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Sample records for intermolecular heck coupling

  1. Phosphite-oxazole/imidazole ligands in asymmetric intermolecular Heck reaction.

    PubMed

    Mazuela, Javier; Tolstoy, Paivi; Pàmies, Oscar; Andersson, Pher G; Diéguez, Montserrat

    2011-02-07

    We describe the application of a new class of ligands--the phosphite-oxazole/imidazole (L1-L5a-g)--in asymmetric intermolecular Pd-catalyzed Heck reactions under thermal and microwave conditions. These ligands combine the advantages of the oxazole/imidazole moiety with those of the phosphite moiety: they are more stable than their oxazoline counterparts, less sensitive to air and other oxidizing agents than phosphines and phosphinites, and easy to synthesize from readily available alcohols. The results indicate that activities, regio- and enantioselectivities, are highly influenced by the type of nitrogen donor group (oxazole or imidazole), the oxazole and biaryl-phosphite substituents and the axial chirality of the biaryl moiety of the ligand. By carefully selecting the ligand components, we achieved high activities, regio- (up to 99%) and enantioselectivities (up to 99%) using several triflate sources. Under microwave-irradiation conditions, reaction times were considerably shorter (from 24 h to 30 min) and regio- and enantioselectivities were still excellent.

  2. Palladium-catalyzed Heck-type cross-couplings of unactivated alkyl iodides.

    PubMed

    McMahon, Caitlin M; Alexanian, Erik J

    2014-06-02

    A palladium-catalyzed, intermolecular Heck-type coupling of alkyl iodides and alkenes is described. This process is successful with a variety of primary and secondary unactivated alkyl iodides as reaction partners, including those with hydrogen atoms in the β position. The mild catalytic conditions enable intermolecular C-C bond formations with a diverse set of alkyl iodides and alkenes, including substrates containing base- or nucleophile-sensitive functionality.

  3. Rational design of cyclopropane-based chiral PHOX ligands for intermolecular asymmetric Heck reaction

    PubMed Central

    Rubina, Marina; Sherrill, William M; Barkov, Alexey Yu

    2014-01-01

    Summary A novel class of chiral phosphanyl-oxazoline (PHOX) ligands with a conformationally rigid cyclopropyl backbone was synthesized and tested in the intermolecular asymmetric Heck reaction. Mechanistic modelling and crystallographic studies were used to predict the optimal ligand structure and helped to design a very efficient and highly selective catalytic system. Employment of the optimized ligands in the asymmetric arylation of cyclic olefins allowed for achieving high enantioselectivities and significantly suppressing product isomerization. Factors affecting the selectivity and the rate of the isomerization were identified. It was shown that the nature of this isomerization is different from that demonstrated previously using chiral diphosphine ligands. PMID:25161709

  4. Probing Intermolecular Coupled Vibrations between Two Molecules

    NASA Astrophysics Data System (ADS)

    Han, Zhumin; Czap, Gregory; Xu, Chen; Chiang, Chi-lun; Yuan, Dingwang; Wu, Ruqian; Ho, W.

    2017-01-01

    Intermolecular interactions can induce energy shifts and coupling of molecular vibrations. However, the detection of intermolecular coupled vibrations has not been reported at the single molecule level. Here we detected an intermolecular coupled vibration between two CO molecules, one on the surface and another on the tip within the gap of a subkelvin scanning tunneling microscope, and analyzed the results by density functional calculations. We attribute the evolution of the energy and intensity of this coupled vibration as a function of tip-sample distance to the tilting and orbital alignment of the two CO molecules.

  5. Heck coupling of haloaromatics with octavinylsilsesquioxane: solution processable nanocomposites for application in electroluminescent devices.

    PubMed

    Sellinger, Alan; Tamaki, Ryo; Laine, Richard M; Ueno, Kazunori; Tanabe, Hiroshi; Williams, Evan; Jabbour, Ghassan E

    2005-08-07

    A new solution processable nanocomposite material has been prepared via the Heck coupling of octavinylsilsesquioxane with a selected bromoaromatic hole transport compound. Resultant electroluminescent devices show an 18% improvement in external quantum efficiencies over their small molecule analogues.

  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.

  7. 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

  8. Nickel and cobalt-catalyzed coupling of alkyl halides with alkenes via heck reactions and radical conjugate addition.

    PubMed

    Qian, Qun; Zang, Zhenhua; Chen, Yang; Tong, Weiqi; Gong, Hegui

    2013-05-01

    Cross-coupling of alkyl halides with alkenes leading to Heck-type and addition products is summarized. The development of Heck reaction with aliphatic halides although has made significant progress in the past decade and particularly recently, it was much less explored in comparison with the aryl halides. The use of Ni- and Co-catalyzed protocols allowed efficient Heck coupling of activated and unactivated alkenes with 1°, 2° and 3° alkyl halides. In addition, radical conjugate addition to activated alkenes has become a well-established method that has led to efficient construction of many natural products. The utilization of Ni- and Co-catalyzed strategies would avoid toxic tin reagents, and therefore worth exploring. The recent development of Ni- and Co-catalyzed addition of alkyl halides to alkenes displays much improved reactivity and functional group tolerance. In this mini-review, we also attempt to overview the mechanisms that are proposed in the reactions, aiming at providing insight into the nickel and cobalt-catalyzed coupling of alkyl halides with alkenes.

  9. Crystalline hybrid solid materials of palladium and decamethylcucurbit[5]uril as recoverable precatalysts for Heck cross-coupling reactions.

    PubMed

    Li, Hongfang; Lü, Jian; Lin, Jingxiang; Huang, Yuanbiao; Cao, Minna; Cao, Rong

    2013-11-11

    A series of MPdMe10 CB[5] (M=Li, Na, K, Rb, and Cs; Me10 CB[5]=decamethylcucurbit[5]uril) hybrid solid materials have been successfully synthesized for the first time through a simple diffusion method. These as-prepared hybrid solids have been applied as phosphine-free precatalysts for Heck cross-coupling reactions with excellent catalytic performance and good recyclability. In the processes of the catalytic reactions, the activated Pd(II) species were released from the crystalline hybrid precatalysts and transformed into catalytically active Pd nanoparticles, which have been demonstrated as key to carry on the catalytic reactions for the recoverable precatalysts MPdMe10 CB[5] (M=K, Rb, and Cs). It has also been rationalized that the introduction of different alkali metals afforded crystalline hybrid precatalysts with different crystal structures, which are responsible for their diversified stability and reusability presented in Heck reactions.

  10. Phenylenevinylene oligomers by Mizoroki-Heck cross coupling reaction. Structural and optoelectronic characterization

    NASA Astrophysics Data System (ADS)

    Estrada, Sandra E.; Ochoa-Puentes, Cristian; Sierra, Cesar A.

    2017-04-01

    In order to study the effect of the molecular structure on the optical properties of totally trans-trans phenylenevinylene oligomers (OPVs), sixteen 1,4-distyrylbenzene derivatives (1a-i and 2a-g) functionalized with different electron-donating (ED) and electron-withdrawing (EW) groups were synthesized by the Mizoroki-Heck cross coupling reaction in moderate to good yields (40-95%). The implemented methodology, with a small modification previously reported by our group, allows obtaining the desired vinyl configuration as well as one novel OPV compound (1h). After structural characterization by several techniques (e.g. FTIR, 1H, 13C and Solid-State NMR), particular emphasis was placed upon the investigation of their optical properties by UV-vis and fluorescence spectroscopies. The results showed that, with only one exception, the ED and EW groups at the ends of OPV systems lead to a bathochromic shift. This effect is intensified with the introduction of methoxy groups on the central ring. Consistent with these, the HOMO-LUMO gaps (ΔE) decreases as the strength of ED and EW substituents increases. The ED and EW substituents also lead to a decrease in the Φf values. This contribution in the area of organic electronics can be used as a reference to better select the most appropriate technological application for each OPV and this can be extrapolated to their respective structurally analogous segmented polymer.

  11. Selectivity control between Mizoroki-Heck and homo-coupling reactions for synthesising multinuclear metal complexes: unique addition effects of tertiary phosphines and O2.

    PubMed

    Yamazaki, Yasuomi; Ishitani, Osamu

    2017-04-05

    The addition of a tertiary phosphine and O2 to reaction solutions strongly affected the reactivity and selectivity of coupling reactions between transition metal complexes. The Mizoroki-Heck reaction between metal complexes with bromo and those with vinyl groups in the diimine ligand did not proceed using Pd(OAc)2 in the presence of 2-dicyclohexylphosphino-2',6'-dimethoxybiphenyl (Sphos) under Ar but proceeded selectively after injection of air into the reaction vessel. In the absence of the phosphine ligand, on the other hand, not only the Mizoroki-Heck reaction but also a homo-coupling reaction between the metal complexes with the bromo groups proceeded at the same time. Mechanistic investigation showed that nanoparticles of Pd species were produced in the absence of the phosphine ligand and worked as catalysts for both the Mizoroki-Heck and homo-coupling reactions. On the other hand, larger Pd particles, which were produced in the presence of Sphos but after addition of air for oxidising Sphos, selectively catalysed the Mizoroki-Heck reaction. 'Molecular' Pd species that were stabilised in the presence of non-oxidised Sphos could not catalyse both coupling reactions under the reaction conditions. Based on these results, reaction conditions were established for the selective progress of the Mizoroki-Heck and the homo-coupling reactions.

  12. A general synthesis of alkenyl-substituted benzofurans, indoles, and isoquinolones by cascade palladium-catalyzed heterocyclization/oxidative Heck coupling.

    PubMed

    Alvarez, Rosana; Martínez, Claudio; Madich, Youssef; Denis, J Gabriel; Aurrecoechea, José M; de Lera, Angel R

    2010-11-08

    Structurally diverse C3-alkenylbenzofurans, C3-alkenylindoles, and C4-alkenylisoquinolones are efficiently prepared by using consecutive Sonogashira and cascade Pd-catalyzed heterocyclization/oxidative Heck couplings from readily available ortho-iodosubstituted phenol, aniline, and benzamide substrates, alkynes, and functionalized olefins. The cyclization of O- and N-heteronucleophiles follows regioselective 5-endo-dig- or 6-endo-dig-cyclization modes, whereas the subsequent Heck-type coupling with both mono- and disubstituted olefins takes place stereoselectively with exclusive formation of the E isomers in most cases.

  13. 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

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

    PubMed

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

    2015-06-09

    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 Pd(0) 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.

  15. Heck-type reactions of imine derivatives: a DFT study.

    PubMed

    Li, Zhe; Fu, Yao; Zhang, Song-Lin; Guo, Qing-Xiang; Liu, Lei

    2010-06-01

    The mechanism of a recently discovered intramolecular Heck-type coupling of oximes with aryl halides (Angew. Chem. Int. Ed. 2007, 46, 6325) was systematically studied by using density functional methods enhanced with a polarized continuum solvation model. The overall catalytic cycle of the reaction was found to consist of four steps: oxidative addition, migratory insertion, beta-H elimination, and catalyst regeneration, whereas an alternative base-promoted C-H activation pathway was determined to be less favorable. Migratory insertion was found to be the rate determining step in the catalytic cycle. The apparent activation barrier of migratory insertion of the (E)-oxime was +20.5 kcal mol(-1), whereas the barrier of (Z)-oxime was as high as +32.7 kcal mol(-1). However, (Z)-oxime could isomerize to form the more active (E)-oxime with the assistance of K(2)CO(3), so that both the (E)- and (Z)-oxime substrates could be transformed to the desired product. Our calculations also indicated that the Z product was predominant in the equilibrium of the isomerization of the imine double bond, which constituted the reason for the good Z-selectivity observed for the reaction. Furthermore, we examined the difference between the intermolecular Heck-type reactions of imines and of olefins. It was found that in the intermolecular Heck-type coupling of imines, the apparent activation barrier of migratory insertion was as high as +35 kcal mol(-1), which should be the main obstacle of the reaction. The analysis also revealed the main problem for the intermolecular Heck-type reactions of imines, which was that the breaking of a C=N pi bond was much more difficult than the breaking of a C=C pi bond. After systematic examination of a series of substituted imines, (Z)-N-amino imine and N-acetyl imine were found to have relatively low barriers of migratory insertion, so that they might be possible substrates for intermolecular Heck-type coupling.

  16. 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.

  17. Tandem intermolecular Suzuki coupling/intramolecular vinyl triflate-arene coupling.

    PubMed

    Willis, Michael C; Claverie, Christelle K; Mahon, Mary F

    2002-04-21

    Treatment of a benzyl substituted meso-ditriflate with boronic acids in the presence of palladium acetate, triphenylphosphine and caesium fluoride results in intermolecular Suzuki coupling followed by vinyl triflate-arene cyclisation to provide, in high yields, single regioisomers of tricyclic-carbocycles.

  18. Mizoroki-Heck Cross-coupling Reactions Catalyzed by Dichloro{bis[1,1',1''-(phosphinetriyl)tripiperidine]}palladium Under Mild Reaction Conditions

    PubMed Central

    Oberholzer, Miriam; Frech, Christian M.

    2014-01-01

    Dichloro-bis(aminophosphine) complexes of palladium with the general formula of [(P{(NC5H10)3-n(C6H11)n})2Pd(Cl)2] (where n = 0-2), belong to a new family of easy accessible, very cheap, and air stable, but highly active and universally applicable C-C cross-coupling catalysts with an excellent functional group tolerance. Dichloro{bis[1,1',1''-(phosphinetriyl)tripiperidine]}palladium [(P(NC5H10)3)2Pd(Cl)2] (1), the least stable complex within this series towards protons; e.g. in the form of water, allows an eased nanoparticle formation and hence, proved to be the most active Heck catalyst within this series at 100 °C and is a very rare example of an effective and versatile catalyst system that efficiently operates under mild reaction conditions. Rapid and complete catalyst degradation under work-up conditions into phosphonates, piperidinium salts and other, palladium-containing decomposition products assure an easy separation of the coupling products from catalyst and ligands. The facile, cheap, and rapid synthesis of 1,1',1"-(phosphinetriyl)tripiperidine and 1 respectively, the simple and convenient use as well as its excellent catalytic performance in the Heck reaction at 100 °C make 1 to one of the most attractive and greenest Heck catalysts available. We provide here the visualized protocols for the ligand and catalyst syntheses as well as the reaction protocol for Heck reactions performed at 10 mmol scale at 100 °C and show that this catalyst is suitable for its use in organic syntheses. PMID:24686532

  19. On certain Hecke rings

    PubMed Central

    Evens, Sam; Bressler, Paul

    1987-01-01

    We examine rings that embed into the smash product of the group algebra of the Weyl group with the field of meromorphic functions on the Cartan subalgebra and are generated by elements that satisfy braid relations. We prove that every such ring is isomorphic to either the Hecke algebra, the nil Hecke ring, or the group algebra of the Weyl group. PMID:16593804

  20. 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.

  1. Rh(I)-Catalyzed Intermolecular Hydroacylation: Enantioselective Cross-Coupling of Aldehydes and Ketoamides

    PubMed Central

    2015-01-01

    Under Rh(I) catalysis, α-ketoamides undergo intermolecular hydroacylation with aliphatic aldehydes. A newly designed Josiphos ligand enables access to α-acyloxyamides with high atom-economy and enantioselectivity. On the basis of mechanistic and kinetic studies, we propose a pathway in which rhodium plays a dual role in activating the aldehyde for cross-coupling. A stereochemical model is provided to rationalize the sense of enantioinduction observed. PMID:24937681

  2. 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.

  3. Coupled effects of substrate adhesion and intermolecular forces on polymer thin film glass-transition behavior.

    PubMed

    Xia, Wenjie; Keten, Sinan

    2013-10-15

    Intermolecular noncovalent forces between polymer chains influence the mobility and glass-transition temperature (Tg), where weaker interchain interactions, all else being the same, typically results in lower bulk polymer Tg. Using molecular dynamics simulations, here we show that this relation can become invalid for supported ultrathin films when the substrate-polymer interaction is extremely strong and the polymer-polymer interactions are much weaker. This contrasting trend is found to be due to a more pronounced substrate-induced appreciation of the film Tg for polymers with weaker intermolecular interactions and low bulk Tg. We show that optimizing this coupling between substrate adhesion and bulk Tg maximizes thin film Tg, paving the way for tuning film properties through interface nanoengineering.

  4. Detection of intermolecular homonuclear dipolar coupling in organic rich shale by transverse relaxation exchange.

    PubMed

    Washburn, Kathryn E; Cheng, Yuesheng

    2017-03-04

    The mechanism behind surface relaxivity within organic porosity in shales has been an unanswered question. Here, we present results that confirm the existence of intermolecular homonuclear dipolar coupling between solid and liquid phases in sedimentary organic matter. Transverse magnetization exchange measurements were performed on an organic-rich shale saturated with liquid hydrocarbon. Liquid and solid constituents were identified through both sample resaturation and through their T1/T2 ratios. Extensive cross peaks are observed in the T2-T2 exchange spectra between the solid and liquid constituents, indicating an exchange of magnetization between the two phases. This result cannot arise from physical molecular diffusion, and the dissolution energies are too high for chemical exchange, such that the magnetization exchange must arise from intermolecular homonuclear dipolar coupling. These results both confirm a possible source of surface relaxivity in organic matter and emphasize caution in the use of standard porous media interpretations of relaxation results in shales because of coupling between different magnetization environments.

  5. 15N- 15N spin-spin coupling constants through intermolecular hydrogen bonds in the solid state

    NASA Astrophysics Data System (ADS)

    Claramunt, Rosa M.; Pérez-Torralba, Marta; María, Dolores Santa; Sanz, Dionisia; Elena, Bénédicte; Alkorta, Ibon; Elguero, José

    2010-10-01

    A 2hJNN intermolecular spin-spin coupling constant (SSCC) of 10.2 ± 0.4 Hz has been measured for the powdered tetrachlorogallate salt of pyridinium solvated by pyridine (pyridine-H +⋯pyridine cation 3). Density Functional Theory (DFT) calculations at the B3LYP/6-311++G( d, p) level reproduced this value and two others reported in the literature for 2hJ intermolecular SSCCs, which were measured for complexes in solution.

  6. Intermolecular Electronic Coupling of Organic Units for Efficient Persistent Room‐Temperature Phosphorescence

    PubMed Central

    Yang, Zhiyong; Mao, Zhu; Zhang, Xuepeng; Ou, Depei; Mu, Yingxiao; Zhao, Cunyuan; Liu, Siwei; Xu, Jiarui; Wu, Yuan‐Chun; Lu, Po‐Yen; Lien, Alan

    2016-01-01

    Abstract Although persistent room‐temperature phosphorescence (RTP) emission has been observed for a few pure crystalline organic molecules, there is no consistent mechanism and no universal design strategy for organic persistent RTP (pRTP) materials. A new mechanism for pRTP is presented, based on combining the advantages of different excited‐state configurations in coupled intermolecular units, which may be applicable to a wide range of organic molecules. By following this mechanism, we have developed a successful design strategy to obtain bright pRTP by utilizing a heavy halogen atom to further increase the intersystem crossing rate of the coupled units. RTP with a remarkably long lifetime of 0.28 s and a very high quantum efficiency of 5 % was thus obtained under ambient conditions. This strategy represents an important step in the understanding of organic pRTP emission. PMID:26836346

  7. X-filtering for a range of coupling constants: application to the detection of intermolecular NOEs

    NASA Astrophysics Data System (ADS)

    Zangger, Klaus; Oberer, Monika; Keller, Walter; Sterk, Heinz

    2003-02-01

    A new method for heteronuclear X-filtering is presented, which relies on repetitive applications of 90°( 1H)-τ(1/4 1J HC)-180°( 1H, 13C)-τ(1/4 1J HC)-90°( 1H, 13C)- PFG building blocks employing gradient-mediated suppression of magnetization built up for directly heteronuclear coupled protons. Thereby, a range of heteronuclear coupling constants can be suppressed by varying the delays of scalar coupling evolution both within and between individual transients. To achieve efficient destruction of 13C-coupled protons in macromolecular systems, the scalar coupling evolution delays were optimized using simulated annealing by including transverse relaxation effects. With a combination of regular hard pulses, delays and pulsed field gradients only, this method yields sufficient X-filtering to allow the observation of intermolecular nuclear overhauser effects in a molecular complex consisting of a 13C, 15N double-labeled, and an unlabeled protein. This is achieved by exciting magnetization of 12C- and 14N-bound protons and detecting 13C-bound 1H magnetization in a 3D 13C-filtered, 13C-edited NOESY-HSQC experiment. The method is tested on the 18 kDa homodimeric bacterial antidote ParD.

  8. Hypervalent Iodine(III)-Promoted Intermolecular C–C Coupling of Vindoline with β-Ketoesters and Related Substrates

    PubMed Central

    Turner, Travis C.; Shibayama, Kotaro

    2013-01-01

    The regioselective intermolecular coupling reaction of vindoline with a wide range of substrates including β-ketoesters, β-diketones, β-ketoaldehydes, β-ketonitriles, malononitriles, and β-cyanoesters provides an opportunity for the synthesis of vinblastine analogues containing deep-seated changes in the upper velbanamine subunit. The transition-metal free hypervalent iodine(III)-promoted intermolecular sp3/sp2 coupling, representing a special class of selective C–H activation with direct carbon–carbon bond formation, proceeds with generation of a quaternary center capable of incorporation of the vinblastine C16′ methyl ester and functionalized for subsequent divergent heterocycle introduction. PMID:23421318

  9. 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

  10. Scope and limitations of the Heck-Matsuda-coupling of phenol diazonium salts and styrenes: a protecting-group economic synthesis of phenolic stilbenes.

    PubMed

    Schmidt, Bernd; Elizarov, Nelli; Berger, René; Hölter, Frank

    2013-06-14

    4-Phenol diazonium salts undergo Pd-catalyzed Heck reactions with various styrenes to 4'-hydroxy stilbenes. In almost all cases higher yields and fewer side products were observed, compared to the analogous 4-methoxy benzene diazonium salts. In contrast, the reaction fails completely with 2- and 3-phenol diazonium salts. For these substitution patterns the methoxy-substituted derivatives are superior.

  11. 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.

  12. Detection of complex formation and determination of intermolecular geometry through electrical anharmonic coupling of molecular vibrations using electron-vibration-vibration two-dimensional infrared spectroscopy.

    PubMed

    Guo, Rui; Fournier, Frederic; Donaldson, Paul M; Gardner, Elizabeth M; Gould, Ian R; Klug, David R

    2009-10-14

    Electrical interactions between molecular vibrations can be non-linear and thereby produce intermolecular coupling even in the absence of a chemical bond. We use this fact to detect the formation of an intermolecular complex using electron-vibration-vibration two-dimensional infrared spectroscopy (EVV 2DIR) and also to determine the distance and angle between the two molecular species.

  13. Residence Times of Molecular Complexes in Solution from NMR Data of Intermolecular Hydrogen-Bond Scalar Coupling.

    PubMed

    Zandarashvili, Levani; Esadze, Alexandre; Kemme, Catherine A; Chattopadhyay, Abhijnan; Nguyen, Dan; Iwahara, Junji

    2016-03-03

    The residence times of molecular complexes in solution are important for understanding biomolecular functions and drug actions. We show that NMR data of intermolecular hydrogen-bond scalar couplings can yield information on the residence times of molecular complexes in solution. The molecular exchange of binding partners via the breakage and reformation of a complex causes self-decoupling of intermolecular hydrogen-bond scalar couplings, and this self-decoupling effect depends on the residence time of the complex. For protein-DNA complexes, we investigated the salt concentration dependence of intermolecular hydrogen-bond scalar couplings between the protein side-chain (15)N and DNA phosphate (31)P nuclei, from which the residence times were analyzed. The results were consistent with those obtained by (15)Nz-exchange spectroscopy. This self-decoupling-based kinetic analysis is unique in that it does not require any different signatures for the states involved in the exchange, whereas such conditions are crucial for kinetic analyses by typical NMR and other methods.

  14. Optical properties of azobenzene-functionalized self-assembled monolayers: Intermolecular coupling and many-body interactions

    NASA Astrophysics Data System (ADS)

    Cocchi, Caterina; Moldt, Thomas; Gahl, Cornelius; Weinelt, Martin; Draxl, Claudia

    2016-12-01

    In a joint theoretical and experimental work, the optical properties of azobenzene-functionalized self-assembled monolayers (SAMs) are studied at different molecular packing densities. Our results, based on density-functional and many-body perturbation theory, as well as on differential reflectance (DR) spectroscopy, shed light on the microscopic mechanisms ruling photo-absorption in these systems. While the optical excitations are intrinsically excitonic in nature, regardless of the molecular concentration, in densely packed SAMs intermolecular coupling and local-field effects are responsible for a sizable weakening of the exciton binding strength. Through a detailed analysis of the character of the electron-hole pairs, we show that distinct excitations involved in the photo-isomerization at low molecular concentrations are dramatically broadened by intermolecular interactions. Spectral shifts in the calculated DR spectra are in good agreement with the experimental results. Our findings represent an important step forward to rationalize the excited-state properties of these complex materials.

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

    PubMed

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

    2014-04-11

    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.

  16. 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.

  17. 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.

  18. 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

  19. NMR Scalar Couplings across Intermolecular Hydrogen Bonds between Zinc-Finger Histidine Side Chains and DNA Phosphate Groups.

    PubMed

    Chattopadhyay, Abhijnan; Esadze, Alexandre; Roy, Sourav; Iwahara, Junji

    2016-10-10

    NMR scalar couplings across hydrogen bonds represent direct evidence for the partial covalent nature of hydrogen bonds and provide structural and dynamic information on hydrogen bonding. In this article, we report heteronuclear (15)N-(31)P and (1)H-(31)P scalar couplings across the intermolecular hydrogen bonds between protein histidine (His) imidazole and DNA phosphate groups. These hydrogen-bond scalar couplings were observed for the Egr-1 zinc-finger-DNA complex. Although His side-chain NH protons are typically undetectable in heteronuclear (1)H-(15)N correlation spectra due to rapid hydrogen exchange, this complex exhibited two His side-chain NH signals around (1)H 14.3 ppm and (15)N 178 ppm at 35 °C. Through various heteronuclear multidimensional NMR experiments, these signals were assigned to two zinc-coordinating His side chains in contact with DNA phosphate groups. The data show that the Nδ1 atoms of these His side chains are protonated and exhibit the (1)H-(15)N cross-peaks. Using heteronuclear (1)H, (15)N, and (31)P NMR experiments, we observed the hydrogen-bond scalar couplings between the His (15)Nδ1/(1)Hδ1 and DNA phosphate (31)P nuclei. These results demonstrate the direct involvement of the zinc-coordinating His side chains in the recognition of DNA by the Cys2His2-class zinc fingers in solution.

  20. Unusual intermolecular "through-space" j couplings in p-se heterocycles.

    PubMed

    Sanz Camacho, Paula; Athukorala Arachchige, Kasun S; Slawin, Alexandra M Z; Green, Timothy F G; Yates, Jonathan R; Dawson, Daniel M; Woollins, J Derek; Ashbrook, Sharon E

    2015-05-20

    Solid-state NMR spectra of new P-Se heterocycles based on peri-substituted naphthalene motifs show the presence of unusual J couplings between Se and P. These couplings are between atoms in adjacent molecules and occur "through space", rather than through conventional covalent bonds. Experimental measurements are supported by relativistic DFT calculations, which confirm the presence of couplings between nonbonded atoms, and provide information on the pathway of the interaction. This observation improves the understanding of J couplings and offers insight into the factors that affect crystal packing in solids, for future synthetic exploitation.

  1. Investigating Unusual Homonuclear Intermolecular "Through-Space" J Couplings in Organochalcogen Systems.

    PubMed

    Sanz Camacho, Paula; McKay, David; Dawson, Daniel M; Kirst, Christin; Yates, Jonathan R; Green, Timothy F G; Cordes, David B; Slawin, Alexandra M Z; Woollins, J Derek; Ashbrook, Sharon E

    2016-11-07

    Although the electron-mediated spin-spin or J coupling is conventionally viewed as transmitted via covalent bonds, examples of J couplings between atoms that are not formally bonded but are in close proximity (termed "through-space" J couplings) have been reported. In this work, we investigate the observation of homonuclear (31)P J couplings in organochalcogen heterocycles, which occur between (31)P in two separate molecules, confirming without doubt their through-space nature. The presence of this interaction is even more surprising for one compound, where it occurs between crystallographically equivalent species. Although crystallographically equivalent species need not be magnetically equivalent in the solid state, owing to the presence of anisotropic interactions, we demonstrate that it is not the shielding anisotropy that lifts magnetic equivalence, in this case, but the presence of heteronuclear couplings to (77)Se. We support our experimental observations with periodic scalar-relativistic density functional theory calculations and coupling density deformation plots to visualize the mechanism of these interesting interactions.

  2. 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.

  3. Strong intermolecular exciton couplings in solid-state circular dichroism of aryl benzyl sulfoxides.

    PubMed

    Padula, Daniele; Di Pietro, Sebastiano; Capozzi, Maria Annunziata M; Cardellicchio, Cosimo; Pescitelli, Gennaro

    2014-09-01

    A series of 13 enantiopure aryl benzyl sulfoxides () with different substituents on the two aromatic rings has been previously analyzed by means of electronic circular dichroism (CD) spectroscopy. Most of these compounds are crystalline and their X-ray structure is established. For almost one-half of the series, CD spectra measured in the solid state were quite different from those in acetonitrile solution. We demonstrate that the difference is due to strong exciton couplings between molecules packed closely together in the crystal. The computational approach consists of time-dependent density functional theory (TDDFT) calculations run on "dimers" composed of nearest neighbors found in the lattice. Solid-state CD spectra are well reproduced by the average of all possible pairwise terms. The relation between the crystal space group and conformation, and the appearance of solid-state CD spectra, is also discussed.

  4. The Origins of - and Inter-Molecular Vibrational Couplings: a Case Study of H_2O-Ar on Full and Reduced-Dimensional Potential Energy Surface

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

    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 H_2O-Ar, which explicitly incorporates interdependence on the intramolecular normal-mode coordinates of the H_2O 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 (νb{1},νb{2},νb{3})=(0,0,0),(0,0,1),(1,0,0),(0,1,0) states of H_2O to the three-dimensional Morse/long-range potential function. The resulting vibrationally averaged PESs provide good representations of the experimental infrared data, with RMS discrepancies smaller than 0.02 wn for all three rotational branches of the asymmetric stretch fundamental transitions. The infrared band origin shifts associated with three fundamental bands of H_2O in H_2O-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. J. Chem. Phys., 144, 014301 (2016)

  5. Closed-shell ring coupled cluster doubles theory with range separation applied on weak intermolecular interactions.

    PubMed

    Toulouse, Julien; Zhu, Wuming; Savin, Andreas; Jansen, Georg; Ángyán, János G

    2011-08-28

    We explore different variants of the random phase approximation to the correlation energy derived from closed-shell ring-diagram approximations to coupled cluster doubles theory. We implement these variants in range-separated density-functional theory, i.e., by combining the long-range random phase approximations with short-range density-functional approximations. We perform tests on the rare-gas dimers He(2), Ne(2), and Ar(2), and on the weakly interacting molecular complexes of the S22 set of Jurečka et al. [P. Jurečka, J. Šponer, J. Černý, and P. Hobza, Phys. Chem. Chem. Phys. 8, 1985 (2006)]. The two best variants correspond to the ones originally proposed by Szabo and Ostlund [A. Szabo and N. S. Ostlund, J. Chem. Phys. 67, 4351 (1977)]. With range separation, they reach mean absolute errors on the equilibrium interaction energies of the S22 set of about 0.4 kcal/mol, corresponding to mean absolute percentage errors of about 4%, with the aug-cc-pVDZ basis set.

  6. Heck's disease: diagnosis and susceptibility.

    PubMed

    Bennett, Lindsey K; Hinshaw, Molly

    2009-01-01

    Focal epithelial hyperplasia, or Heck's disease, is an uncommon proliferation of oral mucosa that presents primarily in Native Central and South American populations. It presents as asymptomatic papules or nodules on the oral mucosa, gingiva, tongue, and lips. In the majority of cases, human papilloma virus 13 or 32 is detected. Factors that determine disease susceptibility are unclear, but genetics, and having the human lymphocytic antigen-DR4 (DRB1*0404) allele in particular, are thought to play a major role in disease vulnerability. We report another case of focal epithelial hyperplasia, hypothesize on disease susceptibility, and review the current understanding of this uncommon disorder.

  7. Magnetically separable Fe3O4@DOPA??Pd: a heterogeneous catalyst for aqueous Heck reaction

    EPA Pesticide Factsheets

    Magnetically separable Fe3O4@DOPA??Pd catalyst has been synthesized via anchoring of palladium over dopamine-coated magnetite via co-ordinate interactionand the catalyst is utilized for expeditious Heck coupling in aqueous media.This dataset is associated with the following publication:Baig, N., J. Leazer , and R. Varma. Magnetically Separable Fe3O4@DOPA-Pd: A Heterogeneous Catalyst for Aqueous Heck Reaction. CLEAN TECHNOLOGIES AND ENVIRONMENTAL POLICY. Springer-Verlag, New York, NY, USA, 17(7): 2073-2077, (2015).

  8. Intermolecular forces.

    PubMed

    Buckingham, A D

    1975-11-06

    The nature of molecular interactions is examined. Intermolecular forces are divided into long-range and short-range components; the former operate at distances where the effects of electron exchange are negligible and decrease as an inverse power of the separation. The long-range interactions may be subdividied into electrostatic, induction and dispersion contributions, where the electrostatic component is the interaction of the permanent charge distributions and the others originate in the fluctuations in the distributions. Typical magnitudes of the various contributions are given. The forces between macroscopic bodies are briefly considered, as are the effects of a medium. Some of the manifestations of molecular interactions are discussed.

  9. Chain models on hecke algebra for corner type representations

    NASA Astrophysics Data System (ADS)

    Isaev, A. P.; Ogievetsky, O. V.; Os'kin, A. F.

    2008-04-01

    We consider the integrable open chain models formulated in terms of generators of the Hecke algebra. The spectrum of Hamiltonians for the open Hecke chains of finite size with free boundary conditions is deduced for special (comer type) irreducible representations of the Hecke algebra.

  10. 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.

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

    PubMed

    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(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.

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

    NASA Astrophysics Data System (ADS)

    Azar, R. Julian; Head-Gordon, Martin

    2012-01-01

    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 Cs-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.

  13. Palladium-catalyzed cyclization/Heck- and cyclization/conjugate-addition-type sequences in the preparation of polysubstituted furans.

    PubMed

    Aurrecoechea, José M; Durana, Aritz; Pérez, Elena

    2008-05-02

    Palladium-catalyzed heterocyclization-coupling sequences have been developed starting from buta-1,2,3-trienyl carbinols and electron-deficient alkenes. Polysubstituted furans are formed where the heterocyclic ring originates from the elements of the butatrienyl carbinol while the electron-deficient olefin is incorporated as a C-3 substituent. In most cases, the reaction proceeds via a Heck-type pathway leading to the efficient formation of 3-vinylfurans. However, couplings with methyl vinyl ketone display a divergent behavior to afford selectively either Heck- or hydroarylation-type products depending on reaction conditions.

  14. Solute-solvent intermolecular vibronic coupling as manifested by the molecular near-field effect in resonance hyper-Raman scattering.

    PubMed

    Shimada, Rintaro; Hamaguchi, Hiro-o

    2011-01-21

    Vibronic coupling within the excited electronic manifold of the solute all-trans-β-carotene through the vibrational motions of the solvent cyclohexane is shown to manifest as the "molecular near-field effect," in which the solvent hyper-Raman bands are subject to marked intensity enhancements under the presence of all-trans-β-carotene. The resonance hyper-Raman excitation profiles of the enhanced solvent bands exhibit similar peaks to those of the solute bands in the wavenumber region of 21,700-25,000 cm(-1) (10,850-12,500 cm(-1) in the hyper-Raman exciting wavenumber), where the solute all-trans-β-carotene shows a strong absorption assigned to the 1A(g) → 1B(u) transition. This fact indicates that the solvent hyper-Raman bands gain their intensities through resonances with the electronic states of the solute. The observed excitation profiles are quantitatively analyzed and are successfully accounted for by an extended vibronic theory of resonance hyper-Raman scattering that incorporates the vibronic coupling within the excited electronic manifold of all-trans-β-carotene through the vibrational motions of cyclohexane. It is shown that the major resonance arises from the B-term (vibronic) coupling between the first excited vibrational level (v = 1) of the 1B(u) state and the ground vibrational level (v = 0) of a nearby A(g) state through ungerade vibrational modes of both the solute and the solvent molecules. The inversion symmetry of the solute all-trans-β-carotene is preserved, suggesting the weak perturbative nature of the solute-solvent interaction in the molecular near-field effect. The present study introduces a new concept, "intermolecular vibronic coupling," which may provide an experimentally accessible∕theoretically tractable model for understanding weak solute-solvent interactions in liquid.

  15. On Ternary Quotients of Cubic Hecke Algebras

    NASA Astrophysics Data System (ADS)

    Cabanes, Marc; Marin, Ivan

    2012-08-01

    We prove that the quotient of the group algebra of the braid group introduced by Funar (Commun Math Phys 173:513-558, 1995) collapses in characteristic distinct from 2. In characteristic 2 we define several quotients of it, which are connected to the classical Hecke and Birman-Wenzl-Murakami quotients, but which admit in addition a symmetry of order 3. We also establish conditions on the possible Markov traces factorizing through it.

  16. Coupled Cluster and Møller-Plesset Perturbation Theory Calculations of Noncovalent Intermolecular Interactions using Density Fitting with Auxiliary Basis Sets from Cholesky Decompositions.

