 1}} = {\\varepsilon _{n + 2}} = + 1 , then {m_i} ≥ {(λ _q^2 + 4)^{1/2}} > h_q' for at least one of i = n - 1,n,n + 1 .

  6. Ligand-free Heck reaction: Pd(OAc)2 as an active catalyst revisited.

    PubMed

    Yao, Qingwei; Kinney, Elizabeth P; Yang, Zhi

    2003-09-19

    Palladium acetate was shown to be an extremely active catalyst for the Heck reaction of aryl bromides. Both the base and the solvent were found to have a fundamental influence on the efficiency of the reaction, with K(3)PO(4) and N,N-dimethylacetamide being the optimal base and solvent, respectively. PMID:12968913

  7. Theoretical study on the effect of solvent and intermolecular fluctuations in proton transfer reactions: General theory

    SciTech Connect

    Kato, Nobuhiko; Ida, Tomonori; Endo, Kazunaka

    2004-04-30

    We present a theory of proton transfer reactions which incorporate the modulation of the proton's potential surface by intermolecular vibrations and the effect of coupling to solvent degree of freedom. The proton tunnels between states corresponding to it being localized in the wells of a double minimum potential. The resulting tunnel splitting depends on the intermolecular separation. The solvent response to the proton's charge is modeled as that of a continuous distribution of harmonic oscillators and the intermolecular stretching mode is also damped because of the interaction with solvent degree of freedom. The transition rate is given by the Fermi Gorlden Rule expression.

  8. A simple and facile Heck-type arylation of alkenes with diaryliodonium salts using magnetically recoverable Pd-catalyst

    EPA Science Inventory

    The Heck-type arylation of alkenes was achieved in aqueous polyethylene glycol using a magnetically recoverable heterogenized palladium catalyst employing diaryliodonium salts under ambient conditions. The benign reaction medium and the stability of the catalyst are the salient f...

  9. Desensitization and recovery of metastable intermolecular composites

    DOEpatents

    Busse, James R.; Dye, Robert C.; Foley, Timothy J.; Higa, Kelvin T.; Jorgensen, Betty S.; Sanders, Victor E.; Son, Steven F.

    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.

  10. Determination of Multidimensional Intermolecular Potential Energy Surfaces

    NASA Astrophysics Data System (ADS)

    Cohen, Ronald Carl

    High resolution spectroscopy of the low frequency van der Waals vibrations (also referred to as Vibration -Rotation-Tunneling (VRT) spectroscopy) in weakly bound complexes provides the means to probe intermolecular forces with unprecedented detail and precision. We present an overview of the experimental information on intermolecular forces and intermolecular dynamics which has been obtained by far infrared VRT spectroscopy of 18 complexes. We then turn to a detailed examination of the Ar-H_2O complex, a simple prototype for the study of intermolecular forces. The measurement and analysis of 9 VRT bands is described. These data are first used to obtain a qualitative description of the intermolecular potential energy surface (IPS). A new simple and efficient method for calculating the eigenvalues of the multidimensional intermolecular dynamics on the IPS has been developed. This algorithm (an adaptation of the Collocation Method) was then used in a direct fit to obtain an accurate and detailed description of the intermolecular forces acting within the Ar-H_2O complex.

  11. On boundary fusion and functional relations in the Baxterized affine Hecke algebra

    SciTech Connect

    Babichenko, A.; Regelskis, V.

    2014-04-15

    We construct boundary type operators satisfying fused reflection equation for arbitrary representations of the Baxterized affine Hecke algebra. These operators are analogues of the fused reflection matrices in solvable half-line spin chain models. We show that these operators lead to a family of commuting transfer matrices of Sklyanin type. We derive fusion type functional relations for these operators for two families of representations.

  12. Palladium was supported on superparamagnetic nanoparticles: A magnetically recoverable catalyst for Heck reaction

    SciTech Connect

    Zhang, Fengwei; Niu, Jianrui; Wang, Haibo; Yang, Honglei; Jin, Jun; Liu, Na; Zhang, Yubin; Li, Rong; Ma, Jiantai

    2012-02-15

    Highlights: Black-Right-Pointing-Pointer Palladium-based heterogeneous catalyst was prepared facilely via the co-precipitation method. Black-Right-Pointing-Pointer The particles are nearly spherical in shape with an average size of 20 {+-} 1.0 nm. Black-Right-Pointing-Pointer The developed magnetic catalyst showed high activity for Heck reaction. Black-Right-Pointing-Pointer The catalyst was easily recovered from the reaction mixture with external magnetic field. Black-Right-Pointing-Pointer The catalytic efficiency for Heck reaction remains unaltered even after 6 repeated cycles. -- Abstract: A novel and high-performance palladium-based catalyst for Heck reaction was prepared easily by the co-precipitation method. The catalyst was characterized by transmission electron microscopy (TEM), X-ray powder diffraction (XRD), vibrating sample magnetometry (VSM), X-ray photoelectron spectroscopy (XPS) and atomic absorption spectrophotometry (AAS). The catalyst afforded a fast conversion of the 4-bromonitrobenzene to 4-nitrostilbene at a catalyst loading of 5 mol%, and the efficiency of the catalyst remains unaltered even after 6 repeated cycles. The excellent catalytic performance of the Pd/Fe{sub 3}O{sub 4} catalyst might be attributed to the enhanced synergistic effect between Pd nanoparticles and magnetite.

  13. Synthesis and characterization of mesoporous poly(N-vinyl-2-pyrrolidone) containing palladium nanoparticles as a novel heterogeneous organocatalyst for Heck reaction

    NASA Astrophysics Data System (ADS)

    Kalbasi, Roozbeh Javad; Negahdari, Meysam

    2014-04-01

    Mesoporous poly(N-vinyl-2-pyrrolidone) (MPVP) was prepared through a nanocasting technique based on mesoporous silica KIT-6 as sacrificial templates, and served as an efficient scaffold for supporting Pd nanoparticles. The physical and chemical properties of Pd-MPVP were characterized using FT-IR, XRD, BET, DRS UV-Vis, SEM, TEM and TGA techniques. The application of this novel purely organic heterogeneous catalyst, which combine the advantage of organic polymers and mesoporous materials, was investigated for Csbnd C bond formation through the Heck coupling reaction of aryl iodides, bromides and chlorides with styrene. It was observed that the activity of this catalyst decreased just 5% after nine regeneration processes were performed. This unique result opens new perspectives for application of purely organic mesoporous polymers as structurally defined hydrophobic catalyst in catalytic reactions.

  14. Dendrimer-templated Pd nanoparticles and Pd nanoparticles synthesized by reverse microemulsions as efficient nanocatalysts for the Heck reaction: A comparative study.

    PubMed

    Noh, Ji-Hyang; Meijboom, Reinout

    2014-02-01

    Palladium nanoparticles (NPs) were prepared using a dendrimer-templated method using G4, G5 and G6 PAMAM-OH dendrimers as well as a reverse microemulsion method using the water/dioctyl sulfosuccinate sodium salt (aerosol-OT, AOT) surfactant/isooctane system with water to surfactant ratios (ω0) of 5, 10 and 13. These 6 catalysts were characterized by UV-Vis spectroscopy, TEM, EDX, and XRD. TEM micrographs showed that the average sizes of 2.74-3.32nm with narrower size distribution were achieved by using dendrimer-templated synthetic methods, whereas the reverse microemulsion method resulted in broad size distribution with an average size of 3.87-5.06nm. The influence of various reaction parameters such as base, catalyst dosing, alkene, aryl halide and temperature on the Heck C-C coupling reaction was evaluated. The activation parameters were derived from the reaction rate of each catalyst obtained at various temperatures. A correlation of catalytic activity, enthalpy of activation and particle size is discussed. Particle size changes of each catalyst were investigated after the catalytic reaction. Overall results indicated that dendrimer-templated Pd NP catalysts showed superior activity as compared to the Pd NPs synthesized by reverse microemulsions, with the dendrimer-templated G5-OH(Pd80) showing the best activity. These catalysts were also reusable for 3 cycles, retaining high yield and showing excellent yields under mild conditions. Therefore, the dendrimer-templated Pd NPs are efficient catalyst systems for the ligand-free Heck C-C coupling reaction. PMID:24267330

  15. Metabolic alkene labeling and in vitro detection of histone acylation via the aqueous oxidative Heck reaction

    PubMed Central

    Ourailidou, Maria E.; Dockerty, Paul; Witte, Martin; Poelarends, Gerrit J.; Dekker, Frank J.

    2016-01-01

    The detection of protein lysine acylations remains a challenge due to a lack of specific antibodies for acylations with various chain lengths. This problem can be addressed by metabolic labeling techniques using carboxylates with reactive functionalities. Subsequent chemoselective reactions with a complementary moiety connected to a detection tag enable the visualization and quantification of the protein lysine acylome. In this study, we present EDTA-Pd(II) as a novel catalyst for the oxidative Heck reaction on protein-bound alkenes, which allows employment of fully aqueous reaction conditions. We used this reaction to monitor histone lysine acylation in vitro after metabolic incorporation of olefinic carboxylates as chemical reporters. PMID:25672493

  16. Noncovalent Substrate-Directed Enantioselective Heck Reactions: Synthesis of S- and P-Stereogenic Heterocycles.

    PubMed

    de Azambuja, Francisco; Carmona, Rafaela C; Chorro, Tomaz H D; Heerdt, Gabriel; Correia, Carlos Roque D

    2016-08-01

    S- and P-Stereogenic heterocycles were synthesized by a remarkably simple enantioselective Heck desymmetrization reaction based on the unprecedented noncovalent directing effect of S=O and P=O functionalities. Selected prochiral symmetric substrates were efficiently arylated using the recently disclosed chiral PyraBOx ligand under mild and open-flask reaction conditions. Several five-membered aryl- sulfones, sulfoxides, and phosphine oxides were synthesized in good to excellent yields, in good to high diastereoselectivity, and enantiomeric ratios up to 98:2. Theoretical calculations also support the noncovalent directing effect of the S=O and P=O functionalities during the arylation process. PMID:27273079

  17. Hauser-Heck: Efficient Synthesis of γ-Aryl-β-ketoesters en Route to Substituted Naphthalenes.

    PubMed

    Wagner, Frederic; Harms, Klaus; Koert, Ulrich

    2015-11-20

    γ-Aryl-β-ketoesters can be prepared in one step from aryl bromides and bis(trimethylsilyl) enol ethers using catalytic amounts of Pd(dba)2/t-Bu3P and stoichiometric amounts of Bu3SnF. The wide range of γ-(hetero)aryl-β-ketoesters that can be obtained illustrate the scope and limitations of this novel Hauser-Heck combination. γ-Aryl-β-ketoesters with a 1,3-dioxane acetal in the ortho position can easily be transformed into the hydroxy naphthoate in very good yield. Aqueous formic acid at 65 °C provides optimal conditions for this deprotective aromatization. PMID:26536142

  18. Rhodium(i)-catalysed intermolecular alkyne insertion into (2-pyridylmethylene)cyclobutenes.

    PubMed

    Matsuda, Takanori; Matsumoto, Takeshi

    2016-06-14

    Cyclobutenes with 2-pyridylmethylene groups at the 3 position underwent an intermolecular alkyne insertion reaction in the presence of a rhodium(i) catalyst at 170 °C to afford substituted benzenes. Among the different 2-pyridylmethylene groups examined, 3-methyl-2-pyridyl derivatives showed superior activity and readily coupled with various alkynes, including sterically demanding, heteroaromatic and terminal alkynes. PMID:27193826

  19. Mapping intermolecular bonding in C60

    PubMed Central

    Sundqvist, Bertil

    2014-01-01

    The formation of intermolecular bonds in C60 has been investigated in detail at pressures below 2.2 GPa and up to 750 K. Fullerene samples were heated in a temperature gradient to obtain data on the formation of dimers and low-dimensional polymers along isobars. Intermolecular bonding was analyzed ex situ by Raman scattering, using both intramolecular modes and intermolecular stretching modes. Semi-quantitative reaction maps are given for the formation of dimers and chains. The activation energy for dimer formation decreases by 0.2 meV pm−1 when intermolecular distances decrease and dimer formation is noticeably affected by the rotational state of molecules. Above 400–450 K larger oligomers are formed; below 1.4 GPa most of these are disordered, with small domains of linear chains, but above this the appearance of stretching modes indicates the existence of ordered one-dimensional polymers. At the highest pressures and temperatures two-dimensional polymers are also observed. PMID:25145952

  20. Estimation of intermolecular interactions in polymer networks

    SciTech Connect

    Subrananian, P.R.; Galiatsatos, V.

    1993-12-31

    Strain-birefringence measurements have been used to estimate intermolecular interactions in polymer networks. The intensity of the interaction has been quantified through a theoretical scheme recently proposed by Erman. The results show that these interactions diminish with decreasing molecular weight between cross-links and decreasing cross-link functionality.

  1. An improved intermolecular potential for sulfur hexafluoride

    SciTech Connect

    Aziz, R.A.; Slaman, M.J. ); Taylor, W.L.; Hurly, J.J. Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221 )

    1991-01-15

    Second virial coefficient data and viscosity were used to evaluate effective isotropic intermolecular potential functions proposed in the literature for sulfur hexafluoride. It was found that none of the potentials could predict the properties simultaneously. We have constructed a Morse--Morse--Spline--van der Waals (MMSV) potential which satisfactorily correlates second virial coefficient and viscosity data at the same time.

  2. Use of the Intramolecular Heck Reaction for Forming Congested Quaternary Carbon Stereoenters. Stereocontrolled Total Synthesis of (±)-Gelsemine

    PubMed Central

    Madin, Andrew; O’Donnell, Christopher J.; Oh, Taeboem; Old, David W.; Overman, Larry E.; Sharp, Matthew J.

    2008-01-01

    Intramolecular Heck reactions of α,β-unsaturated 2-haloanilides derived from azatricyclo[4.4.0.02,8]decanone 5 efficiently install the congested spirooxindole functionality of gelsemine. Depending upon the Heck reaction conditions and the nature of the β-substituent, either products having the natural or unnatural configuration of the spirooxindole group are formed predominantly. Efforts to elaborate the hydropyran ring of gelsemine from the endo-oriented nitrile substituent of pentacyclic Heck product 18 were unsuccessful. Important steps in the ultimately successful route to (±)-gelsemine (1) are: (a) intramolecular Heck reaction of tricyclic β-methoxy α,β-unsaturated 2-iodoanilide 68 in the presence of silver phosphate to form pentacyclic product 69 having the unnatural configuration of the spirooxindole fragment, (b) formation of hexacyclic aziridine 80 from the reaction of cyanide with intermediate 79 containing an N-methoxycarbonyl-β-bromoethylamine fragment, (c) introduction of C17 by ring-opening of the aziridinium ion derived from aziridine 80, and (d) base-promoted skeletal rearrangement of pentacyclic equatorial alcohol 82 to form the oxacyclic ring and invert the spirooxindole functional group to provide hexacyclic gelsemine precursor 83. PMID:16366557

  3. COUPLING

    DOEpatents

    Hawke, B.C.

    1963-02-26

    This patent relates to a releasable coupling connecting a control rod to a control rod drive. This remotely operable coupling mechanism can connect two elements which are laterally and angviarly misaligned, and provides a means for sensing the locked condition of the elements. The coupling utilizes a spherical bayonet joint which is locked against rotation by a ball detent lock. (AEC)

  4. Intermolecular electrostatic energies using density fitting

    PubMed Central

    Cisneros, G. Andrés; Piquemal, Jean-Philip; Darden, Thomas A.

    2009-01-01

    A method is presented to calculate the electron-electron and nuclear-electron intermolecular Coulomb interaction energy between two molecules by separately fitting the unperturbed molecular electron density of each monomer. This method is based on the variational Coulomb fitting method which relies on the expansion of the ab initio molecular electron density in site-centered auxiliary basis sets. By expanding the electron density of each monomer in this way the integral expressions for the intermolecular electrostatic calculations are simplified, lowering the operation count as well as the memory usage. Furthermore, this method allows the calculation of intermolecular Coulomb interactions with any level of theory from which a one-electron density matrix can be obtained. Our implementation is initially tested by calculating molecular properties with the density fitting method using three different auxiliary basis sets and comparing them to results obtained from ab initio calculations. These properties include dipoles for a series of molecules, as well as the molecular electrostatic potential and electric field for water. Subsequently, the intermolecular electrostatic energy is tested by calculating ten stationary points on the water dimer potential-energy surface. Results are presented for electron densities obtained at four different levels of theory using two different basis sets, fitted with three auxiliary basis sets. Additionally, a one-dimensional electrostatic energy surface scan is performed for four different systems (H2O dimer, Mg2+–H2O, Cu+–H2O, and n-methyl-formamide dimer). Our results show a very good agreement with ab initio calculations for all properties as well as interaction energies. PMID:16095348

  5. An isotopic mass effect on the intermolecular potential

    NASA Astrophysics Data System (ADS)

    Herman, Michael F.; Currier, Robert P.; Clegg, Samuel M.

    2015-10-01

    The impact of isotopic variation on the electronic energy and intermolecular potentials is often suppressed when calculating isotopologue thermodynamics. Intramolecular potential energy surfaces for distinct isotopologues are in fact equivalent under the Born-Oppenheimer approximation, which is sometimes used to imply that the intermolecular interactions are independent of isotopic mass. In this communication, the intermolecular dipole-dipole interaction between hetero-nuclear diatomic molecules is considered. It is shown that the intermolecular potential contains mass-dependent terms even though each nucleus moves on a Born-Oppenheimer surface. The analysis suggests that mass dependent variations in intermolecular potentials should be included in comprehensive descriptions of isotopologue thermodynamics.

  6. Palladium-Catalyzed 6-Endo Selective Alkyl-Heck Reactions: Access to 5-Phenyl-1,2,3,6-tetrahydropyridine Derivatives.

    PubMed

    Dong, Xu; Han, Ying; Yan, Fachao; Liu, Qing; Wang, Ping; Chen, Kexun; Li, Yueyun; Zhao, Zengdian; Dong, Yunhui; Liu, Hui

    2016-08-01

    A new type of palladium-catalyzed 6-endo-selective alkyl-Heck reaction of unactivated alkyl iodides has been described. This strategy provides efficient access to a variety of 5-phenyl-1,2,3,6-tetrahydropyridine derivatives, which are important structural motifs for bioactive molecules. This process displays a broad substrate scope with excellent 6-endo selectivity. Mechanistic investigations reveal that this alkyl-Heck reaction performs via a hybrid palladium-radical process. PMID:27409716

  7. An assay for intermolecular exchange of alpha crystallin

    NASA Technical Reports Server (NTRS)

    Gopalakrishnan, S.; Takemoto, L.; Spooner, B. S. (Principal Investigator)

    1992-01-01

    An affinity column of alpha crystallin linked to cyanogen bromide-activated Sepharose was developed to study the exchange of alpha subunits. Alpha crystallin bound to the Sepharose-alpha complex was dissociated with 8 mol/l urea, followed by quantitation using high-performance reverse-phase liquid chromatography. The time course of binding at 37 degrees C showed a hyperbolic binding pattern reaching equilibrium between 6-18 hr. Under these conditions, binding of beta and gamma crystallins to the same matrix was less than 10% of the alpha values, as was binding of alpha to glycine-coupled Sepharose. This assay was used to demonstrate changes in the subunit exchange of alpha crystallins present in high molecular weight versus lower molecular weight aggregates of the human lens. These results show that this binding procedure was a specific reproducible assay that might be used to study intermolecular interactions of the alpha crystallins.

  8. Intermolecular shielding from molecular magnetic susceptibility. A new view of intermolecular ring current effects.

    PubMed

    Facelli, Julio C

    2006-03-01

    This paper presents calculations of the NICS (nuclear independent chemical shieldings) in a rectangular grid surrounding the molecules of benzene, naphthalene and coronene. Using the relationship between calculated NICS and the induced magnetic field, the calculated NICS are used to predict intermolecular effects due to molecular magnetic susceptibility or ring current effects. As expected from approximate ring current models, these intermolecular shielding effects are concentrated along the direction perpendicular to the molecular plane and they approach asymptotically to a dipolar functional dependence, i.e. (1-3 cos(2)theta)/r(3)). The deviations from the dipolar functional form require that the calculations of these intermolecular effects be done using a suitable interpolation scheme of the NICS calculated on the grid. The analysis of the NICS tensor components shows that these intermolecular shielding effects should be primarily expected on shielding components of the neighboring molecules nuclei, which are perpendicular to the molecular plane of the aromatic compound generating the induced field. The analysis of the calculated NICS along the series benzene, naphthalene and coronene shows that these intermolecular effects increase monotonically with the number of aromatic rings. PMID:16477673

  9. Chemoselective and Sequential Palladium-Catalyzed Couplings for the Generation of Stilbene Libraries via Immobilized Substrates.

    PubMed

    Traficante, Carla I; Fagundez, Catherine; Serra, Gloria L; Mata, Ernesto G; Delpiccolo, Carina M L

    2016-05-01

    A versatile palladium-catalyzed tandem synthetic sequence to afford E-stilbenes libraries has been developed. Excellent regio- and stereocontrol have been achieved by means of the sequence of Hiyama and Heck cross-couplings. Undesirable homocoupling byproducts were avoided employing immobilized substrates. PMID:27073985

  10. Simulating two-dimensional infrared-Raman and Raman spectroscopies for intermolecular and intramolecular modes of liquid water.

    PubMed

    Ito, Hironobu; Tanimura, Yoshitaka

    2016-02-21

    Full classical molecular dynamics (MD) simulations of two-dimensional (2D) infrared-Raman and 2D Raman spectroscopies of liquid water were carried out to elucidate a mode-mode coupling mechanism using a polarizable water model for intermolecular and intramolecular vibrational spectroscopy (POLI2VS). This model is capable of describing both infrared and Raman spectra. Second-order response functions, which consist of one molecular polarizability and two molecular dipole moments for 2D IR-Raman and three molecular polarizabilities for 2D Raman spectroscopies, were calculated using an equilibrium-non-equilibrium hybrid MD approach. The obtained signals were analyzed using a multi-mode Brownian oscillator (BO) model with nonlinear system-bath interactions representing the intramolecular OH stretching, intramolecular HOH bending, hydrogen bonded (HB)-intermolecular librational motion and HB-intermolecular vibrational (translational) motion of liquid water. This model was applied through use of hierarchal Fokker-Planck equations. The qualitative features of the peak profiles in the 2D spectra obtained from the MD simulations are accurately reproduced with the BO model. This indicates that this model captures the essential features of the intermolecular and intramolecular motion. We elucidate the mechanisms governing the 2D signal profiles involving anharmonic mode-mode coupling, the nonlinearities of the polarizability and dipole moment, and the vibrational dephasing processes of liquid water even in the case that the 2D spectral peaks obtained from the MD simulation overlap or are unclear. The mode coupling peaks caused by electrical anharmonic coupling (EAHC) and mechanical anharmonic coupling (MAHC) are observed in all of the 2D spectra. We find that the strength of the MAHC between the OH-stretching and HB-intermolecular vibrational modes is comparable to that between the OH-stretching and HOH bending modes. Moreover, we find that this OH-stretching and HB-intermolecular

  11. The nil Hecke ring and cohomology of G/P for a Kac-Moody group G

    PubMed Central

    Kostant, Bertram; Kumar, Shrawan

    1986-01-01

    Let G be the group with Borel subgroup B, associated to a Kac-Moody Lie algebra [unk] (with Weyl group W and Cartan subalgebra [unk]). Then H*(G/B) has, among others, four distinguished structures (i) an algebra structure, (ii) a distinguished basis, given by the Schubert cells, (iii) a module for W, and (iv) a module for Hecke-type operators Aw, for w [unk] W. We construct a ring R, which we refer to as the nil Hecke ring, which is very simply and explicitly defined as a functor of W together with the W-module [unk] alone and such that all these four structures on H*(G/B) arise naturally from the ring R. PMID:16593661

  12. The nil Hecke ring and cohomology of G/P for a Kac-Moody group G.

    PubMed

    Kostant, B; Kumar, S

    1986-03-01

    Let G be the group with Borel subgroup B, associated to a Kac-Moody Lie algebra [unk] (with Weyl group W and Cartan subalgebra [unk]). Then H(*)(G/B) has, among others, four distinguished structures (i) an algebra structure, (ii) a distinguished basis, given by the Schubert cells, (iii) a module for W, and (iv) a module for Hecke-type operators A(w), for w [unk] W. We construct a ring R, which we refer to as the nil Hecke ring, which is very simply and explicitly defined as a functor of W together with the W-module [unk] alone and such that all these four structures on H(*)(G/B) arise naturally from the ring R. PMID:16593661

  13. COUPLING

    DOEpatents

    Frisch, E.; Johnson, C.G.

    1962-05-15

    A detachable coupling arrangement is described which provides for varying the length of the handle of a tool used in relatively narrow channels. The arrangement consists of mating the key and keyhole formations in the cooperating handle sections. (AEC)

  14. Maximizing Singlet Fission by Intermolecular Packing.

    PubMed

    Wang, Linjun; Olivier, Yoann; Prezhdo, Oleg V; Beljonne, David

    2014-10-01

    A novel nonadiabatic molecular dynamics scheme is applied to study the singlet fission (SF) process in pentacene dimers as a function of longitudinal and lateral displacements of the molecular backbones. Detailed two-dimensional mappings of both instantaneous and long-term triplet yields are obtained, characterizing the advantageous and unfavorable stacking arrangements, which can be achieved by chemical substitutions to the bare pentacene molecule. We show that the SF rate can be increased by more than an order of magnitude through tuning the intermolecular packing, most notably when going from cofacial to the slipped stacked arrangements encountered in some pentacene derivatives. The simulations indicate that the SF process is driven by thermal electron-phonon fluctuations at ambient and high temperatures, expected in solar cell applications. Although charge-transfer states are key to construct continuous channels for SF, a large charge-transfer character of the photoexcited state is found to be not essential for efficient SF. The reported time domain study mimics directly numerous laser experiments and provides novel guidelines for designing efficient photovoltaic systems exploiting the SF process with optimum intermolecular packing. PMID:26278443

  15. Pd-N-Heterocyclic Carbene (NHC) Organic Silica: Synthesis and Application in Carbon-Carbon Coupling Reactions

    EPA Science Inventory

    The first Pd-N-heterocyclic carbene (NHC) complex in the form of organic silica was prepared using sol-gel method and its application in Heck and Suzuki reaction were demonstrated. These C-C coupling reactions proceeded efficiently under the influence of microwave irradiation, wi...

  16. Palladium(0)/NHC-Catalyzed Reductive Heck Reaction of Enones: A Detailed Mechanistic Study.

    PubMed

    Raoufmoghaddam, Saeed; Mannathan, Subramaniyan; Minnaard, Adriaan J; de Vries, Johannes G; Reek, Joost N H

    2015-12-14

    We have studied the mechanism of the palladium-catalyzed reductive Heck reaction of para-substituted enones with 4-iodoanisole by using N,N-diisopropylethylamine (DIPEA) as the reductant. Kinetic studies and in situ spectroscopic analysis have provided a detailed insight into the reaction. Progress kinetic analysis demonstrated that neither catalyst decomposition nor product inhibition occurred during the catalysis. The reaction is first order in the palladium and aryl iodide, and zero order in the activated alkene, N-heterocyclic carbene (NHC) ligand, and DIPEA. The experiments with deuterated solvent ([D7]DMF) and deuterated base ([D15]Et3N) supported the role of the amine as a reductant in the reaction. The palladium complex [Pd(0)(NHC)(1)] has been identified as the resting state. The kinetic experiments by stopped-flow UV/Vis also revealed that the presence of the second substrate, benzylideneacetone 1, slows down the oxidative addition of 4-iodoanisole through its competing coordination to the palladium center. The kinetic and mechanistic studies indicated that the oxidative addition of the aryl iodide is the rate-determining step. Various scenarios for the oxidative addition step have been analyzed by using DFT calculations (bp86/def2-TZVP) that supported the inhibiting effect of substrate 1 by formation of resting state [Pd(0)(NHC)(1)] species at the cost of further increase in the energy barrier of the oxidative addition step. PMID:26561034

  17. X-ray Intermolecular Structure Factor (XISF): separation of intra- and intermolecular interactions from total X-ray scattering data

    SciTech Connect

    Mou, Q.; Benmore, C. J.; Yarger, J. L.

    2015-06-01

    XISF is a MATLAB program developed to separate intermolecular structure factors from total X-ray scattering structure factors for molecular liquids and amorphous solids. The program is built on a trust-region-reflective optimization routine with the r.m.s. deviations of atoms physically constrained. XISF has been optimized for performance and can separate intermolecular structure factors of complex molecules.

  18. Palladium-catalyzed Heck-type reaction of oximes with allylic alcohols: synthesis of pyridines and azafluorenones.

    PubMed

    Zheng, Meifang; Chen, Pengquan; Wu, Wanqing; Jiang, Huanfeng

    2016-01-01

    We describe herein a palladium-catalyzed Heck-type reaction of O-acetyl ketoximes and allylic alcohols to synthesise pyridines. This protocol allows the robust synthesis of pyridines and azafluorenones in good to excellent yields with tolerance of various functional groups under mild conditions. The reaction is supposed to go through an oxidative addition of oximes to palladium(0) complexes, generating an alkylideneamino-palladium(II) species, which is utilized as a key intermediate to capture the nonbiased alkenes for carbon-carbon bond formation. PMID:26496814

  19. Fluorescence photoactivation by intermolecular proton transfer.

    PubMed

    Swaminathan, Subramani; Petriella, Marco; Deniz, Erhan; Cusido, Janet; Baker, James D; Bossi, Mariano L; Raymo, Françisco M

    2012-10-11

    We designed a strategy to activate fluorescence under the influence of optical stimulations based on the intermolecular transfer of protons. Specifically, the illumination of a 2-nitrobenzyl derivative at an activating wavelength is accompanied by the release of hydrogen bromide. In turn, the photogenerated acid encourages the opening of an oxazine ring embedded within a halochromic compound. This structural transformation extends the conjugation of an adjacent coumarin fluorophore and enables its absorption at an appropriate excitation wavelength. Indeed, this bimolecular system offers the opportunity to activate fluorescence in liquid solutions, within rigid matrixes and inside micellar assemblies, relying on the interplay of activating and exciting beams. Furthermore, this strategy permits the permanent imprinting of fluorescent patterns on polymer films, the monitoring of proton diffusion within such materials in real time on a millisecond time scale, and the acquisition of images with spatial resolution at the nanometer level. Thus, our operating principles for fluorescence activation can eventually lead to the development of valuable photoswitchable probes for imaging applications and versatile mechanisms for the investigation of proton transport. PMID:22994311

  20. Propagation studies of metastable intermolecular composites (MIC).

    SciTech Connect

    Son, S. F.; Busse, J. R.; Asay, B. W.; Peterson, P. D.; Mang, J. T.; Bockmon, B.; Pantoya, M.

    2002-01-01

    Thermite materials are attractive energetic materials because the reactions are highly exothermic, have high energy densities, and high temperatures of combustion. However, the application of thermite materials has been limited because of the relative slow release of energy compared to other energetic materials. Engineered nano-scale composite energetic materials, such as Al/MoO{sub 3}, show promise for additional energetic material applications because they can react very rapidly. The composite material studied in this work consists of tailored, ultra-fine grain (30-200 nm diameter) aluminum particles that dramatically increase energy release rates of these thermite materials. These reactant clusters of fuel and oxidizer particles are in nearly atomic scale proximity to each other but are constrained from reaction until triggered. Despite the growing importance of nano-scale energetic materials, even the most basic combustion characteristics of these materials have not been thoroughly studied. This paper reports initial studies of the ignition and combustion of metastable intermolecular composites (MIC) materials. The goals were lo obtain an improved understanding of flame propagation mechanisms and combustion behaviors associated with nano-structured energetic materials. Information on issues such as reaction rate and behavior as a function of composition (mixture ratio), initial static charge, and particle size are essential and will allow scientists to design applications incorporating the benefits of these compounds. The materials have been characterized, specifically focusing on particle size, shape, distribution and morphology.

  1. Mechanism of Intermolecular Electron Transfer in Bionanostructures

    NASA Astrophysics Data System (ADS)

    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.

  2. Intermolecular domain docking in the hairpin ribozyme

    PubMed Central

    Sumita, Minako; White, Neil A.; Julien, Kristine R.; Hoogstraten, Charles G.

    2013-01-01

    The hairpin ribozyme is a prototype small, self-cleaving RNA motif. It exists naturally as a four-way RNA junction containing two internal loops on adjoining arms. These two loops interact in a cation-driven docking step prior to chemical catalysis to form a tightly integrated structure, with dramatic changes occurring in the conformation of each loop upon docking. We investigate the thermodynamics and kinetics of the docking process using constructs in which loop A and loop B reside on separate molecules. Using a novel CD difference assay to isolate the effects of metal ions linked to domain docking, we find the intermolecular docking process to be driven by sub-millimolar concentrations of the exchange-inert Co(NH3)63+. RNA self-cleavage requires binding of lower-affinity ions with greater apparent cooperativity than the docking process itself, implying that, even in the absence of direct coordination to RNA, metal ions play a catalytic role in hairpin ribozyme function beyond simply driving loop-loop docking. Surface plasmon resonance assays reveal remarkably slow molecular association, given the relatively tight loop-loop interaction. This observation is consistent with a “double conformational capture” model in which only collisions between loop A and loop B molecules that are simultaneously in minor, docking-competent conformations are productive for binding. PMID:23324606

  3. Aqueous microwaves assisted cross-coupling reactions applied to unprotected nucleosides.

    NASA Astrophysics Data System (ADS)

    Len, Christophe; Hervé, Gwénaelle

    2015-02-01

    Nucleoside analogues have attracted much attention due to their potential biological activities. Amongst all synthetic nucleosides, C5-modified pyrimidines and C7- or C8-modified purines have mostly been prepared using palladium cross-coupling reactions and then studied as antitumoral and antiviral agents. Our objective is to focus this review on the Suzuki-Miyaura and on the Heck cross-couplings of nucleosides using microwave irradiations which are an alternative technology compatible with green chemistry and sustainable development.

  4. Advances in metal-catalyzed cross-coupling reactions of halogenated quinazolinones and their quinazoline derivatives.

    PubMed

    Mphahlele, Malose Jack; Maluleka, Marole Maria

    2014-01-01

    Halogenated quinazolinones and quinazolines are versatile synthetic intermediates for the metal-catalyzed carbon-carbon bond formation reactions such as the Kumada, Stille, Negishi, Sonogashira, Suzuki-Miyaura and Heck cross-coupling reactions or carbon-heteroatom bond formation via the Buchwald-Hartwig cross-coupling to yield novel polysubstituted derivatives. This review presents an overview of the application of these methods on halogenated quinazolin-4-ones and their quinazolines to generate novel polysubstituted derivatives. PMID:25356566

  5. Intermolecular Vibrations of Hydrophobic Amino Acids

    NASA Astrophysics Data System (ADS)

    Williams, Michael Roy Casselman

    Hydrophobic amino acids interact with their chemical environment through a combination of electrostatic, hydrogen bonding, dipole, induced dipole, and dispersion forces. These interactions all have their own characteristic energy scale and distance dependence. The low-frequency (0.1-5 THz, 5-150 cm-1) vibrational modes of amino acids in the solid state are a direct indicator of the interactions between the molecules, which include interactions between an amino acid functional group and its surroundings. This information is central to understanding the dynamics and morphology of proteins. The alpha-carbon is a chiral center for all of the hydrophobic amino acids, meaning that they exist in two forms, traditionally referred to as L- and D-enantiomers. This nomenclature indicates which direction the molecule rotates plane-polarized visible light (levorotory and dextrorotory). Chiral a-amino acids in proteins are exclusively the L-variety In the solid state, the crystal lattice of the pure L-enantiomer is the mirror image of the D-enantiomer crystal lattice. These solids are energetically identical. Enantiomers also have identical spectroscopic properties except when the measurement is polarization sensitive. A mixture of equal amounts D- and L-amino acid enantiomers can crystallize into a racemic (DL-) structure that is different from that of the pure enantiomers. Whether a solution of both enantiomers will crystallize into a racemic form or spontaneously resolve into a mixture of separate D- and L-crystals largely depends on the interactions between molecules available in the various possible configurations. This is an active area of research. Low-frequency vibrations with intermolecular character are very sensitive to changes in lattice geometry, and consequently the vibrational spectra of racemic crystals are usually quite distinct from the spectra of the crystals of the corresponding pure enantiomers in the far-infrared (far-IR). THz time-domain spectroscopy (THz

  6. Interatomic (Intermolecular) Decay Processes in Clusters: Current Status and Outlook

    SciTech Connect

    Averbukh, V.; Cederbaum, L. S.

    2007-11-29

    Since their theoretical prediction a decade ago, interatomic (intermolecular) Coulombic decay (ICD) and related processes have been in the focus of intensive theoretical and experimental research. The spectacular progress in this direction has been stimulated both by the fundamental importance of the new electronic decay phenomena and by the exciting possibility of their practical application, for example in spectroscopy. We review the current status of the research of interatomic (intermolecular) decay phenomena in clusters and discuss some perspectives of this new field.

  7. Frontier orbital symmetry control of intermolecular electron transfer

    SciTech Connect

    Stevens, B.

    1990-11-01

    Research continued on the study of intermolecular electron transfer. This report discusses the following topics: fluorescence quenching by electron transfer and the modification of quenching dynamics by solvent properties and net free energy change; transient absorption measurements following selective excitation of 1:1 EDA complex isomers; selective quenching of dual fluorescence from linked EDA systems; electron-transfer sensitized cycloreversion of rubrene endoperoxide; and vibronic modification of adiabatic requirements for intermolecular electron transfer. (CBS)

  8. Synthesis of epoxybenzo[d]isothiazole 1,1-dioxides via a reductive-Heck, metathesis-sequestration protocol†‡

    PubMed Central

    Asad, Naeem; Hanson, Paul R.; Long, Toby R.; Rayabarapu, Dinesh K.; Rolfe, Alan

    2011-01-01

    An atom-economical purification protocol, using solution phase processing via ring-opening metathesis polymerization (ROMP) has been developed for the synthesis of tricyclic sultams. This chromatography-free method allows for convenient isolation of reductive-Heck products and reclamation of excess starting material via sequestration involving metathesis catalysts and a catalyst-armed Si-surface. PMID:21727956

  9. Rhodium(III)-catalyzed C-C coupling of 7-azaindoles with vinyl acetates and allyl acetates.

    PubMed

    Li, Shuai-Shuai; Wang, Cheng-Qi; Lin, Hui; Zhang, Xiao-Mei; Dong, Lin

    2016-01-01

    The behaviour of electron-rich alkenes with 7-azaindoles in rhodium(III)-catalyzed C-H activation is investigated. Various substituted vinyl acetates and allyl acetates as coupling partners reacted smoothly providing a wide variety of 7-azaindole derivatives, and the selectivity of the coupling reaction is alkene-dependent. In addition, the approaches of rhodium(III)-catalyzed dehydrogenative Heck-type reaction (DHR) and carbonylation reaction were quite novel and simple. PMID:26553424

  10. Intermolecular interactions between imidazole derivatives intercalated in layered solids. Substituent group effect

    SciTech Connect

    González, M.; Lemus-Santana, A.A.; Rodríguez-Hernández, J.; Aguirre-Velez, C.I.; Knobel, M.; Reguera, E.

    2013-08-15

    This study sheds light on the intermolecular interactions between imidazole derive molecules (2-methyl-imidazole, 2-ethyl-imidazole and benzimidazole) intercalated in T[Ni(CN){sub 4}] layers to form a solid of formula unit T(ImD){sub 2}[Ni(CN){sub 4}]. These hybrid inorganic–organic solids were prepared by soft chemical routes and their crystal structures solved and refined from X-ray powder diffraction data. The involved imidazole derivative molecules were found coordinated through the pyridinic N atom to the axial positions for the metal T in the T[Ni(CN){sub 4}] layer. In the interlayers region ligand molecules from neighboring layers remain stacked in a face-to-face configuration through dipole–dipole and quadrupole–quadrupole interactions. These intermolecular interactions show a pronounced dependence on the substituent group and are responsible for an ImD-pillaring concatenation of adjacent layers. This is supported by the structural information and the recorded magnetic data in the 2–300 K temperature range. The samples containing Co and Ni are characterized by presence of spin–orbit coupling and pronounced temperature dependence for the effective magnetic moment except for 2-ethyl-imidazole related to the local distortion for the metal coordination environment. For this last one ligand a weak ferromagnetic ordering ascribed to a super-exchange interaction between T metals from neighboring layers through the ligands π–π interaction was detected. - Graphical abstract: In the interlayers region imidazole derivative molecules are oriented according to their dipolar and quadrupolar interactions and minimizing the steric impediment. Highlights: • Imidazole derivatives intercalation compounds. • Intermolecular interaction between intercalated imidazole derivatives. • Hybrid inorganic–organic solids. • Pi–pi interactions and ferromagnetic coupling. • Dipolar and quadrupolar interactions between intercalated imidazole derivatives.

  11. Rational Design of a Second Generation Catalyst for Preparation of Allylsilanes Using the Silyl-Heck Reaction

    PubMed Central

    2015-01-01

    Using rational ligand design, we have developed of a second-generation ligand, bis(3,5-di-tert-butylphenyl)(tert-butyl)phosphine, for the preparation of allylsilanes using the palladium-catalyzed silyl-Heck reaction. This new ligand provides nearly complete suppression of starting material alkene isomerization that was observed with our first-generation catalyst, providing vastly improved yields of allylsilanes from simple alkene starting materials. The studies quantifying the electronic and steric properties of the new ligand are described. Finally, we report an X-ray crystal structure of a palladium complex resulting from the oxidative addition of Me3SiI using an analogous ligand that provides significant insight into the nature of the catalytic system. PMID:25003502

  12. Investigating the Nature of Palladium Chain-Walking in the Enantioselective Redox-Relay Heck Reaction of Alkenyl Alcohols

    PubMed Central

    2015-01-01

    The mechanism of the redox-relay Heck reaction was investigated using deuterium-labeled substrates. Results support a pathway through a low energy palladium–alkyl intermediate that immediately precedes product formation, ruling out a tautomerization mechanism. DFT calculations of the relevant transition structures at the M06/LAN2DZ+f/6-31+G* level of theory show that the former pathway is favored by 5.8 kcal/mol. Palladium chain-walking toward the alcohol, following successive β-hydride eliminations and migratory insertions, is also supported in this study. The stereochemistry of deuterium labels is determined, lending support that the catalyst remains bound to the substrate during the relay process and that both cis- and trans-alkenes form from β-hydride elimination. PMID:25186804

  13. Case Report of Focal Epithelial Hyperplasia (Heck's Disease) with Polymerase Chain Reaction Detection of Human Papillomavirus 13.

    PubMed

    Brehm, Mary A; Gordon, Katie; Firan, Miahil; Rady, Peter; Agim, Nnenna

    2016-05-01

    Focal epithelial hyperplasia (FEH), or Heck's disease, is an uncommon benign proliferation of oral mucosa caused by the human papillomavirus (HPV), particularly subtypes 13 and 32. The disease typically presents in young Native American patients and is characterized by multiple asymptomatic papules and nodules on the oral mucosa, lips, tongue, and gingiva. The factors that determine susceptibility to FEH are unknown, but the ethnic and geographic distribution of FEH suggests that genetic predisposition, particularly having the human lymphocytic antigen DR4 type, may be involved in pathogenesis. We report a case of FEH with polymerase chain reaction detection of HPV13 in a healthy 11-year-old Hispanic girl and discuss the current understanding of disease pathogenesis, susceptibility, and treatment. PMID:27072123

  14. Intermolecular artifacts in probe microscope images of C60 assemblies

    NASA Astrophysics Data System (ADS)

    Jarvis, Samuel Paul; Rashid, Mohammad Abdur; Sweetman, Adam; Leaf, Jeremy; Taylor, Simon; Moriarty, Philip; Dunn, Janette

    2015-12-01

    Claims that dynamic force microscopy has the capability to resolve intermolecular bonds in real space continue to be vigorously debated. To date, studies have been restricted to planar molecular assemblies with small separations between neighboring molecules. Here we report the observation of intermolecular artifacts over much larger distances in 2D assemblies of C60 molecules, with compelling evidence that in our case the tip apex is terminated by a C60 molecule (rather than the CO termination typically exploited in ultrahigh resolution force microscopy). The complete absence of directional interactions such as hydrogen or halogen bonding, the nonplanar structure of C60, and the fullerene termination of the tip apex in our case highlight that intermolecular artifacts are ubiquitous in dynamic force microscopy.