    PubMed

    Boström, Jonas; Pitoňák, Michal; Aquilante, Francesco; Neogrády, Pavel; Pedersen, Thomas Bondo; Lindh, Roland

    2012-06-12

    We compute noncovalent intermolecular interaction energies for the S22 test set [Phys. Chem. Chem. Phys.2006, 8, 1985-1993] of molecules at the Møller-Plesset and coupled cluster levels of supermolecular theory using density fitting (DF) to approximate all two-electron integrals. The error due to the DF approximation is analyzed for a range of auxiliary basis sets derived from Cholesky decomposition (CD) in conjunction with correlation consistent and atomic natural orbital valence basis sets. A Cholesky decomposition threshold of 10(-4)Eh for full molecular CD and its one-center approximation (1C-CD) generally yields errors below 0.03 kcal/mol, whereas 10(-3)Eh is sufficient to obtain the same level of accuracy or better with the atomic CD (aCD) and atomic compact CD (acCD) auxiliary basis sets. Comparing to commonly used predefined auxiliary basis sets, we find that while the aCD and acCD sets are larger by a factor of 2-4 with triple-ζ AO basis sets, they provide results 1-2 orders of magnitude more accurate.

  17. Enantioselective Heck arylations of acyclic alkenyl alcohols using a redox-relay strategy.

    PubMed

    Werner, Erik W; Mei, Tian-Sheng; Burckle, Alexander J; Sigman, Matthew S

    2012-12-14

    Progress in the development of asymmetric Heck couplings of arenes and acyclic olefins has been limited by a tenuous understanding of the factors that dictate selectivity in migratory insertion and β-hydride elimination. On the basis of key mechanistic insight recently garnered in the exploration of selective Heck reactions, we report here an enantioselective variant that delivers β-, γ-, or δ-aryl carbonyl products from acyclic alkenol substrates. The catalyst system imparts notable regioselectivity during migratory insertion and promotes the migration of the alkene's unsaturation toward the alcohol to ultimately form the ketone product. The reaction uses aryldiazonium salts as the arene source, yields enantiomeric products from opposite starting alkene configurations, and uses a readily accessible ligand. The racemic nature of the alkenol substrate does not bias the enantioselection.

  18. Oxidative Heck vinylation for the synthesis of complex dienes and polyenes.

    PubMed

    Delcamp, Jared H; Gormisky, Paul E; White, M Christina

    2013-06-12

    We introduce an oxidative Heck reaction for selective complex diene and polyene formation. The reaction proceeds via oxidative Pd(II)/sulfoxide catalysis that retards palladium-hydride isomerizations which previously limited the Heck manifold's capacity for furnishing stereodefined conjugated dienes. Limiting quantities of nonactivated terminal olefins (1 equiv) and slight excesses of vinyl boronic esters (1.5 equiv) that feature diverse functionality can be used to furnish complex dienes and polyenes in good yields and excellent selectivities (generally E:Z = >20:1; internal:terminal = >20:1). Because this reaction only requires prior activation of a single vinylic carbon, improvements in efficiency are observed for synthetic sequences relative to ones featuring reactions that require activation of both coupling partners.

  19. Baxter Operator and Archimedean Hecke Algebra

    NASA Astrophysics Data System (ADS)

    Gerasimov, A.; Lebedev, D.; Oblezin, S.

    2008-12-01

    In this paper we introduce Baxter integral {mathcal{Q}} -operators for finite-dimensional Lie algebras {mathfrak{gl}_{ell+1}} and {mathfrak{so}_{2ell+1}} . Whittaker functions corresponding to these algebras are eigenfunctions of the {mathcal{Q}}-operators with the eigenvalues expressed in terms of Gamma-functions. The appearance of the Gamma-functions is one of the manifestations of an interesting connection between Mellin-Barnes and Givental integral representations of Whittaker functions, which are in a sense dual to each other. We define a dual Baxter operator and derive a family of mixed Mellin-Barnes-Givental integral representations. Givental and Mellin-Barnes integral representations are used to provide a short proof of the Friedberg-Bump and Bump conjectures for G = GL( ℓ + 1) proved earlier by Stade. We also identify eigenvalues of the Baxter {mathcal{Q}}-operator acting on Whittaker functions with local Archimedean L-factors. The Baxter {mathcal{Q}}-operator introduced in this paper is then described as a particular realization of the explicitly defined universal Baxter operator in the spherical Hecke algebra {mathcal {H}(G(mathbb{R}), K)} , K being a maximal compact subgroup of G. Finally we stress an analogy between {mathcal{Q}}-operators and certain elements of the non-Archimedean Hecke algebra {mathcal {H}(G(mathbb{Q}_p),G(mathbb{Z}_p))}.

  20. The origins of intra- and inter-molecular vibrational couplings: A case study of H{sub 2}O-Ar on full and reduced-dimensional potential energy surface

    SciTech Connect

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

    2016-01-07

    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 H{sub 2}O–Ar, which explicitly incorporates interdependence on the intramolecular (Q{sub 1},  Q{sub 2},  Q{sub 3}) normal-mode coordinates of the H{sub 2}O 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 (v{sub 1},  v{sub 2},  v{sub 3}) =  (0,  0,  0), (0,  0,  1), (1,  0,  0), (0,  1,  0) states of H{sub 2}O 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{sup −1}, and required only 58 parameters. With the 3D PESs of H{sub 2}O–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{sup −1} for all three rotational branches of the asymmetric stretch fundamental transitions. The infrared band origin shifts associated with three fundamental bands of H{sub 2}O in H{sub 2}O–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

  1. Catalyst-Controlled Regioselectivity in the Synthesis of Branched Conjugated Dienes via Aerobic Oxidative Heck Reactions

    PubMed Central

    Zheng, Changwu; Wang, Dian; Stahl, Shannon S.

    2012-01-01

    Pd-catalyzed aerobic oxidative coupling of vinylboronic acids and electronically unbiased alkyl olefins provides regioselective access to 1,3-disubstituted conjugated dienes. Catalyst-controlled regioselectivity is achieved by using 2,9-dimethylphenanthroline as a ligand. The observed regioselectivity is opposite to that observed from a traditional (non-oxidative) Heck reaction between a vinyl bromide and an alkene. DFT computational studies reveal that steric effects of the 2,9-dimethylphenanthroline ligand promote C–C bond-formation at the internal position of the alkene. PMID:22998540

  2. 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...

  3. Influence of intermolecular interactions on magnetic observables

    NASA Astrophysics Data System (ADS)

    Schnack, Jürgen

    2016-02-01

    Very often it is an implied paradigm of molecular magnetism that magnetic molecules in a crystal interact so weakly that measurements of dc magnetic observables reflect ensemble properties of single molecules. But the number of cases where the assumption of virtually noninteracting molecules does not hold grows steadily. A deviation from the noninteracting case can especially clearly be seen in clusters with antiferromagnetic couplings, where steps of the low-temperature magnetization curve are smeared out with increasing intermolecular interaction. In this investigation we demonstrate with examples in one, two, and three space dimensions how intermolecular interactions influence typical magnetic observables such as magnetization, susceptibility, and specific heat.

  4. 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…

  5. [Focal epithelial hyperplasia (Heck's disease) in a Turkish family].

    PubMed

    Weidner, F

    1996-12-01

    A 31-year-old Turkish patient and some family members suffered from multiple hyperplastic oral mucosal papules. Intralesional papilloma virus was not found but the patient had elevated levels of CD8 lymphocytes in his peripheral blood. We diagnosed focal epithelial hyperplasia of Heck.

  6. Preparation of nonsymmetrically substituted stilbenes in a one-pot two-step heck strategy using ethene as a reagent.

    PubMed

    Kormos, Chad M; Leadbeater, Nicholas E

    2008-05-16

    We present here a strategy for the preparation of nonsymmetrically substituted stilbenes using a one-pot two-step double Heck strategy. First a protocol is developed for the selective preparation of a range of styrenes using ethene as the alkene coupling partner. Then conditions are found for the effective coupling of the styrenes with aryl halides using a 1:1 stoichiometric ratio of the two components. The use of the microwave apparatus to perform the reactions offers a convenient method for synthesis as well as for safely, easily, and accurately loading vessels with gaseous reagents.

  7. Development of (trimethylsilyl)ethyl ester protected enolates and applications in palladium-catalyzed enantioselective allylic alkylation: intermolecular cross-coupling of functionalized electrophiles.

    PubMed

    Reeves, Corey M; Behenna, Douglas C; Stoltz, Brian M

    2014-05-02

    The development of (trimethylsilyl)ethyl ester protected enolates is reported. The application of this class of compounds in palladium-catalyzed asymmetric allylic alkylation is explored, yielding a variety of α-quaternary six- and seven-membered ketones and lactams. Independent coupling partner synthesis engenders enhanced allyl substrate scope relative to traditional β-ketoester substrates; highly functionalized α-quaternary ketones generated by the union of (trimethylsilyl)ethyl β-ketoesters and sensitive allylic alkylation coupling partners serve to demonstrate the utility of this method for complex fragment coupling.

  8. Late-onset adenosine deaminase deficiency presenting with Heck's disease.

    PubMed

    Artac, Hasibe; Göktürk, Bahar; Bozdemir, Sefika Elmas; Toy, Hatice; van der Burg, Mirjam; Santisteban, Ines; Hershfield, Michael; Reisli, Ismail

    2010-08-01

    Focal epithelial hyperplasia, also known as Heck's disease, is a rare but distinctive entity of viral etiology with characteristic clinical and histopathological features. It is a benign, asymptomatic disease of the oral mucosa caused by human papilloma viruses (HPV). Previous studies postulated an association between these lesions and immunodeficiency. Genetic deficiency of adenosine deaminase (ADA) results in varying degrees of immunodeficiency, including neonatal onset severe combined immunodeficiency (ADA-SCID), and milder, later onset immunodeficiency. We report a 12-year-old girl with the late onset-ADA deficiency presenting with Heck's disease. Our case report should draw attention to the possibility of immunodeficiency in patients with HPV-induced focal epithelial hyperplasia.

  9. 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.

  10. Aryl-phenyl scrambling in intermediate organopalladium complexes: a gas-phase study of the Mizoroki-Heck reaction.

    PubMed

    Fiebig, Lukas; Schlörer, Nils; Schmalz, Hans-Günther; Schäfer, Mathias

    2014-04-22

    The intramolecular aryl-phenyl scrambling reaction within palladium-DPPP-aryl complex (DPPP=1,3-bis(diphenylphosphino)propane) ions was analyzed by state-of-the-art tandem MS, including gas-phase ion/molecule reactions. The Mizoroki-Heck cross-coupling reaction was performed in the gas phase, and the intrinsic reactivity of important intermediates could be examined. Moreover, linear free-energy correlations were applied, and a mechanism for the scrambling reaction proceeding via phosphonium cations was assumed.

  11. Non-Abelian Vortices, Hecke Modifications and Singular Monopoles

    NASA Astrophysics Data System (ADS)

    Baptista, J. M.

    2010-06-01

    In this note, we show that for the group G = U( N) the space of Hecke modifications of a rank N vector bundle over a Riemann surface C coincides with the moduli space of solutions of certain non-Abelian vortex equations over C. Through the recent work of Kapustin and Witten this then leads to an isomorphism between the moduli space of vortices and the moduli space of singular monopoles on the product of C with a closed interval I.

  12. Intermolecular interactions in solid benzene.

    PubMed

    Kearley, G J; Johnson, M R; Tomkinson, J

    2006-01-28

    The lattice dynamics and molecular vibrations of benzene and deuterated benzene crystals are calculated from force constants derived from density-functional theory (DFT) calculations and compared with measured inelastic neutron-scattering spectra. A very small change (0.5%) in lattice parameter is required to obtain real lattice-mode frequencies across the Brillouin zone. There is a strong coupling between wagging and breathing modes away from the zone center. This coupling and sensitivity to cell size arises from two basic interactions. Firstly, comparatively strong interactions that hold the benzene molecules together in layers. These include an intermolecular interaction in which H atoms of one molecule link to the center of the aromatic ring of a neighboring molecule. The layers are held to each other by weaker interactions, which also have components that hold molecules together within a layer. Small changes in the lattice parameters change this second type of interaction and account for the changes to the lattice dynamics. The calculations also reveal a small auxetic effect in that elongation of the crystal along the b axis leads to an increase in internal pressure in the ac plane, that is, elongation in the b direction induces expansion in the a and c directions.

  13. Desensitization of metastable intermolecular composites

    SciTech Connect

    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. Palladium catalysts supported on mesoporous molecular sieves bearing nitrogen donor groups: preparation and use in Heck and Suzuki C-C bond-forming reactions.

    PubMed

    Demel, Jan; Lamac, Martin; Cejka, Jirí; Stepnicka, Petr

    2009-01-01

    A series of supported catalysts is prepared by treatment of SBA-15-type mesoporous molecular sieve bearing [triple chemical bond]SiCH(2)CH(2)CH(2)NHCH(2)CH(2)NEt(2) groups with palladium(II) acetate. These catalysts are studied in Suzuki biaryl couplings and in Heck reactions to establish the influence of metal loading and innocent surface modifications (trimethylsilylation). The Suzuki reaction proceeded efficiently with model and practically relevant substrates; the catalyst performance increasing with an increasing degree of metalation (decreasing N/Pd ratio). Catalyst poisoning tests revealed that the reaction takes place in the liquid phase with the catalyst serving as a reservoir of active metal species and also as a stabilizing support once the reaction is performed. In the Heck reactions, on the other hand, the catalyst performance strongly changed with the reaction temperature and with the N/Pd ratio. The material with the lowest metal loading (0.01 mmol palladium per gram of material, N/Pd ratio ca. 100:1) proved particularly attractive in the Heck coupling, being highly active at elevated temperatures, recyclable, and capable of acting as a bifunctional catalyst (i.e., functioning without any external base.

  15. On the Li Coefficients for the Hecke L-functions

    NASA Astrophysics Data System (ADS)

    Omar, Sami; Ouni, Raouf; Mazhouda, Kamel

    2014-06-01

    In this paper, we compute and verify the positivity of the Li coefficients for the Hecke L-functions using an arithmetic formula established in Omar and Mazhouda, J. Number Theory 125(1), 50-58 (2007) and J. Number Theory 130(4), 1098-1108 (2010) and the Serre trace formula. Additional results are presented, including new formulas for the Li coefficients and a formulation of a criterion for the partial Riemann hypothesis. Basing on the numerical computations made below, we conjecture that these coefficients are increasing in n.

  16. Nickel-Catalyzed Heck-Type Reactions of Benzyl Chlorides and Simple Olefins

    PubMed Central

    Matsubara, Ryosuke; Gutierrez, Alicia C.; Jamison, Timothy F.

    2011-01-01

    Nickel-catalyzed intermolecular benzylation and heterobenzylation of unactivated alkenes to provide functionalized allylbenzene derivatives is described. A wide range of both the benzyl chloride and alkene coupling partners are tolerated. In contrast to analogous palladium-catalyzed variants of this process, all reactions described herein employ electronically unbiased aliphatic olefins (including ethylene), proceed at room temperature and provide 1,1-disubstituted olefins over the more commonly observed 1,2-disubstituted olefins with very high selectivity. PMID:22066899

  17. Focal epithelial hyperplasia (Heck's disease) in two Chinese females.

    PubMed

    Liu, N; Li, Y; Zhou, Y; Zeng, X

    2012-08-01

    Focal epithelial hyperplasia, or Heck's disease, is a relatively rare virus-induced benign disease. To the best of the authors' knowledge it has not been reported in an ethnic Chinese population. The authors report two cases of focal epithelial hyperplasia (FEH) in Chinese patients, which were clinically and histologically in accord with FEH. In particular, the lesions in one case were located on the gingival mucosa, which is rarely affected by FEH. DNA extracted from paraffin-embedded specimens from the two patients was tested for the presence of human papilloma virus followed by specific polymerase chain reaction testing for 16, 18, 13, and 32 subtypes in order to confirm the clinical diagnosis.

  18. Perturbation analyses of intermolecular interactions

    NASA Astrophysics Data System (ADS)

    Koyama, Yohei M.; Kobayashi, Tetsuya J.; Ueda, Hiroki R.

    2011-08-01

    Conformational fluctuations of a protein molecule are important to its function, and it is known that environmental molecules, such as water molecules, ions, and ligand molecules, significantly affect the function by changing the conformational fluctuations. However, it is difficult to systematically understand the role of environmental molecules because intermolecular interactions related to the conformational fluctuations are complicated. To identify important intermolecular interactions with regard to the conformational fluctuations, we develop herein (i) distance-independent and (ii) distance-dependent perturbation analyses of the intermolecular interactions. We show that these perturbation analyses can be realized by performing (i) a principal component analysis using conditional expectations of truncated and shifted intermolecular potential energy terms and (ii) a functional principal component analysis using products of intermolecular forces and conditional cumulative densities. We refer to these analyses as intermolecular perturbation analysis (IPA) and distance-dependent intermolecular perturbation analysis (DIPA), respectively. For comparison of the IPA and the DIPA, we apply them to the alanine dipeptide isomerization in explicit water. Although the first IPA principal components discriminate two states (the α state and PPII (polyproline II) + β states) for larger cutoff length, the separation between the PPII state and the β state is unclear in the second IPA principal components. On the other hand, in the large cutoff value, DIPA eigenvalues converge faster than that for IPA and the top two DIPA principal components clearly identify the three states. By using the DIPA biplot, the contributions of the dipeptide-water interactions to each state are analyzed systematically. Since the DIPA improves the state identification and the convergence rate with retaining distance information, we conclude that the DIPA is a more practical method compared with the

  19. 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.

  20. Direct carbocyclizations of benzoic acids: catalyst-controlled synthesis of cyclic ketones and the development of tandem aHH (acyl Heck-Heck) reactions.

    PubMed

    Miles, Kelsey C; Le, Chi Chip; Stambuli, James P

    2014-09-01

    The formation of exo-methylene indanones and indenones from simple ortho-allyl benzoic acid derivatives has been developed. Selective formation of the indanone or indenone products in these reactions is controlled by choice of ancillary ligand. This new process has a low environmental footprint as the products are formed in high yields using low catalyst loadings, while the only stoichiometric chemical waste generated from the reactants in the transformation is acetic acid. The conversion of the active cyclization catalyst into the Hermman-Beller palladacycle was exploited in a one-pot tandem acyl Heck-Heck (aHH) reaction, and utilized in the synthesis of donepezil.

  1. 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.

  2. A rapid microwave protocol for Heck vinylation of aryl chlorides under air.

    PubMed

    Datta, Gopal K; Vallin, Karl S A; Larhed, Mats

    2003-01-01

    In modern high-throughput chemistry, the overall workflow is a crucial factor and much work is devoted to speeding up the process of chemistry development. Since automated microwave-based synthesizers are known to streamline the compound production and to accelerate slow organic transformations, this technology was implemented for Heck reactions with sluggish aryl chlorides. Furthermore, homogeneous palladium-catalyzed Heck vinylations of aryl chlorides can be performed under air under optimized conditions. Based on this finding, controlled microwave heating was utilized to accelerate model reactions down to 30 min employing a mixture of ionic liquid and 1,4-dioxane as solvent.

  3. Intermolecular potentials for hexafluoride gases

    SciTech Connect

    Aziz, R.A. . Dept. of Physics); Taylor, W.L. )

    1989-10-31

    Second virial coefficient and viscosity data were used to evaluate intermolecular potential functions proposed in the literature for SF{sub 6}, UF{sub 6}, and WF{sub 6}. It was found that none of the potentials could predict the properties simultaneously. By suitable adjustment of the repulsive wall, we constructed an inverse power (n{minus}7) potential which correlates second virial coefficient and viscosity data at the same time. The best integer repulsive exponent for SF{sub 6} was found to be n = 40, while that for UF{sub 6} and WF{sub 6} was n = 46. 41 refs., 10 figs., 11 tabs.

  4. 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 .

  5. Preparation of Vinyl Silyl Ethers and Disiloxanes via the Silyl-Heck Reaction of Silyl Ditriflates

    PubMed Central

    Martin, Sara E. S.; Watson, Donald A.

    2013-01-01

    Vinyl silyl ethers and disiloxanes can now be prepared from aryl-substituted alkenes and related substrates using a silyl-Heck reaction. The reaction employs a commercially available catalyst system and mild conditions. This work represents a highly practical means of accessing diverse classes of vinyl silyl ether substrates in an efficient and direct manner with complete regio- and geometric selectivity. PMID:23984876

  6. Focal epithelial hyperplasia (Heck's disease) in three Kenyan girls: case reports.

    PubMed

    Chindia, M L; Awange, D O; Guthua, S W; Mwaniki, D L

    1993-09-01

    We report the first three patients diagnosed with focal epithelial hyperplasia (Heck's disease) in Kenya. Clinically they presented as focal or diffuse papillomatous lesions in the oral mucosa. Histopathological features rule out other similar lesions inter alia multiple fibro-epithelial and viral warts.

  7. Successful topical treatment of focal epithelial hyperplasia (Heck's disease) with interferon-beta.

    PubMed

    Steinhoff, M; Metze, D; Stockfleth, E; Luger, T A

    2001-05-01

    We report the successful topical treatment of focal epithelial hyperplasia (Heck's disease) with interferon-beta (Fiblaferon gel). Topical treatment with interferon-beta appears to be an effective, simple, non-invasive, cheap and low-risk alternative to other invasive or surgical therapeutic modalities.

  8. 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.

  9. Classification of Non-Affine Non-Hecke Dynamical R-Matrices

    NASA Astrophysics Data System (ADS)

    Avan, Jean; Billaud, Baptiste; Rollet, Geneviève

    2012-09-01

    A complete classification of non-affine dynamical quantum R-matrices obeying the Gl_n({C})-Gervais-Neveu-Felder equation is obtained without assuming either Hecke or weak Hecke conditions. More general dynamical dependences are observed. It is shown that any solution is built upon elementary blocks, which individually satisfy the weak Hecke condition. Each solution is in particular characterized by an arbitrary partition {{I}(i),; iin\\{1,dots,n}} of the set of indices {1,dots,n} into classes, {I}(i) being the class of the index i, and an arbitrary family of signs (ɛ_{I})_{{I}in{{I}(i), ; iin{1,dots,n}}} on this partition. The weak Hecke-type R-matrices exhibit the analytical behaviour R_{ij,ji}=f(ɛ_{{I}(i)}Λ_{{I}(i)}-ɛ_{{I}(j)}Λ_{{I}(j)}), where f is a particular trigonometric or rational function, Λ_{{I}(i)}=sumlimits_{jin{I}(i)}λ_j, and (λ_i)_{iin{1,dots,n}} denotes the family of dynamical coordinates.

  10. Intramolecular Imidoylative Heck Reaction: Synthesis of Cyclic Ketoimines from Functionalized Isocyanide.

    PubMed

    Wang, Jian; Tang, Shi; Zhu, Qiang

    2016-07-01

    Efficient access to five- to seven-membered cyclic ketoimines, through palladium-catalyzed intramolecular imidoylative Heck reaction of alkene-containing isocyanides, has been developed. Consecutive isocyanide and alkene insertion into aryl or alkyl Pd(II) intermediates takes place in this process. No byproduct derived from monoinsertion or reversed sequence is detected.

  11. 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...

  12. Focal epithelial hyperplasia (Heck's disease): report of two cases with PCR detection of human papillomavirus DNA.

    PubMed

    Jayasooriya, P R; Abeyratne, S; Ranasinghe, A W; Tilakaratne, W M

    2004-07-01

    Focal epithelial hyperplasia (FEH) (Heck's disease) is essentially a benign oral infection produced by the human papillomavirus (HPV). Although this condition is known to exist in numerous populations and ethnic groups, it is relatively rare in South-East Asia. The following report is based on two cases of adult FEH with histopathological features in favour of the disease. In addition, polymerase chain reaction was performed to detect the presence of HPV DNA in the lesions in order to confirm the histopathological diagnosis.

  13. 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.

  14. A generalization of the Funk-Hecke theorem to the case of hyperbolic spaces

    NASA Astrophysics Data System (ADS)

    Shtepina, T. V.

    2004-10-01

    The well-known Funk-Hecke theorem states that for integral operators whose kernels depend only on the distance between points in spherical geometry and where the integral is taken over the surface of a hypersphere, every surface spherical harmonic is an eigenvector. In this paper we extend this theorem to the case of non-compact Lobachevsky spaces. We compute the corresponding eigenvalue in some physically important cases.

  15. A Family of Finite-Dimensional Representations of Generalized Double Affine Hecke Algebras of Higher Rank

    NASA Astrophysics Data System (ADS)

    Fu, Yuchen; Shelley-Abrahamson, Seth

    2016-06-01

    We give explicit constructions of some finite-dimensional representations of generalized double affine Hecke algebras (GDAHA) of higher rank using R-matrices for U_q(sl_N). Our construction is motivated by an analogous construction of Silvia Montarani in the rational case. Using the Drinfeld-Kohno theorem for Knizhnik-Zamolodchikov differential equations, we prove that the explicit representations we produce correspond to Montarani's representations under a monodromy functor introduced by Etingof, Gan, and Oblomkov.

  16. Many-body effects in intermolecular forces.

    PubMed

    Elrod, M J; Saykally, R J

    1994-11-01

    The authors provide a review and literature survey of many-body effects in intermolecular forces. Topics include experimental methods, theoretical methods, many-body effects in atomic systems, and many-body effects in aqueous and nonaqueous molecular systems.

  17. 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.

  18. 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.

  19. Electroreductive Intermolecular Coupling of Coumarins with Benzophenones: Synthesis of 4-(2-Hydroxyphenyl)-5,5-diaryl-γ-butyrolactones, 2-(2,2-Diaryl-2,3-dihydrobenzofuran-3-yl)acetic Acids, and 4-(Diarylmethyl)coumarins.

    PubMed

    Kise, Naoki; Hamada, Yusuke; Sakurai, Toshihiko

    2016-11-18

    The electroreductive coupling of coumarins with benzophenones in the presence of TMSCl gave adducts reacted at the 4-position of coumarins as trimethylsilyl ethers. From 3-methylcoumarin, 3,4-cis-adducts were formed stereoselectively. The de-trimethylsilylation of the adducts with 1 M HCl aq or TBAF in THF at 25 °C produced 4-(2-hydroxyphenyl)-5,5-diaryl-γ-butyrolactones. The γ-butyrolactones were further transformed to 2-(2,2-diaryl-2,3-dihydrobenzofuran-3-yl)acetic acids by treatment with 1 M HCl aq at reflux temperature. The de-trimethylsilylation of the adducts with 1 M HCl in MeOH afforded 2-(2,2-diaryl-2,3-dihydrobenzofuran-3-yl)acetic acid methyl esters. The de-trimethylsiloxylation of the adducts or dehydration of the γ-butyrolactones brought about 4-(diarylmethyl)coumarins.

  20. Density functional calculation of intermolecular potentials.

    PubMed

    Nyeland, Carl

    2011-06-30

    Calculations of intermolecular potentials following the density functional theory (DFT) turn out to be very complicated without using some appropriate approximations. Most often the following three approximations have been considered. In one approximation the disturbed charge distributions during collisions are reduced to sums of undisturbed charge distributions from the colliding species. In another approximation, the so-called local density approximation (LDA), one neglects the fact that the intermolecular potentials that depend on charge densities also depend on gradients in the densities. In a third approximation one assumes that the intermolecular potential can be considered as a sum of two terms: a term for the long-range geometry and a term for the short-range geometry. In this Article the three approximations mentioned will be discussed for numerical accuracy for calculations of potentials between inert gas atoms and for calculations of potentials between surfaces and inert gas atoms. In the discussion a few other approximations will be mentioned too.

  1. 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.

  2. 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.

  3. Intermolecular Slip Mechanism in Tropocollagen Nanofibrils

    DTIC Science & Technology

    2009-01-01

    Imperfecta or Ehlers - Danlos Syndrome. REPORT DOCUMENTATION PAGE (SF298) (Continuation Sheet) Continuation for Block 13 ARO Report Number Intermolecular slip...our studies could advance our knowledge of mechan- isms underlying important collagen-related diseases like Osteogenesis Imperfecta or Ehlers - Danlos

  4. 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

  5. Mapping intermolecular bonding in C₆₀.

    PubMed

    Sundqvist, Bertil

    2014-08-22

    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.

  6. Catalytic intermolecular alkene oxyamination with nitrenes.

    PubMed

    Dequirez, Geoffroy; Ciesielski, Jennifer; Retailleau, Pascal; Dauban, Philippe

    2014-07-14

    The Rh(II)-catalyzed intermolecular addition of nitrenes to aromatic and aliphatic alkenes provides vicinal amino alcohols with yields of up to 95 % and complete regioselectivity. This 1,2-oxyamination reaction involves the formation of an aziridine intermediate that undergoes in situ ring opening. The latter is induced by the Rh-bound nitrene that behaves as a Lewis acid.

  7. VSCF calculations for the intra- and intermolecular vibrational modes of the water dimer and its isotopologs

    NASA Astrophysics Data System (ADS)

    Monteiro, João G. S.; Barbosa, André G. H.

    2016-11-01

    In this work we show how the VSCF method may be successfully used to describe all fundamental vibrational transitions of several isotopologs of water dimer. By expressing the normal mode displacements in terms of appropriate delocalized internal coordinates we are able to minimize the mode-mode coupling in the PES and thus yield PT2-VSCF frequencies in good agreement with the experiment. The use of curvilinear normal modes is of paramount importance to describe vibrational transitions of the very soft intermolecular modes. Within our approach the maximum calculated error for the (H2O)2 intermolecular frequencies are reduced from 311 cm-1 (Cartesian normal modes) to just 56 cm-1 (curvilinear normal modes). Plots of the diagonal intermolecular potential and of the vibrational wave function illustrate the remarkable effect of different coordinate systems. In conclusion, our PT2-VSCF calculations provide a fair anharmonic description of the fundamental transitions of water dimers.

  8. Unexpected hydrodeiodo Sonogashira-Heck-Casser coupling reaction of 2,2'-diiodobiphenyls with acetylenes.

    PubMed

    Chou, Meng-Yen; Mandal, Ashis Baran; Leung, Man-kit

    2002-03-08

    2,2'-Diiodobiphenyl-4,4'-dicarboxylic acid dimethyl ester (3) undergoes either a ring-closure reaction with phenylacetylene to give 4 or hydrodeiodo phenylethynylation to give 5 under the catalytic conditions of Pd(OAc)(2)/CuI/phosphine in amines. In these reactions, the amine and the phosphine ligands play important roles in controlling the reactivity. Among the ligands we used, tris(o-tolyl)phosphine is the best ligand for hydrodeiodo phenylethynylation, while the bidentate phosphine ligand retards both of the reactions. On the basis of our results, we propose that 5 is formed through a fast hydrodeiodination, followed by a Sonogashira phenylethynylation. The results of the deuterium labeling experiments show that proton exchange between the acetylenic proton and the alkyl protons of amine occurs effectively under the reaction conditions. In addition, the hydrogen that replaces the iodide in the hydrodeiodination process arises mainly from the acetylenic proton.

  9. High-resolution absorptive intermolecular multiple-quantum coherence NMR spectroscopy under inhomogeneous fields

    NASA Astrophysics Data System (ADS)

    Lin, Meijin; Lin, Yanqin; Chen, Xi; Cai, Shuhui; Chen, Zhong

    2012-01-01

    Intermolecular multiple-quantum coherence (iMQC) is capable of improving NMR spectral resolution using a 2D shearing manipulation method. A pulse sequence termed CT-iDH, which combines intermolecular double-quantum filter (iDQF) with a modified constant-time (CT) scheme, is designed to achieve fast acquisition of high-resolution intermolecular zero-quantum coherences (iZQCs) and intermolecular double-quantum coherences (iDQCs) spectra without strong coupling artifacts. Furthermore, double-absorption lineshapes are first realized in 2D intermolecular multi-quantum coherences (iMQCs) spectra under inhomogeneous fields through a combination of iZQC and iDQC signals to double the resolution without loss of sensitivity. Theoretically the spectral linewidth can be further reduced by half compared to original iMQC high-resolution spectra. Several experiments were performed to test the feasibility of the new method and the improvements are evaluated quantitatively. The study suggests potential applications for in vivo spectroscopy.

  10. Mechanism, reactivity, and selectivity in palladium-catalyzed redox-relay Heck arylations of alkenyl alcohols.

    PubMed

    Xu, Liping; Hilton, Margaret J; Zhang, Xinhao; Norrby, Per-Ola; Wu, Yun-Dong; Sigman, Matthew S; Wiest, Olaf

    2014-02-05

    The enantioselective Pd-catalyzed redox-relay Heck arylation of acyclic alkenyl alcohols allows access to various useful chiral building blocks from simple olefinic substrates. Mechanistically, after the initial migratory insertion, a succession of β-hydride elimination and migratory insertion steps yields a saturated carbonyl product instead of the more general Heck product, an unsaturated alcohol. Here, we investigate the reaction mechanism, including the relay function, yielding the final carbonyl group transformation. M06 calculations predict a ΔΔG(‡) of 1 kcal/mol for the site selectivity and 2.5 kcal/mol for the enantioselectivity, in quantitative agreement with experimental results. The site selectivity is controlled by a remote electronic effect, where the developing polarization of the alkene in the migratory insertion transition state is stabilized by the C-O dipole of the alcohol moiety. The enantioselectivity is controlled by steric repulsion between the oxazoline substituent and the alcohol-bearing alkene substituent. The relay efficiency is due to an unusually smooth potential energy surface without high barriers, where the hydroxyalkyl-palladium species acts as a thermodynamic sink, driving the reaction toward the carbonyl product. Computational predictions of the relative reactivity and selectivity of the double bond isomers are validated experimentally.

  11. 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)

  12. 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

    2016-05-09

    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.

  13. Intermolecular Michael reactions: a computational investigation.

    PubMed

    Kwan, Eugene E; Evans, David A

    2010-11-19

    Computational studies have suggested that η(3)-lithium enolates in which the cation is partially bound to both carbon and oxygen may be important reactive intermediates. DFT calculations are used to demonstrate that explicitly solvated acetone enolates are largely O-bound. With this premise in mind, the stereochemical course of intermolecular Michael additions is examined. The results are generally consistent with what is observed experimentally and the model advanced by Heathcock and co-workers.

  14. 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.

  15. An isotopic mass effect on the intermolecular potential

    SciTech Connect

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

    2015-09-28

    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 paper, 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. Finally, the analysis suggests that mass dependent variations in intermolecular potentials should be included in comprehensive descriptions of isotopologue thermodynamics.

  16. Terminating Catalytic Asymmetric Heck Cyclizations by Stereoselective Intramolecular Capture of η3-Allylpalladium Intermediates: Total Synthesis of (−)-Spirotryprostatin B and Three Stereoisomers

    PubMed Central

    Overman, Larry E.; Rosen, Mark D.

    2010-01-01

    A catalytic intramolecular Heck reaction, followed by capture of the resulting η3-allylpalladium intermediate by a tethered diketopiperazine, is the central step in a concise synthetic route to (−)-spirotryprostatin B and three stereoisomers. This study demonstrates that an acyclic, chiral η3-allylpalladium fragment generated in a catalytic asymmetric Heck cyclization can be trapped by even a weakly nucleophilic diketopiperazine more rapidly than it undergoes diastereomeric equilibration. PMID:20725641

  17. A Case Report of Focal Epithelial Hyperplasia (Heck's disease) with PCR Detection of Human Papillomavirus.

    PubMed

    Ozden, Bora; Gunduz, Kaan; Gunhan, Omer; Ozden, Feyza Otan

    2011-12-01

    Focal epithelial hyperplasia or Heck's disease, is a rare viral infection of the oral mucosa caused by human papillomavirus. The frequency of this disease varies widely from one geographic region to another. In Caucasians there have been only few cases reported. This paper reports a case of focal epithelial hyperplasia and demonstrates the association with HPV subtype 32 through polymerase chain reaction (PCR) and sequencing of PCR products. A 7-year-old Caucasian girl was admitted to our clinic for investigation of multiple oral mucosal lesions in the mouth. Lesion was excised under local anesthesia without any complication. The lesion was diagnosed as focal epithelial hyperplasia according to both clinical and histopathological features. Dental staff should be aware of these kind of lesions and histopathological examination together with a careful clinical observation should be carried out for a definitive diagnosis.

  18. Exploring a cascade Heck-Suzuki reaction based route to kinase inhibitors using design of experiments.

    PubMed

    Ekebergh, Andreas; Lingblom, Christine; Sandin, Peter; Wennerås, Christine; Mårtensson, Jerker

    2015-03-21

    Design of Experiments (DoE) has been used to optimize a diversity oriented palladium catalyzed cascade Heck-Suzuki reaction for the construction of 3-alkenyl substituted cyclopenta[b]indole compounds. The obtained DoE model revealed a reaction highly dependent on the ligand. Guided by the model, an optimal ligand was chosen that selectively delivered the desired products in high yields. The conditions were applicable with a variety of boronic acids and were used to synthesize a library of 3-alkenyl derivatized compounds. Focusing on inhibition of kinases relevant for combating melanoma, the library was used in an initial structure-activity survey. In line with the observed kinase inhibition, cellular studies revealed one of the more promising derivatives to inhibit cell proliferation via an apoptotic mechanism.

  19. 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...

  20. Direct access to ketones from aldehydes via rhodium-catalyzed cross-coupling reaction with potassium trifluoro(organo)borates.

    PubMed

    Pucheault, Mathieu; Darses, Sylvain; Genet, Jean-Pierre

    2004-12-01

    A direct cross-coupling reaction of aromatic aldehydes with potassium trifluoro(organo)borates afforded ketones in high yields and under mild conditions in the presence of a rhodium catalyst and acetone. This new reaction, involving a formal aldehyde C-H bond activation, is believed to proceed via a Heck-type mechanism followed by hydride transfer to acetone.

  1. Intermolecular potential energy surface for CS2 dimer.

    PubMed

    Farrokhpour, Hossein; Mombeini, Zainab; Namazian, Mansoor; Coote, Michelle L

    2011-04-15

    A new four-dimensional intermolecular potential energy surface for CS(2) dimer is obtained by ab initio calculation of the interaction energies for a range of configurations and center-of-mass separation distances for the first time. The calculations were performed using the supermolecular approach at the Møller-Plesset second-order perturbation (MP2) level of theory with the augmented correlation consistent basis sets (aug-cc-pVxZ, x = D, T) and corrected for the basis-set superposition error using the full counterpoise correction method. A two-point extrapolation method was used to extrapolate the calculated energy points to the complete basis set limit. The effect of using the higher levels of theory, quadratic configuration interaction containing single, double, and perturbative triple excitations QCISD(T) and coupled cluster singles, doubles and perturbative triples excitations CCSD(T), on the shape of potential energy surface was investigated. It is shown that the MP2 level of theory apparently performs extremely poorly for describing the intermolecular potential energy surface, overestimating the total energy by a factor of nearly 1.73 in comparison with the QCISD(T) and CCSD(T) values. The value of isotropic dipole-dipole dispersion coefficient (C(6) ) of CS(2) fluid was obtained from the extrapolated MP2 potential energy surface. The MP2 extrapolated energy points were fitted to well-known analytical potential functions using two different methods to represent the potential energy surface analytically. The most stable configuration of the dimer was determined at R = 6.23 au, α = 90°, β = 90°, and γ = 90°, with a well depth of 3.980 kcal mol(-1) at the MP2 level of theory. Finally, the calculated second virial coefficients were compared with experimental values to test the quality of the presented potential energy surface.

  2. The First Example of Nickel-Catalyzed Silyl-Heck Reactions: Direct Activation of Silyl Triflates Without Iodide Additives

    PubMed Central

    McAtee, Jesse R.; Martin, Sara E. S.; Cinderella, Andrew P.; Reid, William B.; Johnson, Keywan A.

    2014-01-01

    For the first time, nickel-catalyzed silyl-Heck reactions are reported. Using simple phosphine-supported nickel catalysts, direct activation of silyl triflates has been achieved. These results contrast earlier palladium-catalyzed systems, which require iodide additives to activate silyl-triflates. These nickel-based catalysts exhibit good functional group tolerance in the preparation of vinyl silanes, and unlike earlier systems, allows for the incorporation of trialkylsilanes larger than Me3Si. PMID:24914247

  3. An in Situ Generated Palladium on Aluminum Oxide: Applications in Gram-Scale Matsuda-Heck Reactions.

    PubMed

    Pape, Simon; Daukšaitė, Lauryna; Lucks, Sandra; Gu, Xiaoting; Brunner, Heiko

    2016-12-16

    In situ generated palladium on aluminum oxide provides an active catalytic system for Matsuda-Heck reactions in gram-scale. The novel catalyst proceeded through a significantly higher catalytic activity compared to the classical Pd/C system. Based on the high catalytic activity the first α,β,β-triarylation of methyl acrylate in good yields could be provided in one-step.

  4. Intermolecular interaction approach for TADF (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Wong, Ken-Tsung

    2016-09-01

    Materials with thermally activated delayed fluorescence (TADF) have recently emerged as new fluorescent emitters for highly efficient organic light-emitting diodes (OLEDs). Molecule with TADF behavior needs to have a small singlet-triplet energy difference (ΔES-T) that allows the up-conversion from nonradiative triplet state (T1) to radiative singlet state (S1) via reverse intersystem crossing (RISC) process. Generally, molecules with small ΔES-T can be obtained via carefully manipulate the degree of "intramolecular" charge transfer (ICT) between electron-donating and -accepting components, such that the electron exchange energy that contributes to ΔES-T, can be minimized. Alternatively, excited state with small ΔES-T can be feasibly realized via "intermolecular" charge transfer occurring at the interface between spatially separating donor (D) and acceptor (A) molecules. Because the exchange energy decreases as the HOMO-LUMO separation distance increases, theoretically, the intermolecular D/A charge transfer state (or exciplex) should have rather small ΔES-T, leading to efficient TADF. However, it is still a challenge to access highly efficient exciplex systems. This is mainly because exciplex formation is commonly accompanied with a large red shift of emission spectra and long radiative lifetime, which tend to diminish photoluminescence quantum yield (PLQY) as well as electroluminescence (EL) performance. Until now, exciplex-based OLEDs with external quantum efficiency (EQE) above 10% are still limited. By judicious selection of donor and acceptor, the formation of efficient exciplex can be feasibly achieved. In this conference, our recent efforts on highly efficient exciplexes using C3-symmetry triazine acceptors and various donors, and their device characteristics will be presented.

  5. Some mathematical models of intermolecular autophosphorylation.

    PubMed

    Doherty, Kevin; Meere, Martin; Piiroinen, Petri T

    2015-04-07

    Intermolecular autophosphorylation refers to the process whereby a molecule of an enzyme phosphorylates another molecule of the same enzyme. The enzyme thereby catalyses its own phosphorylation. In the present paper, we develop two generic models of intermolecular autophosphorylation that also include dephosphorylation by a phosphatase of constant concentration. The first of these, a solely time-dependent model, is written as one ordinary differential equation that relies upon mass-action and Michaelis-Menten kinetics. Beginning with the enzyme in its dephosphorylated state, it predicts a lag before the enzyme becomes significantly phosphorylated, for suitable parameter values. It also predicts that there exists a threshold concentration for the phosphorylation of enzyme and that for suitable parameter values, a continuous or discontinuous switch in the phosphorylation of enzyme are possible. The model developed here has the advantage that it is relatively easy to analyse compared with most existing models for autophosphorylation and can qualitatively describe many different systems. We also extend our time-dependent model of autophosphorylation to include a spatial dependence, as well as localised binding reactions. This spatio-temporal model consists of a system of partial differential equations that describe a soluble autophosphorylating enzyme in a spherical geometry. We use the spatio-temporal model to describe the phosphorylation of an enzyme throughout the cell due to an increase in local concentration by binding. Using physically realistic values for model parameters, our results provide a proof-of-concept of the process of activation by local concentration and suggest that, in the presence of a phosphatase, this activation can be irreversible.

  6. 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.

  7. Aqueous microwave-assisted cross-coupling reactions applied to unprotected nucleosides

    PubMed Central

    Hervé, Gwénaëlle; Len, Christophe

    2015-01-01

    Metal catalyzed cross-coupling reactions have been the preferred tools to access to modified nucleosides (on the C5-position of pyrimidines and on the C7- or C8-positions of purines). Our objective is to focus this mini-review on the Suzuki-Miyaura and on the Heck cross-couplings of nucleosides using microwave irradiations which is an alternative technology compatible with green chemistry and sustainable development PMID:25741506

  8. An isotopic mass effect on the intermolecular potential

    DOE PAGES

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

    2015-09-28

    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 paper, 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. Finally, the analysis suggests that mass dependent variations in intermolecular potentials should be included in comprehensive descriptions of isotopologuemore » thermodynamics.« less

  9. 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.

  10. [Imiquimod for the topical treatment of focal epithelial hyperplasia (Heck disease) in a child].

    PubMed

    Maschke, Jan; Brauns, Tilmann C; Goos, Manfred

    2004-10-01

    Focal epithelial hyperplasia (FEH) or Heck disease is a rare skin disease caused by human papilloma viruses (HPV). The case of a 9-year old boy is presented to demonstrate the successful treatment of massive FEH with 5% imiquimod cream. Initially, the patient had noticed several separate papules, which spread and developed into multiple peri- and intraoral papillomatous nodules. The lesions were treated with carbon dioxide laser destruction. However, multiple, skin-coloured papillomatous nodules were found on the tongue, buccal mucosa and lips 1.5 years later. Treatment with imiquimod was initiated, because the patient suffered tremendously from the disease. 5% imiquimod cream was applied 3 times per week. Regression of lesions was obvious after 1 month of treatment. Complete clearance was achieved after 2 additional months of treatment and no recurrence was detected over a follow-up period of 5 months. Our case points out the clinical value of imiquimod for the non-traumatic and almost painless therapy of HPV-induced skin diseases in children.

  11. Relative reactivity of alkenyl alcohols in the palladium-catalyzed redox-relay Heck reaction.

    PubMed

    Hilton, Margaret J; Cheng, Bin; Buckley, Benjamin R; Xu, Liping; Wiest, Olaf; Sigman, Matthew S

    2015-09-16

    The relative rates of alkenyl alcohols in the Pd-catalyzed redox-relay Heck reaction were measured in order to examine the effect of their steric and electronic properties on the rate-determining step. Competition experiments between an allylic alkenyl alcohol and two substrates with differing chain lengths revealed that the allylic alcohol reacts 3-4 times faster in either case. Competition between di- and trisubstituted alkenyl alcohols provided an interesting scenario, in which the disubstituted alkene was consumed first followed by reaction of the trisubstituted alkene. Consistent with this observation, the transition structures for the migratory insertion of the aryl group into the di- and trisubstituted alkenes were calculated with a lower barrier for the former. An internal competition between a substrate containing two alcohols with differing chain lengths demonstrated the catalyst's preference for migrating towards the closest alcohol. Additionally, it was observed that increasing the electron density in the arene boronic acid promotes a faster reaction, which correlates with Hammett σp values to give a ρ of -0.87.

  12. Nickel-Catalyzed Mizoroki–Heck Reaction of Aryl Sulfonates and Chlorides with Electronically Unbiased Terminal Olefins: High Selectivity for Branched Products**

    PubMed Central

    Tasker, Sarah Z.; Gutierrez, Alicia C.

    2014-01-01

    Achieving high selectivity in the Heck reaction of electronically unbiased alkenes has been a longstanding challenge. Using a nickel-catalyzed cationic Heck reaction, we were able to achieve excellent selectivity for branched products (≥19:1 in all cases) over a wide range of aryl electrophiles and aliphatic olefins. A bidentate ligand with a suitable bite angle and steric profile was key to obtaining high branched/linear selectivity, while the appropriate base suppressed alkene isomerization of the product. Though aryl triflates are traditionally used to access the cationic Heck pathway, we have shown that by using triethylsilyl trifluoromethanesulfonate (TESOTf), we can effect a counterion exchange of the catalytic nickel complex such that cheaper and more stable aryl chlorides, mesylates, tosylates, and sulfamates can be used to yield the same branched products with high selectivity. PMID:24402966

  13. 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

  14. 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.

  15. Synthesis and intermolecular interactions of N-benzylidenetyramines

    NASA Astrophysics Data System (ADS)

    Maldonado, Mauricio; Pérez-Redondo, Adrián; Quevedo, Rodolfo

    2017-01-01

    In this paper, the synthesis and intermolecular interactions between N-benzylidenetyramine molecules were investigated. The crystal structure of N-(4-nitrobenzylidene)tyramine shows a molecular organization in zigzag chains with intermolecular O-H⋯N hydrogen bonds between the azomethine and phenolic hydroxyl groups. Those chains are held together by C-H⋯O hydrogen bonds to generate layers, which are connected by C-H⋯O, π⋯π and NO2⋯π interactions.

  16. Intermolecular Singlet and Triplet Exciton Transfer Integrals from Many-Body Green's Functions Theory.

    PubMed

    Wehner, Jens; Baumeier, Björn

    2017-03-08

    A general approach to determine orientation and distance-dependent effective intermolecular exciton transfer integrals from many-body Green's functions theory is presented. On the basis of the GW approximation and the Bethe-Salpeter equation (BSE), a projection technique is employed to obtain the excitonic coupling by forming the expectation value of a supramolecular BSE Hamiltonian with electron-hole wave functions for excitations localized on two separated chromophores. Within this approach, accounting for the effects of coupling mediated by intermolecular charge transfer (CT) excitations is possible via perturbation theory or a reduction technique. Application to model configurations of pyrene dimers shows an accurate description of short-range exchange and long-range Coulomb interactions for the coupling of singlet and triplet excitons. Computational parameters, such as the choice of the exchange-correlation functional in the density-functional theory (DFT) calculations that underly the GW-BSE steps and the convergence with the number of included CT excitations, are scrutinized. Finally, an optimal strategy is derived for simulations of full large-scale morphologies by benchmarking various approximations using pairs of dicyanovinyl end-capped oligothiophenes (DCV5T), which are used as donor material in state-of-the-art organic solar cells.

  17. Continuous-flow Heck synthesis of 4-methoxybiphenyl and methyl 4-methoxycinnamate in supercritical carbon dioxide expanded solvent solutions

    PubMed Central

    Lau, Phei Li; Allen, Ray W K

    2013-01-01

    Summary The palladium metal catalysed Heck reaction of 4-iodoanisole with styrene or methyl acrylate has been studied in a continuous plug flow reactor (PFR) using supercritical carbon dioxide (scCO2) as the solvent, with THF and methanol as modifiers. The catalyst was 2% palladium on silica and the base was diisopropylethylamine due to its solubility in the reaction solvent. No phosphine co-catalysts were used so the work-up procedure was simplified and the green credentials of the reaction were enhanced. The reactions were studied as a function of temperature, pressure and flow rate and in the case of the reaction with styrene compared against a standard, stirred autoclave reaction. Conversion was determined and, in the case of the reaction with styrene, the isomeric product distribution was monitored by GC. In the case of the reaction with methyl acrylate the reactor was scaled from a 1.0 mm to 3.9 mm internal diameter and the conversion and turnover frequency determined. The results show that the Heck reaction can be effectively performed in scCO2 under continuous flow conditions with a palladium metal, phosphine-free catalyst, but care must be taken when selecting the reaction temperature in order to ensure the appropriate isomer distribution is achieved. Higher reaction temperatures were found to enhance formation of the branched terminal alkene isomer as opposed to the linear trans-isomer. PMID:24367454

  18. 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

  19. From α-arylation of olefins to acylation with aldehydes: a journey in regiocontrol of the Heck reaction.

    PubMed

    Ruan, Jiwu; Xiao, Jianliang

    2011-08-16

    The Pd-catalyzed Mizoroki-Heck reaction of olefins with aryl halides, more often simply called the Heck reaction, was recently recognized with the 2010 Nobel Prize in chemistry. Although highly selective with electron-deficient olefins, which generally yield the linear β-arylated product exclusively, the Heck reaction is less satisfactory with electron-rich olefins. This substrate typically generates a mixture of both α- and β-arylated regioisomeric products, hampering wider application of the reaction in chemical synthesis. Pioneering studies by a number of researchers revealed that high α-regioselectivity could be obtained under Pd-diphosphine catalysis either through (i) the substitution of aryl triflates for halides or (ii) the addition of stoichiometric silver or thallium salts when aryl halides are used. Under these conditions, the arylation is believed to proceed via an ionic pathway. However, silver introduces added cost, thallium salts are toxic, and triflates are generally commercially unavailable, base sensitive, and thermally labile. Believing that the ionic pathway would be promoted in an ionic medium, in the early 2000s, we attempted the Pd-catalyzed arylation of the benchmark electron-rich olefin butyl vinyl ether with aryl bromides in an imidazolium ionic liquid. We were delighted to observe that highly regioselective α-arylation could readily be accomplished, with no need for silver additives, thallium additives, or aryl triflates. A range of other electron-rich olefins has since been shown to be viable as well. The high α-selectivity probably results from the high ionic strength of the medium, which facilitates the dissociation of halide anions from the [L(2)Pd(Ar)X] intermediate, channeling the arylation into the ionic pathway. Hydrogen bonding interactions may also play a role, however. We subsequently discovered that the α-arylation can indeed be significantly accelerated by a hydrogen bond donor salt, in both ionic liquids and common

  20. 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

  1. 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.

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

    PubMed

    Renaud, Nicolas; Grozema, Ferdinand C

    2015-02-05

    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.

  3. Rhodium-Catalyzed β-Selective Oxidative Heck-Type Coupling of Vinyl Acetate via C-H Activation.

    PubMed

    Zhang, Hui-Jun; Lin, Weidong; Su, Feng; Wen, Ting-Bin

    2016-12-16

    An efficient Rh(III)-catalyzed direct ortho-C-H olefination of acetanilides with vinyl acetate was developed. This protocol provides a straightforward pathway to a series of (E)-2-acetamidostyryl acetates, giving access to indole derivatives following a simple hydrolysis/cyclization process.

  4. A unique Pd-catalysed Heck arylation as a remote trigger for cyclopropane selective ring-opening

    NASA Astrophysics Data System (ADS)

    Singh, Sukhdev; Bruffaerts, Jeffrey; Vasseur, Alexandre; Marek, Ilan

    2017-02-01

    Combining functionalization at a distant position from a reactive site with the creation of several consecutive stereogenic centres, including the formation of a quaternary carbon stereocentre, in acyclic system represents a pinnacle in organic synthesis. Here we report the regioselective Heck arylation of terminal olefins as a distant trigger for the ring-opening of cyclopropanes. This Pd-catalysed unfolding of the strained cycle, driving force of the chain-walking process, remarkably proved its efficiency and versatility, as the reaction proceeded regardless of the molecular distance between the initiation (double bond) and termination (alcohol) sites. Moreover, employing stereodefined polysubstituted cyclopropane vaults allowed to access sophisticated stereoenriched acyclic scaffolds in good yields. Conceptually, we demonstrated that merging catalytically a chain walking process with a selective C-C bond cleavage represents a powerful approach to construct linear skeleton possessing two stereogenic centres.

  5. 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.

  6. Investigating the nature of palladium chain-walking in the enantioselective redox-relay Heck reaction of alkenyl alcohols.

    PubMed

    Hilton, Margaret J; Xu, Li-Ping; Norrby, Per-Ola; Wu, Yun-Dong; Wiest, Olaf; Sigman, Matthew S

    2014-12-19

    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.

  7. A unique Pd-catalysed Heck arylation as a remote trigger for cyclopropane selective ring-opening

    PubMed Central

    Singh, Sukhdev; Bruffaerts, Jeffrey; Vasseur, Alexandre; Marek, Ilan

    2017-01-01

    Combining functionalization at a distant position from a reactive site with the creation of several consecutive stereogenic centres, including the formation of a quaternary carbon stereocentre, in acyclic system represents a pinnacle in organic synthesis. Here we report the regioselective Heck arylation of terminal olefins as a distant trigger for the ring-opening of cyclopropanes. This Pd-catalysed unfolding of the strained cycle, driving force of the chain-walking process, remarkably proved its efficiency and versatility, as the reaction proceeded regardless of the molecular distance between the initiation (double bond) and termination (alcohol) sites. Moreover, employing stereodefined polysubstituted cyclopropane vaults allowed to access sophisticated stereoenriched acyclic scaffolds in good yields. Conceptually, we demonstrated that merging catalytically a chain walking process with a selective C–C bond cleavage represents a powerful approach to construct linear skeleton possessing two stereogenic centres. PMID:28169276

  8. A unique Pd-catalysed Heck arylation as a remote trigger for cyclopropane selective ring-opening.

    PubMed

    Singh, Sukhdev; Bruffaerts, Jeffrey; Vasseur, Alexandre; Marek, Ilan

    2017-02-07

    Combining functionalization at a distant position from a reactive site with the creation of several consecutive stereogenic centres, including the formation of a quaternary carbon stereocentre, in acyclic system represents a pinnacle in organic synthesis. Here we report the regioselective Heck arylation of terminal olefins as a distant trigger for the ring-opening of cyclopropanes. This Pd-catalysed unfolding of the strained cycle, driving force of the chain-walking process, remarkably proved its efficiency and versatility, as the reaction proceeded regardless of the molecular distance between the initiation (double bond) and termination (alcohol) sites. Moreover, employing stereodefined polysubstituted cyclopropane vaults allowed to access sophisticated stereoenriched acyclic scaffolds in good yields. Conceptually, we demonstrated that merging catalytically a chain walking process with a selective C-C bond cleavage represents a powerful approach to construct linear skeleton possessing two stereogenic centres.

  9. 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…

  10. 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.

  11. 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.

  12. 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…

  13. Connecting Protein Structure to Intermolecular Interactions: A Computer Modeling Laboratory

    ERIC Educational Resources Information Center

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

    2016-01-01

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

  14. 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…

  15. Intermolecular atom-atom bonds in crystals - a chemical perspective.

    PubMed

    Thakur, Tejender S; Dubey, Ritesh; Desiraju, Gautam R

    2015-03-01

    Short atom-atom distances between molecules are almost always indicative of specific intermolecular bonding. These distances may be used to assess the significance of all hydrogen bonds, including the C-H⋯O and even weaker C-H⋯F varieties.

  16. 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.

  17. Intermolecular forces and the glass transition.

    PubMed

    Hall, Randall W; Wolynes, Peter G

    2008-01-17

    Random first-order transition theory is used to determine the role of attractive and repulsive interactions in the dynamics of supercooled liquids. Self-consistent phonon theory, an approximate mean field treatment consistent with random first-order transition theory, is used to treat individual glassy configurations, whereas the liquid phase is treated using common liquid-state approximations. Free energies are calculated using liquid-state perturbation theory. The transition temperature, T*A, the temperature where the onset of activated behavior is predicted by mean field theory; the lower crossover temperature, T*C, where barrierless motions actually occur through fractal or stringy motions (corresponding to the phenomenological mode coupling transition temperature); and T*K, the Kauzmann temperature (corresponding to an extrapolated entropy crisis), are calculated in addition to T*g, the glass transition temperature that corresponds to laboratory cooling rates. Relationships between these quantities agree well with existing experimental and simulation data on van der Waals liquids. Both the isobaric and isochoric behavior in the supercooled regime are studied, providing results for DeltaCV and DeltaCp that can be used to calculate the fragility as a function of density and pressure, respectively. The predicted variations in the alpha-relaxation time with temperature and density conform to the empirical density-temperature scaling relations found by Casalini and Roland. We thereby demonstrate the microscopic origin of their observations. Finally, the relationship first suggested by Sastry between the spinodal temperature and the Kauzmann temperatures, as a function of density, is examined. The present microscopic calculations support the existence of an intersection of these two temperatures at sufficiently low temperatures.

  18. Tuning intermolecular non-covalent interactions for nanowires of organic semiconductors.

    PubMed

    Jiang, Lang; Gao, Jianhua; Fu, Yanyan; Dong, Huanli; Zhao, Huaping; Li, Hongxiang; Tang, Qingxin; Chen, Keqiu; Hu, Wenping

    2010-12-01

    Anthracene and its derivatives are used to demonstrate a simple way to cast assemble nanowires of organic semiconductors with tuning of intermolecular non-covalent interactions by molecular design. The tuning of intermolecular interactions could be achieved by (i) decreasing intermolecular hydrophobic interactions by linking hydrophilic side chains to anthracene rings, (ii) increasing intermolecular interaction for self-assembly with the assistance of hydrogen bonds, and (iii) enhancing molecular π-π interaction by increasing the conjugated dimension of the compounds.

  19. Tuning intermolecular non-covalent interactions for nanowires of organic semiconductors

    NASA Astrophysics Data System (ADS)

    Jiang, Lang; Gao, Jianhua; Fu, Yanyan; Dong, Huanli; Zhao, Huaping; Li, Hongxiang; Tang, Qingxin; Chen, Keqiu; Hu, Wenping

    2010-12-01

    Anthracene and its derivatives are used to demonstrate a simple way to cast assemble nanowires of organic semiconductors with tuning of intermolecular non-covalent interactions by molecular design. The tuning of intermolecular interactions could be achieved by (i) decreasing intermolecular hydrophobic interactions by linking hydrophilic side chains to anthracene rings, (ii) increasing intermolecular interaction for self-assembly with the assistance of hydrogen bonds, and (iii) enhancing molecular π-π interaction by increasing the conjugated dimension of the compounds.

  20. Intermolecular Hydrogen Bonding in Peptide and Modified Jeffamine Organogels

    NASA Astrophysics Data System (ADS)

    Savin, Daniel; Richardson, Adam

    2011-03-01

    In these studies, we present two systems whereby supramolecular assembly results in rigid organogels. First, a series of AB diblock copolymers consisting of poly(Lysine(Z)) (P(Lys(Z)) blocks were synthesized and found to form stable, rigid organogels in THF (ca. 1 - 1.5 wt.% solutions) and chloroform at room temperature. In these systems, the protecting group on the P(Lys) side-chains remains intact and gel formation results from the assembly of the solventphobic P(Lys(Z)) chains through intermolecular beta-sheet formation. The non-peptide block was found to have an effect on organogel properties due to interfacial frustration, which disrupts H-bonding. Second, Jeffamine polymers were modified in a facile way to incorporate intermolecular H-bonding groups to yield networks able to gel various solvents as well as mineral and canola oil. We present the physical and rheological properties of the organogels produced.

  1. 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.

  2. 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

  3. Highly Stereoselective Intermolecular Haloetherification and Haloesterification of Allyl Amides

    PubMed Central

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

    2016-01-01

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

  4. Calciate-mediated intermolecular hydroamination of diphenylbutadiyne with secondary anilines.

    PubMed

    Glock, Carsten; Görls, Helmar; Westerhausen, Matthias

    2012-07-18

    Calciate-mediated intermolecular hydroamination of diphenylbutadiyne with N-phenyl and N-isopropyl-substituted anilines yields E- and Z-isomers of the corresponding 1-anilino-1,4-diphenylbut-1-ene-3-yne. In the case of HNPh(2) solely heterobimetallic K(2)Ca(NPh(2))(4) is able to effectively catalyze this hydroamination reaction in tetrahydrofuran at elevated temperatures.

  5. 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.

  6. Direction-dependent intermolecular interactions: catechol on TiO2(110)-1×1

    NASA Astrophysics Data System (ADS)

    Li, Shao-Chun; Diebold, Ulrike

    2009-08-01

    The adsorption of a submonolayer of catechol (C6H6O2) on the rutile TiO2(110)-1×1 surface has been investigated by Scanning Tunneling Microscopy (STM). The catechol molecules are preferentially adsorbed on the surface 5-fold coordinated Ti4+ sites, and occupy two neighboring lattice Ti sites. No preference for adsorption at surface step edges is observed at room temperature. A statistical analysis of intermolecular distances demonstrates that the interaction between the molecules strongly depends on the surface crystallographic direction: catechol molecules exhibit attractive interaction along [1-1 0], while they repel each other along the [001] direction. The attractive interaction is proposed to be caused by the coupling of π bonding electrons and the repulsive interaction is possibly mediated by substrate.

  7. 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.

  8. Intermolecular interactions in AST zeolites through (14)N NMR and DFT calculations.

    PubMed

    Dib, Eddy; Freire, Mélanie; Pralong, Valérie; Mineva, Tzonka; Alonso, Bruno

    2017-03-01

    The structure of the silica AST zeolites (octadecasil) synthesized in fluoride medium using tetramethylammonium (TMA) as the organic structure-directing agent has been reinvestigated using (14)N NMR quadrupolar parameters and DFT calculations. The value of the experimental (14)N quadrupolar coupling constant (CQ = 27 kHz) is larger than expected for a TMA cation possessing a high degree of motion. The analysis of a DFT-optimized octadecasil cluster along with the comparison between measured and calculated (14)N NMR parameters demonstrate the presence of weak C-H...O hydrogen bonds between the TMA in the [4(6)6(12)] cages and the silica skeleton. These intermolecular interactions can be related to the presence of Si...F tetrel bonds within the [4(6)] cages. These new results provide additional information with regard to the formation mechanisms and structure of the octadecasil zeolites.

  9. 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

  10. 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.

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

    NASA Astrophysics Data System (ADS)

    Huang, Yuanhang; Beran, Gregory J. O.

    2015-07-01

    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(N6) methods like MP2.5 or even spin-component-scaled coupled cluster models for 3-body intermolecular interactions with only O(N5) computational cost.

  12. Second law considerations in Fourier heat conduction of a lattice chain in relation to intermolecular potentials

    NASA Astrophysics Data System (ADS)

    Jesudason, Christopher G.

    2017-01-01

    Two aspects of conductive heat are focused here (i) the nature of conductive heat, defined as that form of energy that is transferred as a result of a temperature difference and (ii) the nature of the intermolecular potentials that induces both thermal energy flow and the temperature profile at the steady state for a 1-D lattice chain. It is found that the standard presuppositions of people like Benofy and Quay (BQ) following Joseph Fourier do not obtain for at least a certain specified regime of intermolecular potential parameters related to harmonic (quadratic) potentials for nearest neighbor interactions. For these harmonic potentials, it appears from the simulation results that steady state solutions exist utilizing non-synthetic thermostats that couple not just the two particles at the extreme ends of the lattice chain, but to a control volume of N particles located at either ends of the chain that does not accord with the unique analytical solutions that obtains for single particle thermostatting at the ends of the lattice with a different thermostatting algorithm that utilizes coupling coefficients. If the method used here is considered a more "realistic" or feasible model of the physical reality, then a re-evaluation of some aspects of the standard theoretical methodology is warranted since the standard model solution profile does not accord with the simulation temperature profile determined here for this related model. We also note that the sinusoidal temperature profile generated suggests that thermal integrated circuits with several thermal P-N junctions may be constructed, opening a way to create more complex thermal transistor circuits. A stationary principle is proposed for regions that violate the Fourier principle Jq.∇T ≤ 0, where Jq is the heat current vector and T the temperature.

  13. Intermolecular vibrations of fluorobenzene-Ar up to 130 cm(-1) in the ground electronic state.

    PubMed

    Gascooke, Jason R; Alexander, Ula N; Lawrance, Warren D

    2012-08-28

    Sixteen intermolecular vibrational levels of the S(0) state of the fluorobenzene-Ar van der Waals complex have been observed using dispersed fluorescence. The levels range up to ~130 cm(-1) in vibrational energy. The vibrational energies have been modelled using a complete set of harmonic and quartic anharmonic constants and a cubic anharmonic coupling between the stretch and long axis bend overtone that becomes near ubiquitous at higher energies. The constants predict the observed band positions with a root mean square deviation of 0.04 cm(-1). The set of vibrational levels predicted by the constants, which includes unobserved bands, has been compared with the predictions of ab initio calculations, which include all vibrational levels up to 70-75 cm(-1). There are small differences in energy, particularly above 60 cm(-1), however, the main differences are in the assignments and are largely due to the limitations of assigning the ab initio wavefunctions to a simple stretch, bend, or combination when the states are mixed by the cubic anharmonic coupling. The availability of these experimental data presents an opportunity to extend ab initio calculations to higher vibrational energies to provide an assessment of the accuracy of the calculated potential surface away from the minimum. The intermolecular modes of the fluorobenzene-Ar(2) trimer complex have also been investigated by dispersed fluorescence. The dominant structure is a pair of bands with a ~35 cm(-1) displacement from the origin band. Based on the set of vibrational modes calculated from the fluorobenzene-Ar frequencies, they are assigned to a Fermi resonance between the symmetric stretch and symmetric short axis bend overtone. The analysis of this resonance provides a measurement of the coupling strength between the stretch and short axis bend overtone in the dimer, an interaction that is not directly observed. The coupling matrix elements determined for the fluorobenzene-Ar stretch-long axis bend

  14. Focal Epithelial Hyperplasia (Heck's Disease) in a 57-Year-Old Brazilian Patient: A Case Report and Literature Review.

    PubMed

    de Castro, Luciano Alberto; de Castro, Joao Gabriel Leite; da Cruz, Alexandre Duarte Lopes; Barbosa, Bruno Henrique de Sousa; de Spindula-Filho, Jose Vieira; Costa, Mauricio Barcelos

    2016-04-01

    Focal epithelial hyperplasia (FEH), or Heck's disease, is a rare disease of the oral mucosa associated with infection by some subtypes of human papilloma virus, especially subtypes 13 or 32. The disease is predominantly found in children and adolescents with indigenous heritage, but other ethnic groups can be affected worldwide. To the best of the authors' knowledge, it has not been reported in Brazil's elderly population. This article describes a case of FEH in a 57-year-old Brazilian patient presenting since childhood, with multiple lesions in the lips, buccal mucosa and tongue. The solitary tongue lesion underwent excisional biopsy and the histopathological analysis showed parakeratosis, acanthosis, rete pegs with a club-shaped appearance, koilocytosis and the presence of mitosoid cells. These microscopic findings in conjunction with clinical presentation were sufficient to establish the accurate diagnosis of FEH. Polymerase chain reaction (PCR) was performed, but no one human papillomavirus (HPV) subtype could be identified. Clinicians must be aware of this rare oral disease, which can even affect elderly patients, as we described here. Treatment may be indicated in selected cases due to esthetic and/or functional problems.

  15. 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.

  16. Effects of intermolecular interaction on inelastic electron tunneling spectra

    NASA Astrophysics Data System (ADS)

    Kula, Mathias; Luo, Yi

    2008-02-01

    We have examined the effects of intermolecular interactions on the inelastic electron tunneling spectroscopy (IETS) of model systems: a pair of benzenethiol or a pair of benzenedithiol sandwiched between gold electrodes. The dependence of the IETS on the mutual position of and distance between the paired molecules has been predicted and discussed in detailed. It is shown that, although in most cases, there are clear spectral fingerprints present which allow identification of the actual structures of the molecules inside the junction. Caution must be exercised since some characteristic lines can disappear at certain symmetries. The importance of theoretical simulation is emphasized.

  17. 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

  18. INTERMOLECULAR FORCES IN ASSOCIATION OF PURINES WITH POLYBENZENOID HYDROCARBONS.

    PubMed

    PULLMAN, B; CLAVERIE, P; CAILLET, J

    1965-03-12

    The interactions in solution between purine or pyrimidine bases and polybenzenoid aromatic hydrocarbons probably consist in a vertical, stacking-type physical association. By molecular orbital calculations the role of the Van der Waals-London intermolecular forces in these interactions is determined. The electrostatic dipole-dipole forces are negligible, the polarization (or induction) dipole-induced dipole forces are contributory, but most important are the dispersion (or fluctuation) forces. This loose, physical type of interaction should not show any specificity with respect to the carcinogenic activity of the hydrocarbons.

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

    NASA Astrophysics Data System (ADS)

    Ye, ChuanXiang; Zhao, Yi; Liang, WanZhen

    2015-10-01

    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.

  20. Intermolecular potential and rovibrational states of the H2O-D2 complex

    NASA Astrophysics Data System (ADS)

    van der Avoird, Ad; Scribano, Yohann; Faure, Alexandre; Weida, Miles J.; Fair, Joanna R.; Nesbitt, David J.

    2012-05-01

    A five-dimensional intermolecular potential for H2O-D2 was obtained from the full nine-dimensional ab initio potential surface of Valiron et al. [P. Valiron, M. Wernli, A. Faure, L. Wiesenfeld, C. Rist, S. Kedžuch, J. Noga, J. Chem. Phys. 129 (2008) 134306] by averaging over the ground state vibrational wave functions of H2O and D2. On this five-dimensional potential with a well depth De of 232.12 cm-1 we calculated the bound rovibrational levels of H2O-D2 for total angular momentum J = 0-3. The method used to compute the rovibrational levels is similar to a scattering approach—it involves a basis of coupled free rotor wave functions for the hindered internal rotations and the overall rotation of the dimer—while it uses a discrete variable representation of the intermolecular distance coordinate R. The basis was adapted to the permutation symmetry associated with the para/ortho (p/o) nature of both H2O and D2, as well as to inversion symmetry. As expected, the H2O-D2 dimer is more strongly bound than its H2O-H2 isotopologue [cf. A. van der Avoird, D.J. Nesbitt, J. Chem. Phys. 134 (2011) 044314], with dissociation energies D0 of 46.10, 50.59, 67.43, and 73.53 cm-1 for pH2O-oD2, oH2O-oD2, pH2O-pD2, and oH2O-pD2. A rotationally resolved infrared spectrum of H2O-D2 was measured in the frequency region of the H2O bend mode. The ab initio calculated values of the rotational and distortion constants agree well with the values extracted from this spectrum.

  1. The rotational spectrum, geometry, and intermolecular force constant of the heterodimer of hydrogen cyanide and fluoroform

    NASA Astrophysics Data System (ADS)

    Goodwin, Elizabeth J.; Legon, A. C.

    1986-02-01

    The ground-state rotational spectra of six isotopic species of an intermolecular complex formed by hydrogen cyanide and fluoroform have been measured using the pulsed-nozzle, Fourier-transform microwave technique. The rotational constant B0, the centrifugal distortion constants DJ,DJK,HJ, HJK, and HKJ, and, where appropriate, the nuclear quadrupole coupling constants χ(14N) and χ(D) have been determined for each of the species HC14NṡṡṡHCF3, DC14NṡṡṡHCF3, HC14ṡṡṡDCF3, HC15NṡṡṡHCF3, HC15NṡṡṡDCF3, and DC15NṡṡṡHCF3. For HC14NṡṡṡHCF3 the values are as follows: B0=1151.2991(4) MHz, DJ=1.91(1) kHz, DJK=282.75(6) kHz, HJ=-0.1(1) Hz, HJK=44.3(5) Hz, HKJ=53(5) Hz, and χ(14N)=3.948(8) MHz. The form of the spectra and magnitudes of the rotational constants allow the conclusion that the geometry of the complex is of C3V symmetry with the nuclei in the order HCNṡṡṡHCF3 and lead to r(NṡṡṡC)=3.489(2) Å for HCF3 species but 3.483(1) Å for DCF3 species. The intermolecular stretching force constant determined from DJ is kσ=3.52 N m-1.

  2. A IR Diode Laser Spectroscopic Study of Adsorption and Intermolecular Interactions on Stepped Metal Surfaces: Carbon Monoxide on Vicinal COPPER(100)

    NASA Astrophysics Data System (ADS)

    Borguet, Eric Urbain

    The kinetics of elementary surface processes, intermolecular interactions and stepped surfaces are intrinsic scientific interest, as well as being important to industrially relevant processes such as catalysis. A novel time-resolved surface sensitive technique, Transient Diode Laser Infrared Reflection-Absorption Spectroscopy, has been developed to investigate adsorption on stepped metal surfaces. The IR spectra display anomalous intensity behavior resulting in a minority step-CO species accounting for a disproportionate fraction of the spectral intensity. A model has been elaborated which successfully accounts for, and simulates, the observed spectra. This enables site specific concentrations to be determined, even in the presence of strong dynamic-dipole coupling. These methods allow the spectroscopy, kinetics and intermolecular interactions of CO on a stepped Cu(100) surface to be probed. In particular, it has been possible to observe a dynamic equilibrium between CO adsorbed at step and terrace sites and to investigate the kinetics of site exchange on this surface. The IR spectra also reveal the nature and range of the intermolecular interactions and the local order which results. The CO/Cu(100) system is characterized by repulsive first and second nearest neighbor interactions. As a consequence, the adsorbates adopt a configuration which maximizes the intermolecular distance. Additionally, a non-resonant, broadband, adsorbate induced change in surface reflectivity is observed both in the IR and visible. This linear dependence of this signal with coverage provides a simple method of determining total adsorbed CO concentration.