  15. Qualitative change of character of dispersive interaction with intermolecular distance.

    PubMed

    Haslmayr, Johannes; Renger, Thomas

    2013-07-28

    The dispersive interaction between molecules results from Coulomb-correlated fluctuations of electrons and for large intermolecular distances it can be related to the molecular polarizabilities as in London's theory (F. London, Trans. Faraday Soc. 33, 8-26 (1937)). Here, we investigate the interaction between molecules with anisotropic polarizabilities at arbitrary distances using symmetry adapted perturbation theory, which allows us to analyze the different parts of the intermolecular potential separately. Whereas at large distances, in accordance with London's theory, there is no way to describe the dispersive interaction by a sum over pairwise isotropic atom-centered energy terms, at short distances such a description becomes possible. This surprising result has consequences for the development of molecular mechanics force fields, supports the dispersion energy terms applied in dispersion corrected density functional theory, and indicates that there is a qualitative change in electron correlation with distance. Apparently, at short distances intermolecular electron correlation is less influenced by intramolecular electron delocalization. PMID:23901956

  16. Intermolecular Vibrational Modes Speed Up Singlet Fission in Perylenediimide Crystals.

    PubMed

    Renaud, Nicolas; Grozema, Ferdinand C

    2015-02-01

    We report numerical simulations based on a non-Markovian density matrix propagation scheme of singlet fission (SF) in molecular crystals. Ab initio electronic structure calculations were used to parametrize the exciton and phonon Hamiltonian as well as the interactions between the exciton and the intramolecular and intermolecular vibrational modes. We demonstrate that the interactions of the exciton with intermolecular vibrational modes are highly sensitive to the stacking geometry of the crystal and can, in certain cases, significantly accelerate SF. This result may help in understanding the fast SF experimentally observed in a broad range of molecular crystals and offers a new direction for the engineering of efficient SF sensitizers. PMID:26261948

  17. Fast acquisition of high-resolution NMR spectra in inhomogeneous fields via intermolecular double-quantum coherences

    PubMed Central

    Chen, Zhong; Cai, Shuhui; Chen, Zhiwei; Zhong, Jianhui

    2009-01-01

    A pulse sequence, IDEAL-II, is proposed based on the concept of intermolecular dipolar-interaction enhanced all lines [Z. Chen et al., J. Am. Chem. Soc. 126, 446 (2004)] for obtaining one-dimensional (1D) high-resolution liquid NMR spectra in inhomogeneous fields via two-dimensional acquisitions. With the new acquisition scheme, the range of magnetic field inhomogeneity rather than chemical shift is sampled in the indirect dimension. This enables a great reduction in acquisition time and amount of data, much improved over the original IDEAL implementation. It is applicable to both isolated and J-coupled spin systems in liquid. For the latter, apparent J coupling constants are magnified threefold in spectra obtained with this sequence. This allows a more accurate measurement of J coupling constants in the cases of small J coupling constants or large inhomogeneous fields. Analytical expression was derived based on intermolecular multiple-quantum coherence treatments. Solution samples that were purposely deshimmed and biological samples with intrinsic field inhomogeneities were tested. Experimental results demonstrate that this sequence retains useful structural information including chemical shifts, relative peak areas, and multiplet patterns of J coupling even when the field inhomogeneity is severe enough to almost erase all spectroscopic information with conventional 1D single-quantum coherence techniques. This sequence is more applicable to weakly coupled and uncoupled spin systems, potentially useful for studying metabolites in in vivo NMR spectroscopy and for characterizing technologically important new materials in combinatorial chemistry. PMID:19256612

  18. Intermolecular energy-band dispersion in PTCDA multilayers

    NASA Astrophysics Data System (ADS)

    Yamane, Hiroyuki; Kera, Satoshi; Okudaira, Koji K.; Yoshimura, Daisuke; Seki, Kazuhiko; Ueno, Nobuo

    2003-07-01

    The electronic structure of a well-oriented perylene-3,4,9,10-tetracarboxylic acid-dianhydride multilayer prepared on MoS2 single crystal surface were studied by angle-resolved ultraviolet photoemission spectroscopy using synchrotron radiation. From the photon energy dependence of normal emission spectra, we observed an intermolecular energy-band dispersion of about 0.2 eV for the highest occupied molecular orbital (HOMO) band of single π character. The observed energy-band dispersion showed a cosine curve, which originates from the intermolecular π-π interaction. Analyses using the tight-binding model gave that the transfer integral of about 0.05 eV for the π-π interaction, the effective mass of HOMO hole m*h=5.28m0, and the hole mobility μh>3.8 cm2/V s. This is the first observation of the intermolecular energy-band dispersion of a conventional single-component organic semiconductor only with the weak intermolecular van der Waals interaction.

  19. Spin radical enhanced magnetocapacitance effect in intermolecular excited states.

    PubMed

    Zang, Huidong; Wang, Jianguo; Li, Mingxing; He, Lei; Liu, Zitong; Zhang, Deqing; Hu, Bin

    2013-11-14

    This article reports the magnetocapacitance effect (MFC) based on both pristine polymer MEH-PPV and its composite system doped with spin radicals (6R-BDTSCSB). We observed that a photoexcitation leads to a significant positive MFC in the pristine MEH-PPV. Moreover, we found that a low doping of spin radicals in polymer MEH-PPV causes a significant change on the MFC signal: an amplitude increase and a line-shape narrowing under light illumination at room temperature. However, no MFC signal was observed under dark conditions in either the pristine MEH-PPV or the radical-doped MEH-PPV. Furthermore, the magnitude increase and line-shape narrowing caused by the doped spin radicals are very similar to the phenomena induced by increasing the photoexcitation intensity. Our studies suggest that the MFC is essentially originated from the intermolecular excited states, namely, intermolecular electron-hole pairs, generated by a photoexcitation in the MEH-PPV. More importantly, by comparing the effects of spin radicals and electrically polar molecules on the MFC magnitude and line shape, we concluded that the doped spin radicals can have the spin interaction with intermolecular excited states and consequently affect the internal spin-exchange interaction within intermolecular excited states in the development of MFC. Clearly, our experimental results indicate that dispersing spin radicals forms a convenient method to enhance the magnetocapacitance effect in organic semiconducting materials. PMID:24144347

  20. Learning about Intermolecular Interactions from the Cambridge Structural Database

    ERIC Educational Resources Information Center

    Battle, Gary M.; Allen, Frank H.

    2012-01-01

    A clear understanding and appreciation of noncovalent interactions, especially hydrogen bonding, are vitally important to students of chemistry and the life sciences, including biochemistry, molecular biology, pharmacology, and medicine. The opportunities afforded by the IsoStar knowledge base of intermolecular interactions to enhance the…

  1. Morphology and the Strength of Intermolecular Contact in Protein Crystals

    NASA Technical Reports Server (NTRS)

    Matsuura, Yoshiki; Chernov, Alexander A.

    2002-01-01

    The strengths of intermolecular contacts (macrobonds) in four lysozyme crystals were estimated based on the strengths of individual intermolecular interatomic interaction pairs. The periodic bond chain of these macrobonds accounts for the morphology of protein crystals as shown previously. Further in this paper, the surface area of contact, polar coordinate representation of contact site, Coulombic contribution on the macrobond strength, and the surface energy of the crystal have been evaluated. Comparing location of intermolecular contacts in different polymorphic crystal modifications, we show that these contacts can form a wide variety of patches on the molecular surface. The patches are located practically everywhere on this surface except for the concave active site. The contacts frequently include water molecules, with specific intermolecular hydrogen-bonds on the background of non-specific attractive interactions. The strengths of macrobonds are also compared to those of other protein complex systems. Making use of the contact strengths and taking into account bond hydration we also estimated crystal-water interfacial energies for different crystal faces.

  2. Intermolecular potentials from shock structure experiments. [for monatomic gases

    NASA Technical Reports Server (NTRS)

    Sturtevant, B.; Steinhilper, E. A.

    1974-01-01

    Ground-state intermolecular interaction potentials determined from shock structure experiments with four monatomic gases are reported. These potentials are assessed for self-consistency, using the law of corresponding states, and their suitability for engineering applications in rarefied gas dynamics is discussed.

  3. Intermolecular Silacarbonyl Ylide Cycloadditions: A Direct Pathway to Oxasilacyclopentenes

    PubMed Central

    Bourque, Laura E.; Woerpel, K. A.

    2009-01-01

    Silacarbonyl ylides, generated by metal-catalyzed silylene transfer to carbonyls, participate in formal intermolecular 1,3-dipolar cycloaddition reactions with carbonyl compounds and alkynes to form dioxasilacyclopentane acetals and oxasilacyclopentenes in an efficient, one-step process. PMID:18922005

  4. Dancing Crystals: A Dramatic Illustration of Intermolecular Forces

    ERIC Educational Resources Information Center

    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…

  5. Student Understanding of Intermolecular Forces: A Multimodal Study

    ERIC Educational Resources Information Center

    Cooper, Melanie M.; Williams, Leah C.; Underwood, Sonia M.

    2015-01-01

    The ability to use representations of molecular structure to predict the macroscopic properties of a substance is central to the development of a robust understanding of chemistry. Intermolecular forces (IMFs) play an important role in this process because they provide a mechanism for how and why molecules interact. In this study, we investigate…

  6. Hydrogen-hydrogen intermolecular structure of polyethylene in the melt

    NASA Astrophysics Data System (ADS)

    Londono, J. D.; Annis, B. K.; Habenschuss, A.; Smith, G. D.; Borodin, O.; Tso, C.; Hsieh, E. T.; Soper, A. K.

    1999-05-01

    Three polyethylene samples, which differed in their degree of deuteration, were studied in neutron diffraction isotopic substitution (NDIS) experiments at 428 K. These results were complemented at small wavevectors by small angle neutron measurements. The intermolecular hydrogen-hydrogen (HH) structure function, hHH(Q), was obtained without recourse to intramolecular structure models, as demonstrated in a prior report. The PE experimental results are compared to computer simulation results for the alkanes C100 at 509 K and C44 at 350, 400, and 450 K. The small temperature dependence of the HH intermolecular radial distribution functions, gHH(r) for C44 indicates that the differences observed between the PE, C100, and C44 (450 K) results are, for the most part, not due to just temperature differences. It is shown that the string model, an analytic result from an integral equation theory of polymers (PRISM), can account approximately for the overall shape of the gHH(r) functions, and that this overall shape is dependent on the radius of gyration of the molecule. Further analysis shows that there are two other contributions to gHH(r), both of which are independent of chain length to first order. The first is due to chain-chain packing, and the second is due to local HH intermolecular correlations. These results are significant because they demonstrate that hHH(Q) is a useful function for studying intermolecular polymer structure, which has been shown to underpin phase behavior in polyolefin blends.

  7. Copper-catalyzed intermolecular asymmetric propargylic dearomatization of indoles.

    PubMed

    Shao, Wen; Li, He; Liu, Chuan; Liu, Chen-Jiang; You, Shu-Li

    2015-06-22

    The first copper-catalyzed intermolecular dearomatization of indoles by an asymmetric propargylic substitution reaction was developed. This method provides a highly efficient synthesis of versatile furoindoline and pyrroloindoline derivatives containing a quaternary carbon stereogenic center and a terminal alkyne moiety with up to 86 % yield and 98 % ee. PMID:25968474

  8. An efficient generation of a functionalized tertiary-alkyl radical for copper-catalyzed tertiary-alkylative Mizoroki-Heck type reaction.

    PubMed

    Nishikata, Takashi; Noda, Yushi; Fujimoto, Ryo; Sakashita, Tomomi

    2013-11-01

    α-Halocarbonyl compounds undergo β-hydrogen elimination to give conjugated olefins in the presence of a transition-metal catalyst. However, a copper/triamine catalyst system can induce the alkylative Mizoroki–Heck reaction of styrenes with tertiary-alkyl halides possessing a withdrawing group under very mild conditions. This reaction provides an efficient synthetic methodology for tertiary-alkylated styrenes. PMID:24143934

  9. Dynamics of intermolecular interactions in CCl4via the isotope effect by femtosecond time-resolved spectroscopy.

    PubMed

    Konarska, Jadwiga; Gadomski, Wojciech; Ratajska-Gadomska, Bożena; Polok, Kamil; Pudłowski, Grzegorz; Kardaś, Tomasz M

    2016-06-21

    We report our study on the ultrafast dynamics of intermolecular interactions in liquid CCl4. A transient transmission time domain signal, obtained in the 40 ps delay range, exhibits beating at the difference frequency of the totally symmetric stretching vibrations of the tetrachloride isotopologues. We show that the spectra obtained as the windowed Fourier transform of different parts of the time domain signal in the range of this totally symmetric vibration, split due to the isotope effect, carry the information about the dynamics of the coherently excited, coupled molecules. We use a simple theoretical model in order to prove that the intermolecular interaction influences the relative amplitudes of the isotopologue peaks in the spectrum. Moreover, we demonstrate that the pump induced coherence in the system leads to additional strengthening of the interaction, which can be observed in the spectra obtained from the experimental time domain signal. PMID:27244535

  10. Probing Intermolecular Interactions in Polycyclic Aromatic Hydrocarbons with 2D IR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Krummel, Amber

    2014-03-01

    Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in the environment and impact geochemical processes that are critical to sustainable energy resources. For example, asphaltenes exist naturally in geologic formations and their aggregates heavily impact the petroleum economy. Unfortunately, the chemical dynamics that drive asphaltene nanoaggregation processes are still poorly understood. Solvent dynamics and intermolecular interactions such as π-stacking interactions play integral roles in asphaltene nanoaggregation. Linear and nonlinear vibrational spectroscopy including two-dimensional infrared spectroscopy (2DIR), are well suited to explore these fundamental interactions. Teasing apart the vibrational characteristics in PAHs that model asphaltenic compounds represents an important step towards utilizing 2D IR spectroscopy to understand the intermolecular interactions that are prevalent in asphaltene nanoaggregation. A solar dye, N,N'-Dioctyl-3,4,9,10-perylenedicarboximide, is used in this work to model aphaltenes. Carbonyl and ring vibrations are used to probe the nanoaggregates of the model compounds. However, the characteristics of these normal modes change as a function of the size of the conjugated ring system. Thus, in order to fully understand the nature of these normal modes, we include a systematic study of a series of quinones. Our investigation employs a combination of 2DIR spectroscopy and electronic structure calculations to explore vibrational coupling in quinones and PAHs. We compare the calculated vibrational characteristics to those extracted from 2DIR spectra. ATK acknowledges the Donors of the American Chemical Society Petroleum Research Fund for support of this research.

  11. The Nature of Intermolecular Interactions Between Aromatic Amino Acid Residues

    SciTech Connect

    Gervasio, Francesco; Chelli, Riccardo; Procacci, Piero; Schettino, Vincenzo

    2002-05-01

    The nature of intermolecular interactions between aromatic amino acid residues has been investigated by a combination of molecular dynamics and ab initio methods. The potential energy surface of various interacting pairs, including tryptophan, phenilalanine, and tyrosine, was scanned for determining all the relevant local minima by a combined molecular dynamics and conjugate gradient methodology with the AMBER force field. For each of these minima, single-point correlated ab initio calculations of the binding energy were performed. The agreement between empirical force field and ab initio binding energies of the minimum energy structures is excellent. Aromatic-aromatic interactions can be rationalized on the basis of electrostatic and van der Waals interactions, whereas charge transfer or polarization phenomena are small for all intermolecular complexes and, particularly, for stacked structures.

  12. Separation of intra- and intermolecular contributions to the PELDOR signal

    NASA Astrophysics Data System (ADS)

    Schöps, Philipp; Plackmeyer, Jörn; Marko, Andriy

    2016-08-01

    Pulsed Electron-electron Double Resonance (PELDOR) is commonly used to measure distances between native paramagnetic centers or spin labels attached to complex biological macromolecules. In PELDOR the energies of electron magnetic dipolar interactions are measured by analyzing the oscillation frequencies of the recorded time resolved signal. Since PELDOR is an ensemble method, the detected signal contains contributions from intramolecular, as well as intermolecular electron spin interactions. The intramolecular part of the signal contains the information about the structure of the studied molecules, thus it is very important to accurately separate intra- and intermolecular contributions to the total signal. This separation can become ambiguous, when the length of the PELDOR signal is not much longer than twice the oscillation period of the signal. In this work we suggest a modulation depth scaling method, which can use short PELDOR signals in order to extract the intermolecular contribution. Using synthetic data we demonstrate the advantages of the new approach and analyze its stability with regard to signal noise. The method was also successfully tested on experimental data of three systems measured at Q-Band frequencies, two model compounds in deuterated and protonated solvents and one biological sample, namely BetP. The application of the new method with an assigned value of the signal modulation depth enables us to determine the interspin distances in all cases. This is especially interesting for the model compound with an interspin distance of 5.2 nm in the protonated solvent and the biological sample, since an accurate separation of the intra- and intermolecular PELDOR signal contributions would be difficult with the standard approach in those cases.

  13. Separation of intra- and intermolecular contributions to the PELDOR signal.

    PubMed

    Schöps, Philipp; Plackmeyer, Jörn; Marko, Andriy

    2016-08-01

    Pulsed Electron-electron Double Resonance (PELDOR) is commonly used to measure distances between native paramagnetic centers or spin labels attached to complex biological macromolecules. In PELDOR the energies of electron magnetic dipolar interactions are measured by analyzing the oscillation frequencies of the recorded time resolved signal. Since PELDOR is an ensemble method, the detected signal contains contributions from intramolecular, as well as intermolecular electron spin interactions. The intramolecular part of the signal contains the information about the structure of the studied molecules, thus it is very important to accurately separate intra- and intermolecular contributions to the total signal. This separation can become ambiguous, when the length of the PELDOR signal is not much longer than twice the oscillation period of the signal. In this work we suggest a modulation depth scaling method, which can use short PELDOR signals in order to extract the intermolecular contribution. Using synthetic data we demonstrate the advantages of the new approach and analyze its stability with regard to signal noise. The method was also successfully tested on experimental data of three systems measured at Q-Band frequencies, two model compounds in deuterated and protonated solvents and one biological sample, namely BetP. The application of the new method with an assigned value of the signal modulation depth enables us to determine the interspin distances in all cases. This is especially interesting for the model compound with an interspin distance of 5.2nm in the protonated solvent and the biological sample, since an accurate separation of the intra- and intermolecular PELDOR signal contributions would be difficult with the standard approach in those cases. PMID:27243966

  14. Energetics of Intermolecular Hydrogen Bonds in a Hydrophobic Protein Cavity

    NASA Astrophysics Data System (ADS)

    Liu, Lan; Baergen, Alyson; Michelsen, Klaus; Kitova, Elena N.; Schnier, Paul D.; Klassen, John S.

    2014-05-01

    This work explores the energetics of intermolecular H-bonds inside a hydrophobic protein cavity. Kinetic measurements were performed on the gaseous deprotonated ions (at the -7 charge state) of complexes of bovine β-lactoglobulin (Lg) and three monohydroxylated analogs of palmitic acid (PA): 3-hydroxypalmitic acid (3-OHPA), 7-hydroxypalmitic acid (7-OHPA), and 16-hydroxypalmitic acid (16-OHPA). From the increase in the activation energy for the dissociation of the (Lg + X-OHPA)7- ions, compared with that of the (Lg + PA)7- ion, it is concluded that the -OH groups of the X-OHPA ligands participate in strong (5 - 11 kcal mol-1) intermolecular H-bonds in the hydrophobic cavity of Lg. The results of molecular dynamics (MD) simulations suggest that the -OH groups of 3-OHPA and 16-OHPA act as H-bond donors and interact with backbone carbonyl oxygens, whereas the -OH group of 7-OHPA acts as both H-bond donor and acceptor with nearby side chains. The capacity for intermolecular H-bonds within the Lg cavity, as suggested by the gas-phase measurements, does not necessarily lead to enhanced binding in aqueous solution. The association constant (Ka) measured for 7-OHPA [(2.3 ± 0.2) × 105 M-1] is similar to the value for the PA [(3.8 ± 0.1) × 105 M-1]; Ka for 3-OHPA [(1.1 ± 0.3) × 106 M-1] is approximately three-times larger, whereas Ka for 16-OHPA [(2.3 ± 0.2) × 104 M-1] is an order of magnitude smaller. Taken together, the results of this study suggest that the energetic penalty to desolvating the ligand -OH groups, which is necessary for complex formation, is similar in magnitude to the energetic contribution of the intermolecular H-bonds.

  15. Covalent intermolecular interaction of the nitric oxide dimer (NO)2

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Zheng, Gui-Li; Lv, Gang; Geng, Yi-Zhao; Ji, Qing

    2015-09-01

    Covalent bonds arise from the overlap of the electronic clouds in the internucleus region, which is a pure quantum effect and cannot be obtained in any classical way. If the intermolecular interaction is of covalent character, the result from direct applications of classical simulation methods to the molecular system would be questionable. Here, we analyze the special intermolecular interaction between two NO molecules based on quantum chemical calculation. This weak intermolecular interaction, which is of covalent character, is responsible for the formation of the NO dimer, (NO)2, in its most stable conformation, a cis conformation. The natural bond orbital (NBO) analysis gives an intuitive illustration of the formation of the dimer bonding and antibonding orbitals concomitant with the breaking of the π bonds with bond order 0.5 of the monomers. The dimer bonding is counteracted by partially filling the antibonding dimer orbital and the repulsion between those fully or nearly fully occupied nonbonding dimer orbitals that make the dimer binding rather weak. The direct molecular mechanics (MM) calculation with the UFF force fields predicts a trans conformation as the most stable state, which contradicts the result of quantum mechanics (QM). The lesson from the investigation of this special system is that for the case where intermolecular interaction is of covalent character, a specific modification of the force fields of the molecular simulation method is necessary. Project supported by the National Natural Science Foundation of China (Grant Nos. 90403007 and 10975044), the Key Subject Construction Project of Hebei Provincial Universities, China, the Research Project of Hebei Education Department, China (Grant Nos. Z2012067 and Z2011133), the National Natural Science Foundation of China (Grant No. 11147103), and the Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China (Grant No. Y5

  16. Calculations of helical twisting powers from intermolecular torques.

    PubMed

    Earl, David J; Wilson, Mark R

    2004-05-22

    We present a Monte Carlo molecular simulation method that calculates the helical twisting power of a chiral molecule by sampling intermolecular torques. The approach is applied to an achiral nematic liquid crystalline system, composed of Gay-Berne particles, that is doped with chiral molecules. Calculations are presented for six chiral dopant molecules and the results show a good correlation with the sign and magnitude of experimentally determined helical twisting powers. PMID:15267981

  17. Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

    PubMed Central

    Nagy, Peter I.

    2014-01-01

    A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed. PMID:25353178

  18. Intermolecular interactions of thrombospondins drive their accumulation in extracellular matrix

    PubMed Central

    Kim, Dae Joong; Christofidou, Elena D.; Keene, Douglas R.; Hassan Milde, Marwah; Adams, Josephine C.

    2015-01-01

    Thrombospondins participate in many aspects of tissue organization in adult tissue homeostasis, and their dysregulation contributes to pathological processes such as fibrosis and tumor progression. The incorporation of thrombospondins into extracellular matrix (ECM) as discrete puncta has been documented in various tissue and cell biological contexts, yet the underlying mechanisms remain poorly understood. We find that collagen fibrils are disorganized in multiple tissues of Thbs1−/− mice. In investigating how thrombospondins become retained within ECM and thereby affect ECM organization, we find that accumulation of thrombospondin-1 or thrombospondin-5 puncta within cell-derived ECM is controlled by a novel, conserved, surface-exposed site on the thrombospondin L-type lectin domain. This site acts to recruit thrombospondin molecules into ECM by intermolecular interactions in trans. This mechanism is fibronectin independent, can take place extracellularly, and is demonstrated to be direct in vitro. The trans intermolecular interactions can also be heterotypic—for example, between thrombospondin-1 and thrombospondin-5. These data identify a novel concept of concentration-dependent, intermolecular “matrix trapping” as a conserved mechanism that controls the accumulation and thereby the functionality of thrombospondins in ECM. PMID:25995382

  19. Competing intramolecular vs. intermolecular hydrogen bonds in solution.

    PubMed

    Nagy, Peter I

    2014-01-01

    A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed. PMID:25353178

  20. Transfer operators for Gamma_{0}(n) and the Hecke operators for the period functions of PSL(2,mathbb{Z})

    NASA Astrophysics Data System (ADS)

    Hilgert, Joachim; Mayer, Dieter; Movasati, Hossein

    2005-07-01

    In this paper we report on a surprising relation between the transfer operators for the congruence subgroups Gamma_{0}(nm),n,min mathbb{N}, and some kind of Hecke operators on the space of vector valued period functions for the groups Gamma_{0}(n). We study special eigenfunctions of the transfer operators for the groups Gamma_{0}(nm) with eigenvalues mp1 which are also solutions of the Lewis equations for these groups and which are determined by eigenfunctions of the transfer operator for the congruence subgroup Gamma_{0}(n). In the language of the Atkin-Lehner theory of old and new forms one should hence call them old eigenfunctions or old solutions of the Lewis equation for Gamma_{0}(n). It turns out that certain linear combinations of the components of these old solutions for the group Gamma_{0}(nm) determine for any m a solution of the Lewis equation for the group Gamma_{0}(n) and hence also an eigenfunction of the transfer operator for this group.

  1. Intermolecular control of thermoswitching and photoswitching phenomena in two spin-crossover polymorphs

    NASA Astrophysics Data System (ADS)

    Buron-Le Cointe, M.; Hébert, J.; Baldé, C.; Moisan, N.; Toupet, L.; Guionneau, P.; Létard, J. F.; Freysz, E.; Cailleau, H.; Collet, E.

    2012-02-01

    We discuss here the important role of intermolecular coupling for the thermal- and light-induced molecular state switching in the solid state. Investigations were performed on the two crystalline polymorphs of the spin-crossover [Fe-(PM-BIA)2(NCS)2] material. In addition to structural studies at thermal equilibrium, light-induced phenomena were investigated through photocrystallography, photomagnetic, and dynamical optical measurements. Strong similarities between the thermal-equilibrium and the out-of-equilibrium light-induced transformations are observed in each polymorph: strong cooperative phenomena in one polymorph versus weak cooperative ones in the second polymorph. These different responses of the two crystalline forms of the compound to external perturbations are discussed at the microscopic level in terms of Ising-like model and two-mode description of on-site molecular potentials.

  2. Nonresonant and resonant mode-specific intermolecular vibrational energy transfers in electrolyte aqueous solutions.

    PubMed

    Bian, Hongtao; Chen, Hailong; Li, Jiebo; Wen, Xiewen; Zheng, Junrong

    2011-10-27

    The donor/acceptor energy mismatch and vibrational coupling strength dependences of interionic vibrational energy transfer kinetics in electrolyte aqueous solutions were investigated with ultrafast multiple-dimensional vibrational spectroscopy. An analytical equation derived from the Fermi's Golden rule that correlates molecular structural parameters and vibrational energy transfer kinetics was found to be able to describe the intermolecular mode specific vibrational energy transfer. Under the assumption of the dipole-dipole approximation, the distance between anions in the aqueous solutions was obtained from the vibrational energy transfer measurements, confirmed with measurements on the corresponding crystalline samples. The result demonstrates that the mode-specific vibrational energy transfer method holds promise as an angstrom molecular ruler. PMID:21916443

  3. Raman Q-branch line shapes as a test of the H2-Ar intermolecular potential

    NASA Technical Reports Server (NTRS)

    Green, Sheldon

    1990-01-01

    The line-shape cross sections of vibrational Raman Q-branch spectra are determined theoretically for D2 and H2 in Ar. The calculations are based on accurate close-coupling matrices and the intermolecular potential obtained by Le Roy and Hutson (1987) from spectra of van der Waals complexes. The calculation techniques applied are explained, and the results are presented in tables and graphs and discussed in detail with reference to published experimental data. Agreement to within about 25 percent is obtained for the line widths, but the line shifts are found to be a factor of two smaller than the measured values, and a temperature dependence of line-width cross sections is predicted which is not observed experimentally.

  4. Effect of intermolecular orientation upon proton transfer within a polarizable medium.

    PubMed Central

    Scheiner, S; Duan, X

    1991-01-01

    Ab initio calculations are used to investigate the proton transfer process in bacteriorhodopsin. HN = CH2 serves as a small prototype of the Schiff base while HCOO- models its carboxylate-containing counterion and HO- the hydroxyl group of water of tyrosine, leading to the HCOO-..H+..NHCH2 and HO-..H+..NHCH2 complexes. In isolation, both complexes prefer a neutral pair configuration wherein the central proton is associated with the anion. However, the Schiff base may be protonated in the former complex, producing the HCOO-..+HNHCH2 ion pair, when there is a high degree of dielectric coupling with an external polarizable medium. Within a range of intermediate level coupling, the equilibrium position of the proton (on either the carboxylate or Schiff base) can be switched by suitable changes in the intermolecular angle. pK shift resulting from a 60 degrees reorientation are calculated to be some 5-12 pK U within the coupling range where proton transfers are possible. The energy barrier to proton transfer reinforces the ability of changes in angle and dielectric coupling to induce a proton transfer. PMID:1660318

  5. Rubrene: The Interplay between Intramolecular and Intermolecular Interactions Determines the Planarization of Its Tetracene Core in the Solid State.

    PubMed

    Sutton, Christopher; Marshall, Michael S; Sherrill, C David; Risko, Chad; Brédas, Jean-Luc

    2015-07-15

    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. PMID:26075966

  6. Reliable prediction of three-body intermolecular interactions using dispersion-corrected second-order Møller-Plesset perturbation theory

    SciTech Connect

    Huang, Yuanhang; Beran, Gregory J. O.

    2015-07-28

    Three-body and higher intermolecular interactions can play an important role in molecular condensed phases. Recent benchmark calculations found problematic behavior for many widely used density functional approximations in treating 3-body intermolecular interactions. Here, we demonstrate that the combination of second-order Møller-Plesset (MP2) perturbation theory plus short-range damped Axilrod-Teller-Muto (ATM) dispersion accurately describes 3-body interactions with reasonable computational cost. The empirical damping function used in the ATM dispersion term compensates both for the absence of higher-order dispersion contributions beyond the triple-dipole ATM term and non-additive short-range exchange terms which arise in third-order perturbation theory and beyond. Empirical damping enables this simple model to out-perform a non-expanded coupled Kohn-Sham dispersion correction for 3-body intermolecular dispersion. The MP2 plus ATM dispersion model approaches the accuracy of O(N{sup 6}) methods like MP2.5 or even spin-component-scaled coupled cluster models for 3-body intermolecular interactions with only O(N{sup 5}) computational cost.

  7. Combination Bands of the Nonpolar OCS Dimer Involving Intermolecular Modes

    NASA Astrophysics Data System (ADS)

    Rezaei, M.; Oliaee, J. Norooz; Moazzen-Ahmadi, N.; McKellar, A. R. W.

    2012-06-01

    Spectra of the nonpolar carbonyl sulfide in the region of the OCS ν_1 fundamental band were observed in a supersonic slit-jet apparatus. The expansion gas was probed using radiation from a tunable diode laser employed in a rapid-scan signal averaging mode. Three bands centered at 2085.906, 2103.504, and 2114.979 cm-1 were observed and anlysed. The rotational assignment and fitting of the bands were made by fixing the lower state parameters to those for the ground state of nonpolar (OCS)_2, thus confirming that they were indeed combination bands of the of the most stable isomer of OCS dimer. The band centered at 2085.906 cm-1 is a combination of the forbidden A_g intramolecular mode plus the geared bend intermolecular mode and that centered at 2114.979 cm-1 is a combination of the allowed B_u intramolecular mode plus the intermolecular van der Waals stretch. The combination at 2103.504 cm-1 can be assigned as a band whose upper state involves four quanta of the intramolecular bend or the B_u intramolecular mode plus two quanta of the intermolecular torsional mode. Isotopic work is needed to conclusively identify the vibrational assignment of this band. Our experimental frequencies for the geared bend and van der Waals modes are in good agreement with a recent high level ab initio calculation by Brown et al. J. Brown, Xiao-Gang Wang, T. Carrington Jr. and Richard Dawes, Journal of Chemical Physics, submitted.

  8. Computing free energy hypersurfaces for anisotropic intermolecular associations.

    PubMed

    Strümpfer, Johan; Naidoo, Kevin J

    2010-01-30

    We previously used an adaptive reaction coordinate force biasing method for calculating the free energy of conformation (Naidoo and Brady, J Am Chem Soc 1999, 121, 2244) and chemical reactions (Rajamani et al., J Comput Chem 2003, 24, 1775) amongst others. Here, we describe a generalized version able to produce free energies in multiple dimensions, descriptively named the free energies from adaptive reaction coordinate forces method. To illustrate it, we describe how we calculate a multidimensional intermolecular orientational free energy, which can be used to investigate complex systems such as protein conformation and liquids. This multidimensional intermolecular free energy W(r, theta(1), theta(2), phi) provides a measure of orientationally dependent interactions that are appropriate for applications in systems that inherently have molecular anisotropic features. It is a highly informative free energy volume, which can be used to parameterize key terms such as the Gay-Berne intermolecular potential in coarse grain simulations. To demonstrate the value of the information gained from the W(r, theta(1), theta(2), phi) hypersurfaces we calculated them for TIP3P, TIP4P, and TIP5P dimer water models in vacuum. A comparison with a commonly used one-dimensional distance free energy profile is made to illustrate the significant increase in configurational information. The W(r) plots show little difference between the three models while the W(r, theta(1), theta(2), phi) hypersurfaces reveal the underlying energetic reasons why these potentials reproduce tetrahedrality in the condensed phase so differently from each. PMID:19462397

  9. Structurally Defined Molecular Hypervalent Iodine Catalysts for Intermolecular Enantioselective Reactions

    PubMed Central

    Haubenreisser, Stefan; Wöste, Thorsten H.; Martínez, Claudio; Ishihara, Kazuaki

    2015-01-01

    Abstract Molecular structures of the most prominent chiral non‐racemic hypervalent iodine(III) reagents to date have been elucidated for the first time. The formation of a chirally induced supramolecular scaffold based on a selective hydrogen‐bonding arrangement provides an explanation for the consistently high asymmetric induction with these reagents. As an exploratory example, their scope as chiral catalysts was extended to the enantioselective dioxygenation of alkenes. A series of terminal styrenes are converted into the corresponding vicinal diacetoxylation products under mild conditions and provide the proof of principle for a truly intermolecular asymmetric alkene oxidation under iodine(I/III) catalysis. PMID:26596513

  10. Photon Antibunching in Complex Intermolecular Fluorescence Quenching Kinetics.

    PubMed

    Sharma, Arjun; Enderlein, Jörg; Kumbhakar, Manoj

    2016-08-18

    We present a novel fluorescence spectroscopic method, which combines fluorescence antibunching, time-correlated single-photon counting (TCSPC), and steady-state emission spectroscopy, to study chemical reactions at the single molecule level. We exemplify our method on investigating intermolecular fluorescence quenching of Rhodamine110 by aniline. We demonstrate that the combination of measurements of fluorescence antibunching, fluorescence lifetime, and fluorescence steady state intensity, captures the full picture of the complex quenching kinetics, which involves static and dynamics quenching, and which cannot be seen by steady-state or lifetime measurements alone. PMID:27468007

  11. Resonance Raman spectra of organic molecules absorbed on inorganic semiconducting surfaces: Contribution from both localized intramolecular excitation and intermolecular charge transfer excitation

    SciTech Connect

    Ye, ChuanXiang; Zhao, Yi E-mail: liangwz@xmu.edu.cn; Liang, WanZhen E-mail: liangwz@xmu.edu.cn

    2015-10-21

    The time-dependent correlation function approach for the calculations of absorption and resonance Raman spectra (RRS) of organic molecules absorbed on semiconductor surfaces [Y. Zhao and W. Z. Liang, J. Chem. Phys. 135, 044108 (2011)] is extended to include the contribution of the intermolecular charge transfer (CT) excitation from the absorbers to the semiconducting nanoparticles. The results demonstrate that the bidirectionally interfacial CT significantly modifies the spectral line shapes. Although the intermolecular CT excitation makes the absorption spectra red shift slightly, it essentially changes the relative intensities of mode-specific RRS and causes the oscillation behavior of surface enhanced Raman spectra with respect to interfacial electronic couplings. Furthermore, the constructive and destructive interferences of RRS from the localized molecular excitation and CT excitation are observed with respect to the electronic coupling and the bottom position of conductor band. The interferences are determined by both excitation pathways and bidirectionally interfacial CT.

  12. Intermolecular Association Provides Specific Optical and NMR Signatures for Serotonin at Intravesicular Concentrations

    PubMed Central

    Nag, Suman; Balaji, J.; Madhu, P. K.; Maiti, S.

    2008-01-01

    Neurotransmitter vesicles contain biomolecules at extraordinarily high concentrations (hundreds of millimoles/liter). Such concentrations can drive intermolecular associations, which may affect vesicular osmolarity and neuronal signaling. Here we investigate whether aqueous serotonin (a monoamine neurotransmitter) forms oligomers at intravesicular concentrations and whether these oligomers have specific spectroscopic signatures that can potentially be used for monitoring neuronal storage and release. We report that, as serotonin concentration is increased from 60 μM to 600 mM, the normalized fluorescence spectrum of serotonin displays a growing long-wavelength tail, with an isoemissive point at 376 nm. The fluorescence decay is monoexponential with a lifetime of 4 ns at low concentrations but is multiexponential with an average lifetime of 0.41 ns at 600 mM. A 600 mM serotonin solution has 30% less osmolarity than expected for monomeric serotonin, indicating oligomer formation. The proton NMR chemical shifts move upfield by as much as 0.3 ppm at 600 mM compared to those at 10 mM, indicating a stacking of the serotonin indole moieties. However, no intermolecular crosspeak is evident in the two-dimensional NMR rotating frame Overhauser effect spectroscopy spectrum even at 600 mM, suggesting that oligomeric structures are possibly weakly coupled. The appearance of a single peak for each proton suggests that the rate of interconversion between the monomeric and the oligomeric structures is faster than 240 Hz. A stopped-flow kinetic experiment also confirms that the rate of dissociation is faster than 100 ms. We conclude that serotonin forms oligomers at intravesicular concentrations but becomes monomeric quickly on dilution. NMR signatures of the oligomers provide potential contrast agents for monitoring the activity of serotonergic neurons in vivo. PMID:18234835

  13. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    SciTech Connect

    Hathwar, Venkatesha R.; Sist, Mattia; Jørgensen, Mads R. V.; Mamakhel, Aref H.; Wang, Xiaoping; Hoffmann, Christina M.; Sugimoto, Kunihisa; Overgaard, Jacob; Iversen, Bo Brummerstedt

    2015-08-14

    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...Cπinteractions 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. Finally, 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.

  14. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    DOE PAGESBeta

    Hathwar, Venkatesha R.; Sist, Mattia; Jørgensen, Mads R. V.; Mamakhel, Aref H.; Wang, Xiaoping; Hoffmann, Christina M.; Sugimoto, Kunihisa; Overgaard, Jacob; Iversen, Bo Brummerstedt

    2015-08-14

    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,more » the presence of Cπ...Cπinteractions 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. Finally, 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.« less

  15. Intermolecular Hybridization Creating Nanopore Orbital in a Supramolecular Hydrocarbon Sheet.

    PubMed

    Zhang, Yi-Qi; Björk, Jonas; Barth, Johannes V; Klappenberger, Florian

    2016-07-13

    Molecular orbital engineering is a key ingredient for the design of organic devices. Intermolecular hybridization promises efficient charge carrier transport but usually requires dense packing for significant wave function overlap. Here we use scanning tunneling spectroscopy to spatially resolve the electronic structure of a surface-confined nanoporous supramolecular sheet of a prototypical hydrocarbon compound featuring terminal alkyne (-CCH) groups. Surprisingly, localized nanopore orbitals are observed, with their electron density centered in the cavities surrounded by the functional moieties. Density functional theory calculations reveal that these new electronic states originate from the intermolecular hybridization of six in-plane π-orbitals of the carbon-carbon triple bonds, exhibiting significant electronic splitting and an energy downshift of approximately 1 eV. Importantly, these nanopore states are distinct from previously reported interfacial states. We unravel the underlying connection between the formation of nanopore orbital and geometric arrangements of functional groups, thus demonstrating the generality of applying related orbital engineering concepts in various types of porous organic structures. PMID:27253516

  16. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    PubMed Central

    Hathwar, Venkatesha R.; Sist, Mattia; Jørgensen, Mads R. V.; Mamakhel, Aref H.; Wang, Xiaoping; Hoffmann, Christina M.; Sugimoto, Kunihisa; Overgaard, Jacob; Iversen, Bo Brummerstedt

    2015-01-01

    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. PMID:26306198

  17. Characterization of intermolecular structure of β(2)-microglobulin core fragments in amyloid fibrils by vacuum-ultraviolet circular dichroism spectroscopy and circular dichroism theory.

    PubMed

    Matsuo, Koichi; Hiramatsu, Hirotsugu; Gekko, Kunihiko; Namatame, Hirofumi; Taniguchi, Masaki; Woody, Robert W

    2014-03-20

    Intermolecular structures are important factors for understanding the conformational properties of amyloid fibrils. In this study, vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy and circular dichroism (CD) theory were used for characterizing the intermolecular structures of β2-microglobulin (β2m) core fragments in the amyloid fibrils. The VUVCD spectra of β2m20-41, β2m21-31, and β2m21-29 fragments in the amyloid fibrils exhibited characteristic features, but they were affected not only by the backbone conformations but also by the aromatic side-chain conformations. To estimate the contributions of aromatic side-chains to the spectra, the theoretical spectra were calculated from the simulated structures of β2m21-29 amyloid fibrils with various types of β-sheet stacking (parallel or antiparallel) using CD theory. We found that the experimental spectrum of β2m21-29 fibrils is largely affected by aromatic-backbone couplings, which are induced by the interaction between transitions within the aromatic and backbone chromophores, and these couplings are sensitive to the type of stacking among the β-sheets of the fibrils. Further theoretical analyses of simulated structures incorporating mutated aromatic residues suggested that the β2m21-29 fibrils are composed of amyloid accumulations in which the parallel β-sheets stack in an antiparallel manner and that the characteristic Phe-Tyr interactions among the β-sheet stacks affect the aromatic-backbone coupling. These findings indicate that the coupling components, which depend on the characteristic intermolecular structures, induce the spectral differences among three fragments in the amyloid fibrils. These advanced spectral analyses using CD theory provide a useful method for characterizing the intermolecular structures of protein and peptide fragment complexes. PMID:24512563

  18. Substituent-induced intermolecular interaction in organic crystals revealed by precise band-dispersion measurements.

    PubMed

    Yamane, Hiroyuki; Kosugi, Nobuhiro

    2013-08-23

    We reveal quite small but different intermolecular valence band dispersions of sub-100-meV scale in crystalline films of Zn and Mn phthalocyanine (ZnPc and MnPc) and fluorinated ZnPc (F16ZnPc). The intermolecular transfer integrals are found to be reasonably dependent on the intermolecular distance with the 75±5 meV/Å relation. Furthermore, the angle-resolved photoemission spectra show anomalous dispersive behaviors such as phase flips and local-dimerization-derived periodicities, which originate from the site-specific intermolecular interaction induced by substituents. PMID:24010459

  19. Substituent-Induced Intermolecular Interaction in Organic Crystals Revealed by Precise Band-Dispersion Measurements

    NASA Astrophysics Data System (ADS)

    Yamane, Hiroyuki; Kosugi, Nobuhiro

    2013-08-01

    We reveal quite small but different intermolecular valence band dispersions of sub-100-meV scale in crystalline films of Zn and Mn phthalocyanine (ZnPc and MnPc) and fluorinated ZnPc (F16ZnPc). The intermolecular transfer integrals are found to be reasonably dependent on the intermolecular distance with the 75±5meV/Å relation. Furthermore, the angle-resolved photoemission spectra show anomalous dispersive behaviors such as phase flips and local-dimerization-derived periodicities, which originate from the site-specific intermolecular interaction induced by substituents.