  3. An IR diode laser spectroscopic study of adsorption and intermolecular interactions on stepped metal surfaces: CO on vicinal Cu(100). [IR (infrared)

    SciTech Connect

    Borguet, E.R.

    1993-01-01

    The kinetics of elementary surface processes, intermolecular interactions and stepped surfaces are intrinsic scientific interest, as well as being important to industrially relevant processes such as catalysis. A novel time-resolved surface sensitive technique. Transient Diode Laser Infrared Reflection-Absorption Spectroscopy, has been developed to investigate adsorption on stepped metal surfaces. The IR spectra display anomalous intensity behavior resulting in a minority step-CO species accounting for a disporportionate fraction of the spectral intensity. A model has been elaborated which successfully accounts for, and simulates, the observed spectra. This enables site specific concentrations to be determined, even in the presence of strong dynamic-dipole coupling. These methods allow the spectroscopy, kinetics and intermolecular interactions of CO on a stepped Cu(100) surface to be probed. In particular, it has been possible to observe a dynamic equilibrium between CO adsorbed at step and terrace sites and to investigate the kinetics of site exchanges on this surface. The IR spectra also reveal the nature and range of the intermolecular interactions and the local order which results. The CO/Cu(100) system is characterized by repulsive first and second nearest neighbor interactions. As a consequence, the adsorbates adopt a configuration which maximizes the intermolecular distance. Additionally, a non-resonant, broadband, adsorbate induced change in surface reflectivity is observed both in the IR and visible. This linear dependence of this signal with coverage provides a simple method of determining total absorbed CO concentration.

  4. 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.

  5. Intermolecular interactions and the thermodynamic properties of supercritical fluids

    NASA Astrophysics Data System (ADS)

    Yigzawe, Tesfaye M.; Sadus, Richard J.

    2013-05-01

    The role of different contributions to intermolecular interactions on the thermodynamic properties of supercritical fluids is investigated. Molecular dynamics simulation results are reported for the energy, pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, Joule-Thomson coefficient, and speed of sound of fluids interacting via both the Lennard-Jones and Weeks-Chandler-Andersen potentials. These properties were obtained for a wide range of temperatures, pressures, and densities. For each thermodynamic property, an excess value is determined to distinguish between attraction and repulsion. It is found that the contributions of intermolecular interactions have varying effects depending on the thermodynamic property. The maxima exhibited by the isochoric and isobaric heat capacities, isothermal compressibilities, and thermal expansion coefficient are attributed to interactions in the Lennard-Jones well. Repulsion is required to obtain physically realistic speeds of sound and both repulsion and attraction are necessary to observe a Joule-Thomson inversion curve. Significantly, both maxima and minima are observed for the isobaric and isochoric heat capacities of the supercritical Lennard-Jones fluid. It is postulated that the loci of these maxima and minima converge to a common point via the same power law relationship as the phase coexistence curve with an exponent of β = 0.32. This provides an explanation for the terminal isobaric heat capacity maximum in supercritical fluids.

  6. Hybrid materials from intermolecular associations between cationic lipid and polymers.

    PubMed

    Pereira, Edla M A; Kosaka, Priscila M; Rosa, Heloísa; Vieira, Débora B; Kawano, Yoshio; Petri, Denise F S; Carmona-Ribeiro, Ana M

    2008-08-07

    Intermolecular associations between a cationic lipid and two model polymers were evaluated from preparation and characterization of hybrid thin films cast on silicon wafers. The novel materials were prepared by spin-coating of a chloroformic solution of lipid and polymer on silicon wafer. Polymers tested for miscibility with the cationic lipid dioctadecyldimethylammonium bromide (DODAB) were polystyrene (PS) and poly(methyl methacrylate) (PMMA). The films thus obtained were characterized by ellipsometry, wettability, optical and atomic force microscopy, Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), and activity against Escherichia coli. Whereas intermolecular ion-dipole interactions were available for the PMMA-DODAB interacting pair producing smooth PMMA-DODAB films, the absence of such interactions for PS-DODAB films caused lipid segregation, poor film stability (detachment from the silicon wafer) and large rugosity. In addition, the well-established but still remarkable antimicrobial DODAB properties were transferred to the novel hybrid PMMA/DODAB coating, which is demonstrated to be highly effective against E. coli.

  7. 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

  8. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    DOE PAGES

    Hathwar, Venkatesha R.; Sist, Mattia; Jørgensen, Mads R. V.; ...

    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

  9. Quaternary Stereogenic Centers through Enantioselective Heck Arylation of Acyclic Olefins with Aryldiazonium Salts: Application in a Concise Synthesis of (R)-Verapamil.

    PubMed

    Oliveira, Caio C; Pfaltz, Andreas; Correia, Carlos Roque Duarte

    2015-11-16

    We describe herein a highly regio- and enantioselective Pd-catalyzed Heck arylation of unactivated trisubstituted acyclic olefins to provide all-carbon quaternary stereogenic centers. Chiral N,N ligands of the pyrimidine- and pyrazino-oxazoline class were developed for that purpose, providing the desired products in good to high yields with enantiomeric ratios up to >99:1. Both linear and branched substituents on the olefins were well-tolerated. The potential of this new method is demonstrated by the straightforward synthesis of several O-methyl lactols and lactones containing quaternary stereocenters, together with a concise enantioselective total synthesis of the calcium channel blocker verapamil.

  10. Stereoselective Synthesis of Spiro Bis-C,C-α-arylglycosides by Tandem Heck Type C-Glycosylation and Friedel-Crafts Cyclization.

    PubMed

    Chen, Yen-Bo; Liu, Shi-Hao; Hsieh, Min-Tsang; Chang, Chih-Shiang; Lin, Chun-Hung; Chen, Chen-Yin; Chen, Po-Yen; Lin, Hui-Chang

    2016-04-01

    Spiro bis-C,C-α-arylglycosides were synthesized in three steps in 78-85% overall yields starting from exo-glycals. The initial Heck type C-aryl addition of exo-glycals with arylboronic acids afforded α-aryl-β-substituted C-glycosides with exclusive α-stereoselectivity. Among the products, β-ethanal α-aryl C-glycosides further reacted with alkylthiol in the presence of InCl3, followed by in situ Friedel-Crafts cyclization to yield the desirable final products. We proposed a mechanism to explain how the α-aryl group serves as a main determinant of the cyclization.

  11. Synthesis of Pd(0) nanocatalyst using lignin in water for the Mizoroki-Heck reaction under solvent-free conditions.

    PubMed

    Marulasiddeshwara, M B; Kumar, P Raghavendra

    2016-02-01

    Palladium(0) nanospheres with an average size of 1-5 nm were synthesized and stabilized by lignin in water without any reducing agent. The lignin supported palladium(0) nanoparticles (lignin@Pd-NPs) were characterized by UV-vis., FT-IR, SEM, TEM, HRICP-AES, EDX and PXRD. Absence of the peak at 430 nm in UV-vis., spectrum confirmed the reduction of Pd(II) to Pd(0). The five characteristic peaks at (111), (200), (220), (311) and (222) corresponding to the 2θ values 40°, 46.7°, 67.9°, 81.9° and 86.9°, respectively, appeared in PXRD spectrum indicated the crystallographic planes of Pd(0) with fcc structure. The Pd(0) loaded on lignin was 0.0467 mmol/g determined by HRICP-AES and 0.89% (w/w) by EDX. The performance of lignin@Pd-NPs catalyst have been investigated for the Mizoroki-Heck CC bond formation reactions between n-butyl propene-2-enoate and halobenzenes and substituted halobenzenes in polar to highly polar solvents as well as under solvent-free conditions in the presence of organic or inorganic bases. The lignin@Pd-NPs was found to be a highly efficient catalyst to yield the desired products of up to 94% under solvent-free conditions in short reaction times. The catalyst was heterogeneous and hence recovered by filtration and reused several times in the subsequent batches of the same reaction.

  12. Adsorption kinetics and intermolecular interactions of CO adsorbed on Cu(100) by transient laser reflection-absorption spectroscopy

    SciTech Connect

    Borguet, E.; Dai, H.L.

    1993-12-31

    IR and visible transient laser spectroscopic techniques have been developed to probe adsorption/desorption kinetics and intermolecular interactions of the CO/Cu(100) system. Vibrational spectroscopy, in general, can provide information about the nature of species adsorbed on surfaces e.g. chemical identity, site, orientation and concentration. In the presence of a few percent of CO adsorbed at step/defect sites, the spectra of the CO adsorbed on the terrace sites are greatly perturbed through dynamic-dipole coupling. This perturbation depends strongly on the intermolecular distance and the short-range order of the adsorbates. An analysis of this dynamic-dipole coupling reveals that the local arrangement of adsorbates is dominant by repulsive nearest-neighbor interactions. Successful modeling of the observed lineshapes allows the populations at each site to be determined at all coverages. The authors have also observed non-resonant adsorbate induced changes in both the IR and visible reflectance for a number of different adsorbates. This provides a simple and sensitive optical means of studying adsorption and desorption kinetics.

  13. On the effect of a radiation field in modifying the intermolecular interaction between two chiral molecules

    NASA Astrophysics Data System (ADS)

    Salam, A.

    2006-01-01

    The change in the mutual energy of interaction between a pair of chiral molecules coupled via the exchange of a single virtual photon and in the presence of an electromagnetic field is calculated using nonrelativistic quantum electrodynamics. The particular viewpoint adopted is one that has an intuitive physical appeal and resembles a classical treatment. It involves the coupling of electric and magnetic dipole moments induced at each center by the incident radiation field to the resonant dipole-dipole interaction tensor. The energy shift is evaluated for fixed as well as random orientations of the molecular pair with respect to the direction of propagation of the field. A complete polarization analysis is carried out for the former situation by examining the effect of incident radiation that is linearly or circularly polarized and traveling in a direction that is parallel or perpendicular to the intermolecular distance vector. After tumble averaging, all polarization dependence of the energy shift vanishes. In both cases the interaction energy is directly proportional to the irradiance of the applied field, and is discriminatory, changing sign when one optically active species is replaced by its enantiomer. The asymptotic behavior of the energy shift at the limits of large and small separations is also studied.

  14. Intermolecular vibrations of (CH2)2O-HF and -DF hydrogen bonded complexes investigated by Fourier transform infrared spectroscopy and ab initio calculations.

    PubMed

    Cirtog, M; Asselin, P; Soulard, P; Madebène, B; Alikhani, M E

    2010-10-14

    A series of Fourier transform infrared spectra (FTIR) of the hydrogen bonded complexes (CH(2))(2)O-HF and -DF have been recorded in the 50-750 cm(-1) range up to 0.1 cm(-1) resolution in a static cell maintained at near room temperature. The direct observation of three intermolecular transitions enabled us to perform band contour analysis of congested cell spectra and to determine reliable rovibrational parameters such as intermolecular frequencies, rovibrational and anharmonic coupling constants involving two l(1) and l(2) librations and one σ stretching intermolecular motion. Inter-inter anharmonic couplings could be identified between ν(l(1)), ν(l(2)), ν(σ) and the two lowest frequency bending modes. The positive sign of coupling constants (opposite with respect to acid stretching intra-inter ones) reveals a weakening of the hydrogen bond upon intermolecular excitation. The four rovibrational parameters ν(σ) and x(σj) (j = σ, δ(1), δ(2)) derived in the present far-infrared study and also in a previous mid-infrared one [Phys. Chem. Chem. Phys. 2005, 1, 592] make deviations appear smaller than 1% for frequencies and 12% for coupling constants which gives confidence to the reliability of the data obtained. Anharmonic frequencies obtained at the MP2 level with Aug-cc-pvTZ basis set agree well with experimental values over a large set of frequencies and coupling constants. An estimated anharmonic corrected value of the dissociation energy D for both oxirane-HF (2424 cm(-1)) and -DF (2566 cm(-1)) has been derived using a level of theory as high as CCSD(T)/Aug-cc-pvQZ, refining the harmonic value previously calculated for oxirane-HF with the MP2 method and a smaller basis set. Finally, contrary to short predissociation lifetimes evidenced for acid stretching excited states, any homogeneous broadening related to vibrational dynamics of (CH(2))(2)O-HF and -DF has been observed within the three highest frequency intermolecular states, as expected with low

  15. Dissecting Anion Effects in Gold(I)-Catalyzed Intermolecular Cycloadditions

    PubMed Central

    Homs, Anna; Obradors, Carla; Lebœuf, David; Echavarren, Antonio M

    2014-01-01

    From a series of gold complexes of the type [t-BuXPhosAu(MeCN)]X (X=anion), the best results in intermolecular gold(I)-catalyzed reactions are obtained with the complex with the bulky and soft anion BAr4F− [BAr4F−=3,5-bis(trifluoromethyl)phenylborate] improving the original protocols by 10–30% yield. A kinetic study on the [2+2] cycloaddition reaction of alkynes with alkenes is consistent with an scenario in which the rate-determining step is the ligand exchange to generate the (η2-phenylacetylene)gold(I) complex. We have studied in detail the subtle differences that can be attributed to the anion in this formation, which result in a substantial decrease in the formation of unproductive σ,π-(alkyne)digold(I) complexes by destabilizing the conjugated acid formed. PMID:26190958

  16. Thermodynamic curvature for attractive and repulsive intermolecular forces.

    PubMed

    May, Helge-Otmar; Mausbach, Peter; Ruppeiner, George

    2013-09-01

    The thermodynamic curvature scalar R for the Lennard-Jones system is evaluated in phase space, including vapor, liquid, and solid state. We paid special attention to the investigation of R along vapor-liquid, liquid-solid, and vapor-solid equilibria. Because R is a measure of interaction strength, we traced out the line R=0 dividing the phase space into regions with effectively attractive (R<0) or repulsive (R>0) interactions. Furthermore, we analyzed the dependence of R on the strength of attraction applying a perturbation ansatz proposed by Weeks-Chandler-Anderson. Our results show clearly a transition from R>0 (for poorly repulsive interaction) to R<0 when loading attraction in the intermolecular potential.

  17. 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.

  18. Bis-diimidazolylidine complexes of nickel: investigations into nickel catalyzed coupling reactions.

    PubMed

    Paulose, Tressia A P; Wu, Shih-Chang; Olson, Jeremy A; Chau, Tony; Theaker, Nikki; Hassler, Matt; Quail, J Wilson; Foley, Stephen R

    2012-01-07

    Air and moisture stable homoleptic bis(diimidazolylidine)nickel(II) complexes, ([(diNHC)(2)Ni](2+)) 3a,b and their corresponding silver(I) 4a,b and palladium(II) 5a,b complexes were synthesized and characterized by NMR and single crystal X-ray analysis. The catalytic potential of complex 3a was assessed in Mizoroki-Heck and Suzuki-Miyaura coupling reactions. In the Suzuki-Miyaura coupling reaction, nickel precatalyst 3a was active for the coupling of aryl chlorides as well as aryl fluorides. The analogously synthesized Pd(II) complexes resulted in formation of (diNHC)PdCl(2) species which were not active for the coupling of aryl fluorides. For the Mizoroki-Heck reaction, it was found that aryl iodides could be activated in the absence of nickel or palladium precatalysts when using Na(2)CO(3) or NEt(3) as base while aryl iodides and aryl bromides could be activated in the Suzuki-Miyaura reaction sans precatalyst when K(3)PO(4) was used as base.

  19. Evaluation of intermolecular forces in a circulating system.

    PubMed

    Guo, Qiuquan; Liu, Mei; Yang, Jun

    2011-11-01

    Intercellular interactions, which are mediated by a variety of complex intercellular molecules through the processes of formation and dissociation of molecular bonds, play a critical role in regulating cellular functions in biological systems. Various approaches are applied to evaluate intercellular or molecular bonding forces. To quantify the intermolecular interaction forces, flow chamber has become a meaningful technique as it can ultimately mimic the cellular microenvironment in vivo under physiological flow conditions. Hydrodynamic forces are usually used to predict the intercellular forces down to the single molecular level. However, results show that only using hydrodynamic force will overestimate up to 30% of the receptor-ligand strength when the non-specific forces such as Derjaguin-Landau-Verway-Overbeek (DLVO) forces become un-neglected. Due to the nature of high ion concentration in the physiological condition, electrostatic force is largely screened which will cause DLVO force unbalanced. In this study, we propose to take account of the DLVO force, including van der Waals (VDW) force and electrostatic force, to predict the intermolecular forces of a cell doublet and cell-substrate model in a circulating system. Results also show that the DLVO force has a nonlinear effect as the cell-cell or cell-substrate distance changes. In addition, we used the framework of high accuracy hydrodynamic theories proved in colloidal systems. It is concluded that DLVO force could not be ignored in quantitative studies of molecular interaction forces in circulating system. More accurate prediction of intercellular forces needs to take account of both hydrodynamic force and DLVO force.

  20. 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.

  1. Intermolecular potential functions from spectroscopic properties of weakly bound complexes

    SciTech Connect

    Muenter, J.S.

    1992-01-01

    Goal is to consolidate the information from high resolution spectroscopy of weakly bound cluster molecules through a theoretical model of intermolecular potential energy surfaces. The ability to construct analytic intermolecular potential functions that accurately predict the interaction energy between small molecules will have a major impact in chemistry, biochemistry, and biology. This document presents the evolution and capabilities of a potential function model developed here, and then describes plans for future developments and applications. This potential energy surface (PES) model was first used on (HCCH){sub 2}, (CO{sub 2}){sub 2}, HCCH - CO{sub 2}; it had to be modified to work with HX dimers and CO{sub 2}-HX complexes. Potential functions have been calculated for 15 different molecular complexes containing 7 different monomer molecules. Current questions, logical extensions and new applications of the model are discussed. The questions are those raised by changing the repulsion and dispersion terms. A major extension of the PES model will be the inclusion of induction effects. Projects in progress include PES calculations on (HCCH){sub 3}, CO{sub 2} containing complexes, (HX){sub 2}, HX - CO{sub 2}, CO{sub 2} - CO, (CO{sub 2}){sub 3}, and (OCS){sub 2}. The first PES calculation for a nonlinear molecule will be for water and ammonia complexes. Possible long-term applications for biological molecules are discussed. Differences between computer programs used for molecular mechanics and dynamics in biological systems are discussed, as is the problem of errors. 12 figs, 74 refs. (DLC)

  2. Direct olefination of benzaldehydes into hydroxy functionalized oligo (p-phenylenevinylene)s via Pd-catalyzed heterodomino Knoevenagel-decarboxylation-Heck sequence and its application for fluoride sensing pi-conjugated units.

    PubMed

    Sharma, Abhishek; Sharma, Naina; Kumar, Rakesh; Shard, Amit; Sinha, Arun K

    2010-05-21

    A new approach for one step olefination of benzaldehydes into hydroxy functionalized OPVs is achieved through the first domino Knoevenagel-decarboxylation-Heck sequence using a single catalyst system. The methodology also led to new oxygen based OPV scaffolds capable of selective and visible fluoride recognition in organic or aqueous medium.

  3. General, mild, and intermolecular Ullmann-type synthesis of diaryl and alkyl aryl ethers catalyzed by diol-copper(I) complex.

    PubMed

    Naidu, Ajay B; Jaseer, E A; Sekar, Govindasamy

    2009-05-15

    A wide range of diaryl ethers and alkyl aryl ethers are synthesized through intermolecular C(aryl)-O bond formation from the corresponding aryl iodides/aryl bromides and phenols/alcohols through Ullmann-type coupling reaction in the presence of a catalytic amount of easily available (+/-)-diol L3-CuI complex under very mild reaction conditions. Less reactive aryl bromides can also be used for O-arylation of phenols under the same reaction conditions without increasing the reaction temperature, catalyst loading, and time. The catalytic system not only is capable of coupling hindered substrate but also tolerates a broad range of a series of functional groups.

  4. 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.

  5. 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.

  6. Meeting the Challenge of Intermolecular Gold(I)-Catalyzed Cycloadditions of Alkynes and Allenes

    PubMed Central

    Muratore, Michael E; Homs, Anna; Obradors, Carla; Echavarren, Antonio M

    2014-01-01

    The development of gold(I)-catalyzed intermolecular carbo- and hetero-cycloadditions of alkynes and allenes has been more challenging than their intramolecular counterparts. Here we review, with a mechanistic perspective, the most fundamental intermolecular cycloadditions of alkynes and allenes with alkenes. PMID:25048645

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

    PubMed

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

    2010-07-29

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

  9. Oriented covalent immobilization of antibodies for measurement of intermolecular binding forces between zipper-like contact surfaces of split inteins

    PubMed Central

    Sorci, Mirco; Dassa, Bareket; Liu, Hongwei; Anand, Gaurav; Dutta, Amit K.; Pietrokovski, Shmuel; Belfort, Marlene; Belfort, Georges

    2013-01-01

    In order to measure the intermolecular binding forces between two halves (or partners) of naturally split protein splicing elements called inteins, a novel thiol-hydrazide linker was designed and used to orient immobilized antibodies specific for each partner. Activation of the surfaces was achieved in one step allowing direct force measurements of the formation of a peptide bond catalyzed by the binding of the two partners of the split intein (called protein trans-splicing). Through this binding process, a whole functional intein is formed resulting in subsequent splicing. Atomic force microscopy (AFM) was used to directly measure the split intein partner binding at 1µm/s between native (wild-type) and mixed pairs of C- and N-terminal partners of naturally occurring split inteins from three cyanobacteria. Native and mixed pairs exhibit similar binding forces within the error of the measurement technique (~52 pN). Bioinformatic sequence analysis and computational structural analysis discovered a zipper-like contact between the two partners with electrostatic and non-polar attraction between multiple aligned ion pairs and hydrophobic residues. Also, we tested the Jarzynski’s equality and demonstrated, as expected, that non-equilibrium dissipative measurements obtained here gave larger energies of interaction as compared with those for equilibrium. Hence, AFM coupled with our immobilization strategy and computational studies provides a useful analytical tool for the direct measurement of intermolecular association of split inteins and could be extended to any interacting protein pair. PMID:23679912

  10. Role of Amino Acid Insertions on Intermolecular Forces between Arginine Peptide Condensed DNA Helices

    PubMed Central

    DeRouchey, Jason E.; Rau, Donald C.

    2011-01-01

    In spermatogenesis, chromatin histones are replaced by arginine-rich protamines to densely compact DNA in sperm heads. Tight packaging is considered necessary to protect the DNA from damage. To better understand the nature of the forces condensing protamine-DNA assemblies and their dependence on amino acid content, the effect of neutral and negatively charged amino acids on DNA-DNA intermolecular forces was studied using model peptides containing six arginines. We have previously observed that the neutral amino acids in salmon protamine decrease the net attraction between protamine-DNA helices compared with the equivalent homo-arginine peptide. Using osmotic stress coupled with x-ray scattering, we have investigated the component attractive and repulsive forces that determine the net attraction and equilibrium interhelical distance as a function of the chemistry, position, and number of the amino acid inserted. Neutral amino acids inserted into hexa-arginine increase the short range repulsion while only slightly affecting longer range attraction. The amino acid content alone of salmon protamine is enough to rationalize the forces that package DNA in sperm heads. Inserting a negatively charged amino acid into hexa-arginine dramatically weakens the net attraction. Both of these observations have biological implications for protamine-DNA packaging in sperm heads. PMID:21994948

  11. 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.

  12. Liquid chloroform structure from computer simulation with a full ab initio intermolecular interaction potential

    NASA Astrophysics Data System (ADS)

    Yin, Chih-Chien; Li, Arvin Huang-Te; Chao, Sheng D.

    2013-11-01

    We have calculated the intermolecular interaction energies of the chloroform dimer in 12 orientations using the second-order Møller-Plesset perturbation theory. Single point energies of important geometries were calibrated by the coupled cluster with single and double and perturbative triple excitation method. Dunning's correlation consistent basis sets up to aug-cc-pVQZ have been employed in extrapolating the interaction energies to the complete basis set limit values. With the ab initio potential data we constructed a 5-site force field model for molecular dynamics simulations. We compared the simulation results with recent experiments and obtained quantitative agreements for the detailed atomwise radial distribution functions. Our results were also consistent with previous results using empirical force fields with polarization effects. Moreover, the calculated diffusion coefficients reproduced the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with existing empirical force fields for liquid chloroform.

  13. 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.

  14. Ab initio intermolecular potential energy surfaces for the Ar-NCCN van der Waals complexes

    NASA Astrophysics Data System (ADS)

    Solimannejad, Mohammad; Jouypazadeh, Hamidreza; Farrokhpour, Hossein

    2014-11-01

    The intermolecular potential energy surface of complex pairing argon with cyanogen molecule (NCCN) was calculated using the coupled cluster with single and double and perturbative triple excitations (CCSD(T)) with aug-cc-pvdz basis set extended with a set of mid-bond (3s3p2d1f1g) functions. The interaction energies were calculated by the supermolecular approach with the full counterpoise correction for the basis set superposition error. The calculated potential energies were fitted to an analytical expression. The calculated Ar-NCCN potential energy surface shows a global minimum at 3.35 Å, the distance between argon and centre of mass of cyanogen, for the T-shaped geometry and two local minimum at distance of 5.54 Å for the linear geometry on one side of cyanogen. Finally, the interaction second virial coefficients were calculated using the fitted potential energy surface and were compared with those obtained by the parameters of the Beattie-Bridgeman equation of states of pure argon and cyanogens fluids, approximately.

  15. 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.

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

    SciTech Connect

    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}{sub 1}) is the measure of the fastest ET rate ({tau}{sub 1}={tau}{sub ET}{sup fast}=(k{sub ET}{sup fast}){sup -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{sub 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}{sub 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{sub A}) is found to be {approx}0.4 for aromatic amines and {approx}0.8 for aliphatic amines. Beyond these dilutions in the two respective cases of the amine systems, the {tau}{sub 1} values are seen to increase very sharply. The large difference in the critical x{sub 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

  17. Noncovalent Intermolecular Forces in Phycobilisomes of Porphyridium cruentum.

    PubMed

    Zilinskas, B A; Glick, R E

    1981-08-01

    Using sensitized fluorescence as a measure of intactness of phycobilisomes isolated from Porphyridium cruentum, the effects of various environmental perturbations on phycobilisome integrity were investigated. The rate of phycobilisome dissociation in 0.75 ionic strength sodium salts proceeds in the order: SCN(-) > NO(3) (-) > Cl(-) > C(6)H(5)O(7) (3-) > SO(4) (2-) > PO(4) (3-), as predicted from the lyotropic series of anions and their effects on hydrophobic interactions in proteins. Similarly, increasing temperature (to 30 C) and pH values approaching the isoelectric points of the biliproteins stabilize phycobilisomes. Deuterium substitution at exchangeable sites on the phycobiliproteins decreases the rate of phycobilisome dissociation, while substitution at nonexchangeable sites increases rates of dissociation. It is concluded that hydrophobic intermolecular interactions are the most important forces in maintaining the phycobilisome structure. Dispersion forces also seem to contribute to phycobilisome stabilization. The adverse effects of electrostatic repulsion must not be ignored; however, it seems that the requirement of phycobilisomes of high salt concentrations is not simply countershielding of charges on the proteins.

  18. Intermolecular forces between the motor protein and the filament.

    PubMed

    Suda, H; Taylor, T W

    1993-03-07

    Intermolecular forces between motor proteins and filaments were evaluated on the basis of the experimental data of an in vitro motility assay by considering the molecular friction in the movement system. The molecular friction was caused by a different mechanism from that of the hydrodynamic drag. However, the molecular frictional forces apparently gave the same expression as the hydrodynamic frictional forces. The resulting equation was very effective in examining the physical properties of the weak interaction in the dynein-microtubules system from basic experiments carried out by Vale et al. (1989). From careful analysis of their experimental data, it was concluded that the hydrodynamic friction was not dominant, even in the weak binding state. The electrostatic interaction between dynein-heads and microtubules in the weak binding state was analyzed by applying the DLVO (Derjaguin-Landau-Verway-Overbeek) theory in colloid science through the ionic dependence of one-dimensional diffusion. The interacting distance between charges which took part in the weak adhesion was estimated to be 3 nm. In the present study, the molecular mechanism of the sliding velocity was also investigated for the myosin-actin filaments and the kinesin-microtubules systems by fitting the ATP-dependence and the ionic dependence in ATP-driven active sliding.

  19. 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

  20. 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).

  1. 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.

  2. 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

    2016-03-11

    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.

  3. 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

  4. 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.

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

    PubMed

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

    2016-01-05

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

  6. 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.

  7. Cobalt complex of cinchonine: intermolecular interactions in two crystalline modifications.

    PubMed

    Skórska, Agnieszka; Oleksyn, Barbara J; Sliwiński, Jan

    2002-01-01

    Two crystalline modifications of cinchonine cobalt complex, C19H23Cl3CoN2O, were obtained from mixture of saturated alcohol solutions of CoCl3 x 6H2O and cinchonine. The X-ray structure analysis revealed that the asymmetric unit of one modification, CoCn1, contains only zwitterionic molecules of the complex. In the asymmetric unit of the other, CoCn2, there are two molecules of the title compound and two molecules of ethanol. The influence of the absolute configuration, the CoCl3 coordination with quinoline, and the presence of alcohol molecules on the studied structures was established by comparison of the crystal and molecular structures of both cobalt complexes with the analogous quinine complex and zinc complex of cinchonine. The interactions that dominate in the packing of the molecules in both structures are intermolecular hydrogen bonds. They form characteristic ring systems, depending on the presence of the alcohol molecules. The ring features are also related to the absolute configuration of the alkaloid.

  8. 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

  9. 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

  10. Simulated imaging of intermolecular bonds using high throughput real-space density functional calculations

    NASA Astrophysics Data System (ADS)

    Lee, Alex; Kim, Minjung; Chelikowsky, James

    2015-03-01

    Recent experimental noncontact atomic force microscopy (AFM) studies on 8-hydroxyquinoline (8-hq) assemblies have imaged distinct lines between molecules that are thought to represent intermolecular bonding. To aid the interpretation of these images, we calculate simulated AFM images of an 8-hq dimer with a CO functionalized tip using a real-space pseudopotential formalism. We examine the effects of Pauli repulsion and tip probe relaxation as explanations for the enhanced resolution that resolves these intermolecular force lines. Our study aims to compute ab initio real-space images of intermolecular interactions.

  11. A Heck-Matsuda Process for the Synthesis of β-Arylethenesulfonyl Fluorides: Selectively Addressable Bis-electrophiles for SuFEx Click Chemistry.

    PubMed

    Qin, Hua-Li; Zheng, Qinheng; Bare, Grant A L; Wu, Peng; Sharpless, K Barry

    2016-11-02

    A Heck-Matsuda process for the synthesis of the otherwise difficult to access compounds, β-arylethenesulfonyl fluorides, is described. Ethenesulfonyl fluoride (i.e., vinylsulfonyl fluoride, or ESF) undergoes β-arylation with stable and readily prepared arenediazonium tetrafluoroborates in the presence of the catalyst palladium(II) acetate to afford the E-isomer sulfonyl analogues of cinnamoyl fluoride in 43-97 % yield. The β-arylethenesulfonyl fluorides are found to be selectively addressable bis-electrophiles for sulfur(VI) fluoride exchange (SuFEx) click chemistry, in which either the alkenyl moiety or the sulfonyl fluoride group can be the exclusive site of nucleophilic attack under defined conditions, making these rather simple cores attractive for covalent drug discovery.

  12. Controlled synthesis of uniform palladium nanoparticles on novel micro-porous carbon as a recyclable heterogeneous catalyst for the Heck reaction.

    PubMed

    Song, Kunpeng; Liu, Peng; Wang, Jingyu; Pang, Lei; Chen, Jian; Hussain, Irshad; Tan, Bien; Li, Tao

    2015-08-21

    Novel dual-porous carbon-supported palladium nanoparticle (Pd NP) catalysts were prepared by sequential carbonization and reduction of microporous organic polymer-encaged PdCl2. The diverse pore structure of microporous organic polymers provides a reservoir for the palladium precursors and prevents Pd NPs from sintering during the carbonization and reaction. The microporous structure has a significant effect on the size and dispersion of palladium NPs. The average size of the Pd NPs (in the range of 4-6 nm) was tuned by changing the pore size distribution and the carbonization temperature. The resulting carbon-supported Pd NPs were characterized by TEM, BET, XRD, and XPS and the Pd loading was calculated by AAS. The encaged Pd NP catalysts prepared by this methodology exhibited outstanding stability and reusability in the Heck reaction and could be reused at least 10 times without appreciable loss of activity.

  13. 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.

  14. Interplay between intramolecular and intermolecular structures of 1,1,2,2-tetrachloro-1,2-difluoroethane

    NASA Astrophysics Data System (ADS)

    Rovira-Esteva, M.; Murugan, N. A.; Pardo, L. C.; Busch, S.; Tamarit, J. Ll.; Pothoczki, Sz.; Cuello, G. J.; Bermejo, F. J.

    2011-08-01

    We report on the interplay between the short-range order of molecules in the liquid phase of 1,1,2,2-tetrachloro-1,2-difluoroethane and the possible molecular conformations, trans and gauche. Two complementary approaches have been used to get a comprehensive picture: analysis of neutron-diffraction data by a Bayesian fit algorithm and a molecular dynamics simulation. The results of both show that the population of trans and gauche conformers in the liquid state can only correspond to the gauche conformer being more stable than the trans conformer. Distinct conformer geometries induce distinct molecular short-range orders around them, suggesting that a deep intra- and intermolecular interaction coupling is energetically favoring one of the conformers by reducing the total molecular free energy.

  15. Intermolecular vibrations and vibrational dynamics of a phenol⋯methanol binary complex studied by LIF spectroscopy

    NASA Astrophysics Data System (ADS)

    Mukhopadhyay, Deb Pratim; Biswas, Souvick; Chakraborty, Tapas

    2017-04-01

    Low-frequency intermolecular vibrations in S0 and S1 states of p-fluorophenol (pFP) methanol binary complex have been studied using laser induced fluorescence (LIF) spectroscopy in a supersonic jet expansion. Vibrational fundamentals of five such modes show up in fluorescence excitation (FE) spectrum, and corresponding ground state frequencies are obtained measuring disperse fluorescence (DF) spectra. Signatures of strong coupling between the hydrogen bond stretching fundamental (σ01) and a ring mode of pFP moiety in S1 state are revealed. In comparison with the analogous pFP-water complex, the present system displays very low threshold (∼170 cm-1) for vibrational energy relaxation in S1 state.

  16. 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.

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

    PubMed

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

    2014-04-05

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

  18. Electronic Structure Theory for Radicaloid Systems and Intermolecular Interactions

    NASA Astrophysics Data System (ADS)

    Kurlancheek, Westin

    associated with unrestriction. Second, the relaxed density matrix itself fails to be N-representable, with natural orbital occupation numbers less than zero and greater than one. Therefore, it is desirable to use a method that is not dependent on the inverse of the Hessian like orbital optimized MP2 (O2). Another system which requires the use of orbital optimization is a neutral soliton on a polyacetylene chain. In this system, the Hartree-Fock reference suffers from severe spin-polarization making the wavefunction physically unreasonable unless a very sophisticated treatment of electron correlation is used to correct this problem. Originally, it was found that computationally expensive methods like CCSD(T) and CASSCF could adequately describe small model chain but not the full system. The O2 method is found to be an dramatic improvement over traditional MP2 which can be feasibly applied to polyenyl chains long enough to characterize the soliton. It is also discovered that density functionals are generally inadequate in describing the half-width of the soliton. Finally, the last chapter takes a slightly different perspective and focuses on the addition of correlation energy to a successful energy decomposition analysis based on absolutely localized molecular orbitals. It is discovered that the resulting new method can adequately describe systems with dispersive intermolecular interactions and large amounts of charge transfer. This scheme is then applied to the water dimer systems and it is found that all of the intermolecular interactions similar in size with the electrostatic interaction being the largest and the dispersive interaction being the smallest. This method is also contrasted with other EDA schemes.

  19. Competing intermolecular interactions in some 'bridge-flipped' isomeric phenylhydrazones.

    PubMed

    Ojala, William H; Arola, Trina M; Brigino, Ann M; Leavell, Jeremy D; Ojala, Charles R

    2012-07-01

    To examine the roles of competing intermolecular interactions in differentiating the molecular packing arrangements of some isomeric phenylhydrazones from each other, the crystal structures of five nitrile-halogen substituted phenylhydrazones and two nitro-halogen substituted phenylhydrazones have been determined and are described here: (E)-4-cyanobenzaldehyde 4-chlorophenylhydrazone, C(14)H(10)ClN(3), (Ia); (E)-4-cyanobenzaldehyde 4-bromophenylhydrazone, C(14)H(10)BrN(3), (Ib); (E)-4-cyanobenzaldehyde 4-iodophenylhydrazone, C(14)H(10)IN(3), (Ic); (E)-4-bromobenzaldehyde 4-cyanophenylhydrazone, C(14)H(10)BrN(3), (IIb); (E)-4-iodobenzaldehyde 4-cyanophenylhydrazone, C(14)H(10)IN(3), (IIc); (E)-4-chlorobenzaldehyde 4-nitrophenylhydrazone, C(13)H(10)ClN(3)O(2), (III); and (E)-4-nitrobenzaldehyde 4-chlorophenylhydrazone, C(13)H(10)ClN(3)O(2), (IV). Both (Ia) and (Ib) are disordered (less than 7% of the molecules have the minor orientation in each structure). Pairs (Ia)/(Ib) and (IIb)/(IIc), related by a halogen exchange, are isomorphous, but none of the 'bridge-flipped' isomeric pairs, viz. (Ib)/(IIb), (Ic)/(IIc) or (III)/(IV), is isomorphous. In the nitrile-halogen structures (Ia)-(Ic) and (IIb)-(IIc), only the bridge N-H group and not the bridge C-H group acts as a hydrogen-bond donor to the nitrile group, but in the nitro-halogen structures (III) (with Z' = 2) and (IV), both the bridge N-H group and the bridge C-H group interact with the nitro group as hydrogen-bond donors, albeit via different motifs. The occurrence here of the bridge C-H contact with a hydrogen-bond acceptor suggests the possibility that other pairs of `bridge-flipped' isomeric phenylhydrazones may prove to be isomorphous, regardless of the change from isomer to isomer in the position of the N-H group within the bridge.