  20. Transetherification on Polyols by Intra- and Intermolecular Nucleophilic Substitutions

    PubMed Central

    Muraoka, Takahiro; Adachi, Kota; Chowdhury, Rainy; Kinbara, Kazushi

    2014-01-01

    Transetherification on polyols involving intra- and intermolecular nucleophilic substitutions is reported. Di- or trialkoxide formation of propane-1,3-diol or 2-(hydroxymethyl)propane-1,3-diol derivatives by NaH triggers the reaction via oxetanes formation, where the order to add NaH and a polyol significantly influences the yields of products. It was demonstrated that the protective group on the pentaerythritol skeleton is apparently transferred to the hydrophilic and hydrophobic chain molecules bearing a leaving group in one-step, and a protective group conversion from tosyl to benzyl was successful using a benzyl-appending triol to afford a desired product in 67% yield. PMID:24663293

  1. Visualizing the orientational dependence of an intermolecular potential

    PubMed Central

    Sweetman, Adam; Rashid, Mohammad A.; Jarvis, Samuel P.; Dunn, Janette L.; Rahe, Philipp; Moriarty, Philip

    2016-01-01

    Scanning probe microscopy can now be used to map the properties of single molecules with intramolecular precision by functionalization of the apex of the scanning probe tip with a single atom or molecule. Here we report on the mapping of the three-dimensional potential between fullerene (C60) molecules in different relative orientations, with sub-Angstrom resolution, using dynamic force microscopy (DFM). We introduce a visualization method which is capable of directly imaging the variation in equilibrium binding energy of different molecular orientations. We model the interaction using both a simple approach based around analytical Lennard–Jones potentials, and with dispersion-force-corrected density functional theory (DFT), and show that the positional variation in the binding energy between the molecules is dominated by the onset of repulsive interactions. Our modelling suggests that variations in the dispersion interaction are masked by repulsive interactions even at displacements significantly larger than the equilibrium intermolecular separation. PMID:26879386

  2. Intermolecular forces and energies between ligands and receptors.

    PubMed

    Moy, V T; Florin, E L; Gaub, H E

    1994-10-14

    The recognition mechanisms and dissociation pathways of the avidin-biotin complex and of actin monomers in actin filaments were investigated. The unbinding forces of discrete complexes of avidin or streptavidin with biotin analogs are proportional to the enthalpy change of the complex formation but independent of changes in the free energy. This result indicates that the unbinding process is adiabatic and that entropic changes occur after unbinding. On the basis of the measured forces and binding energies, an effective rupture length of 9.5 +/- 1 angstroms was calculated for all biotin-avidin pairs and approximately 1 to 3 angstroms for the actin monomer-monomer interaction. A model for the correlation among binding forces, intermolecular potential, and molecular function is proposed. PMID:7939660

  3. Visualizing the orientational dependence of an intermolecular potential

    NASA Astrophysics Data System (ADS)

    Sweetman, Adam; Rashid, Mohammad A.; Jarvis, Samuel P.; Dunn, Janette L.; Rahe, Philipp; Moriarty, Philip

    2016-02-01

    Scanning probe microscopy can now be used to map the properties of single molecules with intramolecular precision by functionalization of the apex of the scanning probe tip with a single atom or molecule. Here we report on the mapping of the three-dimensional potential between fullerene (C60) molecules in different relative orientations, with sub-Angstrom resolution, using dynamic force microscopy (DFM). We introduce a visualization method which is capable of directly imaging the variation in equilibrium binding energy of different molecular orientations. We model the interaction using both a simple approach based around analytical Lennard-Jones potentials, and with dispersion-force-corrected density functional theory (DFT), and show that the positional variation in the binding energy between the molecules is dominated by the onset of repulsive interactions. Our modelling suggests that variations in the dispersion interaction are masked by repulsive interactions even at displacements significantly larger than the equilibrium intermolecular separation.

  4. Intermolecular interactions in the crystalline state of some organotellurium antioxidants

    NASA Astrophysics Data System (ADS)

    Engman, L.; Kania, I.; Oleksyn, B. J.; Śliwiński, J.; Wojtoń, A.

    2002-05-01

    The X-ray crystal structure analysis was performed for single crystals of bis (4-aminophenyl) telluride ( 1), bis [4-( N, N-dimethylamino)phenyl] telluride ( 2) and bis (4-hydroxyphenyl) telluride hemihydrate ( 3). The molecules of the diaryl tellurides 1- 3 display two types of non-planar conformations: 'butterfly' and 'T-shaped'. They differ in the torsion angles around Te-C bonds. Intermolecular hydrogen bonds occur between water molecules and hydroxyl groups in compound 3 and also between phenyl rings and proton donors in compounds 2 and 3 with -H⋯π distances 2.56(8)-2.95(6) Å. Also, in compounds 1 and 2 short -H⋯π contacts (3.02(4)-3.29(5) Å) were observed.

  5. Van der Waals Interactions in Density Functional Theory: Intermolecular Complexes

    NASA Astrophysics Data System (ADS)

    Kannemann, Felix; Becke, Axel

    2010-03-01

    Conventional density functional theory (GGA and hybrid functionals) fails to account for dispersion interactions and is therefore not applicable to systems where van der Waals interactions play a dominant role, such as intermolecular complexes and biomolecules. The exchange-hole dipole moment (XDM) dispersion model of Becke and Johnson [A. D. Becke and E. R. Johnson, J. Chem. Phys. 127, 154108 (2007)] corrects for this deficiency. We have previously shown that the XDM dispersion model can be combined with standard GGA functionals (PW86 for exchange and PBE for correlation) to give accurate binding energy curves for rare-gas diatomics [F. O. Kannemann and A. D. Becke, J. Chem. Theory Comput. 5, 719 (2009)]. Here we present further tests of the GGA-XDM method using benchmark sets including hydrogen bonding, electrostatic, dispersion and stacking interactions, and systems ranging from rare-gas diatomics to biomolecular complexes.

  6. Intermolecular vibrations and fast relaxations in supercooled ionic liquids

    NASA Astrophysics Data System (ADS)

    Ribeiro, Mauro C. C.

    2011-06-01

    Short-time dynamics of ionic liquids has been investigated by low-frequency Raman spectroscopy (4 < ω < 100 cm-1) within the supercooled liquid range. Raman spectra are reported for ionic liquids with the same anion, bis(trifluoromethylsulfonyl)imide, and different cations: 1-butyl-3-methylimidazolium, 1-hexyl-3-methylimidazolium, 1-butyl-1-methylpiperidinium, trimethylbutylammonium, and tributylmethylammonium. It is shown that low-frequency Raman spectroscopy provides similar results as optical Kerr effect (OKE) spectroscopy, which has been used to study intermolecular vibrations in ionic liquids. The comparison of ionic liquids containing aromatic and non-aromatic cations identifies the characteristic feature in Raman spectra usually assigned to librational motion of the imidazolium ring. The strength of the fast relaxations (quasi-elastic scattering, QES) and the intermolecular vibrational contribution (boson peak) of ionic liquids with non-aromatic cations are significantly lower than imidazolium ionic liquids. A correlation length assigned to the boson peak vibrations was estimated from the frequency of the maximum of the boson peak and experimental data of sound velocity. The correlation length related to the boson peak (˜19 Å) does not change with the length of the alkyl chain in imidazolium cations, in contrast to the position of the first-sharp diffraction peak observed in neutron and X-ray scattering measurements of ionic liquids. The rate of change of the QES intensity in the supercooled liquid range is compared with data of excess entropy, free volume, and mean-squared displacement recently reported for ionic liquids. The temperature dependence of the QES intensity in ionic liquids illustrates relationships between short-time dynamics and long-time structural relaxation that have been proposed for glass-forming liquids.

  7. Problem-Based Learning in 9th Grade Chemistry Class: "Intermolecular Forces"

    ERIC Educational Resources Information Center

    Tarhan, Leman; Ayar-Kayali, Hulya; Urek, Raziye Ozturk; Acar, Burcin

    2008-01-01

    This research study aims to examine the effectiveness of a problem-based learning (PBL) on 9th grade students' understanding of intermolecular forces (dipole-dipole forces, London dispersion forces and hydrogen bonding). The student's alternate conceptions about intermolecular bonding and their beliefs about PBL were also measured. Seventy-eight…

  8. Intermolecular interactions in rifabutin—2-hydroxypropyl-β-cyclodextrin—water solutions

    NASA Astrophysics Data System (ADS)

    Anshakova, A. V.; Yermolenko, Yu. V.; Konyukhov, V. Yu.; Polshakov, V. I.; Maksimenko, O. O.; Gelperina, S. E.

    2015-05-01

    The possibility of a intermolecular complex rifabutin (RB)-2-hydroxypropyl-β-cyclodextrin (HP-β-CD) formed as a result of the interaction of the piperidine fragment of the RB molecule and the hydrophobic cavity of the HP-β-CD molecule was found. The stability constant of the intermolecular complex was determined.

  9. The use of intermolecular potential functions in fitting pressure induced spectra

    NASA Technical Reports Server (NTRS)

    Goorvitch, D.; Silvaggio, P. M.; Boese, R. W.

    1981-01-01

    An example is presented which demonstrates the importance of using physically realistic derivatives of the intermolecular potential when fitting pressure-induced spectra. The use of nonrealistic derivatives may mask second-order temperature effects in the theory. As the temperature decreases, the intermolecular potential may have an important angular dependence.

  10. Benchmark Calculations of Three-Body Intermolecular Interactions and the Performance of Low-Cost Electronic Structure Methods.

    PubMed

    Řezáč, Jan; Huang, Yuanhang; Hobza, Pavel; Beran, Gregory J O

    2015-07-14

    Many-body noncovalent interactions are increasingly important in large and/or condensed-phase systems, but the current understanding of how well various models predict these interactions is limited. Here, benchmark complete-basis set coupled cluster singles, doubles, and perturbative triples (CCSD(T)) calculations have been performed to generate a new test set for three-body intermolecular interactions. This "3B-69" benchmark set includes three-body interaction energies for 69 total trimer structures, consisting of three structures from each of 23 different molecular crystals. By including structures that exhibit a variety of intermolecular interactions and packing arrangements, this set provides a stringent test for the ability of electronic structure methods to describe the correct physics involved in the interactions. Both MP2.5 (the average of second- and third-order Møller-Plesset perturbation theory) and spin-component-scaled CCSD for noncovalent interactions (SCS-MI-CCSD) perform well. MP2 handles the polarization aspects reasonably well, but it omits three-body dispersion. In contrast, many widely used density functionals corrected with three-body D3 dispersion correction perform comparatively poorly. The primary difficulty stems from the treatment of exchange and polarization in the functionals rather than from the dispersion correction, though the three-body dispersion may also be moderately underestimated by the D3 correction. PMID:26575743

  11. Chloro({2-[mesityl(quinolin-8-yl-κN)boryl]-3,5-dimethyl-phenyl}methyl-κC)palladium(II) as a catalyst for Heck reactions.

    PubMed

    Tamang, Sem Raj; Hoefelmeyer, James D

    2015-01-01

    We recently reported an air and moisture stable 16-electron borapalladacycle formed upon combination of 8-quinolyldimesitylborane with bis(benzonitrile)dichloropalladium(II). The complex features a tucked mesityl group formed upon metalation of an ortho-methyl group on a mesityl; however it is unusually stable due to contribution of the boron pz orbital in delocalizing the carbanion that gives rise to an η4-boratabutadiene fragment coordinated to Pd(II), as evidenced from crystallographic data. This complex was observed to be a highly active catalyst for the Heck reaction. Data of the catalyst activity are presented alongside data found in the literature, and initial comparison reveals that the borapalladacycle is quite active. The observed catalysis suggests the borapalladacycle readily undergoes reductive elimination; however the Pd(0) complex has not yet been isolated. Nevertheless, the ambiphilic ligand 8-quinolyldimesitylborane may be able to support palladium in different redox states. PMID:26193250

  12. Intercalation of organic molecules in 2D copper (II) nitroprusside: Intermolecular interactions and magnetic properties

    SciTech Connect

    Osiry, H.; Cano, A.; Lemus-Santana, A.A.; Rodríguez, A.; Carbonio, R.E.; Reguera, E.

    2015-10-15

    This contribution discusses the intercalation of imidazole and its 2-ethyl derivative, and pyridine in 2D copper nitroprusside. In the interlayer region, neighboring molecules remain interacting throu gh their dipole and quadrupole moments, which supports the solid 3D crystal structure. The crystal structure of this series of intercalation compounds was solved and refined from powder X-ray diffraction patterns complemented with spectroscopic information. The intermolecular interactions were studied from the refined crystal structures and low temperature magnetic measurements. Due to strong attractive forces between neighboring molecules, the resulting π–π cloud overlapping enables the ferromagnetic coupling between metal centers on neighboring layers, which was actually observed for the solids containing imidazole and pyridine as intercalated molecules. For these two solids, the magnetic data were properly described with a model of six neighbors. For the solid containing 2-ethylimidazole and for 2D copper nitroprusside, a model of four neighbors in a plane is sufficient to obtain a reliable data fitting. - Highlights: • Intercalation of organic molecules in 2D copper (II) nitroprusside. • Molecular properties of intercalation compounds of 2D copper (II) nitroprusside. • Magnetic properties of hybrid inorganic–organic solids. • Hybrid inorganic–organic 3D framework.

  13. Ground state analytical ab initio intermolecular potential for the Cl{sub 2}-water system

    SciTech Connect

    Hormain, Laureline; Monnerville, Maurice Toubin, Céline; Duflot, Denis; Pouilly, Brigitte; Briquez, Stéphane; Bernal-Uruchurtu, Margarita I.; Hernández-Lamoneda, Ramón

    2015-04-14

    The chlorine/water interface is of crucial importance in the context of atmospheric chemistry. Modeling the structure and dynamics at this interface requires an accurate description of the interaction potential energy surfaces. We propose here an analytical intermolecular potential that reproduces the interaction between the Cl{sub 2} molecule and a water molecule. Our functional form is fitted to a set of high level ab initio data using the coupled-cluster single double (triple)/aug-cc-p-VTZ level of electronic structure theory for the Cl{sub 2} − H{sub 2}O complex. The potential fitted to reproduce the three minima structures of 1:1 complex is validated by the comparison of ab initio results of Cl{sub 2} interacting with an increasing number of water molecules. Finally, the model potential is used to study the physisorption of Cl{sub 2} on a perfectly ordered hexagonal ice slab. The calculated adsorption energy, in the range 0.27 eV, shows a good agreement with previous experimental results.

  14. Intercalation of organic molecules in 2D copper (II) nitroprusside: Intermolecular interactions and magnetic properties

    NASA Astrophysics Data System (ADS)

    Osiry, H.; Cano, A.; Lemus-Santana, A. A.; Rodríguez, A.; Carbonio, R. E.; Reguera, E.

    2015-10-01

    This contribution discusses the intercalation of imidazole and its 2-ethyl derivative, and pyridine in 2D copper nitroprusside. In the interlayer region, neighboring molecules remain interacting throu gh their dipole and quadrupole moments, which supports the solid 3D crystal structure. The crystal structure of this series of intercalation compounds was solved and refined from powder X-ray diffraction patterns complemented with spectroscopic information. The intermolecular interactions were studied from the refined crystal structures and low temperature magnetic measurements. Due to strong attractive forces between neighboring molecules, the resulting π-π cloud overlapping enables the ferromagnetic coupling between metal centers on neighboring layers, which was actually observed for the solids containing imidazole and pyridine as intercalated molecules. For these two solids, the magnetic data were properly described with a model of six neighbors. For the solid containing 2-ethylimidazole and for 2D copper nitroprusside, a model of four neighbors in a plane is sufficient to obtain a reliable data fitting.

  15. Impact of Intermolecular Distance on Singlet Fission in a Series of TIPS Pentacene Compounds.

    PubMed

    Wu, Yishi; Liu, Ke; Liu, Huiying; Zhang, Yi; Zhang, Haoli; Yao, Jiannian; Fu, Hongbing

    2014-10-16

    Singlet fission has attracted considerable interest for its potential application in organic photovoltaics. However, the underlying microscopic mechanism is not well understood and the molecular parameters that govern SF efficiency remain unclear. We herein study the primary exciton photogeneration and evolution in the thin film of a series of pentacene derivatives (TIPS-Pn and ADPD-Pn) using femtosecond transient absorption spectroscopy. With a favorable "long-edge on" packing motif, the singlet-excited slip-stacked TIPS-Pn and ADPD-Pn molecules undergo ultrafast fission to produce triplet excitonic states with time constants of ∼0.3 ps. More importantly, the ADPD-Pn compound features a considerably higher triplet yield than TIPS-Pn (162 ± 10% vs 114 ± 15%). The enhanced electronic coupling as a result of closer interchromophore distance (3.33 Å for ADPD-Pn vs 3.40 Å for TIPS-Pn) is suggested to account for the much higher triplet yield for ADPD-Pn relative to that for TIPS-Pn, proving SF can be readily modulated by adjusting the intermolecular distance. PMID:26278592

  16. Intermolecular forces between low generation PAMAM dendrimer condensed DNA helices: role of cation architecture.

    PubMed

    An, Min; Parkin, Sean R; DeRouchey, Jason E

    2014-01-28

    In recent years, dendriplexes, complexes of cationic dendrimers with DNA, have become attractive DNA delivery vehicles due to their well-defined chemistries. To better understand the nature of the forces condensing dendriplexes, we studied low generation poly(amidoamine) (PAMAM) dendrimer-DNA complexes and compared them to comparably charged linear arginine peptides. Using osmotic stress coupled with X-ray scattering, we have investigated the effect of molecular chain architecture on DNA-DNA intermolecular forces that determine the net attraction and equilibrium interhelical distance within these polycation condensed DNA arrays. In order to compact DNA, linear cations are believed to bind in DNA grooves and to interact with the phosphate backbone of apposing helices. We have previously shown a length dependent attraction resulting in higher packaging densities with increasing charge for linear cations. Hyperbranched polycations, such as polycationic dendrimers, presumably would not be able to bind to DNA and correlate their charges in the same manner as linear cations. We show that attractive and repulsive force amplitudes in PAMAM-DNA assemblies display significantly different trends than comparably charged linear arginines resulting in lower DNA packaging densities with increasing PAMAM generation. The salt and pH dependencies of packaging in PAMAM dendrimer-DNA and linear arginine-DNA complexes were also investigated. Significant differences in the force curve behaviour and salt and pH sensitivities suggest that different binding modes may be present in DNA condensed by dendrimers when compared to linear polycations. PMID:24651934

  17. Accessing a Biologically Relevant Benzofuran Skeleton by a One-Pot Tandem Heck Alkynylation/Cyclization Reaction Using Well-Defined Palladium N-Heterocyclic Carbene Complexes.

    PubMed

    Kumar, Anuj; Gangwar, Manoj Kumar; Prakasham, A P; Mhatre, Darshan; Kalita, Alok Ch; Ghosh, Prasenjit

    2016-03-21

    Well-defined palladium N-heterocyclic carbene (NHC) complexes were employed in the one-pot tandem Heck alkynylation/cyclization sequence for preparing biologically relevant benzofuran compounds under copper-free conditions in a time-efficient step-reduced fashion. In particular, a series of binuclear palladium complexes, 1b-1e and 2b-2e, of the alkyl-bridged NHC ligands, namely, {1,1'-di-R1-4,4'-R2-di-1,2,4-triazoline-5,5'-diylid-2-ene] (R1 = i-Pr; R2 = -(CH2)2-, -(CH2)3-), and their mononuclear analogues, trans-(NHC)PdBr2(pyridine) (3b) and cis-(NHC)PdBr2(PPh3) (3c), successfully catalyzed the one-pot tandem Heck alkynylation/cyclization reaction of 2-iodophenol with a variety of terminal alkyne substrates, yielding 2-substituted benzofuran derivatives. The mononuclear complexes 3b and 3c were nearly half as active as the representative dinuclear analogue 1c under analogous reaction conditions, thereby implying that, at the same mole percent of the palladium loading, the monometallic 3b and 3c and the bimetallic 1c complexes were equally effective as catalysts. The two sites of the bimetallic complex 1c performed as two separate independent catalytic sites, displaying no cooperativity effect in the catalysis. Finally, the practical utility of the aforementioned catalysts was demonstrated for a representative catalyst 1c through the convenient synthesis of a key intermediate, 3-[2-(benzo[d][1,3]dioxol-5-yl)-7-methoxybenzofuran-5-yl]propan-1-ol, in a total-synthesis protocol of the natural product Egonol. PMID:26928799

  18. Femtosecond Fourier-transform spectroscopy of low-frequency intermolecular motions in weakly interacting liquids

    SciTech Connect

    Castner, E.W. Jr.; Chang, Y.J.; Melinger, J.S.; McMorrow, D.

    1993-07-01

    Recent work on the subject of solvation dynamics has concentrated on understanding the ultrafast dynamics of intermolecular interactions in strongly interacting, polar, and hydrogen-bonding solvents. In general, investigations into the effects of solvation dynamics on chemical reactions have concentrated on the highly polar liquids because it is in these solvents that the largest spectroscopic changes with solvent relaxation are observed. In these very polar liquids, however, the intermolecular dynamics are very complex, consisting of contributions from reorientational diffusion, inertially limited rotations, intermolecular vibrations involving both reorientational (librational) and translational degrees of freedom, and interaction-induced collisional effects. The role of collisional interaction-induced effects in shaping the intermolecular dynamics of molecular liquids has been a subject of considerable discussion. Molecular dynamics simulations have suggested that collisional effects can have a significant role in shaping the femtosecond dynamics and nonlinear-optical properties of molecular liquids. However, for anisotropic molecules, it is difficult to separate experimentally the collisional effects from other phenomena. In this paper the authors examine the intermolecular dynamics of the weakly interacting liquid carbon tetrachloride (CCl{sub 4}). Because carbon tetrachloride is a spherical top molecule (belonging to the T{sub d} point group), its intermolecular light-scattering spectrum is purely interaction-induced. By studying this purely collision-induced feature in CCl{sub 4}, the authors hope to gain insight on the lowest-frequency intermolecular vibrational behavior of more complex systems.

  19. Quantitative tomographic imaging of intermolecular FRET in small animals

    PubMed Central

    Venugopal, Vivek; Chen, Jin; Barroso, Margarida; Intes, Xavier

    2012-01-01

    Forster resonance energy transfer (FRET) is a nonradiative transfer of energy between two fluorescent molecules (a donor and an acceptor) in nanometer range proximity. FRET imaging methods have been applied to proteomic studies and drug discovery applications based on intermolecular FRET efficiency measurements and stoichiometric measurements of FRET interaction as quantitative parameters of interest. Importantly, FRET provides information about biomolecular interactions at a molecular level, well beyond the diffraction limits of standard microscopy techniques. The application of FRET to small animal imaging will allow biomedical researchers to investigate physiological processes occurring at nanometer range in vivo as well as in situ. In this work a new method for the quantitative reconstruction of FRET measurements in small animals, incorporating a full-field tomographic acquisition system with a Monte Carlo based hierarchical reconstruction scheme, is described and validated in murine models. Our main objective is to estimate the relative concentration of two forms of donor species, i.e., a donor molecule involved in FRETing to an acceptor close by and a nonFRETing donor molecule. PMID:23243567

  20. Thermal selectivity of intermolecular versus intramolecular reactions on surfaces

    PubMed Central

    Cirera, Borja; Giménez-Agulló, Nelson; Björk, Jonas; Martínez-Peña, Francisco; Martin-Jimenez, Alberto; Rodriguez-Fernandez, Jonathan; Pizarro, Ana M.; Otero, Roberto; Gallego, José M.; Ballester, Pablo; Galan-Mascaros, José R.; Ecija, David

    2016-01-01

    On-surface synthesis is a promising strategy for engineering heteroatomic covalent nanoarchitectures with prospects in electronics, optoelectronics and photovoltaics. Here we report the thermal tunability of reaction pathways of a molecular precursor in order to select intramolecular versus intermolecular reactions, yielding monomeric or polymeric phthalocyanine derivatives, respectively. Deposition of tetra-aza-porphyrin species bearing ethyl termini on Au(111) held at room temperature results in a close-packed assembly. Upon annealing from room temperature to 275 °C, the molecular precursors undergo a series of covalent reactions via their ethyl termini, giving rise to phthalocyanine tapes. However, deposition of the tetra-aza-porphyrin derivatives on Au(111) held at 300 °C results in the formation and self-assembly of monomeric phthalocyanines. A systematic scanning tunnelling microscopy study of reaction intermediates, combined with density functional calculations, suggests a [2+2] cycloaddition as responsible for the initial linkage between molecular precursors, whereas the monomeric reaction is rationalized as an electrocyclic ring closure. PMID:26964764

  1. Determination of stepsize parameters for intermolecular vibrational energy transfer

    SciTech Connect

    Tardy, D.C.

    1992-03-01

    Intermolecular energy transfer of highly excited polyatomic molecules plays an important role in many complex chemical systems: combustion, high temperature and atmospheric chemistry. By monitoring the relaxation of internal energy we have observed trends in the collisional efficiency ({beta}) for energy transfer as a function of the substrate's excitation energy and the complexities of substrate and deactivator. For a given substrate {beta} increases as the deactivator's mass increase to {approximately}30 amu and then exhibits a nearly constant value; this is due to a mass mismatch between the atoms of the colliders. In a homologous series of substrate molecules (C{sub 3}{minus}C{sub 8}) {beta} decreases as the number of atoms in the substrate increases; replacing F with H increases {beta}. All substrates, except for CF{sub 2}Cl{sub 2} and CF{sub 2}HCl below 10,000 cm{sup {minus}1}, exhibited that {beta} is independent of energy, i.e. <{Delta}E>{sub all} is linear with energy. The results are interpreted with a simple model which considers that {beta} is a function of the ocillators energy and its vibrational frequency. Limitations of current approximations used in high temperature unimolecular reactions were evaluated and better approximations were developed. The importance of energy transfer in product yields was observed for the photoactivation of perfluorocyclopropene and the photoproduction of difluoroethyne. 3 refs., 18 figs., 4 tabs.

  2. Evolutionary meandering of intermolecular interactions along the drift barrier

    PubMed Central

    Lynch, Michael; Hagner, Kyle

    2015-01-01

    Many cellular functions depend on highly specific intermolecular interactions, for example transcription factors and their DNA binding sites, microRNAs and their RNA binding sites, the interfaces between heterodimeric protein molecules, the stems in RNA molecules, and kinases and their response regulators in signal-transduction systems. Despite the need for complementarity between interacting partners, such pairwise systems seem to be capable of high levels of evolutionary divergence, even when subject to strong selection. Such behavior is a consequence of the diminishing advantages of increasing binding affinity between partners, the multiplicity of evolutionary pathways between selectively equivalent alternatives, and the stochastic nature of evolutionary processes. Because mutation pressure toward reduced affinity conflicts with selective pressure for greater interaction, situations can arise in which the expected distribution of the degree of matching between interacting partners is bimodal, even in the face of constant selection. Although biomolecules with larger numbers of interacting partners are subject to increased levels of evolutionary conservation, their more numerous partners need not converge on a single sequence motif or be increasingly constrained in more complex systems. These results suggest that most phylogenetic differences in the sequences of binding interfaces are not the result of adaptive fine tuning but a simple consequence of random genetic drift. PMID:25535374

  3. Interpreting the widespread nonlinear force spectra of intermolecular bonds

    PubMed Central

    Friddle, Raymond W.; Noy, Aleksandr; De Yoreo, James J.

    2012-01-01

    Single molecule force spectroscopy probes the strength, lifetime, and energetic details of intermolecular interactions in a simple experiment. A growing number of these studies have reported distinctly nonlinear trends in rupture force with loading rate that are typically explained in conventional models by invoking complex escape pathways. Recent analyses suggested that these trends should be expected even for simple barriers based on the basic assumptions of bond rupture dynamics and thus may represent the norm rather than the exception. Here we explore how these nonlinear trends reflect the two fundamental regimes of bond rupture: (i) a near-equilibrium regime, produced either by bond reforming in the case of a single bond or by asynchronized rupture of multiple individual bonds, and (ii) a kinetic regime produced by fast, non-equilibrium bond rupture. We analyze both single- and multi-bonded cases, describe the full evolution of the system as it transitions between near- and far-from-equilibrium loading regimes, and show that both interpretations produce essentially identical force spectra. Data from 10 different molecular systems show that this model provides a comprehensive description of force spectra for a diverse suite of bonds over experimentally relevant loading rates, removes the inconsistencies of previous interpretations of transition state distances, and gives ready access to both kinetic and thermodynamic information about the interaction. These results imply that single-molecule binding free energies for a vast number of bonds have already been measured. PMID:22869712

  4. Thermal selectivity of intermolecular versus intramolecular reactions on surfaces

    NASA Astrophysics Data System (ADS)

    Cirera, Borja; Giménez-Agulló, Nelson; Björk, Jonas; Martínez-Peña, Francisco; Martin-Jimenez, Alberto; Rodriguez-Fernandez, Jonathan; Pizarro, Ana M.; Otero, Roberto; Gallego, José M.; Ballester, Pablo; Galan-Mascaros, José R.; Ecija, David

    2016-03-01

    On-surface synthesis is a promising strategy for engineering heteroatomic covalent nanoarchitectures with prospects in electronics, optoelectronics and photovoltaics. Here we report the thermal tunability of reaction pathways of a molecular precursor in order to select intramolecular versus intermolecular reactions, yielding monomeric or polymeric phthalocyanine derivatives, respectively. Deposition of tetra-aza-porphyrin species bearing ethyl termini on Au(111) held at room temperature results in a close-packed assembly. Upon annealing from room temperature to 275 °C, the molecular precursors undergo a series of covalent reactions via their ethyl termini, giving rise to phthalocyanine tapes. However, deposition of the tetra-aza-porphyrin derivatives on Au(111) held at 300 °C results in the formation and self-assembly of monomeric phthalocyanines. A systematic scanning tunnelling microscopy study of reaction intermediates, combined with density functional calculations, suggests a [2+2] cycloaddition as responsible for the initial linkage between molecular precursors, whereas the monomeric reaction is rationalized as an electrocyclic ring closure.

  5. Development of an optimized intermolecular potential for sulfur dioxide.

    PubMed

    Ketko, MaryBeth H; Kamath, Ganesh; Potoff, Jeffrey J

    2011-05-01

    A new force field for sulfur dioxide, capable of predicting accurately the vapor-liquid equilibria, critical properties, vapor pressure, and heats of vaporization is presented. The new force field reproduces the saturated liquid densities, vapor pressures and heats of vaporization to within 0.5, 2, and 2% of experiment, respectively. The predicted critical properties and the normal boiling point are in excellent agreement with experimental results. Pair distribution functions are calculated for the S-S, S-O, and O-O interactions are in close agreement with neutron and X-ray scattering experiments. In addition to the new force field, similar calculations are performed for four SO(2) intermolecular potentials proposed by Sokolic et al. (Sokolic, F.; Guissani, Y. and Guillot, B. J. Phys. Chem. 1985, 89, 3023], which show that these models work reasonably well near the state point where they were originally parametrized, but large errors in the predicted coexistence properties are displayed at higher and lower temperatures. Comparison of the radial distribution functions show the local structure is only weakly affected by the different force field parameters. PMID:21476503

  6. Intermolecular interactions of reduced nicotinamide adenine dinucleotide (NADH) in solution

    NASA Astrophysics Data System (ADS)

    Jasensky, Joshua; Junaid Farooqi, M.; Urayama, Paul

    2008-10-01

    Nicotinamide adenine dinucleotide (NAD^+/NADH) is a coenzyme involved in cellular respiration as an electron transporter. In aqueous solution, the molecule exhibits a folding transition characterized by the stacking of its aromatic moieties. A transition to an unfolded conformation is possible using chemical denaturants like methanol. Because the reduced NADH form is fluorescent, the folding transition can be monitored using fluorescence spectroscopy, e.g., via a blue-shift in the UV-excited emission peak upon methanol unfolding. Here we present evidence of interactions between NADH molecules in solution. We measure the excited-state emission from NADH at various concentrations (1-100 μM in MOPS buffer, pH 7.5; 337-nm wavelength excitation). Unlike for the folded form, the emission peak wavelength of the unfolded form is concentration dependent, exhibiting a red-shift with higher NADH concentration, suggesting the presence of intermolecular interactions. An understanding of NADH spectra in solution would assist in interpreting intercellular NADH measurements used for the in vivo monitoring cellular energy metabolism.

  7. Combined Electrostatics and Hydrogen Bonding Determine PIP2 Intermolecular Interactions

    PubMed Central

    Levental, Ilya; Cebers, Andrejs; Janmey, Paul A.

    2010-01-01

    Membrane lipids are active contributors to cell function as key mediators in signaling pathways of inflammation, apoptosis, migration, and proliferation. Recent work on multimolecular lipid structures suggests a critical role for lipid organization in regulating the function of both lipids and proteins. Of particular interest in this context are the polyphosphoinositides (PPI’s), specifically phosphatidylinositol (4,5) bisphosphate (PIP2). The cellular functions of PIP2 are numerous but the factors controlling targeting of PIP2 to specific proteins and organization of PIP2 in the inner leaflet of the plasma membrane remain poorly understood. To analyze the organization of PIP2 in a simplified planar system, we used Langmuir monolayers to study the effects of subphase conditions on monolayers of purified naturally derived PIP2 and other anionic or zwitterionic phospholipids. We report a significant molecular area expanding effect of subphase monovalent salts on PIP2 at biologically relevant surface densities. This effect is shown to be specific to PIP2 and independent of subphase pH. Chaotropic agents (e.g. salts, trehalose, urea, temperature) that disrupt water structure and the ability of water to mediate intermolecular hydrogen bonding also specifically expanded PIP2 monolayers. These results suggest a combination of water-mediated hydrogen bonding and headgroup charge in determining the organization of PIP2, and may provide an explanation for the unique functionality of PIP2 compared to other anionic phospholipids. PMID:18572937

  8. The origins of the directionality of noncovalent intermolecular interactions.

    PubMed

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

    2016-01-01

    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. PMID:26010349

  9. When do we need attractive-repulsive intermolecular potentials?

    SciTech Connect

    Venkattraman, Ayyaswamy

    2014-12-09

    The role of attractive-repulsive interactions in direct simulation Monte Carlo (DSMC) simulations is studied by comparing with traditional purely repulsive interactions. The larger collision cross section of the long-range LJ potential is shown to result in a higher collision frequency and hence a lower mean free path, by at least a factor of two, for given conditions. This results in a faster relaxation to equilibrium as is shown by comparing the fourth and sixth moments of the molecular velocity distribution obtained using 0-D DSMC simulations. A 1-D Fourier-Couette flow with a large temperature and velocity difference between the walls is used to show that matching transport properties will result in identical solutions using both LJPA and VSS models in the near-continuum regime. However, flows in the transitional regime with Knudsen number, Kn ∼ 0.5 show a dependence on the intermolecular potential in spite of matching the viscosity coefficient due to differences in the collision frequency. Attractive-repulsive potentials should be used when both transport coefficients and collision frequencies should be matched.

  10. Polyelectrolyte brushes in mixed ionic medium studied via intermolecular forces

    NASA Astrophysics Data System (ADS)

    Farina, Robert; Laugel, Nicolas; Pincus, Philip; Tirrell, Matthew

    2011-03-01

    The vast uses and applications of polyelectrolyte brushes make them an attractive field of research especially with the growing interest in responsive materials. Polymers which respond via changes in temperature, pH, and ionic strength are increasingly being used for applications in drug delivery, chemical gating, etc. When polyelectrolyte brushes are found in either nature (e.g., surfaces of cartilage and mammalian lung interiors) or commercially (e.g., skin care products, shampoo, and surfaces of medical devices) they are always surrounded by mixed ionic medium. This makes the study of these brushes in varying ionic environments extremely relevant for both current and future potential applications. The polyelectrolyte brushes in this work are diblock co-polymers of poly-styrene sulfonate (N=420) and poly-t-butyl styrene (N=20) which tethers to a hydrophobic surface allowing for a purely thermodynamic study of the polyelectrolyte chains. Intermolecular forces between two brushes are measured using the SFA. As multi-valent concentrations are increased, the brushes collapse internally and form strong adhesion between one another after contact (properties not seen in a purely mono-valent environment).

  11. Evolutionary meandering of intermolecular interactions along the drift barrier.

    PubMed

    Lynch, Michael; Hagner, Kyle

    2015-01-01

    Many cellular functions depend on highly specific intermolecular interactions, for example transcription factors and their DNA binding sites, microRNAs and their RNA binding sites, the interfaces between heterodimeric protein molecules, the stems in RNA molecules, and kinases and their response regulators in signal-transduction systems. Despite the need for complementarity between interacting partners, such pairwise systems seem to be capable of high levels of evolutionary divergence, even when subject to strong selection. Such behavior is a consequence of the diminishing advantages of increasing binding affinity between partners, the multiplicity of evolutionary pathways between selectively equivalent alternatives, and the stochastic nature of evolutionary processes. Because mutation pressure toward reduced affinity conflicts with selective pressure for greater interaction, situations can arise in which the expected distribution of the degree of matching between interacting partners is bimodal, even in the face of constant selection. Although biomolecules with larger numbers of interacting partners are subject to increased levels of evolutionary conservation, their more numerous partners need not converge on a single sequence motif or be increasingly constrained in more complex systems. These results suggest that most phylogenetic differences in the sequences of binding interfaces are not the result of adaptive fine tuning but a simple consequence of random genetic drift. PMID:25535374

  12. Thermal selectivity of intermolecular versus intramolecular reactions on surfaces.

    PubMed

    Cirera, Borja; Giménez-Agulló, Nelson; Björk, Jonas; Martínez-Peña, Francisco; Martin-Jimenez, Alberto; Rodriguez-Fernandez, Jonathan; Pizarro, Ana M; Otero, Roberto; Gallego, José M; Ballester, Pablo; Galan-Mascaros, José R; Ecija, David

    2016-01-01

    On-surface synthesis is a promising strategy for engineering heteroatomic covalent nanoarchitectures with prospects in electronics, optoelectronics and photovoltaics. Here we report the thermal tunability of reaction pathways of a molecular precursor in order to select intramolecular versus intermolecular reactions, yielding monomeric or polymeric phthalocyanine derivatives, respectively. Deposition of tetra-aza-porphyrin species bearing ethyl termini on Au(111) held at room temperature results in a close-packed assembly. Upon annealing from room temperature to 275 °C, the molecular precursors undergo a series of covalent reactions via their ethyl termini, giving rise to phthalocyanine tapes. However, deposition of the tetra-aza-porphyrin derivatives on Au(111) held at 300 °C results in the formation and self-assembly of monomeric phthalocyanines. A systematic scanning tunnelling microscopy study of reaction intermediates, combined with density functional calculations, suggests a [2+2] cycloaddition as responsible for the initial linkage between molecular precursors, whereas the monomeric reaction is rationalized as an electrocyclic ring closure. PMID:26964764

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

    PubMed

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

    2008-09-21

    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 (tau(1)) is the measure of the fastest ET rate (tau(1)=tau(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 tau(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 approximately 0.4 for aromatic amines and approximately 0.8 for aliphatic amines. Beyond these dilutions in the two respective cases of the amine systems, the tau(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 (pi-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 pi-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

  14. Non-covalent intermolecular carbon-carbon interactions in polyynes.

    PubMed

    Remya, Karunakaran; Suresh, Cherumuttathu H

    2015-10-28

    Polyynes, the smaller analogues of one dimensional infinite chain carbon allotrope carbyne, have been studied for the type and strength of the intermolecular interactions in their dimer and tetramer complexes using density functional theory. The nature of end group functionalities and the chain length of the polyynes are varied to assess their role in modulating the non-covalent interaction energy. As seen in molecular electrostatic potential analysis, all the polyyne complexes showed a multitude of non-covalent CC interactions, resulting from complementary electrostatic interactions between relatively electron rich formal triple bond region of one monomer and the electron deficient formal single bond region of the other monomer. This type of paired (C[triple bond, length as m-dash]C)(C-C) bonding interaction, also characterized using quantum theory of atoms-in-molecules, increases with increase in the monomer chain length leading to substantial increase in interaction energy (Eint); -1.07 kcal mol(-1) for the acetylene dimer to -45.83 kcal mol(-1) for the 50yne dimer. The magnitude of Eint increases with substitutions at end positions of the polyyne and this effect persists even up to 50 triple bonds, the largest chain length analyzed in this paper. The role of CC interactions in stabilizing the polyyne dimers is also shown by sliding one monomer in a dimer over the other, which resulted in multiple minima with a reduced number of CC interactions and lower values of Eint. Furthermore, strong cooperativity in the CC bond strength in tetramers is observed as the interaction energy per monomer (Em) of the polyyne is 2.5-2.8 times higher compared to that of the dimer in a test set of four tetramers. The huge gain in energy observed in large polyyene dimers and tetramers predicts the formation of polyyne bundles which may find use in the design of new functional molecular materials. PMID:26412713

  15. Kinetic theory for flows of nonhomogeneous rodlike liquid crystalline polymers with a nonlocal intermolecular potential.

    PubMed

    Wang, Qi; E, Weinan; Liu, Chun; Zhang, Pingwen

    2002-05-01

    The Doi kinetic theory for flows of homogeneous, rodlike liquid crystalline polymers (LCPs) is extended to model flows of nonhomogeneous, rodlike LCPs through a nonlocal (long-range) intermolecular potential. The theory features (i) a nonlocal, anisotropic, effective intermolecular potential in an integral form that is consistent with the chemical potential, (ii) short-range elasticity as well as long-range isotropic and anisotropic elasticity, (iii) a closed-form stress expression accounting for the nonlocal molecular interaction, and (iv) an extra elastic body force exclusively associated with the integral form of the intermolecular potential. With the effective intermolecular potential, the theory is proven to be well posed in that it warrants a positive entropy production and thereby the second law of thermodynamics. Approximate theories are obtained by gradient expansions of the number density function in the free energy density. PMID:12059561

  16. The intermolecular vibrational dynamics of substituted benzene and cyclohexane liquids, studied by femtosecond OHD-RIKES

    SciTech Connect

    Castner, E.W. Jr.; Chang, Yong Joon

    1995-06-01

    By using the femtosecond optical-heterodyne detected, Raman-induced Kerr effect spectroscopy (OHD-RIKES), we have studied the intermolecular dynamics of toluene, benzyl alcohol, benzonitrile, cyclohexane, and methylcyclohexane in both the time and frequency domains.

  17. Determining the Intermolecular Potential Energy in a Gas: A Physical Chemistry Experiment

    ERIC Educational Resources Information Center

    Olbregts, J.; Walgraeve, J. P.

    1976-01-01

    Describes an experiment in which gas viscosity coefficients over a large temperature range are used to determine the parameters of the intermolecular potential energy and other properties such as virial coefficients. (MLH)

  18. Identification and measurement of intermolecular interaction in polyester/polystyrene blends by FTIR-photoacoustic spectrometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fourier transform infrared photoacoustic spectrometry was used to reveal and identify n-p type intermolecular interaction formed in plastic comprising binary blends of polystyrene and a biodegradable polymer, either polylactic acid, polycaprolactone or poly(tetramethyleneadipate-co-terephthalate)....

  19. Relativistic effects in the intermolecular interaction-induced nuclear magnetic resonance parameters of xenon dimer.

    PubMed

    Hanni, Matti; Lantto, Perttu; Ilias, Miroslav; Jensen, Hans Jorgen Aagaard; Vaara, Juha

    2007-10-28

    Relativistic effects on the (129)Xe nuclear magnetic resonance shielding and (131)Xe nuclear quadrupole coupling (NQC) tensors are examined in the weakly bound Xe(2) system at different levels of theory including the relativistic four-component Dirac-Hartree-Fock (DHF) method. The intermolecular interaction-induced binary chemical shift delta, the anisotropy of the shielding tensor Deltasigma, and the NQC constant along the internuclear axis chi( parallel) are calculated as a function of the internuclear distance. DHF shielding calculations are carried out using gauge-including atomic orbitals. For comparison, the full leading-order one-electron Breit-Pauli perturbation theory (BPPT) is applied using a common gauge origin. Electron correlation effects are studied at the nonrelativistic (NR) coupled-cluster singles and doubles with perturbational triples [CCSD(T)] level of theory. The fully relativistic second-order Moller-Plesset many-body perturbation (DMP2) theory is used to examine the cross coupling between correlation and relativity on NQC. The same is investigated for delta and Deltasigma by BPPT with a density functional theory model. A semiquantitative agreement between the BPPT and DHF binary property curves is obtained for delta and Deltasigma in Xe(2). For these properties, the currently most complete theoretical description is obtained by a piecewise approximation where the uncorrelated relativistic DHF results obtained close to the basis-set limit are corrected, on the one hand, for NR correlation effects and, on the other hand, for the BPPT-based cross coupling of relativity and correlation. For chi( parallel), the fully relativistic DMP2 results obtain a correction for NR correlation effects beyond MP2. The computed temperature dependence of the second virial coefficient of the (129)Xe nuclear shielding is compared to experiment in Xe gas. Our best results, obtained with the piecewise approximation for the binary chemical shift combined with the

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

    PubMed

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

    2015-10-21

    Theoretical studies of the potential energy surface (PES) and bound states are performed for the N2-N2O 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 N2O monomer is near the N2 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)N2-N2O and (15)N2-N2O. The accuracy of the PES is validated by the good agreement between theoretical and experimental results for the transition frequencies and spectroscopic parameters. PMID:26493904

  1. Theoretical studies for the N{sub 2}–N{sub 2}O van der Waals complex: The potential energy surface, intermolecular vibrations, and rotational transition frequencies

    SciTech Connect

    Zheng, Rui; Zheng, Limin; Yang, Minghui E-mail: yangmh@wipm.ac.cn; Lu, Yunpeng E-mail: yangmh@wipm.ac.cn

    2015-10-21

    Theoretical studies of the potential energy surface (PES) and bound states are performed for the N{sub 2}–N{sub 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{sub 2}O monomer is near the N{sub 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{sup −1}, which is in good agreement with the available experimental data of 22.334 cm{sup −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 {sup 14}N{sub 2}–N{sub 2}O and {sup 15}N{sub 2}–N{sub 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.

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

    SciTech Connect

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

    1994-11-15

    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[sub 2], N[sub 2], HCl, CO[sub 2], and --fluorene), fluorobenzene--Ar and --Kr, aniline--Ar, and fluorene--Ar and --Ar[sub 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.