  20. Hydrogen-Bonding Polarizable Intermolecular Potential Model for Water.

    PubMed

    Jiang, Hao; Moultos, Othonas A; Economou, Ioannis G; Panagiotopoulos, Athanassios Z

    2016-12-08

    A polarizable intermolecular potential model with short-range directional hydrogen-bonding interactions was developed for water. The model has a rigid geometry, with bond lengths and angles set to experimental gas-phase values. Dispersion interactions are represented by the Buckingham potential assigned to the oxygen atom, whereas electrostatic interactions are modeled by Gaussian charges. Polarization is handled by a Drude oscillator site, using a negative Gaussian charge attached to the oxygen atom by a harmonic spring. An explicit hydrogen-bonding term is included in the model to account for the effects of charge transfer. The model parameters were optimized to density, configurational energy, pair correlation function, and the dielectric constant of water under ambient conditions, as well as the minimum gas-phase dimer energy. Molecular dynamics and Gibbs ensemble Monte Carlo simulations were performed to evaluate the new model with respect to the thermodynamic and transport properties over a wide range of temperature and pressure conditions. Good agreement between model predictions and experimental data was found for most of the properties studied. The new model yields better performance relative to the majority of existing models and outperforms the BK3 model, which is one of the best polarizable models, for vapor-liquid equilibrium properties, whereas the new model is not better than the BK3 model for representation of other properties. The model can be efficiently simulated with the thermalized Drude oscillator algorithm, resulting in computational costs only 3 times higher than those of the nonpolarizable TIP4P/2005 model, whereas having significantly improved properties. Because it involves only a single Drude oscillator site, the new model is significantly faster than polarizable models with multiple sites. With the explicit inclusion of hydrogen-bond interactions, the model may provide a better description of the phase behavior of aqueous mixtures.

  1. Intermolecular Forces in Introductory Chemistry Studied by Gas Chromatography, Computer Models, and Viscometry

    NASA Astrophysics Data System (ADS)

    Wedvik, Jonathan C.; McManaman, Charity; Anderson, Janet S.; Carroll, Mary K.

    1998-07-01

    An experiment on intermolecular forces for first-term introductory college chemistry is presented. The experiment integrates traditional viscometry-based measurements with modern chromatographic analysis and use of computer-based molecular models. Students performing gas chromatographic (GC) analyses of mixtures of n-alkanes and samples that simulate crime scene evidence discover that liquid mixtures can be separated rapidly into their components based upon intermolecular forces. Each group of students is given a liquid sample that simulates one collected at an arson scene, and the group is required to determine the identity of the accelerant. Students also examine computer models to better visualize how molecular structure affects intermolecular forces: London forces, dipole-dipole interactions, and hydrogen bonding. The relative viscosities of organic liquids are also measured to relate physical properties to intermolecular forces.

  2. The effects of intramolecular and intermolecular coordination on (31)P nuclear shielding: phosphorylated azoles.

    PubMed

    Chernyshev, Kirill A; Larina, Ludmila I; Chirkina, Elena A; Krivdin, Leonid B

    2012-02-01

    The effects of intramolecular and intermolecular coordination on (31)P nuclear shielding have been investigated in the series of tetracoordinated, pentacoordinated and hexacoordinated N-vinylpyrazoles and intermolecular complexes of N-vinylimidazole and 1-allyl-3,5-dimethylpyrazole with phosphorous pentachloride both experimentally and theoretically. It was shown that either intramolecular or intermolecular coordination involving phosphorous results in a dramatic (31)P nuclear shielding amounting to approximately 150 ppm on changing the phosphorous coordination number by one. A major importance of solvent effects on (31)P nuclear shielding of intramolecular and intermolecular complexes involving N → P coordination bond has been demonstrated. It was found that the zeroth-order regular approximation-gauge-including atomic orbital-B1PW91/DZP method was sufficiently accurate for the calculation of (31)P NMR chemical shifts, provided relativistic corrections are taken into account, the latter being of crucial importance in the description of (31)P nuclear shielding.

  3. 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)....

  4. 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)

  5. Investigation on intermolecular interaction between two solutes where one solute occurs in two states

    NASA Astrophysics Data System (ADS)

    Kang, Xiaoyan; He, Anqi; Guo, Ran; Chen, Jing; Zhai, Yanjun; Xu, Yizhuang; Noda, Isao; Wu, Jinguang

    2016-11-01

    The spectral behavior of a pair of 2D asynchronous spectra generated by using the double asynchronous orthogonal sample design (DAOSD) approach on a chemical system is investigated. Two solutes (P and Q) are dissolved in the solution and intermolecular interaction between P and Q is characterized. In this particular system, P occurs in two exchangeable states when it is dissolved in the solutions. Results on mathematical analysis and computer simulation demonstrated that interference unrelated to the intermolecular interaction can be completely removed. Hence the resultant 2D asynchronous spectra generated by using the DAOSD approach can reflect intermolecular interaction reliably. Moreover, properties of cross peaks in different regions of the pair of asynchronous spectra are discussed. In our previous works, cross peaks generated by using the DAOSD and relevant techniques reflect variations on peak position, bandwidth or absorptivity of the characteristic peaks of solutes caused by intermolecular interaction. However, we find that cross peak can still be produced even if intermolecular interaction do not bring about any changes on the characteristic peaks of solutes. Mathematical analysis demonstrates that cross peaks are related to the variations of chemical systems caused by intermolecular interaction at a network level.

  6. Intermolecular forces and scaling relations between heterogeneous macromolecular surfaces

    NASA Astrophysics Data System (ADS)

    Rosenberg, Kenneth J.

    Most theories regarding the behavior of intermolecular forces assume perfectly smooth surfaces with well-defined chemical and material properties. In this thesis, three separate systems are studied to explore the accuracy of this assumption in very different situations. In the first system, the effects of milli-molar amounts of dissolved gas (the amount typically present in normal atmospheric conditions) have been studied at a pristine oil/water interface. It was found that the removal of the dissolved gas significantly increased the lifetime of the oil droplets, effectively reducing the long-range hydrophobic attractive force present under standard conditions. In the second system, the effect of varying normal and lateral roughness of solid surfaces in understanding the long-range steric forces and shorter-range adhesive (van der Waals) forces are studied. Various techniques to reproducibly control and vary the roughness were developed for a number of different types of polymeric surfaces. A strong correlation between the roughness and the repulsive steric force was observed for randomly rough surfaces. Similar scaling relations between the roughness and the magnitude of the adhesive force were measured. Friction measurements between these surfaces show that even a few nanometers of roughness significantly reduces the critical shear stress required to initiate sliding. However, the coefficient of friction was relatively unaffected by the range of roughness considered, in agreement with the macroscopic Amontons' law. The third and final system dealt with the properties of adsorbed layers of polyampholytes (containing both positively and negatively charged groups), as opposed to the more common classes of neutral polymers or polyelectrolytes. These measurements took advantage of a naturally occurring family of proteins (a class of polyampholytes), known as tau, which exist in six different well-defined lengths and charge densities. Force measurements were made with

  7. 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

  8. Generalized spin-ratio scaled MP2 method for accurate prediction of intermolecular interactions for neutral and ionic species

    NASA Astrophysics Data System (ADS)

    Tan, Samuel; Barrera Acevedo, Santiago; Izgorodina, Ekaterina I.

    2017-02-01

    The accurate calculation of intermolecular interactions is important to our understanding of properties in large molecular systems. The high computational cost of the current "gold standard" method, coupled cluster with singles and doubles and perturbative triples (CCSD(T), limits its application to small- to medium-sized systems. Second-order Møller-Plesset perturbation (MP2) theory is a cheaper alternative for larger systems, although at the expense of its decreased accuracy, especially when treating van der Waals complexes. In this study, a new modification of the spin-component scaled MP2 method was proposed for a wide range of intermolecular complexes including two well-known datasets, S22 and S66, and a large dataset of ionic liquids consisting of 174 single ion pairs, IL174. It was found that the spin ratio, ɛΔ s=E/INT O SEIN T S S , calculated as the ratio of the opposite-spin component to the same-spin component of the interaction correlation energy fell in the range of 0.1 and 1.6, in contrast to the range of 3-4 usually observed for the ratio of absolute correlation energy, ɛs=E/OSES S , in individual molecules. Scaled coefficients were found to become negative when the spin ratio fell in close proximity to 1.0, and therefore, the studied intermolecular complexes were divided into two groups: (1) complexes with ɛΔ s< 1 and (2) complexes with ɛΔ s≥ 1 . A separate set of coefficients was obtained for both groups. Exclusion of counterpoise correction during scaling was found to produce superior results due to decreased error. Among a series of Dunning's basis sets, cc-pVTZ and cc-pVQZ were found to be the best performing ones, with a mean absolute error of 1.4 kJ mol-1 and maximum errors below 6.2 kJ mol-1. The new modification, spin-ratio scaled second-order Møller-Plesset perturbation, treats both dispersion-driven and hydrogen-bonded complexes equally well, thus validating its robustness with respect to the interaction type ranging from ionic

  9. Intermolecular interactions of oligothienoacenes: Do S⋯S interactions positively contribute to crystal structures of sulfur-containing aromatic molecules?

    PubMed

    Tsuzuki, Seiji; Orita, Hideo; Sato, Naoki

    2016-11-07

    Intermolecular interactions in the crystals of tetra- and penta-thienoacene were studied using ab initio molecular orbital calculations for evaluating the magnitude of characteristic S⋯S interactions with great attention paid to their origin. The interactions between the π-stacked neighboring molecules are significantly greater than those between the neighboring molecules exhibiting the S⋯S contact, although it has sometimes been claimed that the S⋯S interactions play important roles in adjusting the molecular arrangement of sulfur-containing polycyclic aromatic molecules in the crystals owing to short S⋯S contacts. The coupled cluster calculations with single and double substitutions with noniterative triple excitation interaction energies at the basis set limit estimated for the π-stacked and S⋯S contacted neighboring molecules in the tetrathienoacene crystal are -11.17 and -4.27 kcal/mol, respectively. Those for π-stacked molecules in the pentathienoacene crystal is -14.38 kcal/mol, while those for S⋯S contacted molecules are -7.02 and -6.74 kcal/mol. The dispersion interaction is the major source of the attraction between the π-stacked and S⋯S contacted molecules, while the orbital-orbital interactions are repulsive: The orbital-orbital interactions, which are significant for charge carrier transport properties, are not much more than the results of the short S⋯S contact caused by the strong dispersion interactions. Besides, the intermolecular interaction energy calculated for a trithienoacene dimer has strong orientation dependence.

  10. Rational targeting of subclasses of intermolecular interactions: elimination of nonspecific binding for analyte sensing.

    PubMed

    Lane, Jordan S; Richens, Joanna L; Vere, Kelly-Ann; O'Shea, Paul

    2014-08-12

    The ability to target and control intermolecular interactions is crucial in the development of several different technologies. Here we offer a tool to rationally design liquid media systems that can modulate specific intermolecular interactions. This has broad implications in deciphering the nature of intermolecular forces in complex solutions and offers insight into the forces that govern both specific and nonspecific binding in a given system. Nonspecific binding still continues to be a problem when dealing with analyte detection across a range of different detection technologies. Here, we exemplify the problem of nonspecific binding on model membrane systems and when dealing with low-abundance protein detection on commercially available SPR technology. A range of different soluble reagents that target specific subclasses of intermolecular interactions have been tested and optimized to virtually eliminate nonspecific binding while leaving specific interactions unperturbed. Thiocyanate ions are used to target nonpolar interactions, and small reagents such as glycylglycylglycine are used to modulate the dielectric constant, which targets charge-charge and dipole interactions. We show that with rational design and careful modulation these reagents offer a step forward in dissecting the intermolecular forces that govern binding, alongside offering nonspecific binding elimination in detection systems.

  11. Asymmetric Palladium-Catalyzed Directed Intermolecular Fluoroarylation of Styrenes

    PubMed Central

    2015-01-01

    A mild catalytic asymmetric direct fluoro-arylation of styrenes has been developed. The palladium-catalyzed three-component coupling of Selectfluor, a styrene and a boronic acid, provides chiral monofluorinated compounds in good yield and in high enantiomeric excess. A mechanism proceeding through a Pd(IV)-fluoride intermediate is proposed for the transformation and synthesis of an sp3 C–F bond. PMID:24617344

  12. Localization of the dominant non-enzymatic intermolecular cross-linking sites on fibrous collagen.

    PubMed

    Chiue, Hiroko; Yamazoye, Tsutako; Matsumura, Sueo

    2015-06-05

    Previous studies have shown that fibrous collagen undergoes intermolecular cross-linking at multiple sites of the elongated triple-helical regions among adjacent juxtaposed collagen molecules on incubation with a very high concentration of reducing sugar such as 200 mM ribose, and the similarity of the changes in its physicochemical properties to that of senescent collagen aged in vivo has been emphasized. In the present study, however, it was found that when incubated with less than 30 mM ribose, fibrous collagen underwent intermolecular cross-linking primarily between the telopeptide region of a collagen molecule and the triple-helical region of another adjacent collagen molecule, and intermolecular cross-linking between the triple-helical regions of adjacent collagen molecules was very small. Physiological significance of the previous studies thus needs to be reevaluated.

  13. Definition and computation of intermolecular contact in liquids using additively weighted Voronoi tessellation.

    PubMed

    Isele-Holder, Rolf E; Rabideau, Brooks D; Ismail, Ahmed E

    2012-05-10

    We present a definition of intermolecular surface contact by applying weighted Voronoi tessellations to configurations of various organic liquids and water obtained from molecular dynamics simulations. This definition of surface contact is used to link the COSMO-RS model and molecular dynamics simulations. We demonstrate that additively weighted tessellation is the superior tessellation type to define intermolecular surface contact. Furthermore, we fit a set of weights for the elements C, H, O, N, F, and S for this tessellation type to obtain optimal agreement between the models. We use these radii to successfully predict contact statistics for compounds that were excluded from the fit and mixtures. The observed agreement between contact statistics from COSMO-RS and molecular dynamics simulations confirms the capability of the presented method to describe intermolecular contact. Furthermore, we observe that increasing polarity of the surfaces of the examined molecules leads to weaker agreement in the contact statistics. This is especially pronounced for pure water.

  14. 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.

  15. Experimental and computational investigation of intermolecular interactions in cyclopentanone with methanol mixture

    NASA Astrophysics Data System (ADS)

    Zhang, Yu-Feng; Huang, Rong-Yi; Wang, Jun-Wei; Geng, Tong-Mou; Zhao, Shun-Ping; Wu, Gen-Hua

    2014-09-01

    In this Letter, excess molar volumes, refractive index deviations, Raman spectra and quantum-chemical calculations have been used to explore the underlying intermolecular interactions in the binary mixture containing cyclopentanone (CPN) and methanol. The experimental data reveal that the 1:1 (Ia) and 1:2 (Ib) cross-associations between CPN and methanol are formed in the studied binary mixture. This result has been further corroborated via theoretical calculations. In addition, the observed 1747 and 1732 cm-1 bands can be assigned to the Cdbnd O stretching vibrations of the intermolecular cross-associations Ia and Ib, respectively, in distinct contradiction with the previous explanations.

  16. Intermolecular associations in an equimolar formamide-water solution based on neutron scattering and DFT calculations.

    PubMed

    Abdelmoulahi, Hafedh; Ghalla, Houcine; Nasr, Salah; Darpentigny, Jacques; Bellissent-Funel, Marie-Claire

    2016-10-07

    In the present work, we have investigated the intermolecular associations of formamide with water in an equimolar formamide-water solution (FA-Water) by means of neutron scattering in combination with density functional theory calculations. The neutron scattering data were analyzed to deduce the structure factor SM(q) and the intermolecular pair correlation function gL(r). By considering different hydrogen bonded FA-Water associations, it has been shown that some of them describe well the local order in the solution. Natural bond orbital and atoms in molecules analyses have been performed to give more insight into the properties of hydrogen bonds involved in the more probable models.

  17. 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.

  18. 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.

  19. Two-dimensional infrared spectroscopy of intermolecular hydrogen bonds in the condensed phase.

    PubMed

    Elsaesser, Thomas

    2009-09-15

    Hydrogen bonding plays a key role in the structural, physical, and chemical properties of liquids such as water and in macromolecular structures such as proteins. Vibrational spectroscopy is an important tool for understanding hydrogen bonding because it provides a way to observe local molecular geometries and their interaction with the environment. Linear vibrational spectroscopy has mapped characteristic changes of vibrational spectra and the occurrence of new bands that form upon hydrogen bonding. However, linear vibrational spectroscopy gives very limited insight into ultrafast dynamics of the underlying molecular interactions, such as the motions of hydrogen-bonded groups, energy dissipation and delocalization, and the fluctuations within hydrogen-bonded structures that occur in the ultrafast time domain. Nonlinear vibrational spectroscopy with its femtosecond time resolution can discern these dynamic processes in real time and has emerged as an important tool for unraveling molecular dynamics and for quantifying interactions that govern the vibrational and structural dynamics of hydrogen bonds. This Account reviews recent progress originating from third-order nonlinear methods of coherent multidimensional vibrational spectroscopy. Ultrafast dynamics of intermolecular hydrogen bonds are addressed for a number of prototype systems: hydrogen-bonded carboxylic acid dimers in an aprotic liquid environment, the disordered fluctuating hydrogen-bond network of liquid water, and DNA oligomers interacting with water. Cyclic carboxylic acid dimers display a rich scheme of vibrational couplings, resulting in OH stretching absorption bands with highly complex spectral envelopes. Two-dimensional spectroscopy of acetic acid dimers in a nonpolar liquid environment demonstrates that multiple Fermi resonances of the OH stretching mode with overtones and combination tones of fingerprint vibrations dominate both the 2D and linear absorption spectra. The coupling of the OH

  20. Fluorous oxime palladacycle: a precatalyst for carbon-carbon coupling reactions in aqueous and organic medium.

    PubMed

    Susanto, Woen; Chu, Chi-Yuan; Ang, Wei Jie; Chou, Tzyy-Chao; Lo, Lee-Chiang; Lam, Yulin

    2012-03-16

    To facilitate precatalyst recovery and reuse, we have developed a fluorous, oxime-based palladacycle 1 and demonstrated that it is a very efficient and versatile precatalyst for a wide range of carbon-carbon bond formation reactions (Suzuki-Miyaura, Sonogashira, Stille, Heck, Glaser-type, and Kumada) in either aqueous or organic medium under microwave irradiation. Palladacycle 1 could be recovered through F-SPE in various coupling reactions with recovery ranging from 84 to 95% for the first cycle. Inductively coupled plasma optical emission spectrometry (ICP-OES) analyses of the Pd content in the crude product from each class of transformation indicated extremely low levels of leaching and the palladacycle could be reused four to five times without significant loss of activity.

  1. Accurate first principles model potentials for intermolecular interactions.

    PubMed

    Gordon, Mark S; Smith, Quentin A; Xu, Peng; Slipchenko, Lyudmila V

    2013-01-01

    The general effective fragment potential (EFP) method provides model potentials for any molecule that is derived from first principles, with no empirically fitted parameters. The EFP method has been interfaced with most currently used ab initio single-reference and multireference quantum mechanics (QM) methods, ranging from Hartree-Fock and coupled cluster theory to multireference perturbation theory. The most recent innovations in the EFP model have been to make the computationally expensive charge transfer term much more efficient and to interface the general EFP dispersion and exchange repulsion interactions with QM methods. Following a summary of the method and its implementation in generally available computer programs, these most recent new developments are discussed.

  2. 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.

  3. 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.

  4. Selective intermolecular amination of C-H bonds at tertiary carbon centers.

    PubMed

    Roizen, Jennifer L; Zalatan, David N; Du Bois, J

    2013-10-18

    C-H insertion: A method for intermolecular amination of tertiary CH bonds is described that uses limiting amounts of substrate and a convenient phenol-derived nitrogen source. Structure-selectivity and mechanistic studies suggest that steric interaction between the substrate and active oxidant is the principal determinant of product selectivity.

  5. 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…

  6. The B-box module of CYLD is responsible for its intermolecular interaction and cytoplasmic localization.

    PubMed

    Xie, Songbo; Chen, Miao; Gao, Siqi; Zhong, Tao; Zhou, Peng; Li, Dengwen; Zhou, Jun; Gao, Jinmin; Liu, Min

    2017-02-07

    The tumor suppressor protein cylindromatosis (CYLD), as a microtubule-associated deubiquitinase, plays a pivotal role in a wide range of cellular activities, including innate immunity, cell division, and ciliogenesis. Structural characterization reveals a small zinc-binding B-box inserted within the ubiquitin specific protease (USP) domain of CYLD; however, the exact role for this module remains yet to be elucidated. Here we identify a critical role for the B-box in facilitating the intermolecular interaction and subcellular localization of CYLD. By co-immunoprecipitation assays we uncover that CYLD has the ability to form an intermolecular complex. Native gel electrophoresis analysis and pull down assays show that the USP domain of CYLD is essential for its intermolecular interaction. Further investigation reveals that deletion of the B-box from the USP domain disrupts the intermolecular interaction of CYLD. Importantly, although loss of the B-box has no obvious effect on the deubiquitinase activity of CYLD, it abolishes the USP domain-mediated retention of CYLD in the cytoplasm. Collectively, these data demonstrate an important role for the B-box module of CYLD in mediating its assembly and subcellular distribution, which might be related to the functions of CYLD in various biological processes.

  7. Intermolecular C-H Quaternary Alkylation of Aniline Derivatives Induced by Visible-Light Photoredox Catalysis.

    PubMed

    Cheng, Jie; Deng, Xia; Wang, Guoqiang; Li, Ying; Cheng, Xu; Li, Guigen

    2016-09-16

    The intermolecular direct C-H alkylation of aniline derivatives with α-bromo ketones to build a quaternary carbon center was reported with a visible-light catalysis procedure. The reaction covers a variety of functional groups with good to excellent yields. A regioselectivity favoring the ortho position for the amine group was observed and investigated with Fukui indices and spectral methods.

  8. NMR detection of intermolecular interaction sites in the dimeric 5'-leader of the HIV-1 genome.

    PubMed

    Keane, Sarah C; Van, Verna; Frank, Heather M; Sciandra, Carly A; McCowin, Sayo; Santos, Justin; Heng, Xiao; Summers, Michael F

    2016-11-15

    HIV type-1 (HIV-1) contains a pseudodiploid RNA genome that is selected for packaging and maintained in virions as a noncovalently linked dimer. Genome dimerization is mediated by conserved elements within the 5'-leader of the RNA, including a palindromic dimer initiation signal (DIS) that has been proposed to form kissing hairpin and/or extended duplex intermolecular contacts. Here, we have applied a (2)H-edited NMR approach to directly probe for intermolecular interactions in the full-length, dimeric HIV-1 5'-leader (688 nucleotides; 230 kDa). The interface is extensive and includes DIS:DIS base pairing in an extended duplex state as well as intermolecular pairing between elements of the upstream Unique-5' (U5) sequence and those near the gag start site (AUG). Other pseudopalindromic regions of the leader, including the transcription activation (TAR), polyadenylation (PolyA), and primer binding (PBS) elements, do not participate in intermolecular base pairing. Using a (2)H-edited one-dimensional NMR approach, we also show that the extended interface structure forms on a time scale similar to that of overall RNA dimerization. Our studies indicate that a kissing dimer-mediated structure, if formed, exists only transiently and readily converts to the extended interface structure, even in the absence of the HIV-1 nucleocapsid protein or other RNA chaperones.

  9. 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…

  10. Orthogonal adsorption onto nano-graphene oxide using different intermolecular forces for multiplexed delivery.

    PubMed

    Wang, Feng; Liu, Biwu; Ip, Alexander C-F; Liu, Juewen

    2013-08-14

    Nano-graphene oxide can adsorb both doxorubicin and zwitterionic dioleoyl-sn-glycero-3-phosphocholine (DOPC) liposomes in an orthogonal and non-competing manner with high capacities based on different surface and intermolecular forces taking place on the heterogeneous surface of the graphene oxide. The system forms stable colloids, allowing co-delivery of both cargos to cancer cells.

  11. Head-to-tail intermolecular hydrogen bonding of OH and NH groups with fluoride.

    PubMed

    Ashokkumar, Pichandi; Ramakrishnan, Vayalakkavoor T; Ramamurthy, Perumal

    2011-02-07

    To explore the anion-recognition ability of the phenolic hydroxyl group and the amino hydrogen, we synthesized three different acridinedione (ADD) based anion receptors, 1, 2 and 3, having OH, NH, and combination of OH and NH groups, respectively. Absorption, emission and (1)H NMR spectral studies revealed that receptor 1, having only a phenolic OH group, shows selective deprotonation of the hydroxyl proton towards F(-), which results in an "ON-OFF"-type signal in the fluorescence spectral studies. Receptor 2, which only has an amino hydrogen, also shows deprotonation of the amino hydrogen with F(-), whereas receptor 3 (having both OH and NH groups) shows head-to-tail intermolecular hydrogen bonding of OH and NH groups with F(-) prior to deprotonation. The observation of hydrogen bonding of the OH and NH groups in a combined solution of 1 and 2 with F(-) in a head-to-tail hetero-intermolecular fashion, and the absence of head-to-head and tail-to-tail intermolecular hydrogen bonding in 1 and 2 with F(-), prove that the difference in the acidity of the OH and NH protons leads to the formation of an intermolecular hydrogen-bonding complex with F(-) prior to deprotonation. The presence of this hydrogen-bonding complex was confirmed by absorption spectroscopy, 3D emission contour studies, and (1)H NMR titration.

  12. 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.

  13. High-frequency intermolecular homologous recombination during herpes simplex virus-mediated plasmid DNA replication.

    PubMed

    Fu, Xinping; Wang, Hua; Zhang, Xiaoliu

    2002-06-01

    Homologous recombination is a prominent feature of herpes simplex virus (HSV) type 1 DNA replication. This has been demonstrated and traditionally studied in experimental settings where repeated sequences are present or are being introduced into a single molecule for subsequent genome isomerization. In the present study, we have designed a pair of unique HSV amplicon plasmids to examine in detail intermolecular homologous recombination (IM-HR) between these amplicon plasmids during HSV-mediated DNA replication. Our data show that IM-HR occurred at a very high frequency: up to 60% of the amplicon concatemers retrieved from virion particles underwent intermolecular homologous recombination. Such a high frequency of IM-HR required that both plasmids be replicated by HSV-mediated replication, as IM-HR events were not detected when either one or both plasmids were replicated by simian virus 40-mediated DNA replication, even with the presence of HSV infection. In addition, the majority of the homologous recombination events resulted in sequence replacement or targeted gene repair, while the minority resulted in sequence insertion. These findings imply that frequent intermolecular homologous recombination may contribute directly to HSV genome isomerization. In addition, HSV-mediated amplicon replication may be an attractive model for studying intermolecular homologous recombination mechanisms in general in a mammalian system. In this regard, the knowledge obtained from such a study may facilitate the development of better strategies for targeted gene correction for gene therapy purposes.

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

    PubMed

    Jarvis, Samuel Paul

    2015-08-21

    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.

  15. 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.

  16. 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

  17. Ultrasonic and IR study of intermolecular association through hydrogen bonding in ternary liquid mixtures.

    PubMed

    Awasthi, Aashees; Shukla, J P

    2003-08-01

    Complex formation in ternary liquid mixtures of dimethylsulfoxide (DMSO) with phenol and o-cresol in carbontetrachloride has been studied by measuring ultrasonic velocity at 2 MHz, in the concentration range of 0.019-0.162 (in mole fraction of DMSO) at varying temperatures of 20, 30 and 40 degrees C. Using measured values of ultrasonic velocity, other parameters such as adiabatic compressibility, intermolecular free length, molar sound velocity, molar compressibility, specific acoustic impedance and molar volume have been evaluated. These parameters have been utilized to study the solute-solute interactions in these systems. The ultrasonic velocity shows a maxima and adiabatic compressibility a corresponding minima as a function of concentration for these mixtures. The results indicate the occurrence of complex formation between unlike molecules through intermolecular hydrogen bonding between oxygen atom of DMSO molecule and hydrogen atom of phenol and o-cresol molecules. The excess values of adiabatic compressibility and intermolecular free length have also been evaluated. The variation of both these parameters with concentration also indicates the possibility of the complex formation in these systems. Further, to investigate the presence of O-HO bond complexes and the strength of molecular association with concentrations, the infrared spectra of both the systems, DMSO-phenol and DMSO-o-cresol, have been recorded for various concentrations at room temperature (20 degrees C). The results obtained using infrared spectroscopy for both the systems also support the occurrence of complex formation through intermolecular hydrogen bonding in these ternary liquid mixtures.

  18. 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…

  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. Synthesis of Functionalized Cinnamaldehyde Derivatives by an Oxidative Heck Reaction and Their Use as Starting Materials for Preparation of Mycobacterium tuberculosis 1-Deoxy-d-xylulose-5-phosphate Reductoisomerase Inhibitors

    PubMed Central

    2011-01-01

    Cinnamaldehyde derivatives were synthesized in good to excellent yields in one step by a mild and selective, base-free palladium(II)-catalyzed oxidative Heck reaction starting from acrolein and various arylboronic acids. Prepared α,β-unsaturated aldehydes were used for synthesis of novel α-aryl substituted fosmidomycin analogues, which were evaluated for their inhibition of Mycobacterium tuberculosis 1-deoxy-d-xylulose 5-phosphate reductoisomerase. IC50 values between 0.8 and 27.3 μM were measured. The best compound showed activity comparable to that of the most potent previously reported α-aryl substituted fosmidomycin-class inhibitor. PMID:21936546

  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.

  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 General Transformation to Canonical Form for Potentials in Pairwise Intermolecular Interactions

    NASA Astrophysics Data System (ADS)

    Walton, Jay R.; Rivera-Rivera, Luis A.; Lucchese, Robert R.; Bevan, John W.

    2015-06-01

    A generalized formulation of explicit transformations is introduced to investigate the concept of a canonical potential in both fundamental chemical and intermolecular bonding. Different classes of representative ground electronic state pairwise interatomic interactions are referenced to a single canonical potential illustrating application of explicit transformations. Specifically, accurately determined potentials of the diatomic molecules H_2, H_2^+, HF, LiH, argon dimer, and one-dimensional dissociative coordinates in Ar-HBr, OC-HF, and OC-Cl_2 are investigated throughout their bound potentials. The advantages of the current formulation for accurately evaluating equilibrium dissociation energies and a fundamentally different unified perspective on nature of intermolecular interactions will be emphasized. In particular, this canonical approach has relevance to previous assertions that there is no very fundamental distinction between van der Waals bonding and covalent bonding or for that matter hydrogen and halogen bonds.

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

    PubMed

    Berry, David J; Steed, Jonathan W

    2017-03-23

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

  6. 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.

  7. Intermolecular potential and second virial coefficient of the water-nitrogen complex.

    PubMed

    Tulegenov, Akyl S; Wheatley, Richard J; Hodges, Matthew P; Harvey, Allan H

    2007-03-07

    The authors construct a rigid-body (five-dimensional) potential energy surface for the water-nitrogen complex using the systematic intermolecular potential extrapolation routine. The intermolecular potential is then extrapolated to the limit of a complete basis set. An analytic fit of this surface is obtained, and, using this, the global minimum energy is found. The minimum is located in an arrangement in which N2 is near the H atom of H2O, almost collinear with the OH bond. The best estimate of the binding energy is 441 cm-1 (1 cm-1 approximately 1.986 43x10(-23) J). The extrapolated potential is then used to calculate the second cross virial coefficient over a wide temperature range (100-3000 K). These calculated second virial coefficients are generally consistent with experimental data, but for the most part the former have smaller uncertainties.

  8. Investigation of intermolecular interactions in perylene films on Au(111) by infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Ding, Li; Schulz, Philip; Farahzadi, Azadeh; Shportko, Kostiantyn V.; Wuttig, Matthias

    2012-02-01

    Intermolecular interactions in crystalline perylene films on Au(111) have been investigated by Fourier transform infrared spectroscopy. Dimer modes of vibrations are observed in the crystalline film, in contrast to the monomer modes found for isolated perylene molecules. These dimers are formed via hydrogen bonding in the sandwich herringbone structure of the crystalline α-phase. Davydov splitting of both the monomer and the dimer modes is observed due to resonance dynamic intermolecular interaction. The splitting of monomer modes into three distinct vibrations and the occurrence of the dimer modes confirm that the film crystallizes in the α phase, which is in line with the x-ray diffraction results. The frequency shift and band broadening at elevated temperature have been attributed to the cubic and quartic anharmonic interactions.

  9. Distinguishability and chiral stability in solution: Effects of decoherence and intermolecular interactions

    SciTech Connect

    Han, Heekyung; Wardlaw, David M.; Frolov, Alexei M.

    2014-05-28

    We examine the effect of decoherence and intermolecular interactions (chiral discrimination energies) on the chiral stability and the distinguishability of initially pure versus mixed states in an open chiral system. Under a two-level approximation for a system, intermolecular interactions are introduced by a mean-field theory, and interaction between a system and an environment is modeled by a continuous measurement of a population difference between the two chiral states. The resultant equations are explored for various parameters, with emphasis on the combined effects of the initial condition of the system, the chiral discrimination energies, and the decoherence in determining: the distinguishability as measured by a population difference between the initially pure and mixed states, and the decoherence process; the chiral stability as measured by the purity decay; and the stationary state of the system at times long relative to the time scales of the system dynamics and of the environmental effects.

  10. 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.

  11. Tip relaxation in atomic force microscopy imaging simulations to resolve intermolecular bonds

    NASA Astrophysics Data System (ADS)

    Lee, Alex; Sakai, Yuki; Chelikowsky, Jim

    Experimental noncontact atomic force microscopy (AFM) studies have reported distinct lines in regions with no electron density for a variety of systems. The appearance of these lines is unexpected because Pauli repulsion is thought to be the dominant factor in the AFM imaging mechanism. These lines have been proposed to represent intermolecular bonding. Recent theoretical studies have shown that accounting for tip probe relaxation can sharpen images and highlight features that make simulations more comparable to experiment. We will apply a similar tip relaxation scheme to our computational method-which uses an ab initio real-space pseudopotential formalism with frozen density embedding theory added-to the study of dibenzo[a,h]thianthrene and an 8-hydroxyquinoline dimer to develop our interpretation of imaged intermolecular bonds. Work is supported by the DOE under DOE/DE-FG02-06ER46286 and by the Welch Foundation under Grant F-1837. Computational resources were provided by NERSC and XSEDE.

  12. Investigation of intermolecular double-quantum off-resonance longitudinal relaxation in the tilted rotating frame

    NASA Astrophysics Data System (ADS)

    Cai, Honghao; Zheng, Bingwen; Ke, Hanping; Chen, Zhong

    2015-11-01

    A modified correlation spectroscopy revamped by asymmetric z-gradients echo detection (CRAZED) sequence was applied to investigate the behavior of intermolecular double-quantum longitudinal relaxation processes in the tilted rotating frame. Theoretical formalism based on dipolar field theory was presented in detail. Spectroscopic measurements and quantitative analysis demonstrated that the signal intensities and intermolecular double-quantum off-resonance longitudinal relaxation time in the rotating frame (T1ρ, DQC eff) are inversely correlated with the tilt angle (θ), while positively correlated with the effective frequency of spin-locking field (ωe). Magnetic resonance imaging experiments of an agarose phantom also prove the validity of the theoretical analysis and demonstrated the feasibility of imaging based on T1ρ, DQC eff . The rotating-frame double-quantum relaxation measurements are useful for probing slow-motion molecules and this study provides the guidance for optimization of the spin-lock experiments.

  13. Nucleophilic Additions to Coordinated 1,10-Phenanthroline: Intramolecular, Intermolecular, Reversible, and Irreversible.

    PubMed

    Arévalo, Rebeca; Menéndez, M Isabel; López, Ramón; Merino, Isabel; Riera, Lucía; Pérez, Julio

    2016-12-12

    KN(SiMe3 )2 reacts with [Re(CO)3 (phen)(PMe3 )]OTf via reversible addition to the phen ligand and irreversible deprotonation of the PMe3 ligand followed by intramolecular attack to phen by the deprotonated phosphane, whereas MeLi irreversibly adds to phen. The addition of MeLi has been shown to be intermolecular, unlike previously known nucleophilic additions to pyridines.

  14. Intermolecular interactions in rifabutin-2-hydroxypropyl-β-cyclodextrin-water solutions, according to solubility data

    NASA Astrophysics Data System (ADS)

    Anshakova, A. V.; Vinogradov, E. V.; Sedush, N. G.; Kurtikyan, T. S.; Zhokhov, S. S.; Polshakov, V. I.; Ermolenko, Yu. V.; Konyukhov, V. Yu.; Maksimenko, O. O.; Gelperin, S. E.

    2016-05-01

    The formulations of rifabutin (RB) and 2-hydroxypropyl-β-cyclodextrin (HP-β-CD), obtained using different preparation techniques, are studied by means of differential scanning calorimetry and molecular spectroscopy (FTIR, NMR, Raman scattering, and photon correlation light scattering). It is established that molecules of RB do not form inclusion complexes with the molecules of HP-β-CD, and an increase in the solubility of RB determined earlier is caused by the formation of weak intermolecular associates.

  15. Carbon dioxide hydrate phase equilibrium and cage occupancy calculations using ab initio intermolecular potentials.

    PubMed

    Velaga, Srinath C; Anderson, Brian J

    2014-01-16

    Gas hydrate deposits are receiving increased attention as potential locations for CO2 sequestration, with CO2 replacing the methane that is recovered as an energy source. In this scenario, it is very important to correctly characterize the cage occupancies of CO2 to correctly assess the sequestration potential as well as the methane recoverability. In order to predict accurate cage occupancies, the guest–host interaction potential must be represented properly. Earlier, these potential parameters were obtained by fitting to experimental equilibrium data and these fitted parameters do not match with those obtained by second virial coefficient or gas viscosity data. Ab initio quantum mechanical calculations provide an independent means to directly obtain accurate intermolecular potentials. A potential energy surface (PES) between H2O and CO2 was computed at the MP2/aug-cc-pVTZ level and corrected for basis set superposition error (BSSE), an error caused due to the lower basis set, by using the half counterpoise method. Intermolecular potentials were obtained by fitting Exponential-6 and Lennard-Jones 6-12 models to the ab initio PES, correcting for many-body interactions. We denoted this model as the “VAS” model. Reference parameters for structure I carbon dioxide hydrate were calculated using the VAS model (site–site ab initio intermolecular potentials) as Δμ(w)(0) = 1206 ± 2 J/mol and ΔH(w)(0) = 1260 ± 12 J/mol. With these reference parameters and the VAS model, pure CO2 hydrate equilibrium pressure was predicted with an average absolute deviation of less than 3.2% from the experimental data. Predictions of the small cage occupancy ranged from 32 to 51%, and the large cage is more than 98% occupied. The intermolecular potentials were also tested by calculating the pure CO2 density and diffusion of CO2 in water using molecular dynamics simulations.