  3. A supramolecular photoswitch constructed by intermolecular hydrogen bond between BTEPy and TTF COOH

    NASA Astrophysics Data System (ADS)

    Feng, Yanli; Zhang, Qiong; Tan, Wenjuan; Zhang, Deqing; Tu, Yaoquan; Ågren, Hans; Tian, He

    2008-04-01

    A novel supramolecular photoswitch containing bisthienylethene-pyridine (BTEPy) and carboxyl attached tetrathiafluvalene (TTF-COOH) was constructed via intermolecular hydrogen bond. FT-IR spectra, XPS characterizations, 1H NMR and theoretical calculation were carried out to verify the formation of the intermolecular hydrogen bond. The supramolecular self-assemblies BTEPy · 2TTF show good photochromic properties. A molecular switch with UV/vis light as inputs and electrochemical signals as outputs was obtained.

  4. Catalysis in the Service of Green Chemistry: Nobel Prize-Winning Palladium-Catalysed Cross-Couplings, Run in Water at Room Temperature

    PubMed Central

    Lipshutz, Bruce H.; Taft, Benjamin R.; Abela, Alexander R.; Ghorai, Subir; Krasovskiy, Arkady; Duplais, Christophe

    2012-01-01

    Palladium-catalysed cross-couplings, in particular Heck, Suzuki-Miyaura and Negishi reactions developed over three decades ago, are routinely carried out in organic solvents. However, alternative media are currently of considerable interest given an increasing emphasis on making organic processes ‘greener’; for example, by minimising organic waste in the form of organic solvents. Water is the obvious leading candidate in this regard. Hence, this review focuses on the application of micellar catalysis, in which a ‘designer’ surfactant enables these award-winning coupling reactions to be run in water at room temperature. PMID:23555153

  5. Interatomic and intermolecular Coulombic decay: the coming of age story

    NASA Astrophysics Data System (ADS)

    Jahnke, T.

    2015-04-01

    In pioneering work by Cederbaum et al an excitation mechanism was proposed that occurs only in loosely bound matter (Cederbaum et al 1997 Phys. Rev. Lett. 79 4778): it turned out, that (in particular) in cases where a local Auger decay is energetically forbidden, an excited atom or molecule is able to decay in a scheme which was termed ‘interatomic Coulombic decay’ (or ‘intermolecular Coulombic decay’) (ICD). As ICD occurs, the excitation energy is released by transferring it to an atomic or molecular neighbor of the initially excited particle. As a consequence the neighboring atom or molecule is ionized as it receives the energy. A few years later the existence of ICD was confirmed experimentally (Marburger et al 2003 Phys. Rev. Lett. 90 203401; Jahnke et al 2004 Phys. Rev. Lett. 93 163401; Öhrwall et al 2004 Phys. Rev. Lett. 93 173401) by different techniques. Since this time it has been found that ICD is not (as initially suspected) an exotic feature of van der Waals or hydrogen bonded systems, but that ICD is a very general and common feature occurring after a manifold of excitation schemes and in numerous weakly bound systems, as revealed by more than 200 publications. It was even demonstrated, that ICD can become more efficient than a local Auger decay in some system. This review will concentrate on recent experimental investigations on ICD. It will briefly introduce the phenomenon and give a short summary of the ‘early years’ of ICD (a detailed view on this episode of investigations can be found in the review article by U Hergenhahn with the same title (Hergenhahn 2011 J. Electron Spectrosc. Relat. Phenom. 184 78)). More recent articles will be presented that investigate the relevance of ICD in biological systems and possible radiation damage of such systems due to ICD. The occurrence of ICD and ICD-like processes after different excitation schemes and in different systems is covered in the middle section: in that context the helium dimer (He2

  6. Direct Synthesis of Palladium Catalyst on Supporting WS2 Nanotubes and its Reactivity in Cross-Coupling Reactions.

    PubMed

    Višić, Bojana; Cohen, Hagai; Popovitz-Biro, Ronit; Tenne, Reshef; Sokolov, Viacheslav I; Abramova, Natalya V; Buyanovskaya, Anastasiya G; Dzvonkovskii, Sergei L; Lependina, Olga L

    2015-10-01

    Palladium nanoparticles were deposited on multiwall WS2 nanotubes. The composite nanoparticles were characterized by a variety of techniques. The Pd nanoparticles were deposited uniformly on the surface of WS2 nanotubes. An epitaxial relationship between the (111) plane of Pd and the (013) plane of WS2 was mostly observed. The composite nanoparticles were found to perform efficiently as catalysts for cross-coupling (Heck and Suzuki) reactions. The role of the nanotubes' support in the catalytic process is briefly discussed. PMID:26097214

  7. Ferromagnetic intermolecular interactions in a series of organic mixed crystals of galvinoxyl radical and its precursory closed shell compound

    NASA Astrophysics Data System (ADS)

    Awaga, Kunio; Sugano, Tadashi; Kinoshita, Minoru

    1986-08-01

    The magnetic properties of the 4:1, 6:1, 9:1, and 19:1 mixed crystals of galvinoxyl (4-[[3,5-bis(1,1-dimethylethyl)-4-oxo-2,5-cyclohexadien-1-ylidene]methyl]-2,6 -bis(1,1-dimethylethyl) phenoxy) radical and its precursory closed shell compound, hydrogalvinoxyl, have been studied. From the measurements of the temperature dependence of the magnetic susceptibility, it is found that the ferromagnetic intermolecular interactions, which are lost below about 85 K in pure galvinoxyl because of the phase transition, are maintained down to 2 K in these mixed crystals, and that the number of galvinoxyl radicals keeping the ferromagnetically coupled structure at low temperature increases as the concentration of hydrogalvinoxyl increases. The magnetic behavior of the mixed crystals at low temperature depends on the thermal history of the sample and is well interpreted by assuming the presence of a glassy state into which the high-temperature, ferromagnetically coupled phase is quenched. The magnetization curves show the spin multiplicity to be almost in proportion to the radical concentration in the mixed crystal and may be qualitatively understood by assuming that the mixed crystal is an assembly of one-dimensional chain segments partitioned by hydrogalvinoxyl within which the galvinoxyl radicals are coupled ferromagnetically.

  8. Comment on 'Intermolecular interaction potentials of the methane dimer from the local density approximation'

    SciTech Connect

    Li, Arvin H.-T.; Chao, S.D.

    2006-01-15

    To verify the recently calculated intermolecular interaction potentials of the methane dimer within the density functional theory using the (Perdew) local density approximation (LDA) [Chen et al., Phys. Rev. A 69, 034701 (2004)], we have performed a parallel series of calculations using the LDA/6-311++G (3df, 3pd) level of theory with selected exchange functionals (B, G96, MPW, O, PBE, PW91, S, and XA). None of the above calculated intermolecular interaction potentials from the local density approximation reproduce the results reported in the commented paper. In addition, we point out the inappropriateness of using the Lennard-Jones function to model the long-range parts of the calculated intermolecular interaction potentials, as suggested positively by Chen et al.

  9. Enantioselective intermolecular cross Rauhut-Currier reactions of activated alkenes with acrolein.

    PubMed

    Zhou, Wei; Chen, Peng; Tao, Mengna; Su, Xiao; Zhao, Qingjie; Zhang, Junliang

    2016-06-18

    The enantioselective intermolecular cross Rauhut-Currier reaction of acrolein with active olefins has been a long-standing challenge because of the competitive MBH reaction and polymerization. Herein a highly enantioselective intermolecular cross Rauhut-Currier reaction of acrolein with 3-acyl acrylates and 2-ene-1,4-diones, which is enabled by newly designed Peng-Phos catalysts. This method is scalable and highly enantioselective (up to 96% ee). Several transformations of the R-C products are carried out to showcase the synthetic utility. PMID:27225510

  10. Computational Analysis of Intermolecular Coulombic Decay Effects in DNA nucleotide Photoionization

    NASA Astrophysics Data System (ADS)

    Vargas, E. L.; Robertson, J.; Andrianarijaona, V. M.

    2016-03-01

    Intermolecular Coulombic Decay (ICD) is the process of how electrons return to their original state after excitation and how this affects their immediate environment. In a previous research presentationwe had considered the hypothetical applications of Intermolecular Coulombic Decay on the adhesiveness of coding proteins within DNA molecules. This presentation is a continuation of the previous in that the results of our DFT-based computational calculations of the ionization potentials of nucleotides and their excitation energies will be presented, as well as how they influence their surroundings. Author would like to acknowledge the PUC Student Senate for financial assistance.

  11. Intermolecular potential functions and high resolution molecular spectroscopy of weakly bound complexes. Final progress report

    SciTech Connect

    Muenter, J.S.

    1997-04-01

    This report describes accomplishments over the past year in research supported by this grant. Two papers published in this period are briefly discussed. The general goal of the work is to consolidate the understanding of experimental results through a theoretical model of intermolecular potential energy surfaces. Progress in the experimental and theoretical phases of the program are presented and immediate goals outlined. The ability to construct analytic intermolecular potential functions that accurately predict the energy of interaction between small molecules will have great impact in many areas of chemistry, biochemistry, and biology.

  12. Analysis of hypersonic nozzles including vibrational nonequilibrium and intermolecular force effects

    NASA Technical Reports Server (NTRS)

    Canupp, Patrick W.; Candler, Graham V.; Perkins, John N.; Erickson, Wayne D.

    1992-01-01

    A computational fluid dynamics algorithm is developed for the study of high-pressure axisymmetric hypersonic nozzle flows. The effects of intermolecular forces and vibrational nonequilibrium are included in the analysis. The numerical simulation of gases with an arbitrary equation of state is discussed. Simulations for a high pressure nozzle (p(0) = 138 MPa) demonstrate that both intermolecular forces and vibrational nonequilibrium have a significant affect on the flow. These nonideal effects tend to increase the Mach number at the nozzle exit plane. Thus, they must be included in the design and analysis of high pressure hypersonic nozzles.

  13. Modulation of the intermolecular interaction of myoglobin by removal of the heme

    PubMed Central

    Imamura, Hiroshi; Morita, Takeshi; Sumi, Tomonari; Isogai, Yasuhiro; Kato, Minoru; Nishikawa, Keiko

    2013-01-01

    Toward understanding intermolecular interactions governing self-association of proteins, the present study investigated a model protein, myoglobin, using a small-angle X-ray scattering technique. It has been known that removal of the heme makes myoglobin aggregation-prone. The interparticle interferences of the holomyoglobin and the apomyoglobin were compared in terms of the structure factor. Analysis of the structure factor using a model potential of Derjaguin–Laudau–Verwey–Overbeek (DLVO) suggests that the intermolecular interaction potential of apomyoglobin is more attractive than that of holomyoglobin at short range from the protein molecule. PMID:24121340

  14. Virtual photon exchange, intermolecular interactions and optical response functions

    NASA Astrophysics Data System (ADS)

    Salam, A.

    2015-11-01

    According to molecular quantum electrodynamics, coupling between material particles occurs due to an exchange of one or more virtual photons. In this work, the relationship between polarisability and hyperpolarisability tensors of atoms and molecules that feature in linear and nonlinear optical processes, and their analytically continued form in the complex frequency domain that appear in formulae describing fundamental inter-particle interactions, is studied. Examples involving a single virtual photon exchange, which are linearly proportional to electric dipole moments at each centre, include the electrostatic energy and the resonant transfer of excitation energy. The Casimir-Polder dispersion potential, and its discriminatory counterpart applicable to coupled chiral molecules, are used to illustrate response properties depending on the exchange of two virtual photons. Meanwhile, the energy shift between two hyperpolarisable species, a higher order discriminatory contribution to the dispersion potential, is employed to represent forces arising from the three virtual photon exchange. It is shown that for energy shifts that are quadratic or bilinear or cubic in the transition dipole moment, it is necessary to account for all two- and three-photon optical processes, such as absorption, emission and linear and nonlinear scattering of light in order to arrive at the correct form of the molecular response tensor.

  15. Pigment Spectra and Intermolecular Interaction Potentials in Glasses and Proteins

    PubMed Central

    Renge, I.; van Grondelle, R.; Dekker, J. P.

    2007-01-01

    A model is proposed for chromophore optical spectra in solids over a wide range of temperatures and pressures. Inhomogeneous band shapes and their pressure dependence, as well as baric shift coefficients of spectral lines, selected by the frequency, were derived using Lennard-Jones potentials of the ground and excited states. Quadratic electron-phonon coupling constants, describing the thermal shift and broadening of zero-phonon lines, were also calculated. Experimentally, thermal shift and broadening of spectral holes were studied between 5 and 40 K for a synthetic pigment, chlorin, embedded in polymer hosts. The baric effects on holes were determined by applying hydrostatic He gas pressure up to 200 bar, at 6 K. Absorption spectra of pheophytin a, chlorophyll a, and β-carotene in polymers and plant photosystem II CP47 complex were measured between 5 (or 77) and 300 K, and subject to Voigtian deconvolution. A narrowing of inhomogeneous bandwidth with increasing temperature, predicted on the basis of hole behavior, was observed as the shrinking of Gaussian spectral component. The Lorentzian broadening was ascribed to optical dephasing up to 300 K in transitions with weak to moderate linear electron-phonon coupling strength. The thermal broadening is purely Gaussian in multiphonon transitions (S2 band of β-carotene, Soret bands of tetrapyrrolic pigments), and the Lorentz process appears to be suppressed, indicating a lack of exponential dephasing. Density, polarity, polarizability, compressibility, and other local parameters of the pigment binding sites in biologically relevant systems can be deduced from spectroscopic data, provided that sufficient background information is available. PMID:17557783

  16. Solvent-Controlled, Tunable β-OAc and β-H Elimination in Rh(III)-Catalyzed Allyl Acetate and Aryl Amide Coupling via C-H Activation.

    PubMed

    Dai, Huimin; Yu, Chao; Wang, Zihao; Yan, Hong; Lu, Changsheng

    2016-07-15

    The Heck reaction between arenes and allyl acetate has led to cinnamyl derivatives and allyl products depending on the regioselectivity of β-elimination. The regioselectivity can be controlled by the solvent in the Rh(III)-catalyzed arene-allyl acetate coupling via C-H activation: (1) in THF, cinnamyl derivatives via β-H elimination were generated; (2) in MeOH, allyl products via β-OAc elimination were produced. Both routes have advantages such as excellent γ-selectivity toward allyl acetate, good to excellent yields, and broad substrate scope. PMID:27351917

  17. THE INTERACTION OF PARAMAGNETIC RELAXATION REAGENTS WITH INTRA- AND INTERMOLECULAR HYDROGEN BONDED PHENOLS

    EPA Science Inventory

    Intermolecular electron-nuclear 13-C relaxation times (T(1)sup e's) from solutions containing the paramagnetic relaxation reagent (PARR), Cr(acac)3, used in conjunction with 13-C T(1)'s in diamagnetic solutions (intramolecular 13-C - (1)H dipolar T(1)'s) provide a significant inc...

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

    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.

  19. Using Molecular Dynamics Simulation to Reinforce Student Understanding of Intermolecular Forces

    ERIC Educational Resources Information Center

    Burkholder, Phillip R.; Purser, Gordon H.; Cole, Renee S.

    2008-01-01

    Intermolecular forces play an important role in many aspects of chemistry ranging from inorganic to biological chemistry. These forces dictate molecular conformation, species aggregation (including self-assembly), trends in solubility and boiling points, adsorption characteristics, viscosity, phase changes, surface tension, capillary action, vapor…

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

    ERIC Educational Resources Information Center

    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…

  1. An Analysis of Two Textbooks on the Topic of Intermolecular Forces

    ERIC Educational Resources Information Center

    Tan, Daniel Kim Chwee; Seng, Chan Kim

    2004-01-01

    This paper describes the analysis of two commonly used high school (Grades 11 and 12) chemistry textbooks in Singapore to determine if the content presented in the topic of intermolecular forces is consistent with the concepts and propositional knowledge identified by the authors as essential for the learning and understanding of the topic…

  2. Palladium-Catalyzed Intermolecular Aerobic Annulation of o-Alkenylanilines and Alkynes for Quinoline Synthesis.

    PubMed

    Zheng, Jia; Li, Zun; Huang, Liangbin; Wu, Wanqing; Li, Jianxiao; Jiang, Huanfeng

    2016-08-01

    A new approach to construct 2,3-disubstituted quinolines is described via Pd-catalyzed oxidative cyclization of o-vinylanilines and alkynes with molecular oxygen. This transformation is supposed to undergo intermolecular amination of alkyne, insertion of the olefin, and oxidative cleavage of C-C bond sequence. PMID:27418021

  3. Palladium(0)-Catalyzed Intermolecular Allylic Dearomatization of Indoles by a Formal [4+2] Cycloaddition Reaction.

    PubMed

    Gao, Run-Duo; Xu, Qing-Long; Zhang, Bo; Gu, Yiting; Dai, Li-Xin; You, Shu-Li

    2016-08-01

    Bridged indoline derivatives were synthesized by an intermolecular Pd-catalyzed allylic dearomatization reaction of substituted indoles. The reaction between indoles and allyl carbonates bearing a nucleophilic alcohol side-chain proceeds in a cascade fashion, providing bridged indolines in excellent enantioselectivity. PMID:27321285

  4. Copper-catalyzed intermolecular chloroazidation of α,β-unsaturated amides.

    PubMed

    Chen, Long; Xing, Haotian; Zhang, Huaibin; Jiang, Zhong-Xing; Yang, Zhigang

    2016-08-21

    A highly practical copper-catalyzed intermolecular chloroazidation of α,β-unsaturated amides has been described, giving a series of azidochlorides in good-to-excellent yields. The stable azidoiodine(iii) reagent and SOCl2 were used as azide and chlorine sources, respectively. The synthetic applications of this protocol were also explored by a variety of synthetically useful transformations. PMID:27462802

  5. Intermolecular Sulfur···Oxygen Interactions: Theoretical and Statistical Investigations.

    PubMed

    Zhang, Xuejin; Gong, Zhen; Li, Jian; Lu, Tao

    2015-10-26

    Intermolecular S···O interactions are very common and are important in biological systems, but until recently, the presence of these contacts in protein-ligand systems largely depended on serendipitous discovery instead of rational design. Here we provide insight into the phenomenon of intermolecular S···O contacts by focusing on three sulfur-containing aromatic rings. Quantum mechanics is employed to characterize the strength and directionality of the S···O interactions and to determine their energy dependence on their geometric parameters. Protein Data Bank mining is performed to systematically determine the occurrence and geometry of intermolecular S···O interactions, and several representative examples are discussed. Three typical cases are investigated using a combined quantum mechanics/molecular mechanics approach to demonstrate the potential of these interactions in improving binding affinities and physiochemical properties. Overall, our work elucidates the structures and energy features of intermolecular S···O interactions and addresses their use in molecular design. PMID:26393532

  6. Resolving Intra- and Inter-Molecular Structure with Non-Contact Atomic Force Microscopy

    PubMed Central

    Jarvis, Samuel Paul

    2015-01-01

    A major challenge in molecular investigations at surfaces has been to image individual molecules, and the assemblies they form, with single-bond resolution. Scanning probe microscopy, with its exceptionally high resolution, is ideally suited to this goal. With the introduction of methods exploiting molecularly-terminated tips, where the apex of the probe is, for example, terminated with a single CO, Xe or H2 molecule, scanning probe methods can now achieve higher resolution than ever before. In this review, some of the landmark results related to attaining intramolecular resolution with non-contact atomic force microscopy (NC-AFM) are summarised before focussing on recent reports probing molecular assemblies where apparent intermolecular features have been observed. Several groups have now highlighted the critical role that flexure in the tip-sample junction plays in producing the exceptionally sharp images of both intra- and apparent inter-molecular structure. In the latter case, the features have been identified as imaging artefacts, rather than real intermolecular bonds. This review discusses the potential for NC-AFM to provide exceptional resolution of supramolecular assemblies stabilised via a variety of intermolecular forces and highlights the potential challenges and pitfalls involved in interpreting bonding interactions. PMID:26307976

  7. Investigation of intermolecular interactions between fluorene-based conjugated polymers using the dispersion-corrected DFT

    NASA Astrophysics Data System (ADS)

    Ayoub, Sarah; Lagowski, Jolanta B.

    2015-03-01

    Alternating triphenylamine-fluorene, TPAFn (n=1-3), and fluorene-oxadiazole OxFn (n=1-3) conjugated copolymers are important components of novel high-efficiency multi-layer organic light-emitting diodes (OLEDs). In this work, we investigate the intermolecular interactions between the various combinations of monomers of OxFn-TPAFn (n=1-3) copolymers using the dispersion-corrected density functional theory (B97D) method. The monomer combinations are taken with and without the presence of long alkyl chains in order to study the effect of side-chains on the polymer backbone intermolecular interactions. The dispersion effect is studied by comparing the structures of the interacting monomers with those in vacuum. In addition, we calculate intermolecular distances, energy gaps and binding energies of monomer dimers corresponding to different pairings of OxFn-TPAFn (n=1-3) monomers. Our results show that the combination of OxF3-TPAF2 monomers exhibites the highest binding energy, closest intermolecular distance, and the best matching of chain lengths amongst all of the combinations of OxFn-TPAFn (n=1-3) monomers. Experiments have shown that OxF3-TPAF2 combination gives the best performance for OLEDS made of OxF-TPAF polymer layers.

  8. Frontier orbital symmetry control of intermolecular electron transfer. Final report, September 15, 1988--December 31, 1994

    SciTech Connect

    Stevens, B.

    1997-07-01

    This report discusses the following topics: the recovery of intermolecular transfer parameters from fluorescence quenching in liquids; photoinduced intramolecular electron transfer in flexible donor/space/acceptor systems containing an extended unsaturated spacer; electron transfer sensitized reaction; the recovery of solute and fractal dimensions from electron transfer quenching data; and frontier orbital symmetry control of back electron transfer.

  9. Intermolecular forces and nonbonded interactions: Superoperator nonlinear time-dependent density-functional-theory response approach

    SciTech Connect

    Harbola, Upendra; Mukamel, Shaul

    2004-11-01

    Electrostatic and dispersive interactions of polarizable molecules are expressed in terms of generalized (nonretarded) charge-density response functions of the isolated molecules, which in turn are expanded using the collective electronic oscillator (CEO) eigenmodes of linearized time-dependent density-functional theory. Closed expressions for the intermolecular energy are derived to sixth order in charge fluctuation amplitudes.