  16. Intermolecular dynamical charge fluctuations in water: a signature of the H-bond network.

    PubMed

    Sharma, Manu; Resta, Raffaele; Car, Roberto

    2005-10-28

    We report a simulation of deuterated water using a Car-Parrinello approach based on maximally localized Wannier functions. This provides local information on the dynamics of the hydrogen-bond network and on the origin of the low-frequency infrared activity. The oscillator strength of the translational modes, peaked around approximately 200 cm-1, is anisotropic and originates from intermolecular--not intramolecular--charge fluctuations. These fluctuations are a signature of a tetrahedral hydrogen-bonding environment.

  17. A Catalytic, Brønsted Base Strategy for Intermolecular Allylic C—H Amination

    PubMed Central

    Reed, Sean A.; Mazzotti, Anthony R.; White, M. Christina

    2009-01-01

    A Brønsted base activation mode for oxidative, Pd(II)/sulfoxide catalyzed, intermolecular C—H allylic amination is reported. N,N-diisopropylethylamine was found to promote amination of unactivated terminal olefins, forming the corresponding linear allylic amine products with high levels of stereo-, regio-, and chemoselectivity. The predictable and high selectivity of this C—H oxidation method enables late-stage incorporation of nitrogen into advanced synthetic intermediates and natural products. PMID:19645492

  18. Supramolecular methods for controlling intermolecular [2+2] photocycloaddition reactions of unsaturated compounds in solutions

    NASA Astrophysics Data System (ADS)

    Ushakov, E. N.; Gromov, S. P.

    2015-08-01

    This review deals with the methods of supramolecular chemistry used for controlling the efficiency and stereoselectivity of intermolecular [2+2] photocycloaddition of olefins and other unsaturated compounds in homogeneous solutions. The best-studied methods are self-assembly through cation-macrocycle interactions, complexation with molecular templates through hydrogen bonding, and confinement of the reactants in supramolecular containers. The possibilities of using anionic templates and combined supramolecular approaches are discussed. The bibliography includes 107 references.

  19. Metal-free intermolecular formal cycloadditions enable an orthogonal access to nitrogen heterocycles

    PubMed Central

    Xie, Lan-Gui; Niyomchon, Supaporn; Mota, Antonio J.; González, Leticia; Maulide, Nuno

    2016-01-01

    Nitrogen-containing heteroaromatic cores are ubiquitous building blocks in organic chemistry. Herein, we present a family of metal-free intermolecular formal cycloaddition reactions that enable highly selective and orthogonal access to isoquinolines and pyrimidines at will. Applications of the products are complemented by a density functional theory mechanistic analysis that pinpoints the crucial factors responsible for the selectivity observed, including stoichiometry and the nature of the heteroalkyne. PMID:26975182

  20. The CO-Ne van der Waals complex: ab initio intermolecular potential energy, interaction induced electric dipole moment and polarizability surfaces, and second virial coefficients.

    PubMed

    Baranowska, Angelika; Fernández, Berta; Rizzo, Antonio; Jansík, Branislav

    2009-11-14

    The intermolecular potential energy, interaction induced electric dipole moment and polarizability surfaces of the CO-Ne van der Waals complex are calculated using coupled cluster methods and the d-aug-cc-pVTZ basis set extended with a set of 3s3p2d1f1g midbond functions placed in the middle of the van der Waals bond. After fitting the interaction properties to appropriate analytical functions the surfaces are further used in semiclassical calculations of the pressure, the dielectric and the refractivity second virial coefficients of the system. The interaction potential energy surface has a single minimum (-49.9952 cm(-1)), which corresponds to R = 3.383 A and theta = 79.4 degrees. The computed dielectric second virial coefficient B(epsilon) approximately -0.27 cm(6) mol(-2) around the room temperature.

  1. Intermolecular interactions in multi-component crystals of acridinone/thioacridinone derivatives: Structural and energetics investigations

    NASA Astrophysics Data System (ADS)

    Wera, Michał; Storoniak, Piotr; Trzybiński, Damian; Zadykowicz, Beata

    2016-12-01

    A single crystal X-ray analysis of two multi-component crystals consisting of an acridinone/thioacridinone moiety and a solvent moiety - water and ammonia (1 and 2), respectively, was carried out to determine the crystal structures of obtained crystals. A theoretical approach was undertaken - using the DFT method, lattice energies calculations and Hirshfeld surfaces (HS) - to qualitatively and quantitatively assess the intermolecular interactions within the crystal. HS analysis was showed that the H⋯H, C⋯H/H⋯C and C⋯C contacts for both structures (altogether 81.6% of total Hirshfeld surface area for 1 and 79.3% for 2) and the O⋯H/H⋯O (14.3%) for 1 and the S⋯H/H⋯S (15.2%) contacts for 2 were the characteristic intermolecular contacts in the related crystal structures. Using a computational methods were confirmed that the main contribution to the stabilization of the crystal lattice of compound 1 comes from the Coulombic interactions, whereas in compound 2 electrostatic and van der Waals appear to have similar contribution to the crystal lattice energy. Theoretical calculations of the investigated compounds have also allowed to determine the energy of a single specific intermolecular interaction.

  2. Inter-molecular crosslinking activity is engendered by the dimeric form of transglutaminase 2.

    PubMed

    Kim, Nayeon; Lee, Won-Kyu; Lee, Seon-Hyeong; Jin, Kyeong Sik; Kim, Kyung-Hee; Lee, Younho; Song, Minsoo; Kim, Soo-Youl

    2017-03-01

    Transglutaminase 2 (TGase 2) catalyzes a crosslink between protein bound-glutamine and -lysine. We proposed the mechanism of TGase 2 activation depends on conformation change from unfolded monomer to unfolded dimer. We found that TGase 2 has temperature-sensitive conformation change system at 30 °C. Small-angle X-ray scattering analysis showed that the enzyme was maintained as an unfolded monomer at temperatures below 30 °C, but changed to an unfolded dimer at over 30 °C. Mass analysis revealed that the C-terminus of TGase 2 was the critical region for dimerization. Furthermore, this conformational switch creates new biochemical reactivity that catalyzed inter-molecular crosslink at above 30 °C as an unfolded dimer of TGase 2 while catalyzed intra-molecular crosslink at below 30 °C as an unfolded monomer of TGase 2. The mechanism of TGase 2 activation depends on temperature-sensitive conformation change from unfolded monomer to unfolded dimer at over 30 °C. Furthermore, inter-molecular crosslinking activity is generated by the dimeric form of TGase 2. TGase 2 switches its conformation from a monomer to a dimer following a change in temperature, which engendered unique catalytic function of enzyme as inter-molecular crosslinking activity with calcium.

  3. The intermolecular hydrogen-hydrogen structure of chain-molecule liquids from neutron diffraction

    NASA Astrophysics Data System (ADS)

    Londono, J. D.; Annis, B. K.; Turner, J. Z.; Soper, A. K.

    1994-11-01

    Neutron diffraction isotopic substitution experiments on liquid n-decane (C10H22) and n-eicosane (C20H42) are described. The intermolecular H-H structure function hHH(Q) and the intermolecular H-H correlation function ginterHH(r) are obtained without recourse to models of the intramolecular structure. The structure of the ginterHH(r) found at 2.5, 5.0, and 7.0 Å corresponds to different shells in the H-H pair correlation function. In addition, ginterHH(r)<1 for a considerable range, due to the screening of intermolecular correlations by intramolecular correlations. This ``correlation hole'' effect is accentuated by extrapolation of the structure functions to the expected infinite wavelength limit, and shows good agreement with values determined from small-angle neutron scattering (SANS) data. All of these features are in good agreement with the results of molecular dynamics simulations for the closely related system C13H28.

  4. Boiling points of halogenated ethanes: an explanatory model implicating weak intermolecular hydrogen-halogen bonding.

    PubMed

    Beauchamp, Guy

    2008-10-23

    This study explores via structural clues the influence of weak intermolecular hydrogen-halogen bonds on the boiling point of halogenated ethanes. The plot of boiling points of 86 halogenated ethanes versus the molar refraction (linked to polarizability) reveals a series of straight lines, each corresponding to one of nine possible arrangements of hydrogen and halogen atoms on the two-carbon skeleton. A multiple linear regression model of the boiling points could be designed based on molar refraction and subgroup structure as independent variables (R(2) = 0.995, standard error of boiling point 4.2 degrees C). The model is discussed in view of the fact that molar refraction can account for approximately 83.0% of the observed variation in boiling point, while 16.5% could be ascribed to weak C-X...H-C intermolecular interactions. The difference in the observed boiling point of molecules having similar molar refraction values but differing in hydrogen-halogen intermolecular bonds can reach as much as 90 degrees C.

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

    PubMed Central

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

    2015-01-01

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

  6. Intermolecular disintegration and intramolecular strand transfer activities of wild-type and mutant HIV-1 integrase.

    PubMed Central

    Mazumder, A; Engelman, A; Craigie, R; Fesen, M; Pommier, Y

    1994-01-01

    We report the activities of HIV integrase protein on a novel DNA substrate, consisting of a pair of gapped duplex molecules. Integrase catalyzed an intermolecular disintegration reaction that requires positioning of a pair of the gapped duplexes in a configuration that resembles the intgration intermediate. However, the major reaction resulted from an intramolecular reaction involving a single gapped duplex, giving rise to a hairpin. Surprisingly, a deletion mutant of integrase that lacks both the amino and carboxyl terminal regions still catalyzed the intermolecular disintegration reaction, but supported only a very low level of the intramolecular reaction. The central core region of integrase is therefore sufficient to both bind the gapped duplex DNA and juxtapose a pair of such molecules through protein-protein interactions. We suggest that the branched DNA structures of the previously reported disintegration substrate, and the intermolecular disintegration substrate described here, assist in stabilizing protein-protein interactions that otherwise require the amino and carboxy terminal regions of integrase. Images PMID:8152908

  7. The effect of intermolecular hydrogen bonding on the fluorescence of a bimetallic platinum complex.

    PubMed

    Zhao, Guang-Jiu; Northrop, Brian H; Han, Ke-Li; Stang, Peter J

    2010-09-02

    The bimetallic platinum complexes are known as unique building blocks and arewidely utilized in the coordination-driven self-assembly of functionalized supramolecular metallacycles. Hence, photophysical study of the bimetallic platinum complexes will be very helpful for the understanding on the optical properties and further applications of coordination-driven self-assembled supramolecular metallacycles. Herein, we report steady-state and time-resolved spectroscopic experiments as well as quantum chemistry calculations to investigate the significant intermolecular hydrogen bonding effects on the intramolecular charge transfer (ICT) fluorescence of a bimetallic platinum compound 4,4'-bis(trans-Pt(PEt(3))(2)OTf)benzophenone 3 in solution. We demonstrated that the fluorescent state of compound 3 can be assigned as a metal-to-ligand charge transfer (MLCT) state. Moreover, it was observed that the formation of intermolecular hydrogen bonds can effectively lengthen the fluorescence lifetime of 3 in alcoholic solvents compared with that in hexane solvent. At the same time, the electronically excited states of 3 in solution are definitely changed by intermolecular hydrogen bonding interactions. As a consequence, we propose a new fluorescence modulation mechanism by hydrogen bonding to explain different fluorescence emissions of 3 in hydrogen-bonding solvents and nonhydrogen-bonding solvents.

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

    PubMed

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

    2015-08-18

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

  9. One-pot hydrothermal synthesis of magnetically recoverable palladium/reduced graphene oxide nanocomposites and its catalytic applications in cross-coupling reactions.

    PubMed

    Fu, Wenzhi; Zhang, Zhuqing; Zhuang, Peiyuan; Shen, Jianfeng; Ye, Mingxin

    2017-07-01

    A facile, green, economical approach was designed to deposit palladium nanoparticles on magnetic reduced graphene oxide nanosheets (Pd-Fe3O4/rGO) via a one-pot hydrothermal synthesis method. The prepared Pd-Fe3O4/rGO nanocomposites were thoroughly characterized by Transmission electron microscopy, Scanning electron microscopy, Fourier-transform infrared spectroscopy, X-ray diffraction, and Raman spectroscopy. Importantly, the highly efficient catalytic property of the as-obtained Pd-Fe3O4/rGO catalyst was demonstrated for the Suzuki-Miyaura coupling reaction and Mizoroki-Heck coupling reaction. Significantly, the Suzuki-Miyaura coupling reactions could be efficiently performed in an environmentally friendly aqueous solution with no need for further additives. Besides, the nanocomposites could be conveniently separated from reaction system with an external permanent magnet for recycling and the inherent catalytic activity of the nanocomposites did not exacerbate after six repeated applications.

  10. Altering intra- to inter-molecular hydrogen bonding by dimethylsulfoxide: A TDDFT study of charge transfer for coumarin 343

    NASA Astrophysics Data System (ADS)

    Liu, Xiaochun; Yin, Hang; Li, Hui; Shi, Ying

    2017-04-01

    DFT and TDDFT methods were carried out to investigate the influences of intramolecular and intermolecular hydrogen bonding on excited state charge transfer for coumarin 343 (C343). Intramolecular hydrogen bonding is formed between carboxylic acid group and carbonyl group in C343 monomer. However, in dimethylsulfoxide (DMSO) solution, DMSO 'opens up' the intramolecular hydrogen bonding and forms solute-solvent intermolecular hydrogen bonded C343-DMSO complex. Analysis of frontier molecular orbitals reveals that intramolecular charge transfer (ICT) occurs in the first excited state both for C343 monomer and complex. The results of optimized geometric structures indicate that the intramolecular hydrogen bonding interaction is strengthened while the intermolecular hydrogen bonding is weakened in excited state, which is confirmed again by monitoring the shifts of characteristic peaks of infrared spectra. We demonstrated that DMSO solvent can not only break the intramolecular hydrogen bonding to form intermolecular hydrogen bonding with C343 but also alter the mechanism of excited state hydrogen bonding strengthening.

  11. Accurate description of intermolecular interactions involving ions using symmetry-adapted perturbation theory.

    PubMed

    Lao, Ka Un; Schäffer, Rainer; Jansen, Georg; Herbert, John M

    2015-06-09

    Three new data sets for intermolecular interactions, AHB21 for anion-neutral dimers, CHB6 for cation-neutral dimers, and IL16 for ion pairs, are assembled here, with complete-basis CCSD(T) results for each. These benchmarks are then used to evaluate the accuracy of the single-exchange approximation that is used for exchange energies in symmetry-adapted perturbation theory (SAPT), and the accuracy of SAPT based on wave function and density-functional descriptions of the monomers is evaluated. High-level SAPT calculations afford poor results for these data sets, and this includes the recently proposed "gold", "silver", and "bronze standards" of SAPT, namely, SAPT2+(3)-δMP2/aug-cc-pVTZ, SAPT2+/aug-cc-pVDZ, and sSAPT0/jun-cc-pVDZ, respectively [ Parker , T. M. , et al. , J. Chem. Phys. 2014 , 140 , 094106 ]. Especially poor results are obtained for symmetric shared-proton systems of the form X(-)···H(+)···X(-), for X = F, Cl, or OH. For the anionic data set, the SAPT2+(CCD)-δMP2/aug-cc-pVTZ method exhibits the best performance, with a mean absolute error (MAE) of 0.3 kcal/mol and a maximum error of 0.7 kcal/mol. For the cationic data set, the highest-level SAPT method, SAPT2+3-δMP2/aug-cc-pVQZ, outperforms the rest of the SAPT methods, with a MAE of 0.2 kcal/mol and a maximum error of 0.4 kcal/mol. For the ion-pair data set, the SAPT2+3-δMP2/aug-cc-pVTZ performs the best among all SAPT methods with a MAE of 0.3 kcal/mol and a maximum error of 0.9 kcal/mol. Overall, SAPT2+3-δMP2/aug-cc-pVTZ affords a small and balanced MAE (<0.5 kcal/mol) for all three data sets, with an overall MAE of 0.4 kcal/mol. Despite the breakdown of perturbation theory for ionic systems at short-range, SAPT can still be saved given two corrections: a "δHF" correction, which requires a supermolecular Hartree-Fock calculation to incorporate polarization effects beyond second order, and a "δMP2" correction, which requires a supermolecular MP2 calculation to account for higher

  12. Production of Protonated Methanol Ions Via Intermolecular Reactions within Van der Waals Clusters of Dime Dimethyl Ether. Revision

    DTIC Science & Technology

    1990-02-02

    preparation (17) This result also suggests that the protonated methanol ion is not produced via a reaction between the DME cluster and a water impurity. In...include Security Classification) Production ol Protonated Methanol Ions via "Intermolecular" Reactions within van der Waals Clusters of Dimethyl Ether...2/90 Production of Protonated Methanol Ions via "Intermolecular" Reactions within van der Waals Clusters of Dimethyl Ether M. Todd Coolbaugh, William

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

    DOE PAGES

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

    2015-02-19

    Modulation of intermolecular interactions in response to external electric fields could be fundamental to the formation of unusual forms of water, such as water whiskers. However, a detailed understanding of the nature of intermolecular interactions in such systems is lacking. In this study, we present novel theoretical results based on electron correlation calculations regarding the nature of H-bonds in water whiskers, which is revealed by studying their evolution under external electric fields with various field strengths. We find that the water whiskers consisting of 2-7 water molecules all have a chain-length dependent critical electric field. Under the critical electric field,more » the most compact chain structures are obtained, featuring very strong H-bonds, herein referred to as covalent H-bonds. In the case of a water dimer whisker, the bond length of the novel covalent H-bond shortens by 25%, the covalent bond order increases by 9 times, and accordingly the H-bond energy is strengthened by 5 times compared to the normal H-bond in a (H2O)2 cluster. Below the critical electric field, it is observed that with increasing field strength, H-bonding orbitals display gradual evolutions in the orbital energy, orbital ordering, and orbital nature (i.e., from typical -style orbital to unusual -style double H-bonding orbital). We also show that beyond the critical electric field, a single water whisker may disintegrate to form a loosely bound zwitterionic chain due to a relay-style proton transfer, whereas two water whiskers may undergo intermolecular cross-linking to form a quasi-two-dimensional water network. In conclusion, these results help shed new insight on the effects of electric fields on water whisker formation.« less

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

    SciTech Connect

    Bai, Yang; He, Hui-Min; Li, Ying; Zhou, Zhong-Jun; Wang, Jia-Jun; Wu, Di; Chen, Wei; Gu, Feng-Long; Sumpter, Bobby G.; Huang, Jingsong

    2015-02-19

    Modulation of intermolecular interactions in response to external electric fields could be fundamental to the formation of unusual forms of water, such as water whiskers. However, a detailed understanding of the nature of intermolecular interactions in such systems is lacking. In this study, we present novel theoretical results based on electron correlation calculations regarding the nature of H-bonds in water whiskers, which is revealed by studying their evolution under external electric fields with various field strengths. We find that the water whiskers consisting of 2-7 water molecules all have a chain-length dependent critical electric field. Under the critical electric field, the most compact chain structures are obtained, featuring very strong H-bonds, herein referred to as covalent H-bonds. In the case of a water dimer whisker, the bond length of the novel covalent H-bond shortens by 25%, the covalent bond order increases by 9 times, and accordingly the H-bond energy is strengthened by 5 times compared to the normal H-bond in a (H2O)2 cluster. Below the critical electric field, it is observed that with increasing field strength, H-bonding orbitals display gradual evolutions in the orbital energy, orbital ordering, and orbital nature (i.e., from typical -style orbital to unusual -style double H-bonding orbital). We also show that beyond the critical electric field, a single water whisker may disintegrate to form a loosely bound zwitterionic chain due to a relay-style proton transfer, whereas two water whiskers may undergo intermolecular cross-linking to form a quasi-two-dimensional water network. In conclusion, these results help shed new insight on the effects of electric fields on water whisker formation.

  15. Modelling organic crystal structures using distributed multipole and polarizability-based model intermolecular potentials.

    PubMed

    Price, Sarah L; Leslie, Maurice; Welch, Gareth W A; Habgood, Matthew; Price, Louise S; Karamertzanis, Panagiotis G; Day, Graeme M

    2010-08-14

    Crystal structure prediction for organic molecules requires both the fast assessment of thousands to millions of crystal structures and the greatest possible accuracy in their relative energies. We describe a crystal lattice simulation program, DMACRYS, emphasizing the features that make it suitable for use in crystal structure prediction for pharmaceutical molecules using accurate anisotropic atom-atom model intermolecular potentials based on the theory of intermolecular forces. DMACRYS can optimize the lattice energy of a crystal, calculate the second derivative properties, and reduce the symmetry of the spacegroup to move away from a transition state. The calculated terahertz frequency k = 0 rigid-body lattice modes and elastic tensor can be used to estimate free energies. The program uses a distributed multipole electrostatic model (Q, t = 00,...,44s) for the electrostatic fields, and can use anisotropic atom-atom repulsion models, damped isotropic dispersion up to R(-10), as well as a range of empirically fitted isotropic exp-6 atom-atom models with different definitions of atomic types. A new feature is that an accurate model for the induction energy contribution to the lattice energy has been implemented that uses atomic anisotropic dipole polarizability models (alpha, t = (10,10)...(11c,11s)) to evaluate the changes in the molecular charge density induced by the electrostatic field within the crystal. It is demonstrated, using the four polymorphs of the pharmaceutical carbamazepine C(15)H(12)N(2)O, that whilst reproducing crystal structures is relatively easy, calculating the polymorphic energy differences to the accuracy of a few kJ mol(-1) required for applications is very demanding of assumptions made in the modelling. Thus DMACRYS enables the comparison of both known and hypothetical crystal structures as an aid to the development of pharmaceuticals and other speciality organic materials, and provides a tool to develop the modelling of the

  16. Multiple intermolecular bend vibrational excitation of a hydrogen bond: An extended infrared study of OCOHF

    NASA Astrophysics Data System (ADS)

    Nesbitt, David J.; Lovejoy, Christopher M.

    1990-12-01

    We report the use of near infrared tunable difference frequency laser absorption methods to investigate low-frequency bending of the intermolecular hydrogen bond in OCOHF complexes. By deliberate thermal warming of the slit jet expansion to 16 K, we observe bending ``hot band'' transitions built on the fundamental vHF=1←0 HF stretch from the lowest five internally excited bending states (i.e., vlbend=00←00, 11←11, 20←20, 22←22, and 31←31) which correspond to low-frequency, skeletal bending of the intermolecular hydrogen bond. In addition, much weaker parallel (Δl=0) combination band transitions (vlbend=20←00 and 31←11 ) are observed at ≲5% of the 00←00 intensity. Furthermore, measurements of the extremely weak 11←00 perpendicular (Δl=1) band are obtained at ≲1% of the 00←00 intensity. The fundamental, hot band, and combination band data permit quantitative measurement of the absolute vibrational energies of all vibrational levels for the l=0 and 1 manifolds in both HF excited (vHF=1) and ground-state (vHF=0) complexes. The bending frequencies are surprisingly low (˜10 cm-1 ) and exhibit positive anharmonicity (i.e., the energy level spacings increase with vlbend ). The results suggest nearly unrestricted bending of the hydrogen bond in a very flat, highly anharmonic angular potential. In contrast with many other weakly bound complexes, the lowest bending frequency decreases dramatically upon HF excitation, which signals a vHF vibrationally induced shift from a linear to a nonlinear equilibrium geometry for the vHF=1 excited OCOHF potential surface. Excess Lorentzian line widths are observed in all OCOHF transitions, attributable to vibrational predissociation lifetimes that vary smoothly from 1.2 ns (vlbend=00) to 650 ps (vlbend=31) as a function of intermolecular bending excitation.

  17. N-heterocyclic carbene catalyzed asymmetric intermolecular Stetter reaction: origin of enantioselectivity and role of counterions.

    PubMed

    Kuniyil, Rositha; Sunoj, Raghavan B

    2013-10-04

    The mechanism and the role of KOtBu in an enantioselective NHC-catalyzed Stetter reaction between p-chlorobenzaldehyde and N-acylamido acrylate is established using DFT(M06-2X) methods. The Gibbs free energies are found to be significantly lower for transition states with explicit bound KOtBu as compared to the conventional pathways without the counterions. An intermolecular proton transfer from HOtBu to the prochiral carbon is identified as the stereocontrolling step. The computed enantioselectivities are in excellent agreement with the experimental results.

  18. Correlated and cooperative motions in segmental relaxation: Influence of constitutive unit weight and intermolecular interactions

    NASA Astrophysics Data System (ADS)

    Rijal, Bidur; Soto Puente, Jorge Arturo; Atawa, Bienvenu; Delbreilh, Laurent; Fatyeyeva, Kateryna; Saiter, Allisson; Dargent, Eric

    2016-12-01

    This work clarifies the notion of correlated and cooperative motions appearing during the α-relaxation process through the role of the molecular weight of the constitutive units and of the interchain dipolar interactions. By studying amorphous copolymers of poly(ethylene-co-vinyl acetate) with different vinyl acetate contents, we show that the correlated motions are not sensitive to the interchain dipolar interactions, in contrast to the cooperative motions, which increase with a strengthening of the intermolecular interactions for this sample family. Concerning the influence of the molecular weight m0, the notion of "correlated motions" seems to be equivalent to the notion of "cooperative motions" only for low m0 systems.

  19. Dielectric spectroscopy investigation of ion-containing and intermolecular hydrogen-bonded polymer systems

    NASA Astrophysics Data System (ADS)

    Atorngitjawat, Pornpen

    Ion-containing and intermolecular hydrogen-bonded polymers are used widely in a variety of industrial and commercial applications, from food packaging to battery electrolytes to pharmaceuticals. Yet the dynamics of these polymers, which are both complex and important to the application, are poorly understood. This thesis provides the first systematic study of the dynamics of several ion-containing and intermolecular hydrogen-bonded polymers by broadband dielectric relaxation spectroscopy. The systems under consideration include sulfonated polystyrene (SPS) in acid (SPS-H) and neutralized forms, and mixtures of poly(2-vinylpyridine) (P2VPy) with lithium perchlorate (LiClO4) and low molecular weight phenolic molecules. Dynamic mechanical analysis, Fourier transform infrared spectroscopy, differential scanning calorimetry, small-angle X-ray scattering and wide-angle X-ray diffraction were employed in a complementary role. Multiple relaxations were generally observed at high temperatures. For SPS ionomers, the segmental process, Maxwell-Wagner-Sillars interfacial polarization, and electrode polarization were detected. Three relaxations were also found in spectra of SPS-H, attributed to the segmental process, hydrogen bond association/dissociation, and electrode polarization. Three dielectric relaxations above the segmental process were observed for P2VPy-LiClO4 mixtures: ion-mode relaxation, slow hindered segmental relaxation and electrode polarization. However, only electrode polarization was observed above the segmental relaxation for all P2VPy--small phenolic molecule mixtures, except P2VPy + 10 mol% 2,3,3,4,4,5-hexahydroxybenzophenone. This mixture exhibited an additional relaxation due to Maxwell-Wagner-Sillars interfacial polarization, arising from the existence of phase-separated complexes within the P2VPy matrix. Sub-Tg local relaxations were suppressed by ionic intermolecular interactions for SPS ionomers and P2VPy-LiClO4 mixtures. Intermolecular hydrogen

  20. Direct measurement of the intermolecular forces confining a single molecule in an entangled polymer solution.

    PubMed

    Robertson, Rae M; Smith, Douglas E

    2007-09-21

    We use optical tweezers to directly measure the intermolecular forces acting on a single polymer imposed by surrounding entangled polymers (115 kbp DNA, 1 mg/ml). A tubelike confining field was measured in accord with the key assumption of reptation models. A time-dependent harmonic potential opposed transverse displacement, in accord with recent simulation findings. A tube radius of 0.8 microm was determined, close to the predicted value (0.5 microm). Three relaxation modes (approximately 0.4, 5, and 34 s) were measured following transverse displacement, consistent with predicted relaxation mechanisms.

  1. Profile of the intermolecular forces governing the interaction of drugs with mucin.

    PubMed

    Caron, Giulia; Visentin, Sonja; Pontremoli, Carlotta; Ermondi, Giuseppe

    2015-07-05

    The study highlights the balance of the intermolecular forces governing the interaction between drugs and mucin. The interaction strength is expressed as a retention factor k (data retrieved from the literature (Gargano et al., 2014)) obtained by a new bio-affinity chromatographic method in which the stationary phase is based on covalently immobilized mucin (porcine gastric mucin, PGM). A quantitative structure-property relationship (QSPR) between logk and 82 VolSurf+ descriptors was established and mechanistically interpreted. Results evidence that all blocks contribute similarly to the model; moreover, hydrogen bonding donor (HBD) properties of solutes favor the interaction with mucin; and thus, support their detrimental role on drug permeability.

  2. ORGANIC CHEMISTRY. Iron-catalyzed intermolecular [2+2] cycloadditions of unactivated alkenes.

    PubMed

    Hoyt, Jordan M; Schmidt, Valerie A; Tondreau, Aaron M; Chirik, Paul J

    2015-08-28

    Cycloadditions, such as the [4+2] Diels-Alder reaction to form six-membered rings, are among the most powerful and widely used methods in synthetic chemistry. The analogous [2+2] alkene cycloaddition to synthesize cyclobutanes is kinetically accessible by photochemical methods, but the substrate scope and functional group tolerance are limited. Here, we report iron-catalyzed intermolecular [2+2] cycloaddition of unactivated alkenes and cross cycloaddition of alkenes and dienes as regio- and stereoselective routes to cyclobutanes. Through rational ligand design, development of this base metal-catalyzed method expands the chemical space accessible from abundant hydrocarbon feedstocks.

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

    PubMed Central

    Okuom, Macduff O.; Wilson, Mark V.; Jackson, Abby; Holmes, Andrea E.

    2014-01-01

    DETECHIP has been used in testing analytes including caffeine, cocaine, and tetrahydrocannabinol (THC) from marijuana, as well as date rape and club drugs such as flunitrazepam, gamma-hydroxybutyric acid (GHB), and methamphetamine. This study investigates the intermolecular interaction between DETECHIP sensor eosin Y (DC1) and the analyte (caffeine) that is responsible for the fluorescence and color changes observed in the actual array. Using 1H-NMR, 1H-COSY, and 1H-DOSY NMR methods, a proton exchange from C-8 of caffeine to eosin Y is proposed. PMID:25018772

  4. New openings for porous systems research from intermolecular double-quantum NMR.

    PubMed

    Capuani, S; Alesiani, M; Branca, R T; Maraviglia, B

    2004-01-01

    It has been recently recognized that residual intermolecular double-quantum coherences (iDQcs) provide a novel contrast mechanism to study heterogeneity in liquid systems. This is of much interest in the field of the physics of matter and biomedicine. Nowadays, literature concerning the behaviour of the iDQc signal originated by highly heterogeneous systems such as fluids in porous media is scarce. In this paper, we report and discuss our principal results about iDQc signal behaviour in confined liquid systems (trabecular bone, travertine, porous standard systems) and also some new results obtained on doped water in glass capillary pipes.

  5. Vibrational Circular Dichroism (VCD) Reveals Subtle Conformational Aspects and Intermolecular Interactions in the Carnitine Family.

    PubMed

    Mazzeo, Giuseppe; Abbate, Sergio; Longhi, Giovanna; Castiglioni, Ettore; Villani, Claudio

    2015-12-01

    Vibrational circular dichroism spectra (VCD) in the mid-IR region and electronic circular dichroism (ECD) spectra for three carnitine derivatives in the form of hydrochloride salts were recorded in deuterated methanol solutions. Density Functional Theory calculations help one to understand the significance of the observed VCD bands. VCD and ECD spectra are informative about the absolute configuration of the molecule, but VCD data reveal also some conformational aspects in the N,N,N-trimethyl moiety and inform us about intermolecular interactions gained from the carbonyl stretching region for the acyl substituted carnitines.

  6. Catalytic Selenium-Promoted Intermolecular Friedel-Crafts Alkylation with Simple Alkenes.

    PubMed

    Tang, E; Zhao, Yinjiao; Li, Wen; Wang, Weilin; Zhang, Meng; Dai, Xin

    2016-03-04

    A method for conducting selenium-promoted intermolecular Friedel-Crafts (F-C) alkylation reactions has been developed with simple alkenes using trimethylsilyl trifluoromethanesulfonate as a catalyst and N-phenylselenophthalimide as an efficient selenium source. Electron-rich arenes smoothly underwent F-C alkylation with a variety of alkenes to afford alkylated products in good yield and with high regioselectivity and diastereoselectivity. The regioselectivity and stereoselectivity of arenes and alkenes as well as a preliminary mechanism of the F-C alkylation reaction are discussed.

  7. Catalytic intermolecular amination of C-H bonds: method development and mechanistic insights.

    PubMed

    Fiori, Kristin Williams; Du Bois, J

    2007-01-24

    Reaction methodology for intermolecular C-H amination of benzylic and 3 degrees C-H bonds is described. This process uses the starting alkane as the limiting reagent, gives optically pure tetrasubstituted amines through stereospecific insertion into enantiomeric 3 degrees centers, displays high chemoselectivity for benzylic oxidation, and enables the facile preparation of isotopically enriched 15N-labeled compounds. Access to substituted amines, amino alcohols, and diamines is thereby made possible in a single transformation. Important information relevant to understanding the initial steps in the catalytic cycle, reaction chemoselectivity, the nature of the active oxidant, and pathways for catalyst inactivation has been gained through mechanistic analysis; these studies are also presented.

  8. Character of intermolecular interaction in pyridine-argon complex: Ab initio potential energy surface, internal dynamics, and interrelations between SAPT energy components.

    PubMed

    Makarewicz, Jan; Shirkov, Leonid

    2016-05-28

    The pyridine-Ar (PAr) van der Waals (vdW) complex is studied using a high level ab initio method. Its structure, binding energy, and intermolecular vibrational states are determined from the analytical potential energy surface constructed from interaction energy (IE) values computed at the coupled cluster level of theory with single, double, and perturbatively included triple excitations with the augmented correlation consistent polarized valence double-ζ (aug-cc-pVDZ) basis set complemented by midbond functions. The structure of the complex at its global minimum with Ar at a distance of 3.509 Å from the pyridine plane and shifted by 0.218 Å from the center of mass towards nitrogen agrees well with the corresponding equilibrium structure derived previously from the rotational spectrum of PAr. The PAr binding energy De of 392 cm(-1) is close to that of 387 cm(-1) calculated earlier at the same ab initio level for the prototypical benzene-Ar (BAr) complex. However, under an extension of the basis set, De for PAr becomes slightly lower than De for BAr. The ab initio vdW vibrational energy levels allow us to estimate the reliability of the methods for the determination of the vdW fundamentals from the rotational spectra. To disclose the character of the intermolecular interaction in PAr, the symmetry-adapted perturbation theory (SAPT) is employed for the analysis of different physical contributions to IE. It is found that SAPT components of IE can be approximately expressed in the binding region by only two of them: the exchange repulsion and dispersion energy. The total induction effect is negligible. The interrelations between various SAPT components found for PAr are fulfilled for a few other complexes involving aromatic molecules and Ar or Ne, which indicates that they are valid for all rare gas (Rg) atoms and aromatics.

  9. Polarizable intermolecular potentials for water and benzene interacting with halide and metal ions

    PubMed Central

    Archambault, Fabien; Soteras, Ignacio; Luque, F. Javier; Schulten, Klaus

    2010-01-01

    A complete derivation of polarizable intermolecular potentials based on high-level, gas-phase quantum-mechanical calculations is proposed. The importance of appreciable accuracy together with inherent simplicity represents a significant endeavor when enhancement of existing force fields for biological systems is sought. Toward this end, symmetry-adapted perturbation theory (SAPT) can provide an expansion of the total interaction energy into physically meaningful e.g. electrostatic, induction and van der Waals terms. Each contribution can be readily compared with its counterpart in classical force fields. Since the complexity of the different intermolecular terms cannot be fully embraced using a minimalist description, it is necessary to resort to polyvalent expressions capable of encapsulating overlooked contributions from the quantum-mechanical expansion. This choice results in consistent force field components that reflect the underlying physical principles of the phenomena. This simplified potential energy function is detailed and definitive guidelines are drawn. As a proof of concept, the methodology is illustrated through a series of test cases that include the interaction of water and benzene with halide and metal ions. In each case considered, the total energy is reproduced accurately over a range of biologically relevant distances. PMID:21113276

  10. Role of intermolecular interaction in crystal packing: A competition between halogen bond and electrostatic interaction

    NASA Astrophysics Data System (ADS)

    Chen, Peng-Yuan; Zhang, Lin; Zhu, Shun-Guan; Cheng, Guang-Bin

    2017-03-01

    To investigate the competition between halogen bond and electrostatic interaction and their influence on the crystal packing, four novel solvates of 1,3,5-trichloro-2,4,6-trinitrobenzene (TCTNB) and 1,3,5-tribromo-2,4,6-trinitrobenzene (TBTNB) were synthesized while the intermolecular forces and the contribution of each interaction were analyzed quantitatively. The electrostatic interaction is the main link between TCTNB, TBTNB and 1,4-dioxane respectively, while π-π interaction dominates in these two solvates of TCTNB/1,4-dimethylbenzene (PX) and TCTNB/mesitylene. The solvate interaction changes and varieties were illuminated by Hirshfeld surface analysis, and the group contributions were illustrated respectively. Molecular electrostatic potential surface (MEPs) with density functional theory (DFT) calculation was performed to compare the relative strength of electrostatic interaction and halogen bond. The result shows that MEPs can be used as a descriptor for determining the most possible intermolecular interaction under certain circumstances. The study presented here may provide the guidance for the design and synthesis of the complex with desired properties.

  11. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics.

    PubMed

    Pyzer-Knapp, Edward O; Thompson, Hugh P G; Day, Graeme M

    2016-08-01

    We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%.

  12. Rattusin structure reveals a novel defensin scaffold formed by intermolecular disulfide exchanges

    PubMed Central

    Min, Hye Jung; Yun, Hyosuk; Ji, Sehyeon; Rajasekaran, Ganesan; Kim, Jae Il; Kim, Jeong-Sun; Shin, Song Yub; Lee, Chul Won

    2017-01-01

    Defensin peptides are essential for innate immunity in humans and other living systems, as they provide protection against infectious pathogens and regulate the immune response. Here, we report the solution structure of rattusin (RTSN), an α-defensin-related peptide, which revealed a novel C2-symmetric disulfide-linked dimeric structure. RTSN was synthesized by solid-phase peptide synthesis (SPPS) and refolded by air oxidation in vitro. Dimerization of the refolded RTSN (r-RTSN) resulted from five intermolecular disulfide (SS) bond exchanges formed by ten cysteines within two protomer chains. The SS bond pairings of r-RTSN were determined by mass analysis of peptide fragments cleaved by trypsin digestion. In addition to mass analysis, nuclear magnetic resonance (NMR) experiments for a C15S mutant and r-RTSN confirmed that the intermolecular SS bond structure of r-RTSN showed an I-V’, II-IV’, III-III’, IV-II’, V-I’ arrangement. The overall structure of r-RTSN exhibited a cylindrical array, similar to that of β-sandwich folds, with a highly basic surface. Furthermore, fluorescence spectroscopy results suggest that r-RTSN exerts bactericidal activity by damaging membrane integrity. Collectively, these results provide a novel structural scaffold for designing highly potent peptide-based antibiotics suitable for use under various physiological conditions. PMID:28345637

  13. Intermolecular Forces as a Key to Understanding the Environmental Fate of Organic Xenobiotics

    NASA Astrophysics Data System (ADS)

    Casey, Ryan E.; Pittman, Faith A.

    2005-02-01

    Environmental education for undergraduate nonscience majors and high school students is key in fostering an increased understanding of environmental issues among the general public. We have developed an environmental chemistry module that can be used in high schools or undergraduate nonscience courses to relate chemical structures and properties to the macroscopic behavior of environmentally relevant organic chemicals like pesticides, PCBs, and solvents. The module introduces the concepts of intermolecular forces, polarity, and partitioning to explain complex phenomena such as environmental transport and biomagnification of xenobiotics (human-made chemicals). The level 1 version 2.11 model, developed by Trent University, is used in a laboratory segment that allows students to explore the relationship between chemical properties and environmental distribution. The initial material on polarity and intermolecular forces can lead to additional applications, including: bioaccumulation and biomagnification of organic chemicals; toxicology or pharmacology (ability of molecules to cross membranes); and groundwater contamination. This module can enhance chemistry courses by presenting detailed applications and allowing students to make powerful, verifiable predictions. See Featured Molecules .

  14. Glass-Forming Tendency of Molecular Liquids and the Strength of the Intermolecular Attractions

    PubMed Central

    Koperwas, Kajetan; Adrjanowicz, Karolina; Wojnarowska, Zaneta; Jedrzejowska, Agnieszka; Knapik, Justyna; Paluch, Marian

    2016-01-01

    When we cool down a liquid below the melting temperature, it can either crystallize or become supercooled, and then form a disordered solid called glass. Understanding what makes a liquid to crystallize readily in one case and form a stable glass in another is a fundamental problem in science and technology. Here we show that the crystallization/glass-forming tendencies of the molecular liquids might be correlated with the strength of the intermolecular attractions, as determined from the combined experimental and computer simulation studies. We use van der Waals bonded propylene carbonate and its less polar structural analog 3-methyl-cyclopentanone to show that the enhancement of the dipole-dipole forces brings about the better glass-forming ability of the sample when cooling from the melt. Our finding was rationalized by the mismatch between the optimal temperature range for the nucleation and crystal growth, as obtained for a modeled Lennard-Jones system with explicitly enhanced or weakened attractive part of the intermolecular 6–12 potential. PMID:27883011

  15. Intermolecular hydrogen bonding in chlorine dioxide photochemistry: A time-resolved resonance Raman study

    NASA Astrophysics Data System (ADS)

    Philpott, Matthew P.; Hayes, Sophia C.; Thomsen, Carsten L.; Reid, Philip J.

    2001-01-01

    The geminate-recombination and vibrational-relaxation dynamics of chlorine dioxide (OClO) dissolved in ethanol and 2,2,2-trifluoroethanol (TFE) are investigated using time-resolved resonance Raman spectroscopy. Stokes spectra are measured as a function of time following photoexcitation using degenerate pump and probe wavelengths of 398 nm. For OClO dissolved in ethanol, subpicosecond geminate recombination occurs resulting in the reformation of ground-state OClO with a quantum yield of 0.5±0.1. Following recombination, intermolecular-vibrational relaxation of OClO occurs with a time constant of 31±10 ps. For OClO dissolved in TFE, recombination occurs with a time constant of 1.8±0.8 ps and a quantum yield of only 0.3±0.1. The intermolecular-vibrational-relaxation time constant of OClO in TFE is 79±27 ps. The reduced geminate-recombination quantum yield, delayed recombination, and slower vibrational relaxation for OClO in TFE is interpreted in terms of greater self-association of the solvent. Degenerate pump-probe experiments are also presented that demonstrate decay of the Cl-solvent charge-transfer complex on the ˜1-ns time scale in ethanol and TFE. This time is significantly longer than the abstraction times observed for other systems demonstrating that Cl hydrogen abstraction from alcohols occurs in the presence of a significant energy barrier.

  16. Probing the contribution of different intermolecular forces to the adsorption of spheroproteins onto hydrophilic surfaces.

    PubMed

    Borges, João; Campiña, José M; Silva, A Fernando

    2013-12-27

    Protein adsorption is a delicate process, which results from the balance between the properties of proteins and their solid supports. Although the relevance of some of these parameters has been already unveiled, the precise involvement of electrostatics and other weaker intermolecular forces requires further comprehension. Aiming to contribute to this task, this work explores the attachment, rearrangement, and surface aggregation of a model spheroprotein, such as bovine β-lactoglobulin (β-LG), onto hydrophilic substrates prefunctionalized with different alkylthiol films. Thereby, a variety of electrostatic scenarios for the adsorption of β-LG could be recreated through the variation of the pH and the functional chemistry of the surfaces. The changes in surface mass density (plus associated water) and film flexibility were followed in situ with quartz crystal microbalance with dissipation monitoring. Film packing and aggregation were assessed by faradaic electrochemical measurements and ex situ atomic force microscopy and field effect scanning electron microscopy. In contrast to previous hypotheses arguing that electrostatic interactions between charged substrates and proteins would be the only driving force, a complex interplay between Coulombic and non-Coulombic intermolecular forces (which would depend upon the experimental conditions) has been suggested to explain the results.

  17. Conformational diversity in prion protein variants influences intermolecular [beta]-sheet formation

    SciTech Connect

    Lee, Seungjoo; Antony, Lizamma; Hartmann, Rune; Knaus, Karen J.; Surewicz, Krystyna; Surewicz, Witold K.; Yee, Vivien C.

    2010-04-19

    A conformational transition of normal cellular prion protein (PrP{sup C}) to its pathogenic form (PrP{sup Sc}) is believed to be a central event in the transmission of the devastating neurological diseases known as spongiform encephalopathies. The common methionine/valine polymorphism at residue 129 in the PrP influences disease susceptibility and phenotype. We report here seven crystal structures of human PrP variants: three of wild-type (WT) PrP containing V129, and four of the familial variants D178N and F198S, containing either M129 or V129. Comparison of these structures with each other and with previously published WT PrP structures containing M129 revealed that only WT PrPs were found to crystallize as domain-swapped dimers or closed monomers; the four mutant PrPs crystallized as non-swapped dimers. Three of the four mutant PrPs aligned to form intermolecular {beta}-sheets. Several regions of structural variability were identified, and analysis of their conformations provides an explanation for the structural features, which can influence the formation and conformation of intermolecular {beta}-sheets involving the M/V129 polymorphic residue.

  18. Five intermolecular vibrations of the CO2 dimer observed via infrared combination bands.

    PubMed

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

    2016-11-07

    The weakly bound van der Waals dimer (CO2)2 has long been of considerable theoretical and experimental interest. Here, we study its low frequency intermolecular vibrations by means of combination bands in the region of the CO2 monomer ν3 fundamental (≈2350 cm(-1)), which are observed using a tunable infrared laser to probe a pulsed supersonic slit jet expansion. With the help of a recent high level ab initio calculation by Wang, Carrington, and Dawes, four intermolecular frequencies are assigned: the in-plane disrotatory bend (22.26 cm(-1)); the out-of-plane torsion (23.24 cm(-1)); twice the disrotatory bend (31.51 cm(-1)); and the in-plane conrotatory bend (92.25 cm(-1)). The disrotatory bend and torsion, separated by only 0.98 cm(-1), are strongly mixed by Coriolis interactions. The disrotatory bend overtone is well behaved, but the conrotatory bend is highly perturbed and could not be well fitted. The latter perturbations could be due to tunneling effects, which have not previously been observed experimentally for CO2 dimer. A fifth combination band, located 1.3 cm(-1) below the conrotatory bend, remains unassigned.

  19. Foot-and-mouth disease virus leader proteinase: structural insights into the mechanism of intermolecular cleavage.

    PubMed

    Steinberger, Jutta; Grishkovskaya, Irina; Cencic, Regina; Juliano, Luiz; Juliano, Maria A; Skern, Tim

    2014-11-01

    Translation of foot-and-mouth disease virus RNA initiates at one of two start codons leading to the synthesis of two forms of leader proteinase L(pro) (Lab(pro) and Lb(pro)). These forms free themselves from the viral polyprotein by intra- and intermolecular self-processing and subsequently cleave the cellular eukaryotic initiation factor (eIF) 4 G. During infection, Lb(pro) removes six residues from its own C-terminus, generating sLb(pro). We present the structure of sLb(pro) bound to the inhibitor E64-R-P-NH2, illustrating how sLb(pro) can cleave between Lys/Gly and Gly/Arg pairs. In intermolecular cleavage on polyprotein substrates, Lb(pro) was unaffected by P1 or P1' substitutions and processed a substrate containing nine eIF4GI cleavage site residues whereas sLb(pro) failed to cleave the eIF4GI containing substrate and cleaved appreciably more slowly on mutated substrates. Introduction of 70 eIF4GI residues bearing the Lb(pro) binding site restored cleavage. These data imply that Lb(pro) and sLb(pro) may have different functions in infected cells.

  20. Glass-Forming Tendency of Molecular Liquids and the Strength of the Intermolecular Attractions

    NASA Astrophysics Data System (ADS)

    Koperwas, Kajetan; Adrjanowicz, Karolina; Wojnarowska, Zaneta; Jedrzejowska, Agnieszka; Knapik, Justyna; Paluch, Marian

    2016-11-01

    When we cool down a liquid below the melting temperature, it can either crystallize or become supercooled, and then form a disordered solid called glass. Understanding what makes a liquid to crystallize readily in one case and form a stable glass in another is a fundamental problem in science and technology. Here we show that the crystallization/glass-forming tendencies of the molecular liquids might be correlated with the strength of the intermolecular attractions, as determined from the combined experimental and computer simulation studies. We use van der Waals bonded propylene carbonate and its less polar structural analog 3-methyl-cyclopentanone to show that the enhancement of the dipole-dipole forces brings about the better glass-forming ability of the sample when cooling from the melt. Our finding was rationalized by the mismatch between the optimal temperature range for the nucleation and crystal growth, as obtained for a modeled Lennard-Jones system with explicitly enhanced or weakened attractive part of the intermolecular 6–12 potential.

  1. Curcumin amorphous solid dispersions: the influence of intra and intermolecular bonding on physical stability.

    PubMed

    Wegiel, Lindsay A; Zhao, Yuhong; Mauer, Lisa J; Edgar, Kevin J; Taylor, Lynne S

    2014-12-01

    We have investigated the physical stability of amorphous curcumin dispersions and the role of curcumin-polymer intermolecular interactions in delaying crystallization. Curcumin is an interesting model compound as it forms both intra and intermolecular hydrogen bonds in the crystal. A structurally diverse set of amorphous dispersion polymers was investigated; poly(vinylpyrrolidone), Eudragit E100, carboxymethyl cellulose acetate butyrate, hydroxypropyl methyl cellulose (HPMC) and HPMC-acetate succinate. Mid-infrared spectroscopy was used to determine and quantify the extent of curcumin-polymer interactions. Physical stability under different environmental conditions was monitored by powder X-ray diffraction. Curcumin chemical stability was monitored by UV-Vis spectroscopy. Isolation of stable amorphous curcumin was difficult in the absence of polymers. Polymers proved to be effective curcumin crystallization inhibitors enabling the production of amorphous solid dispersions; however, the polymers showed very different abilities to inhibit crystallization during long-term storage. Curcumin intramolecular hydrogen bonding reduced the extent of its hydrogen bonding with polymers; hence most polymers were not highly effective crystallization inhibitors. Overall, polymers proved to be crystallization inhibitors, but inhibition was limited due to the intramolecular hydrogen bonding in curcumin, which leads to a decrease in the ability of the polymers to interact at a molecular level.

  2. Energy relaxation of intermolecular motions in supercooled water and ice: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Yagasaki, Takuma; Saito, Shinji

    2011-12-01

    We investigate the energy relaxation of intermolecular motions in liquid water at temperatures ranging from 220 K to 300 K and in ice at 220 K using molecular dynamics simulations. We employ the recently developed frequency resolved transient kinetic energy analysis, which provides detailed information on energy relaxation in condensed phases like two-color pump-probe spectroscopy. It is shown that the energy cascading in liquid water is characterized by four processes. The temperature dependences of the earlier three processes, the rotational-rotational, rotational-translational, and translational-translational energy transfers, are explained in terms of the density of states of the intermolecular motions. The last process is the slow energy transfer arising from the transitions between potential energy basins caused by the excitation of the low frequency translational motion. This process is absent in ice because the hydrogen bond network rearrangement, which accompanies the interbasin transitions in liquid water, cannot take place in the solid phase. We find that the last process in supercooled water is well approximated by a stretched exponential function. The stretching parameter, β, decreases from 1 to 0.72 with decreasing temperature. This result indicates that the dynamics of liquid water becomes heterogeneous at lower temperatures.

  3. Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of 4-chlorobenzothioamide

    NASA Astrophysics Data System (ADS)

    Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

    2013-09-01

    In the present work, the experimental and theoretical vibrational spectra of 4-chlorobenzothioamide were investigated. The FT-IR (400-4000 cm-1) and μ-Raman spectra (100-4000 cm-1) of 4-chlorobenzothioamide in the solid phase were recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared and Raman intensities of the title molecule in the ground state were calculated using ab initio Hartree-Fock and density functional theory (B3LYP) methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and the theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 4-chlorobenzothioamide was also simulated to evaluate the effect of intermolecular hydrogen bonding on the vibrational frequencies. It was observed that the Nsbnd H stretching modes shifted to lower frequencies, while the in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular Nsbnd H⋯S hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.

  4. Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of 4-chlorobenzothioamide.

    PubMed

    Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

    2013-09-01

    In the present work, the experimental and theoretical vibrational spectra of 4-chlorobenzothioamide were investigated. The FT-IR (400-4000 cm(-1)) and μ-Raman spectra (100-4000 cm(-1)) of 4-chlorobenzothioamide in the solid phase were recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared and Raman intensities of the title molecule in the ground state were calculated using ab initio Hartree-Fock and density functional theory (B3LYP) methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and the theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 4-chlorobenzothioamide was also simulated to evaluate the effect of intermolecular hydrogen bonding on the vibrational frequencies. It was observed that the N-H stretching modes shifted to lower frequencies, while the in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular N-H···S hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.

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

    NASA Astrophysics Data System (ADS)

    Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

    2014-06-01

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

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

    PubMed

    Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

    2014-06-05

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

  7. Effect of the electronic structure of quinoline and its derivatives on the capacity for intermolecular interactions

    SciTech Connect

    Privalova, N.Yu.; Sokolova, I.V.

    1985-05-01

    Calculations of the ground and excited states of quinoline and its 20H-, 70H-, 7NH2-, 7N(CH3)2-, and 7N(C2H5)2- substituted derivatives were undertaken by the INDO method, and the effect of intramolecular proton transfer (IPT) on their electronic structure was studied. The proton-accepting capacity of the compounds for intermolecular interactions was estimated by the molecular electrostatic potential method. It was shown that the proton-accepting capacity with respect to intermolecular interactions increases during the tautomeric transformation of the enolic form of 2-OH-quinoline to its keto form. The change in the basicity of the two forms of the molecules is affected by the orbital nature, and the multiplicity of the state is also important for the keto form. Substitution by electron-donating groups leads to increase in the proton-accepting capacity of both forms of the compounds in the S0, S/sub */, and T/sub */ states.

  8. Validation of intermolecular transfer integral and bandwidth calculations for organic molecular materials.

    PubMed

    Huang, Jingsong; Kertesz, Miklos

    2005-06-15

    We present an interpretation of the intermolecular transfer integral that is independent from the origin of the energy scale allowing convergence studies of this important parameter of organic molecular materials. We present extensive numerical studies by using an ethylene pi dimer to investigate the dependence of transfer integrals on the level of theory and intermolecular packing. Transfer integrals obtained from semiempirical calculations differ substantially from one another and from ab initio results. The ab initio results are consistent across all the levels used including Hartree-Fock, outer valence Green's function, and various forms of density functional theory (DFT). Validation of transfer integrals and bandwidths is performed by comparing the calculated values with the experimental values of tetrathiafulvalene-tetracyanoquinodimethane (TTF-TCNQ), bis[1,2,5]thiadiazolo-p-quinobis(1,3-dithiole), (BTQBT) K-TCNQ, and hexagonal graphite. DFT in one of its presently popular forms, such as Perdew-Wang functionals (PW91), in combination with sufficient basis sets provides reliable transfer integrals, and therefore can serve as a basis for energy band calculations for soft organic materials with van der Waals gaps.

  9. Unravelling the origin of intermolecular interactions using absolutely localized molecular orbitals.

    PubMed

    Khaliullin, Rustam Z; Cobar, Erika A; Lochan, Rohini C; Bell, Alexis T; Head-Gordon, Martin

    2007-09-13

    An energy decomposition analysis (EDA) method is proposed to isolate physically relevant components of the total intermolecular interaction energies such as the contribution from interacting frozen monomer densities, the energy lowering due to polarization of the densities, and the further energy lowering due to charge-transfer effects. This method is conceptually similar to existing EDA methods such as Morokuma analysis but includes several important new features. The first is a fully self-consistent treatment of the energy lowering due to polarization, which is evaluated by a self-consistent field calculation in which the molecular orbital coefficients are constrained to be block-diagonal (absolutely localized) in the interacting molecules to prohibit charge transfer. The second new feature is the ability to separate forward and back-donation in the charge-transfer energy term using a perturbative approximation starting from the optimized block-diagonal reference. The newly proposed EDA method is used to understand the fundamental aspects of intermolecular interactions such as the degree of covalency in the hydrogen bonding in water and the contributions of forward and back-donation in synergic bonding in metal complexes. Additionally, it is demonstrated that this method can be used to identify the factors controlling the interaction of the molecular hydrogen with open metal centers in potential hydrogen storage materials and the interaction of methane with rhenium complexes.

  10. Symmetry-adapted perturbation theory calculation of the He-HF intermolecular potential energy surface

    NASA Astrophysics Data System (ADS)

    Moszynski, Robert; Wormer, Paul E. S.; Jeziorski, Bogumil; van der Avoird, Ad

    1994-08-01

    Symmetry-adapted perturbation theory has been applied to compute the HeHF intermolecular potential energy surface for three internuclear distances in the HF subunit. The interaction energy is found to be dominated by the first-order exchange contribution and by the dispersion energy (including the intramonomer correlation effects). However, smaller corrections as the electrostatics, induction, and second-order exchange are found to be nonnegligible, and the final shape of the potential results from a delicate balance of attractive and repulsive contributions due to the four fundamental intermolecular interactions: electrostatics, exchange, induction, and dispersion. For a broad range of He-HF configurations the theoretical potential agrees very well with the empirical potential of Lovejoy and Nesbitt [C. M. Lovejoy and D. J. Nesbitt, J. Chem. Phys. 93, 5387 (1990)], which was adjusted to reproduce the near-infrared spectrum of the complex. Our potential has a global minimum of ɛm=-39.68 cm-1 for the linear He-HF geometry at Rm=6.16 bohr, and a secondary minimum of ɛm=-36.13 cm-1 for the linear He-FH geometry at Rm=5.59 bohr. These values are in very good agreement with the corresponding empirical results: ɛm=-39.20 cm-1 and Rm=6.17 bohr for the global minimum, and ɛm=-35.12 cm-1 and Rm=5.67 bohr for the secondary minimum.

  11. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics

    PubMed Central

    Pyzer-Knapp, Edward O.; Thompson, Hugh P. G.; Day, Graeme M.

    2016-01-01

    We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%. PMID:27484370

  12. Pressure Effects on the Intermolecular Interaction Potential of Condensed Protein Solutions.

    PubMed

    Winter, Roland

    2015-01-01

    Knowledge of the intermolecular interaction potential of proteins as a function of their solution conditions is essential for understanding protein aggregation, crystallization, and the phase behavior of proteins in general. Here, we report on a combined small-angle X-ray scattering and liquid-state theoretical approach to study dense lysozyme solutions as a function of temperature and pressure, but also in the presence of salts and osmolytes of different nature. We show that the pressure-dependent interaction potential of lysozyme changes in a nonlinear fashion over a wide range of temperatures, salt and protein concentrations, indicating that changes of the bulk water structure mediate the pressure dependence of the intermolecular forces. We present also results on the effect of high hydrostatic pressure on the phase behavior of dense lysozyme solutions in the liquid-liquid phase-coexistence region. As also shown in this study, the application of pressure can be used to fine-tune the second virial coefficient of protein solutions, which can be used to control nucleation rates and hence protein crystallization, or to prevent protein aggregation. Moreover, these results are also important for understanding the hydration behavior of biological matter under extreme environmental conditions, and the high stability of dense protein solutions (as they occur intracellularly) in organisms thriving under hydrostatic pressure conditions such as in the deep sea, where pressures up to the 100 MPa-level are reached.

  13. Intermolecular Interactions and the Release Pattern of Electrospun Curcumin-Polyvinyl(pyrrolidone) Fiber.

    PubMed

    Rahma, Annisa; Munir, Muhammad Miftahul; Khairurrijal; Prasetyo, Anton; Suendo, Veinardi; Rachmawati, Heni

    2016-01-01

    An electrospun fiber of polyvinyl(pyrrolidone) (PVP)-Tween 20 (T20) with curcumin as the encapsulated drug has been developed. A study of intermolecular interactions was performed using Raman spectroscopy, Fourier transform infrared (FT-IR), differential scanning calorimetry (DSC), and X-ray diffraction (XRD). The Raman and FT-IR studies showed that curcumin preferrably interacted with T20 and altered PVP chain packing, as supported by XRD and physical stability data. The hydroxyl stretching band in PVP shifted to a lower wavenumber with higher intenstity in the presence of curcumin and PVP, indicating that hydrogen bond formation is more intense in a curcumin or curcumin-T20 containing fiber. The thermal pattern of the fiber did not indicate phase separation. The conversion of curcumin into an amorphous state was confirmed by XRD analysis. An in vitro release study in phosphate buffer pH 6.8 showed that intermolecular interactions between each material influenced the drug release rate. However, low porosity was found to limit the hydrogen bond-mediated release.

  14. Rh-Catalyzed Intermolecular Syn-Carboamination of Alkenes via a Transient Directing Group

    PubMed Central

    Piou, Tiffany; Rovis, Tomislav

    2015-01-01

    Alkenes are the most ubiquitous pro-chiral functional groups accessible to synthetic chemists. For this reason, difunctionalization reactions of alkenes are particularly important, as they can be used to access highly complex molecular architectures.1,2 Stereoselective oxidation reactions, including dihydroxylation, aminohydroxylation and halogenation reactions,3,4,5,6 are well-established methods for functionalizing alkenes. However, the intermolecular incorporation of both carbon- and nitrogen-based functionalities stereoselectively across an alkene has not been reported. In this manuscript, we describe the Rh(III)-catalyzed syn carboamination of alkenes initiated by a C–H activation event that uses enoxyphthalimides as the source of the carbon and the nitrogen functionalities. The reaction methodology allows for the stereospecific formation of one C–C and one C–N bond across an alkene in a fully intermolecular sense, which is unprecedented. The reaction design involves the in situ generation of a bidentate directing group and the use of a novel cyclopentadienyl ligand to control the reactivity of Rh(III). The results provide a new route to functionalized alkenes and are expected to lead to the more convergent and stereoselective assembly of amine-containing acyclic molecules. PMID:26503048

  15. Five intermolecular vibrations of the CO2 dimer observed via infrared combination bands

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

    The weakly bound van der Waals dimer (CO2)2 has long been of considerable theoretical and experimental interest. Here, we study its low frequency intermolecular vibrations by means of combination bands in the region of the CO2 monomer ν3 fundamental (≈2350 cm-1), which are observed using a tunable infrared laser to probe a pulsed supersonic slit jet expansion. With the help of a recent high level ab initio calculation by Wang, Carrington, and Dawes, four intermolecular frequencies are assigned: the in-plane disrotatory bend (22.26 cm-1); the out-of-plane torsion (23.24 cm-1); twice the disrotatory bend (31.51 cm-1); and the in-plane conrotatory bend (92.25 cm-1). The disrotatory bend and torsion, separated by only 0.98 cm-1, are strongly mixed by Coriolis interactions. The disrotatory bend overtone is well behaved, but the conrotatory bend is highly perturbed and could not be well fitted. The latter perturbations could be due to tunneling effects, which have not previously been observed experimentally for CO2 dimer. A fifth combination band, located 1.3 cm-1 below the conrotatory bend, remains unassigned.

  16. Intermolecular interaction studies of winter flounder antifreeze protein reveal the existence of thermally accessible binding state.

    PubMed

    Nguyen, Dat H; Colvin, Michael E; Yeh, Yin; Feeney, Robert E; Fink, William H

    2004-10-05

    The physical nature underlying intermolecular interactions between two rod-like winter flounder antifreeze protein (AFP) molecules and their implication for the mechanism of antifreeze function are examined in this work using molecular dynamics simulations, augmented with free energy calculations employing a continuum solvation model. The energetics for different modes of interactions of two AFP molecules is examined in both vacuum and aqueous phases along with the water distribution in the region encapsulated by two antiparallel AFP backbones. The results show that in a vacuum two AFP molecules intrinsically attract each other in the antiparallel fashion, where their complementary charge side chains face each other directly. In the aqueous environment, this attraction is counteracted by both screening and entropic effects. Therefore, two nearly energetically degenerate states, an aggregated state and a dissociated state, result as a new aspect of intermolecular interaction in the paradigm for the mechanism of action of AFP. The relevance of these findings to the mechanism of function of freezing inhibition in the context of our work on Antarctic cod antifreeze glycoprotein (Nguyen et al., Biophysical Journal, 2002, Vol. 82, pp. 2892-2905) is discussed.

  17. Problem-Based Learning in 9th Grade Chemistry Class: `Intermolecular Forces'

    NASA Astrophysics Data System (ADS)

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

    2008-05-01

    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 9th grade students were stratified by cognitive levels and then randomly assigned to experimental (PBL, 40 students) and control (lecture-style teaching, 38 students) groups. Following a preparatory lesson where activation and remediation of existing knowledge occur, a pre-test was given, and no significant difference was found between the two groups of students ( p > .05). After the instruction was completed, a post-test and also a questionnaire related to the quality of the problem, the teacher’s role and group functioning were administered. Results from the post-test of both groups ( p < .05) and questionnaire showed that PBL is affective on students’ achievement, remedying formation of alternate conceptions and also social skills.

  18. Quantitative determination of the lateral density and intermolecular correlation between proteins anchored on the membrane surfaces using grazing incidence small-angle X-ray scattering and grazing incidence X-ray fluorescence

    NASA Astrophysics Data System (ADS)

    Abuillan, Wasim; Vorobiev, Alexei; Hartel, Andreas; Jones, Nicola G.; Engstler, Markus; Tanaka, Motomu

    2012-11-01

    As a physical model of the surface of cells coated with densely packed, non-crystalline proteins coupled to lipid anchors, we functionalized the surface of phospholipid membranes by coupling of neutravidin to biotinylated lipid anchors. After the characterization of fine structures perpendicular to the plane of membrane using specular X-ray reflectivity, the same membrane was characterized by grazing incidence small angle X-ray scattering (GISAXS). Within the framework of distorted wave Born approximation and two-dimensional Percus-Yevick function, we can analyze the form and structure factors of the non-crystalline, membrane-anchored proteins for the first time. As a new experimental technique to quantify the surface density of proteins on the membrane surface, we utilized grazing incidence X-ray fluorescence (GIXF). Here, the mean intermolecular distance between proteins from the sulfur peak intensities can be calculated by applying Abelé's matrix formalism. The characteristic correlation distance between non-crystalline neutravidin obtained by the GISAXS analysis agrees well with the intermolecular distance calculated by GIXF, suggesting a large potential of the combination of GISAXS and GIXF in probing the lateral density and correlation of non-crystalline proteins displayed on the membrane surface.

  19. Quantitative determination of the lateral density and intermolecular correlation between proteins anchored on the membrane surfaces using grazing incidence small-angle X-ray scattering and grazing incidence X-ray fluorescence.

    PubMed

    Abuillan, Wasim; Vorobiev, Alexei; Hartel, Andreas; Jones, Nicola G; Engstler, Markus; Tanaka, Motomu

    2012-11-28

    As a physical model of the surface of cells coated with densely packed, non-crystalline proteins coupled to lipid anchors, we functionalized the surface of phospholipid membranes by coupling of neutravidin to biotinylated lipid anchors. After the characterization of fine structures perpendicular to the plane of membrane using specular X-ray reflectivity, the same membrane was characterized by grazing incidence small angle X-ray scattering (GISAXS). Within the framework of distorted wave Born approximation and two-dimensional Percus-Yevick function, we can analyze the form and structure factors of the non-crystalline, membrane-anchored proteins for the first time. As a new experimental technique to quantify the surface density of proteins on the membrane surface, we utilized grazing incidence X-ray fluorescence (GIXF). Here, the mean intermolecular distance between proteins from the sulfur peak intensities can be calculated by applying Abelé's matrix formalism. The characteristic correlation distance between non-crystalline neutravidin obtained by the GISAXS analysis agrees well with the intermolecular distance calculated by GIXF, suggesting a large potential of the combination of GISAXS and GIXF in probing the lateral density and correlation of non-crystalline proteins displayed on the membrane surface.

  20. Role of silver ions in destabilization of intermolecular adhesion forces measured by atomic force microscopy in Staphylococcus epidermidis biofilms.

    PubMed

    Chaw, K C; Manimaran, M; Tay, Francis E H

    2005-12-01

    In this paper, we report on the potential use of atomic force microscopy (AFM) as a tool to measure the intermolecular forces in biofilm structures and to study the effect of silver ions on sessile Staphylococcus epidermidis cell viability and stability. We propose a strategy of destabilizing the biofilm matrix by reducing the intermolecular forces within the extracellular polymeric substances (EPSs) using a low concentration (50 ppb) of silver ions. Our AFM studies on the intermolecular forces within the EPSs of S. epidermidis RP62A and S.epidermidis 1457 biofilms suggest that the silver ions can destabilize the biofilm matrix by binding to electron donor groups of the biological molecules. This leads to reductions in the number of binding sites for hydrogen bonds and electrostatic and hydrophobic interactions and, hence, the destabilization of the biofilm structure.

  1. Focal epithelial hyperplasia: Heck disease.

    PubMed

    Cohen, P R; Hebert, A A; Adler-Storthz, K

    1993-09-01

    Two sisters of Mexican ancestry had focal epithelial hyperplasia (FEH). The lesions on the oral mucosa of the older child were initially misinterpreted as representing sexual abuse. Microscopic evaluation of a hematoxylin and eosin-stained section from a lower lip papule demonstrated the histologic features of FEH. Although human papillomavirus (HPV) type 13 and HPV32 have been most consistently present in FEH lesions, types 6, 11, 13, and 32 were not detected in the paraffin-embedded tissue specimen of our patient using an in situ hybridization technique. The lesions persisted or recurred during management using destructive modalities; subsequently, they completely resolved spontaneously.

  2. CO2 Dimer: Four Intermolecular Modes Observed via Infrared Combination Bands

    NASA Astrophysics Data System (ADS)

    Norooz Oliaee, Jalal; Dehghany, Mehdi; Rezaei, Mojtaba; McKellar, Bob; Moazzen-Ahmadi, Nasser

    2016-06-01

    Study of the carbon dioxide dimer has a long history, but there is only one previous observation of an intermolecular vibration [1]. Here we analyze four new combination bands of (CO2)2 in the CO2 νb{3} region (˜2350 wn), observed using tunable infrared lasers and a pulsed slit-jet supersonic expansion. The previous combination band at 2382.2 wn was simple to assign [1]. A much more complicated band (˜2370 wn) turns out to involve two upper states, one at 2369.0 wn (Bu symmetry), and the other at 2370.0 wn (Au). The spectrum can be nicely fit by including the Coriolis interactions between these states. Another complicated band around 2443 wn also involves two nearby upper states which are highly perturbed in so-far unexplained ways (possibly related to tunneling shifts). With the help of new ab initio calculations [2], we assign the results as follows. The 2369.0 wn band is the combination of the forbidden Ag intramolecular fundamental (probably [1] at about 2346.76 wn) and the intermolecular geared bend (Bu). The 2370.0 wn band is the combination of the same Ag fundamental and the intermolecular torsion (Au). This gives about 22.3 and 23.2 wn for the geared bend and torsion. The previous 2382.2 wn band [1] is the allowed Bu fundamental (2350.771 wn) plus two quanta of the geared bend (Bu), giving 31.509 wn for this overtone. The highly perturbed 2442.7 wn band is the Bu fundamental plus the antigeared bend (Ag), giving about 91.9 wn for the antigeared bend. Finally, the perturbed 2442.1 wn band is due to an unknown combination of modes which gains intensity from the antigeared bend by a Fermi-type interaction. Calculated values [2] are: 20.64 (geared bend), 24.44 (torsion), 32.34 (geared bend overtone), and 92.30 wn (antigeared bend), in good agreement with experiment. \\vskip 0.2 truecm [1] M. Dehghany, A.R.W. McKellar, Mahin Afshari, and N. Moazzen-Ahmadi, Mol. Phys. 108, 2195 (2010). [2] X.-G. Wang, T. Carrington, Jr., and R. Dawes, private communication.

  3. Anharmonic and harmonic intermolecular vibrational modes of the DNA base pairs

    NASA Astrophysics Data System (ADS)

    Špirko, Vladimír; Šponer, Jiří; Hobza, Pavel

    1997-01-01

    Intermolecular vibrational modes of the H-bonded adenine…thymine Watson-Crick (AT) base pair were studied for the first time using multidimensional nonharmonic treatment. Relying on a Born-Oppenheimer-like separation of the fast and slow vibrational motions, the complete multidimensional vibrational problem is reduced to a six-dimensional subproblem in which all rearrangements between the pair fragments (i.e., adenine and thymine) can be described. Following the Hougen-Bunker-Johns approach and using appropriate vibrational coordinates, a nonrigid reference is defined which covers all motions on the low-lying part of the intermolecular potential surface and which facilitates the derivation of a suitable model Hamiltonian. The potential energy surface is determined at the ab initio Hartree-Fock level with minimal basis set (HF/MINI-1) and an analytic potential energy function is obtained by fitting to the ab initio data. This function is used to calculate vibrational energy levels and effective geometries within the framework of the model Hamiltonian, disregarding the role of the kinematic and potential (in-plane)-(out-of-plane) interactions. The calculations are in reasonable agreement with the normal coordinate analysis (harmonic treatment) thus indicating physical correctness of this standard approach for an approximate description of the lowest vibrational states of the AT base pair. In addition, to get a deeper insight, harmonic vibrational frequencies of the AT pair and 28 other base pairs are evaluated at the same and higher levels of theory [ab initio Hartree-Fock level with split-valence basis set (HF/6-31G**)]. The HF/MINI-1 and HF/6-31G** intermolecular harmonic vibrational frequencies differ by less than 30%. For all the base pairs, the buckle and propeller vibrational modes [for definition and nomenclature see R. E. Dickerson et al., EMBO J. 8, 1 (1989)] are the lowest ones, all being in the narrow interval (from 4 to 30 cm-1 in the harmonic

  4. Intermolecular Redox-Neutral Amine C-H Functionalization Induced by the Strong Boron Lewis Acid B(C6 F5 )3 in the Frustrated Lewis Pair Regime.

    PubMed

    Chen, Guo-Qiang; Kehr, Gerald; Daniliuc, Constantin G; Bursch, Markus; Grimme, Stefan; Erker, Gerhard

    2017-02-06

    N,N-Dimethylmesitylamine undergoes an intermolecular redox-neutral C-H activation/C-C coupling process upon treatment with dimethyl acetylenedicarboxylate and the strong boron Lewis acid B(C6 F5 )3 . Similarly, N,N-dimethylmesitylamine reacts with two molar equivalents of ethyl acrylate to give the respective unsaturated coupling product with H2 transfer to the acrylic ester to form the ethyl propionate/B(C6 F5 )3 adduct. N,N-Dimethylmesitylamine also undergoes a C-H activation at the benzylic ortho sp(3) -carbon atom with dihydrogen formation upon treatment with Piers' borane [HB(C6 F5 )2 ]. The last two reactions of N,N-dimethylmesitylamine were analyzed by DFT calculations.

  5. Helix coupling

    DOEpatents

    Ginell, William S.