  10. Resolving Intra- and Inter-Molecular Structure with Non-Contact Atomic Force Microscopy.

    PubMed

    Jarvis, Samuel Paul

    2015-01-01

    A major challenge in molecular investigations at surfaces has been to image individual molecules, and the assemblies they form, with single-bond resolution. Scanning probe microscopy, with its exceptionally high resolution, is ideally suited to this goal. With the introduction of methods exploiting molecularly-terminated tips, where the apex of the probe is, for example, terminated with a single CO, Xe or H2 molecule, scanning probe methods can now achieve higher resolution than ever before. In this review, some of the landmark results related to attaining intramolecular resolution with non-contact atomic force microscopy (NC-AFM) are summarised before focussing on recent reports probing molecular assemblies where apparent intermolecular features have been observed. Several groups have now highlighted the critical role that flexure in the tip-sample junction plays in producing the exceptionally sharp images of both intra- and apparent inter-molecular structure. In the latter case, the features have been identified as imaging artefacts, rather than real intermolecular bonds. This review discusses the potential for NC-AFM to provide exceptional resolution of supramolecular assemblies stabilised via a variety of intermolecular forces and highlights the potential challenges and pitfalls involved in interpreting bonding interactions. PMID:26307976

  11. Intermolecular Cyclopropanation of Styrenes Using Iodine and Visible Light via Carbon-Iodine Bond Cleavage.

    PubMed

    Usami, Kaoru; Nagasawa, Yoshitomo; Yamaguchi, Eiji; Tada, Norihiro; Itoh, Akichika

    2016-01-01

    The intermolecular cyclopropanation of aromatic olefins with activated methylene compounds using iodine and visible light irradiation was described. This reaction proceeds under rare-metal-free conditions. Styrenes with various substituted groups (alkyl and electron-withdrawing groups) provided corresponding cyclopropanes in moderate to good yields. PMID:26654114

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

    SciTech Connect

    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.

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

    SciTech Connect

    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 CF{sub 3}X—B that involve one trifluorohalomethane CF{sub 3}X (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 (NH{sub 3} and PH{sub 3}), two n-pairs (H{sub 2}O and H{sub 2}S), two n-pairs with an unsaturated bond (H{sub 2}CO and H{sub 2}CS), and a single π-pair (C{sub 2}H{sub 4}) and two π-pairs (C{sub 2}H{sub 2}). 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.

  14. Intermolecular electronic interactions in the primary charge separation in bacterial photosynthesis

    SciTech Connect

    Plato, M.; Moebius, K.; Michel-Beyerle, M.E.; Bixon, M.; Jortner, J. )

    1988-10-26

    In this paper the intermolecular overlap approximation is used to calculate the relative magnitudes of the electronic transfer integrals between the excited singlet state ({sup 1}P*) of the bacteriochlorophyll dimer (P) and the accessory bacteriochlorophyll (B) and between B{sup {minus}} and bacteriopheopytin (H), along the L and M subunits of the reaction center (RC) of Rps. viridis. The ratio of the electron-transfer integrals for B{sub L}{sup {minus}}H{sub L}{sup {minus}}B{sub L}H{sub L}{minus} and for B{sub M}{sup {minus}}H{sub M}{minus}B{sub M}H{sub M}{sup {minus}} was calculated to be 2.1 {plus minus} 0.5, which together with the value of 2.8 {plus minus} 0.7 for the ratio of the transfer integrals for {sup 1}P*B{sub L}-P{sup +}B{sub L}- and for {sup 1}P*B{sub M}-P{sup +}B{sub M}- results in the electronic contribution of 33 {plus minus} 16 to the ratio k{sub L}/k{sub m} of the rate constants k{sub L} and k{sub M} for the primary charge separation across the L and M branches of the RC, respectively. The asymmetry of the electronic coupling terms, which originates from the combination of the asymmetry in the charge distribution of {sup 1}P* and of structural asymmetry of the P-M and B-H arrangements across the L and M subunits, provides a major contribution to the unidirectionality of the charge separation in bacterial photosynthesis. A significant contribution to the transfer integrals between adjacent pigments originates from nearby methyl groups through hyperconjugation. The ratio 6 {plus minus} 2 of the transfer integrals for {sup 1}P*B{sub L}-P{sup +}B{sub L}- and for B{sub L}-H{sub L}-B{sub L}H{sub L}- was utilized to estimate the energetic parameters required to ensure the dominance of the superexchange mediated unistep electron transfer {sup 1}P*BH {yields} P{sup +}BH{sup {minus}} over the thermally activated {sup 1}P*B {yields} P{sup +}B{sup {minus}} process. 31 refs., 6 figs., 2 tabs.

  15. Pd-Catalyzed Intramolecular Heck Reaction, C(sp(2))-H Activation, 1,4-Pd Migration, and Aminopalladation: Chemoselective Synthesis of Dihydroindeno[1,2,3-kl]acridines and 3-Arylindoles.

    PubMed

    Gu, Zheng-Yang; Liu, Cheng-Guo; Wang, Shun-Yi; Ji, Shun-Jun

    2016-05-20

    Palladium-catalyzed intramolecular Heck reaction and aminopalladation of N-(2-(1-phenylvinyl)phenyl)aniline for the efficient synthesis of dihydroindeno[1,2,3-kl]acridines and 3-arylindoles via tuning of the phosphine ligands and solvents under two optimized conditions are reported. The reaction follows a 1,4-Pd migration, aminopalladation, C(sp(2))-H activation, as well as five- and six-membered-ring fusion to form different products. The dihydroindeno[1,2,3-kl]acridine derivatives showed higher triplet energy (ET) levels than common blue phosphorescent dopant and may serve as good host candidates for blue triplet emitters. PMID:27137482

  16. Accurate ab initio intermolecular potential energy surface for the quintet state of the O2(3Σg-)-O2(3Σg-) dimer

    NASA Astrophysics Data System (ADS)

    Bartolomei, Massimiliano; Carmona-Novillo, Estela; Hernández, Marta I.; Campos-Martínez, José; Hernandez-Lamoneda, Ramón

    2008-06-01

    A new potential energy surface (PES) for the quintet state of rigid O2(3Σg-)+O2(3Σg-) has been obtained using restricted coupled-cluster theory with singles, doubles, and perturbative triple excitations [RCCSD(T)]. A large number of relative orientations of the monomers (65) and intermolecular distances (17) have been considered. A spherical harmonic expansion of the interaction potential has been built from the ab initio data. It involves 29 terms, as a consequence of the large anisotropy of the interaction. The spherically averaged term agrees quite well with the one obtained from analysis of total integral cross sections. The absolute minimum of the PES corresponds to the crossed (D2d) structure (X shape) with an intermolecular distance of 6.224 bohrs and a well depth of 16.27 meV. Interestingly, the PES presents another (local) minimum close in energy (15.66 meV) at 6.50 bohrs and within a planar skewed geometry (S shape). We find that the origin of this second structure is due to the orientational dependence of the spin-exchange interactions which break the spin degeneracy and leads to three distinct intermolecular PESs with singlet, triplet, and quintet multiplicities. The lowest vibrational bound states of the O2-O2 dimer have been obtained and it is found that they reflect the above mentioned topological features of the PES: The first allowed bound state for the 16O isotope has an X structure but the next state is just 0.12 meV higher in energy and exhibits an S shape.

  17. Target-catalyzed hairpin assembly and intramolecular/intermolecular co-reaction for signal amplified electrochemiluminescent detection of microRNA.

    PubMed

    Yu, Yan-Qing; Wang, Ji-Peng; Zhao, Min; Hong, Lin-Ru; Chai, Ya-Qin; Yuan, Ruo; Zhuo, Ying

    2016-03-15

    Herein, a new electrochemiluminescence (ECL) strategy for enzyme-free microRNA-21 (miR-21) amplified detection was designed based on target-catalyzed hairpin assembly by combining the signal-amplification capability of both intramolecular and intermolecular ECL co-reaction. In this strategy, two hairpin DNA probes of H1 and H2 were designed as capture probes and detection probes, respectively. To be specific, the capture probes of H1 were immobilized on the multilayer interface of AuNPs and thiosemicarbazide (TSC) assembly on the single-walled carbon nanohorns decorated electrode, while the detection probes of H2 was anchored on the nanocarriers of gold nanoparticals functionalized reduced graphene oxide (Au-rGO) which were tagged with the self-enhanced ruthenium complex (PEI-Ru(ΙΙ)) in advance. Based on the target-catalyzed hairpin assembly, target miR-21 could trigger the hybridization of H1 and H2 to further be released for initiating the next hybridization process to capture a large number of H2 bioconjugates on the sensing surface. Herein, the TSC was used not only as a coupling reagent to attach the AuNPs via Au-S and Au-N bonds but also as a novel intermolecular coreactant to enhance the ECL intensity, and the PEI-Ru(ΙΙ) as emitters exhibited enhanced ECL efficiency. Therefore, a strong ECL signal was achieved by the dual amplification strategies of target recycle and the intramolecular/intermolecular co-reaction of PEI-Ru(ΙΙ) and TSC. The designed protocol provided an ultrasensitive ECL detection of miR-21 down to the sub-femtomolar level with a linear response about 6 orders of magnitude (from 1.0 × 10(-16)M to 1.0 × 10(-11)M) with a relatively low detection limit of 0.03 fM (S/N=3). PMID:26453905

  18. The Development of Versatile Methods for Palladium-Catalyzed Coupling Reactions of Aryl Electrophiles Through the Use of P(t-Bu)3 and PCy3 as Ligands

    PubMed Central

    FU, GREGORY C.

    2009-01-01

    CONSPECTUS Metal-catalyzed coupling reactions of aryl electrophiles with organometallics and with olefins serve as unusually effective tools for forming new carbon-carbon bonds. By 1998, researchers had developed catalysts that achieved reactions of aryl iodides, bromides, and triflates. Nevertheless, many noteworthy challenges remained, among them: couplings of aryl iodides, bromides, and triflates under mild conditions (at room temperature, for example); couplings of hindered reaction partners; and, couplings of inexpensive aryl chlorides. This Account highlights some of the progress that has been made over the past decade, largely through the appropriate choice of ligand, in achieving these synthetic objectives. In particular, we have established that palladium in combination with a bulky trialkylphosphine accomplishes a broad spectrum of coupling processes, including Suzuki, Stille, Negishi, and Heck reactions. These methods have been applied in a wide array of settings, such as natural-product synthesis, materials science, and bioorganic chemistry. PMID:18947239

  19. Intermolecular potential parameters and combining rules determined from viscosity data

    SciTech Connect

    Bastien, Lucas A.J.; Price, Phillip N.; Brown, Nancy J.

    2010-05-07

    The Law of Corresponding States has been demonstrated for a number of pure substances and binary mixtures, and provides evidence that the transport properties viscosity and diffusion can be determined from a molecular shape function, often taken to be a Lennard-Jones 12-6 potential, that requires two scaling parameters: a well depth {var_epsilon}{sub ij} and a collision diameter {sigma}{sub ij}, both of which depend on the interacting species i and j. We obtain estimates for {var_epsilon}{sub ij} and {sigma}{sub ij} of interacting species by finding the values that provide the best fit to viscosity data for binary mixtures, and compare these to calculated parameters using several 'combining rules' that have been suggested for determining parameter values for binary collisions from parameter values that describe collisions of like molecules. Different combining rules give different values for {sigma}{sub ij} and {var_epsilon}{sub ij} and for some mixtures the differences between these values and the best-fit parameter values are rather large. There is a curve in ({var_epsilon}{sub ij}, {sigma}{sub ij}) space such that parameter values on the curve generate a calculated viscosity in good agreement with measurements for a pure gas or a binary mixture. The various combining rules produce couples of parameters {var_epsilon}{sub ij}, {sigma}{sub ij} that lie close to the curve and therefore generate predicted mixture viscosities in satisfactory agreement with experiment. Although the combining rules were found to underpredict the viscosity in most of the cases, Kong's rule was found to work better than the others, but none of the combining rules consistently yields parameter values near the best-fit values, suggesting that improved rules could be developed.

  20. Intermolecular electron transfer from intramolecular excitation and coherent acoustic phonon generation in a hydrogen-bonded charge-transfer solid.

    PubMed

    Rury, Aaron S; Sorenson, Shayne; Dawlaty, Jahan M

    2016-03-14

    Organic materials that produce coherent lattice phonon excitations in response to external stimuli may provide next generation solutions in a wide range of applications. However, for these materials to lead to functional devices in technology, a full understanding of the possible driving forces of coherent lattice phonon generation must be attained. To facilitate the achievement of this goal, we have undertaken an optical spectroscopic study of an organic charge-transfer material formed from the ubiquitous reduction-oxidation pair hydroquinone and p-benzoquinone. Upon pumping this material, known as quinhydrone, on its intermolecular charge transfer resonance as well as an intramolecular resonance of p-benzoquinone, we find sub-cm(-1) oscillations whose dispersion with probe energy resembles that of a coherent acoustic phonon that we argue is coherently excited following changes in the electron density of quinhydrone. Using the dynamical information from these ultrafast pump-probe measurements, we find that the fastest process we can resolve does not change whether we pump quinhydrone at either energy. Electron-phonon coupling from both ultrafast coherent vibrational and steady-state resonance Raman spectroscopies allows us to determine that intramolecular electronic excitation of p-benzoquinone also drives the electron transfer process in quinhydrone. These results demonstrate the wide range of electronic excitations of the parent of molecules found in many functional organic materials that can drive coherent lattice phonon excitations useful for applications in electronics, photonics, and information technology. PMID:26979698

  1. Intermolecular electron transfer from intramolecular excitation and coherent acoustic phonon generation in a hydrogen-bonded charge-transfer solid

    NASA Astrophysics Data System (ADS)

    Rury, Aaron S.; Sorenson, Shayne; Dawlaty, Jahan M.

    2016-03-01

    Organic materials that produce coherent lattice phonon excitations in response to external stimuli may provide next generation solutions in a wide range of applications. However, for these materials to lead to functional devices in technology, a full understanding of the possible driving forces of coherent lattice phonon generation must be attained. To facilitate the achievement of this goal, we have undertaken an optical spectroscopic study of an organic charge-transfer material formed from the ubiquitous reduction-oxidation pair hydroquinone and p-benzoquinone. Upon pumping this material, known as quinhydrone, on its intermolecular charge transfer resonance as well as an intramolecular resonance of p-benzoquinone, we find sub-cm-1 oscillations whose dispersion with probe energy resembles that of a coherent acoustic phonon that we argue is coherently excited following changes in the electron density of quinhydrone. Using the dynamical information from these ultrafast pump-probe measurements, we find that the fastest process we can resolve does not change whether we pump quinhydrone at either energy. Electron-phonon coupling from both ultrafast coherent vibrational and steady-state resonance Raman spectroscopies allows us to determine that intramolecular electronic excitation of p-benzoquinone also drives the electron transfer process in quinhydrone. These results demonstrate the wide range of electronic excitations of the parent of molecules found in many functional organic materials that can drive coherent lattice phonon excitations useful for applications in electronics, photonics, and information technology.

  2. Molecular and intermolecular effects in collagen fibril mechanics: a multiscale analytical model compared with atomistic and experimental studies.

    PubMed

    Marino, Michele

    2016-02-01

    Both atomistic and experimental studies reveal the dependence of collagen fibril mechanics on biochemical and biophysical features such as, for instance, cross-link density, water content and protein sequence. In order to move toward a multiscale structural description of biological tissues, a novel analytical model for collagen fibril mechanics is herein presented. The model is based on a multiscale approach that incorporates and couples: thermal fluctuations in collagen molecules; the uncoiling of collagen triple helix; the stretching of molecular backbone; the straightening of the telopeptide in which covalent cross-links form; slip-pulse mechanisms due to the rupture of intermolecular weak bonds; molecular interstrand delamination due to the rupture of intramolecular weak bonds; the rupture of covalent bonds within molecular strands. The effectiveness of the proposed approach is verified by comparison with available atomistic results and experimental data, highlighting the importance of cross-link density in tuning collagen fibril mechanics. The typical three-region shape and hysteresis behavior of fibril constitutive response, as well as the transition from a yielding-like to a brittle-like behavior, are recovered with a special insight on the underlying nanoscale mechanisms. The model is based on parameters with a clear biophysical and biochemical meaning, resulting in a promising tool for analyzing the effect of pathological or pharmacological-induced histochemical alterations on the functional mechanical response of collagenous tissues. PMID:26220454

  3. The weakly bound He-HCCCN complex: High-resolution microwave spectra and intermolecular potential-energy surface

    NASA Astrophysics Data System (ADS)

    Topic, Wendy C.; Jäger, Wolfgang

    2005-08-01

    Rotational spectra of the weakly bound He-HCCCN and He-DCCCN van der Waals complexes were observed using a pulsed-nozzle Fourier-transform microwave spectrometer in the 7-26-GHz frequency region. Nuclear quadrupole hyperfine structures due to the N14 and D nuclei (both with nuclear-spin quantum number I =1) were resolved and assigned. Both strong a and weaker b-type transitions were observed and the assigned transitions were used to fit the parameters of a distortable asymmetric rotor model. The dimers are floppy, near T-shaped complexes. Three intermolecular potential-energy surfaces were calculated using the coupled-cluster method with single and double excitations and noniterative inclusion of triple excitations. Bound-state rotational energy levels supported by these surfaces were determined. The quality of the potential-energy surfaces was assessed by comparing the experimental and calculated transition frequencies and also the corresponding spectroscopic parameters. Simple scaling of the surfaces improved both the transition frequencies and spectroscopic constants. Five other recently reported surfaces [O. Akin-Ojo, R. Bukowski, and K. Szalewicz, J. Chem. Phys. 119, 8379 (2003)], calculated using a variety of methods, and their agreement with spectroscopic properties of He-HCCCN are discussed.

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

    NASA Astrophysics Data System (ADS)

    Chavda, Bhavin R.; Gandhi, Sahaj A.; Dubey, Rahul P.; Patel, Urmila H.; Barot, Vijay M.

    2016-05-01

    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.

  5. Changes of microstructure characteristics and intermolecular interactions of preserved egg white gel during pickling.

    PubMed

    Zhao, Yan; Chen, Zhangyi; Li, Jianke; Xu, Mingsheng; Shao, Yaoyao; Tu, Yonggang

    2016-07-15

    Changes in gel microstructure characteristics and in intermolecular interactions of preserved egg whites during pickling were investigated. Spin-spin relaxation times of preserved egg whites significantly decreased in the first 8 days and remained unchanged after the 16th day. SEM images revealed a three-dimensional gel network, interwoven with a loose linear fibrous mesh structure. The protein gel mesh structure became more regular, smaller, and compacted with pickling time. Free sulfhydryl contents in the egg whites increased significantly, while total sulfhydryl contents dramatically decreased during pickling. The primary intermolecular forces in the preserved egg white gels were ionic and disulfide bonds. Secondary forces included hydrophobic interaction and relatively few hydrogen bonds. During the first 8 days, the proportion of ionic bonds sharply decreased, and that of disulfide bonds increased over the first 24 days. PMID:26948621

  6. Intramolecular and Intermolecular Interactions in Hybrid Organic-Inorganic Alucone Films Grown by Molecular Layer Deposition.

    PubMed

    Park, Yi-Seul; Kim, Hyein; Cho, Boram; Lee, Chaeyun; Choi, Sung-Eun; Sung, Myung Mo; Lee, Jin Seok

    2016-07-13

    Investigation of molecular interactions in polymeric films is crucial for understanding and engineering multiscale physical phenomena correlated to device function and performance, but this often involves a compromise between theoretical and experimental data, because of poor film uniformity. Here, we report the intramolecular and intermolecular interactions inside the ultrathin and conformal hybrid organic-inorganic alucone films grown by molecular layer deposition, based on sequential and self-limiting surface reactions. Varying the carbon chain length of organic precursors, which affects their molecular flexibility, caused intramolecular interactions such as double reactions by bending of the molecular backbone, resulting in formation of hole vacancies in the films. Furthermore, intermolecular interactions in alucone polymeric films are dependent on the thermal kinetics of molecules, leading to binding failures and cross-linking at low and high growth temperatures, respectively. We illustrate these key interactions and identify molecular geometries and potential energies by density functional theory calculations. PMID:27314844

  7. Influence of intermolecular potentials on rarefied gas flows: Fast spectral solutions of the Boltzmann equation

    NASA Astrophysics Data System (ADS)

    Wu, Lei; Liu, Haihu; Zhang, Yonghao; Reese, Jason M.

    2015-08-01

    The Boltzmann equation with an arbitrary intermolecular potential is solved by the fast spectral method. As examples, noble gases described by the Lennard-Jones potential are considered. The accuracy of the method is assessed by comparing both transport coefficients with variational solutions and mass/heat flow rates in Poiseuille/thermal transpiration flows with results from the discrete velocity method. The fast spectral method is then applied to Fourier and Couette flows between two parallel plates, and the influence of the intermolecular potential on various flow properties is investigated. It is found that for gas flows with the same rarefaction parameter, differences in the heat flux in Fourier flow and the shear stress in Couette flow are small. However, differences in other quantities such as density, temperature, and velocity can be very large.

  8. Controlled electrical doping of organic semiconductors: a combined intra- and intermolecular perspective from first principles.

    PubMed

    Joo, Bora; Kim, Eung-Gun

    2016-07-21

    The process of introducing extra charge carriers into organic semiconductors, or simply molecular doping, takes place via intermolecular charge transfer from the donor to the acceptor molecule. Using density functional theory calculations on diverse donor-acceptor pairs, we show that there are two modes of charge transfer; in one, charge transfer is controlled by the sign and in the other, by the magnitude of the donor HOMO-acceptor LUMO level offset. Despite doping being an intermolecular process, the identification of the transfer modes requires a full account of intramolecular geometric changes during charge transfer. We further show that the degree of charge transfer can be represented entirely by the reorganization energy, a common measure of geometric changes, of either the donor or the acceptor. PMID:27314750

  9. Probing acid-amide intermolecular hydrogen bonding by NMR spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Chaudhari, Sachin Rama; Suryaprakash, N.

    2012-05-01

    Benzene carboxylic acids and benzamide act as their self-complement in molecular recognition to form inter-molecular hydrogen bonded dimers between amide and carboxylic acid groups, which have been investigated by 1H, 13C and 15N NMR spectroscopy. Extensive NMR studies using diffusion ordered spectroscopy (DOSY), variable temperature 1D, 2D NMR, established the formation of heterodimers of benzamide with benzoic acid, salicylic acid and phenyl acetic acid in deuterated chloroform solution. Association constants for the complex formation in the solution state have been determined. The results are ascertained by X-ray diffraction in the solid state. Intermolecular interactions in solution and in solid state were found to be similar. The structural parameters obtained by X-ray diffraction studies are compared with those obtained by DFT calculations.

  10. Study of intermolecular interactions in binary mixtures of ethanol in methanol

    NASA Astrophysics Data System (ADS)

    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.