    1989-04-25

    A coupling for connecting helix members in series, which consists of a pair of U-shaped elements, one of which is attached to each helix end with the "U" sections of the elements interlocked. The coupling is particularly beneficial for interconnecting helical Nitinol elements utilized in thermal actuators or engines. Each coupling half is attached to the associated helix at two points, thereby providing axial load while being easily removed from the helix, and reusable.

  6. Helix coupling

    DOEpatents

    Ginell, W.S.

    1982-03-17

    A coupling for connecting helix members in series, which consists of a pair of U-shaped elements, one of which is attached to each helix end with the U sections of the elements interlocked. The coupling is particularly beneficial for interconnecting helical Nitinol elements utilized in thermal actuators or engines. Each coupling half is attached to the associated helix at two points, thereby providing axial load while being easily removed from the helix, and reusable.

  7. Communication: Frequency shifts of an intramolecular hydrogen bond as a measure of intermolecular hydrogen bond strengths

    NASA Astrophysics Data System (ADS)

    Gu, Quanli; Trindle, Carl; Knee, J. L.

    2012-09-01

    Infrared-ultraviolet double resonance spectroscopy has been applied to study the infrared spectra of the supersonically cooled gas phase complexes of formic acid, acetic acid, propionic acid, formamide, and water with 9-hydroxy-9-fluorenecarboxylic acid (9HFCA), an analog of glycolic acid. In these complexes each binding partner to 9HFCA can function as both proton donor and acceptor. Relative to its frequency in free 9HFCA, the 9-hydroxy (9OH) stretch is blue shifted in complexes with formic, acetic, and propionic acids, but is red shifted in the complexes with formamide and water. Density functional calculations on complexes of 9HFCA to a variety of H bonding partners with differing proton donor and acceptor abilities reveal that the quantitative frequency shift of the 9OH can be attributed to the balance struck between two competing intermolecular H bonds. More extensive calculations on complexes of glycolic acid show excellent consistency with the experimental frequency shifts.

  8. Communication: Frequency shifts of an intramolecular hydrogen bond as a measure of intermolecular hydrogen bond strengths.

    PubMed

    Gu, Quanli; Trindle, Carl; Knee, J L

    2012-09-07

    Infrared-ultraviolet double resonance spectroscopy has been applied to study the infrared spectra of the supersonically cooled gas phase complexes of formic acid, acetic acid, propionic acid, formamide, and water with 9-hydroxy-9-fluorenecarboxylic acid (9HFCA), an analog of glycolic acid. In these complexes each binding partner to 9HFCA can function as both proton donor and acceptor. Relative to its frequency in free 9HFCA, the 9-hydroxy (9OH) stretch is blue shifted in complexes with formic, acetic, and propionic acids, but is red shifted in the complexes with formamide and water. Density functional calculations on complexes of 9HFCA to a variety of H bonding partners with differing proton donor and acceptor abilities reveal that the quantitative frequency shift of the 9OH can be attributed to the balance struck between two competing intermolecular H bonds. More extensive calculations on complexes of glycolic acid show excellent consistency with the experimental frequency shifts.

  9. Projectile containing metastable intermolecular composites and spot fire method of use

    DOEpatents

    Asay, Blaine W.; Son, Steven F.; Sanders, V. Eric; Foley, Timothy; Novak, Alan M.; Busse, James R.

    2012-07-31

    A method for altering the course of a conflagration involving firing a projectile comprising a powder mixture of oxidant powder and nanosized reductant powder at velocity sufficient for a violent reaction between the oxidant powder and the nanosized reductant powder upon impact of the projectile, and causing impact of the projectile at a location chosen to draw a main fire to a spot fire at such location and thereby change the course of the conflagration, whereby the air near the chosen location is heated to a temperature sufficient to cause a spot fire at such location. The invention also includes a projectile useful for such method and said mixture preferably comprises a metastable intermolecular composite.

  10. Intramolecular and intermolecular vibrational energy relaxation of CH 2I 2 dissolved in supercritical fluid

    NASA Astrophysics Data System (ADS)

    Sekiguchi, K.; Shimojima, A.; Kajimoto, O.

    2002-04-01

    A pump-probe experiment was performed to examine vibrational population relaxation of diiodomethane (CH 2I 2) molecule dissolved in supercritical CO 2. Using an apparatus with femtosecond time resolution, we observed the contributions of intramolecular vibrational energy redistribution (IVR) and intermolecular vibrational energy transfer (VET) separately. IVR and VET rates were measured with varying solvent densities at a constant temperature. It is shown that the IVR rate is not density dependent while the VET rate increases with increasing density from 0.4 to 0.8 g cm-3. This observation suggests that the rate of the VET process is determined by solute-solvent collisions whereas the IVR rate is not much affected by solute-solvent interaction.

  11. Cobalt-catalysed site-selective intra- and intermolecular dehydrogenative amination of unactivated sp3 carbons

    PubMed Central

    Wu, Xuesong; Yang, Ke; Zhao, Yan; Sun, Hao; Li, Guigen; Ge, Haibo

    2015-01-01

    Cobalt-catalysed sp2 C–H bond functionalization has attracted considerable attention in recent years because of the low cost of cobalt complexes and interesting modes of action in the process. In comparison, much less efforts have been devoted to the sp3 carbons. Here we report the cobalt-catalysed site-selective dehydrogenative cyclization of aliphatic amides via a C–H bond functionalization process on unactivated sp3 carbons with the assistance of a bidentate directing group. This method provides a straightforward synthesis of monocyclic and spiro β- or γ-lactams with good to excellent stereoselectivity and functional group tolerance. In addition, a new procedure has been developed to selectively remove the directing group, which enables the synthesis of free β- or γ-lactam compounds. Furthermore, the first cobalt-catalysed intermolecular dehydrogenative amination of unactivated sp3 carbons is also realized. PMID:25753366

  12. Graphene-enhanced intermolecular interaction at interface between copper- and cobalt-phthalocyanines

    SciTech Connect

    Dou, Wei-Dong; Huang, Shu-Ping; Lee, Chun-Sing

    2015-10-07

    Interfacial electronic structures of copper-phthalocyanine (CuPc), cobalt-phthalocyanine (CoPc), and graphene were investigated experimentally by using photoelectron spectroscopy. While the CuPc/graphene interface shows flat band structure and negligible interfacial dipole indicating quite weak molecule-substrate interaction, the CuPc/CoPc/graphene interface shows a large interfacial dipole and obvious energy level bending. Controlled experiments ruled out possible influences from the change in film structure of CuPc and pure π–π interaction between CoPc and CuPc. Analysis based on X-ray photoelectron spectroscopy and density functional theory reveals that the decrease in the work function for the CuPc/CoPc/graphene system is induced by the intermolecular interaction between CuPc and CoPc which is enhanced owning to the peculiar electronic properties at the CoPc-graphene interface.

  13. Numerical solution of the linearized Boltzmann equation for an arbitrary intermolecular potential

    SciTech Connect

    Sharipov, Felix Bertoldo, Guilherme

    2009-05-20

    A numerical procedure to solve the linearized Boltzmann equation with an arbitrary intermolecular potential by the discrete velocity method is elaborated. The equation is written in terms of the kernel, which contains the differential cross section and represents a singularity. As an example, the Lennard-Jones potential is used and the corresponding differential cross section is calculated and tabulated. Then, the kernel is calculated so that to overcome its singularity. Once, the kernel is known and stored it can be used for many kinds of gas flows. In order to test the method, the transport coefficients, i.e. thermal conductivity and viscosity for all noble gases, are calculated and compared with those obtained by the variational method using the Sonine polynomials expansion. The fine agreement between the results obtained by the two different methods shows the feasibility of application of the proposed technique to calculate rarefied gas flows over the whole range of the Knudsen number.

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

    SciTech Connect

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

    2015-06-28

    We present an analytical intermolecular potential energy surface (PES) for two rigid nitrous oxide (N{sub 2}O) molecules derived from high-level quantum-chemical ab initio calculations. Interaction energies for 2018 N{sub 2}O–N{sub 2}O configurations were computed utilizing the counterpoise-corrected supermolecular approach at the CCSD(T) level of theory using basis sets up to aug-cc-pVQZ supplemented with bond functions. A site-site potential function with seven sites per N{sub 2}O molecule was fitted to the pair interaction energies. We validated our PES by computing the second virial coefficient as well as shear viscosity and thermal conductivity in the dilute-gas limit. The values of these properties are substantiated by the best experimental data.

  15. Phase Competition and Superconductivity in κ-(BEDT-TTF)2X: Importance of Intermolecular Coulomb Interactions

    NASA Astrophysics Data System (ADS)

    Watanabe, Hiroshi; Seo, Hitoshi; Yunoki, Seiji

    2017-03-01

    We theoretically study the competition among different electronic phases in molecular conductors κ-(BEDT-TTF)2X. The ground-state properties of a 3/4-filled extended Hubbard model with the κ-type geometry are investigated by a variational Monte Carlo method. We find various competing phases: dimer-Mott insulator, polar charge-ordered insulator, 3-fold charge-ordered metal, and superconductivity, whose pairing symmetry is an "extended-s + dx2 - y2"-wave type. Our results show that the superconducting phase is stabilized not on the verge of the Mott metal-insulator transition but near charge order instabilities, clearly indicating the importance of the intradimer charge degree of freedom and the intermolecular Coulomb interactions, beyond the simple description of the half-filled Hubbard model.

  16. Graphene-enhanced intermolecular interaction at interface between copper- and cobalt-phthalocyanines.

    PubMed

    Dou, Wei-Dong; Huang, Shu-Ping; Lee, Chun-Sing

    2015-10-07

    Interfacial electronic structures of copper-phthalocyanine (CuPc), cobalt-phthalocyanine (CoPc), and graphene were investigated experimentally by using photoelectron spectroscopy. While the CuPc/graphene interface shows flat band structure and negligible interfacial dipole indicating quite weak molecule-substrate interaction, the CuPc/CoPc/graphene interface shows a large interfacial dipole and obvious energy level bending. Controlled experiments ruled out possible influences from the change in film structure of CuPc and pure π-π interaction between CoPc and CuPc. Analysis based on X-ray photoelectron spectroscopy and density functional theory reveals that the decrease in the work function for the CuPc/CoPc/graphene system is induced by the intermolecular interaction between CuPc and CoPc which is enhanced owning to the peculiar electronic properties at the CoPc-graphene interface.

  17. Generation of the SCF3 Radical by Photoredox Catalysis: Intra- and Intermolecular Carbotrifluoromethylthiolation of Alkenes.

    PubMed

    Dagousset, Guillaume; Simon, Cédric; Anselmi, Elsa; Tuccio, Béatrice; Billard, Thierry; Magnier, Emmanuel

    2017-02-17

    We report herein the first use of N-trifluoromethylthiosaccharin as the source of SCF3 radical under photoredox catalysis. This allowed an efficient and general visible-light-mediated carbotrifluoromethylthiolation of alkenes. Under the optimized conditions using fac-Ir(ppy)3 as the photocatalyst, various N-aryl acrylamides as well as a wide range of substituted styrenes can readily be difunctionalized in an intra- or intermolecular fashion, affording the corresponding SCF3-containing products in good to excellent yield. Importantly, the formation of this SCF3 radical along with other key radical intermediates was unambiguously demonstrated thanks to spin trapping/electron paramagnetic resonance (ST/EPR) experiments, which enabled a clear understanding of the reaction mechanism.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  19. Role of long-range intermolecular forces in the formation of inorganic nanoparticle clusters.

    PubMed

    Gibbs, G V; Crawford, T D; Wallace, A F; Cox, D F; Parrish, R M; Hohenstein, E G; Sherrill, C D

    2011-11-17

    An understanding of the role played by intermolecular forces in terms of the electron density distribution is fundamental to the understanding of the self-assembly of molecules in the formation of a molecular crystal. Using ab initio methods capable of describing both short-range intramolecular interactions and long-range London dispersion interactions arising from electron correlation, analyses of inorganic dimers of As(4)S(4) and As(4)O(6) molecules cut from the structures of realgar and arsenolite, respectively, reveal that the molecules adopt a configuration that closely matches that observed for the crystal. Decomposition of the interaction energies using symmetry-adapted perturbation theory reveals that both model dimers feature significant stabilization from electrostatic forces as anticipated by a Lewis acid/Lewis base picture of the interaction. London dispersion forces also contribute significantly to the interaction, although they play a greater role in the realgar structure near equilibrium than in arsenolite.

  20. Intermolecular forces in bovine serum albumin solutions exhibiting solidlike mechanical behaviors.

    PubMed

    Ikeda, S; Nishinari, K

    2000-01-01

    Mechanical properties of bovine serum albumin (BSA) solutions were analyzed to gain information on intermolecular forces that stabilize the system under normal physiological conditions. BSA solutions showed unexpectedly large zero shear viscosity values under steady shear flows but responded like solids to sinusoidal linear strains: the storage shear moduli were always larger than the loss shear moduli in the frequency range 1-100 rad/s. These results suggest that BSA solutions are so-called colloidal crystals in which colloidal particles are ordered in an array due to strong repulsive forces among particles. However, the pair potential between BSA molecules predicted based on the conventional Derjaguin-Landau-Verwey-Overbeek theory failed to explain these remarkable mechanical properties of BSA solutions. Additional repulsive forces other than electrostatic must be introduced to explain stability of BSA aqueous dispersions.

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  2. Study on the effects of intermolecular interactions on firefly multicolor bioluminescence.

    PubMed

    da Silva, Luís Pinto; da Silva, Joaquim C G Esteves

    2011-11-18

    Firefly luciferase exhibits a color-tuning mechanism based on pH-induced changes in the structure of the active site. These changes increase the polarity of the active site, and thus modulate the intermolecular interactions between the light emitter and active site molecules. In this study, the effects exerted by adenosine monophosphate (AMP), water molecules, and amino acids of Luciola cruciata luciferase active site on the emission wavelength of oxyluciferin were assessed by TD-DFT calculations. The redshift results mainly from decreased interaction of oxyluciferin with AMP and increased interaction of the emitter with a water molecule and Phe249. Breaking of a hydrogen bond between the benzothiazole oxygen atom with formation of a similar bond to the thiazolone oxygen atom is also instrumental.

  3. Intermolecular hydrogen bonded and self-assembled β-pleated sheet structures of β-sulfidocarbonyls

    NASA Astrophysics Data System (ADS)

    Hussain, Sahid; Das, Gopal; Chaudhuri, Mihir K.

    2007-06-01

    The three crystal structures of β-sulfidocarbonyls 1, 2 and 3 synthesized from the reaction of acryl amide with cystiene, 1,2-dithiol and 1,3-dithiols, respectively, in water catalyzed by borax, have been determined at 273 K. The characteristic features of the structures are self-assembly through intermolecular hydrogen bonding leading to infinite chains of molecules in one direction, in addition to the stacking of layers of such molecular chains in the perpendicular direction ultimately giving rise to β-pleated sheets of 3D molecular network involving N-H⋯O, C-H⋯O and C-H⋯S bonding in the crystal lattice.

  4. Insights into the Complexity of Weak Intermolecular Interactions Interfering in Host-Guest Systems.

    PubMed

    Zhang, Dawei; Chatelet, Bastien; Serrano, Eloisa; Perraud, Olivier; Dutasta, Jean-Pierre; Robert, Vincent; Martinez, Alexandre

    2015-10-05

    The recognition properties of heteroditopic hemicryptophane hosts towards anions, cations, and neutral pairs, combining both cation-π and anion-π interaction sites, were investigated to probe the complexity of interfering weak intermolecular interactions. It is suggested from NMR experiments, and supported by CASSCF/CASPT2 calculations, that the binding constants of anions can be modulated by a factor of up to 100 by varying the fluorination sites on the electron-poor aromatic rings. Interestingly, this subtle chemical modification can also reverse the sign of cooperativity in ion-pair recognition. Wavefunction calculations highlight how short- and long-range interactions interfere in this recognition process, suggesting that a disruption of anion-π interactions can occur in the presence of a co-bound cation. Such molecules can be viewed as prototypes for examining complex processes controlled by the competition of weak interactions.

  5. [Intermolecular hydrogen bond between protein and flavonoid and its contribution to the stability of the flavonoids].

    PubMed

    Fang, Ru; Leng, Xiao-jing; Wu, Xia; Li, Qi; Hao, Rui-fang; Ren, Fa-zheng; Jing, Hao

    2012-01-01

    The interactions between three proteins (BSA, lysozyme and myoglobin) and three flavonoids (quercetin, kaempferol and rutin) were analyzed, using three-dimensional fluorescence spectrometry in combination with UV-Vis spectrometry and Fourier transform infrared (FTIR) spectroscopy. The stabilities of unbound flavonoids and protein-bound flavonoids were compared. The correlation between the interaction and stability was analyzed. The results showed that the hydrophobic interaction was the main binding code in all proteins and flavonoids systems. However, the hydrogen bond has been involved merely in the BSA system. The stability of all three flavonoids (quercetin, kaempferol and rutin) was improved by BSA. There was a great correlation between the hydrogen bonding and the stability of the flavonoids in the presence of BSA. It suggested that the protection of BSA on the flavonoids was due to the intermolecular hydrogen bonding between BSA and flavonoid, and the stronger hydrogen bonding resulted in more protection.

  6. Interfacial and intermolecular interactions determining the rotational orientation of C60 adsorbed on Au(111)

    NASA Astrophysics Data System (ADS)

    Paßens, Michael; Karthäuser, Silvia

    2015-12-01

    Close-packed monolayers of fullerenes on metallic substrates are very rich systems with respect to their rotational degrees of freedom and possible interactions with different adsorption sites or next neighbours. In this connection, we report in detail on the (2√3 × 2√3)R30°-superstructure of C60 with respect to the Au(111)-surface. We use molecular orbital imaging in systematic UHV-STM studies to reveal the delicate balance of interfacial and intermolecular interactions in this system. Thus, bright C60-molecules in 5:6-top and 6:6-top geometries are observed depending on the respective next neighbours. Moreover, tiny changes in the appearance of the unoccupied molecular orbitals of dim C60-molecules in hex-vac positions are identified which are caused by the respective interaction with the facets surrounding the Au-vacancy.

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

    SciTech Connect

    Karayel, A. E-mail: yccaoh@hotmail.com; Özbey, S.; Ayhan-Kılcıgil, G.; Kuş, C.

    2015-12-15

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

  8. In Vivo Brown Adipose Tissue Detection and Characterization using Water-lipid Intermolecular Zero Quantum Coherences

    PubMed Central

    Branca, Rosa T.; Warren, Warren S.

    2010-01-01

    Brown Adipose Tissue (BAT) and White Adipose Tissue (WAT) depots are non-invasively characterized in vitro and in vivo in healthy and obese mice using intermolecular Zero-Quantum Coherence (iZQC) transitions between lipid and water spins. IZQCs enable selective detection of spatial correlation between water and lipid spins and thereby the hydration of fatty deposits with subvoxel resolution. At about a 100 micrometer distance scale, the major observed peaks are between water, methylene protons at 1.3ppm, and olefinic protons at 5.3 ppm. Our in vitro results show that the methylene-olefinic iZQC signal is strong both in BAT and in WAT, but that the water-methylene iZQC signal is characteristic only of BAT tissue. In vivo, the ratio of these peaks is substantially higher in lean or young mice than in old or obese mice. PMID:20939093

  9. Influence of intermolecular hydrogen bonds on the luminescence properties of {alpha}-substituted cinnamonitriles

    SciTech Connect

    Mikhlina, Ya. A.; Bolotin, B. M.; Uzhinov, B. M. Volchkov, V. V.; Kuz'mina, L. G.

    2013-03-15

    In view of the dramatic difference in the spectral-luminescence properties of {alpha}-(p-chlorobenzoyl)-4-diethylaminocinnamonitrile and {alpha}-ethoxycarbonyl-4-diethylaminocinnamonitrile in solutions and in the crystalline state, X-ray diffraction analysis has been applied to study crystals of these compounds. The intermolecular C-H...N and C-H...O hydrogen bonds are found to contribute to the quinoidization of molecules, which leads to a bathochromic shift in the absorption and fluorescence spectra. A spectral-luminescence study of the aforementioned compounds has revealed that the solvent temperature and polarity affect the position of absorption and luminescence peaks: a decrease in these parameters causes a hypsochromic shift.

  10. Local Intermolecular Order Controls Photoinduced Charge Separation at Donor/Acceptor Interfaces in Organic Semiconductors

    SciTech Connect

    Feier, Hilary M.; Reid, Obadiah G.; Pace, Natalie A.; Park, Jaehong; Bergkamp, Jesse J.; Sellinger, Alan; Gust, Devens; Rumbles, Garry

    2016-03-23

    How free charge is generated at organic donor-acceptor interfaces is an important question, as the binding energy of the lowest energy (localized) charge transfer states should be too high for the electron and hole to escape each other. Recently, it has been proposed that delocalization of the electronic states participating in charge transfer is crucial, and aggregated or otherwise locally ordered structures of the donor or the acceptor are the precondition for this electronic characteristic. The effect of intermolecular aggregation of both the polymer donor and fullerene acceptor on charge separation is studied. In the first case, the dilute electron acceptor triethylsilylhydroxy-1,4,8,11,15,18,22,25-octabutoxyphthalocyaninatosilicon(IV) (SiPc) is used to eliminate the influence of acceptor aggregation, and control polymer order through side-chain regioregularity, comparing charge generation in 96% regioregular (RR-) poly(3-hexylthiophene) (P3HT) with its regiorandom (RRa-) counterpart. In the second case, ordered phases in the polymer are eliminated by using RRa-P3HT, and phenyl-C61-butyric acid methyl ester (PC61BM) is used as the acceptor, varying its concentration to control aggregation. Time-resolved microwave conductivity, time-resolved photoluminescence, and transient absorption spectroscopy measurements show that while ultrafast charge transfer occurs in all samples, long-lived charge carriers are only produced in films with intermolecular aggregates of either RR-P3HT or PC61BM, and that polymer aggregates are just as effective in this regard as those of fullerenes.

  11. Probing the self-association, intermolecular contacts, and folding propensity of amelogenin

    PubMed Central

    Ndao, Moise; Dutta, Kaushik; Bromley, Keith M; Lakshminarayanan, Rajamani; Sun, Zhi; Rewari, Gita; Moradian-Oldak, Janet; Evans, John Spencer

    2011-01-01

    Amelogenins are an intrinsically disordered protein family that plays a major role in the development of tooth enamel, one of the most highly mineralized materials in nature. Monomeric porcine amelogenin possesses random coil and residual secondary structures, but it is not known which sequence regions would be conformationally attractive to potential enamel matrix targets such as other amelogenins (self-assembly), other matrix proteins, cell surfaces, or biominerals. To address this further, we investigated recombinant porcine amelogenin (rP172) using “solvent engineering” techniques to simultaneously promote native-like structure and induce amelogenin oligomerization in a manner that allows identification of intermolecular contacts between amelogenin molecules. We discovered that in the presence of 2,2,2-trifluoroethanol (TFE) significant folding transitions and stabilization occurred primarily within the N- and C-termini, while the polyproline Type II central domain was largely resistant to conformational transitions. Seven Pro residues (P2, P127, P130, P139, P154, P157, P162) exhibited conformational response to TFE, and this indicates these Pro residues act as folding enhancers in rP172. The remaining Pro residues resisted TFE perturbations and thus act as conformational stabilizers. We also noted that TFE induced rP172 self-association via the formation of intermolecular contacts involving P4–H6, V19–P33, and E40–T58 regions of the N-terminus. Collectively, these results confirm that the N- and C-termini of amelogenin are conformationally responsive and represent potential interactive sites for amelogenin–target interactions during enamel matrix mineralization. Conversely, the Pro, Gln central domain is resistant to folding and this may have important functional significance for amelogenin. PMID:21351181

  12. Testing electronic structure methods for describing intermolecular H...H interactions in supramolecular chemistry.

    PubMed

    Casadesús, Ricard; Moreno, Miquel; González-Lafont, Angels; Lluch, José M; Repasky, Matthew P

    2004-01-15

    In this article a wide variety of computational approaches (molecular mechanics force fields, semiempirical formalisms, and hybrid methods, namely ONIOM calculations) have been used to calculate the energy and geometry of the supramolecular system 2-(2'-hydroxyphenyl)-4-methyloxazole (HPMO) encapsulated in beta-cyclodextrin (beta-CD). The main objective of the present study has been to examine the performance of these computational methods when describing the short range H. H intermolecular interactions between guest (HPMO) and host (beta-CD) molecules. The analyzed molecular mechanics methods do not provide unphysical short H...H contacts, but it is obvious that their applicability to the study of supramolecular systems is rather limited. For the semiempirical methods, MNDO is found to generate more reliable geometries than AM1, PM3 and the two recently developed schemes PDDG/MNDO and PDDG/PM3. MNDO results only give one slightly short H...H distance, whereas the NDDO formalisms with modifications of the Core Repulsion Function (CRF) via Gaussians exhibit a large number of short to very short and unphysical H...H intermolecular distances. In contrast, the PM5 method, which is the successor to PM3, gives very promising results. Our ONIOM calculations indicate that the unphysical optimized geometries from PM3 are retained when this semiempirical method is used as the low level layer in a QM:QM formulation. On the other hand, ab initio methods involving good enough basis sets, at least for the high level layer in a hybrid ONIOM calculation, behave well, but they may be too expensive in practice for most supramolecular chemistry applications. Finally, the performance of the evaluated computational methods has also been tested by evaluating the energetic difference between the two most stable conformations of the host(beta-CD)-guest(HPMO) system.

  13. Structure and intermolecular interactions in selected binary solutions studied by X-ray methods

    NASA Astrophysics Data System (ADS)

    Drozdowski, Henryk; Romaniuk, Anna; Błaszczak, Zdzisław

    2013-12-01

    The results of X-ray structural studies of liquid chloroanisole C6H4OCH3Cl and 10% solutions of chloroanisole in 1,4-dimethylbenzene C8H10 are presented. It is the first paper on an X-ray diffraction study of the liquid solutions of chloroanisole. The X-ray measurements were made at 293 K for the scattering angle range 2Θ varying from 6° to 120°. Averaged scattered X-ray angular distributions I¯(S) were determined. The angular distributions of the intensity of X-ray scattered by 10% solutions of chloroanisole in 1,4-dimethylbenzene were compared to the angular distributions obtained for liquid ortho-, meta- and para-chloroanisole. The differential radial distribution functions of electron density 4πr∑j,knK[ρk(r)-ρ0] were numerically found using the Fourier analysis from a modified Warren, Krutter and Morningstar equation. To the maxima of DRDFs, interatomic and intermolecular distances were assigned. The use of short-wave radiation from an X-ray tube with a molybdenum anode permitted determination of the spheres of intermolecular ordering in the studied liquids and their solutions. The experimental results were used to plot models of the most highly probable mutual disposition of the molecules in liquid chloroanisole and their solutions. The benzene rings of two molecules are situated in parallel plane what results in antiparallel setting of the dipole moments of the chloroanisole molecules. X-ray structural analysis was applied to determine the packing coefficients of chloroanisole molecules. The results obtained in this paper confirm the specific structural properties of the solutions studied.

  14. Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization

    SciTech Connect

    Christensen, Anders S. E-mail: cui@chem.wisc.edu; Cui, Qiang E-mail: cui@chem.wisc.edu; Elstner, Marcus

    2015-08-28

    Semi-empirical quantum mechanical methods traditionally expand the electron density in a minimal, valence-only electron basis set. The minimal-basis approximation causes molecular polarization to be underestimated, and hence intermolecular interaction energies are also underestimated, especially for intermolecular interactions involving charged species. In this work, the third-order self-consistent charge density functional tight-binding method (DFTB3) is augmented with an auxiliary response density using the chemical-potential equalization (CPE) method and an empirical dispersion correction (D3). The parameters in the CPE and D3 models are fitted to high-level CCSD(T) reference interaction energies for a broad range of chemical species, as well as dipole moments calculated at the DFT level; the impact of including polarizabilities of molecules in the parameterization is also considered. Parameters for the elements H, C, N, O, and S are presented. The Root Mean Square Deviation (RMSD) interaction energy is improved from 6.07 kcal/mol to 1.49 kcal/mol for interactions with one charged species, whereas the RMSD is improved from 5.60 kcal/mol to 1.73 for a set of 9 salt bridges, compared to uncorrected DFTB3. For large water clusters and complexes that are dominated by dispersion interactions, the already satisfactory performance of the DFTB3-D3 model is retained; polarizabilities of neutral molecules are also notably improved. Overall, the CPE extension of DFTB3-D3 provides a more balanced description of different types of non-covalent interactions than Neglect of Diatomic Differential Overlap type of semi-empirical methods (e.g., PM6-D3H4) and PBE-D3 with modest basis sets.

  15. Vibrational dependence of the anisotropic intermolecular potential of Ar-HF

    NASA Astrophysics Data System (ADS)

    Hutson, Jeremy M.

    1992-05-01

    A new intermolecular potential for Ar-HF is obtained by fitting to results from high-resolution microwave, far-infrared, and infrared spectroscopy. The new potential, designated H6(4,3,2), is a function of the diatom mass-reduced vibrational quantum number η=(v+ (1)/(2) )/(μHX)1/2 as well as the intermolecular distance R and angle θ, and has 22 adjustable parameters. It reproduces all the available spectroscopic data for levels of Ar-HF correlating with HF, v=0, 1, and 2, and DF, v=0 and 1. The H6(4,3,2) potential is qualitatively similar to previous potentials, with a linear Ar-H-F equilibrium geometry and a secondary minimum at the linear Ar-F-H geometry. Compared to the potential of Nesbitt et al. [J. Chem. Phys. 90, 4855 (1989)], obtained from spectra of Ar-HF (v=1), the H6(4,3,2) potential is rather deeper near the equilibrium geometry (Ar-H-F), but shallower around the secondary minimum (Ar-F-H). The absolute well depth increases by 19 cm-1 between HF v=0 and v=1. The vibrationally averaged induction energy is calculated to be substantially (8.1 cm-1 ) greater for v=1 than for v=0, and is responsible for most of the observed red shift in the complex. Predictions of additional spectroscopic properties that would test the new potential are given, including far-infrared and overtone spectra of Ar-DF and dipole moments of excited states of Ar-HF and Ar-DF.

  16. Multi-referenced excited states and intermolecular forces from the anti-Hermitian contracted Schrodinger equation

    NASA Astrophysics Data System (ADS)

    Sturm, Erica J.

    Strong correlation due to multi-referenced electronic states of quantum chemical systems are crucial for a proper understanding of important phenomena including excited states, bond breakage and formation, singlet fission and biological transport. By solving for the 2-electron reduced density matrix (2-RDM) directly via the anti-Hermitian contracted Schrodinger equation (ACSE) we provide a balanced treatment of single and multi-referenced correlation effects without utilizing the N-electron wave function. This significantly reduces the computational expense while still maintaining near full configuration interaction accuracy when available. When provided with an initial 2-RDM guess from an active-space multi-configuration self consistent field wave function the ACSE scales as [special characters omitted] where ra is the number of active molecular orbitals (MOs) and ra is the number of external MOs. This work demonstrates the energetic accuracy of ACSE calculations with several small multi-referenced systems and presents a novel approach for investigating intermolecular interactions, using a simple dimer test case. In this monomer-optimized basis set approach we compute each monomer's properties in isolation and obtain a set of natural orbitals that best describe the monomer. We then remove or truncate orbitals deemed excessive as a function of occupation number, defining a monomer molecular orbital basis uniquely suited to that monomer. Combining two such monomers yields a super-system expressed in the monomer basis which we then rotate to a dimer basis at a desired geometry before creating a new initial 2-RDM for the final optimization by an ACSE calculation. It is found that the intermolecular properties calculated in this fashion from larger atomic basis sets maintain their high accuracy but at a fraction of the computational cost. Furthermore this basis set optimization is free of basis set superposition error, circumventing the need for an expensive

  17. Importance of the donor:fullerene intermolecular arrangement for high-efficiency organic photovoltaics.

    PubMed

    Graham, Kenneth R; Cabanetos, Clement; Jahnke, Justin P; Idso, Matthew N; El Labban, Abdulrahman; Ngongang Ndjawa, Guy O; Heumueller, Thomas; Vandewal, Koen; Salleo, Alberto; Chmelka, Bradley F; Amassian, Aram; Beaujuge, Pierre M; McGehee, Michael D

    2014-07-09

    The performance of organic photovoltaic (OPV) material systems are hypothesized to depend strongly on the intermolecular arrangements at the donor:fullerene interfaces. A review of some of the most efficient polymers utilized in polymer:fullerene PV devices, combined with an analysis of reported polymer donor materials wherein the same conjugated backbone was used with varying alkyl substituents, supports this hypothesis. Specifically, the literature shows that higher-performing donor-acceptor type polymers generally have acceptor moieties that are sterically accessible for interactions with the fullerene derivative, whereas the corresponding donor moieties tend to have branched alkyl substituents that sterically hinder interactions with the fullerene. To further explore the idea that the most beneficial polymer:fullerene arrangement involves the fullerene docking with the acceptor moiety, a family of benzo[1,2-b:4,5-b']dithiophene-thieno[3,4-c]pyrrole-4,6-dione polymers (PBDTTPD derivatives) was synthesized and tested in a variety of PV device types with vastly different aggregation states of the polymer. In agreement with our hypothesis, the PBDTTPD derivative with a more sterically accessible acceptor moiety and a more sterically hindered donor moiety shows the highest performance in bulk-heterojunction, bilayer, and low-polymer concentration PV devices where fullerene derivatives serve as the electron-accepting materials. Furthermore, external quantum efficiency measurements of the charge-transfer state and solid-state two-dimensional (2D) (13)C{(1)H} heteronuclear correlation (HETCOR) NMR analyses support that a specific polymer:fullerene arrangement is present for the highest performing PBDTTPD derivative, in which the fullerene is in closer proximity to the acceptor moiety of the polymer. This work demonstrates that the polymer:fullerene arrangement and resulting intermolecular interactions may be key factors in determining the performance of OPV material

  18. Control of the intermolecular photodimerization of anthracene derivatives by hydrogen bonding of urea groups in dilute solution.

    PubMed

    Matsumoto, Hisato; Nishimura, Yoshinobu; Arai, Tatsuo

    2016-08-04

    The photodimerization reaction of anthracene derivatives was performed by capitalizing on intermolecular hydrogen bonds. Anthracene derivatives that can control the dimerization reaction depending on the substitution site were designed by using two anthryl moieties and one urea group, referred to as N,N'-dianthracen-n-ylurea, nDAU (n = 1, 2 and 9), which are symmetrically substituted by 1-anthryl, 2-anthryl and 9-anthryl groups, respectively. We investigated the excimer emission and photodimerization reaction of these anthracene-urea derivatives using absorption, emission, and (1)H NMR spectroscopy along with fluorescence decay measurements. All derivatives showed a concentration dependence of their fluorescence spectra and multiple fluorescence lifetime components even at 10(-6) M. Significantly, 9DAU resulted in an intermolecular photodimerization reaction. These differences in photoreactivity of nDAU may depend on variations in the overlap of the intermolecularly associated anthracene rings of nDAU by hydrogen bonding between intermolecular urea moieties. Furthermore, the dimerization quantum yield of 9DAU was reduced by the addition of tetrabutylammonium acetate (TBAAc). Consequently, we revealed that the substitution site and the addition of TBAAc affected the dimerization reaction of anthracene-urea derivatives.

  19. Highly enantioselective and anti-diastereoselective catalytic intermolecular glyoxylate-ene reactions: effect of the geometrical isomers of alkenes.

    PubMed

    Zhang, Xiang; Wang, Min; Ding, Ran; Xu, Yun-He; Loh, Teck-Peng

    2015-06-05

    An efficient method for the synthesis of homoallylic alcohols with high enantioselectivities and anti-diastereoselectivities via an In(III)-catalyzed intermolecular glyoxylate-ene reaction has been developed. The geometrical isomers of alkenes were shown to have different reactivities. Only the isomers of the alkenes having a proton β-cis to the substituent reacted in this catalytic system.

  20. NMR detection of intermolecular interaction sites in the dimeric 5′-leader of the HIV-1 genome

    PubMed Central

    Keane, Sarah C.; Van, Verna; Frank, Heather M.; Sciandra, Carly A.; McCowin, Sayo; Santos, Justin; Heng, Xiao; Summers, Michael F.

    2016-01-01

    HIV type-1 (HIV-1) contains a pseudodiploid RNA genome that is selected for packaging and maintained in virions as a noncovalently linked dimer. Genome dimerization is mediated by conserved elements within the 5′-leader of the RNA, including a palindromic dimer initiation signal (DIS) that has been proposed to form kissing hairpin and/or extended duplex intermolecular contacts. Here, we have applied a 2H-edited NMR approach to directly probe for intermolecular interactions in the full-length, dimeric HIV-1 5′-leader (688 nucleotides; 230 kDa). The interface is extensive and includes DIS:DIS base pairing in an extended duplex state as well as intermolecular pairing between elements of the upstream Unique-5′ (U5) sequence and those near the gag start site (AUG). Other pseudopalindromic regions of the leader, including the transcription activation (TAR), polyadenylation (PolyA), and primer binding (PBS) elements, do not participate in intermolecular base pairing. Using a 2H-edited one-dimensional NMR approach, we also show that the extended interface structure forms on a time scale similar to that of overall RNA dimerization. Our studies indicate that a kissing dimer-mediated structure, if formed, exists only transiently and readily converts to the extended interface structure, even in the absence of the HIV-1 nucleocapsid protein or other RNA chaperones. PMID:27791166

  1. A Hands-On Activity to Build Mastery of Intermolecular Forces and Its Impacts on Student Learning

    ERIC Educational Resources Information Center

    Bruck, Laura B.

    2016-01-01

    The intermolecular forces activity presented in this article is designed to foster concept-building through students' use of concrete, manipulative objects, and it was developed to be pedagogically sound. Data analysis via pre- and posttesting and subsequent exam questions indicated that students who had the opportunity to participate in the…

  2. Magneto-dielectric effects induced by optically-generated intermolecular charge-transfer states in organic semiconducting materials.

    PubMed

    Zang, Huidong; Yan, Liang; Li, Mingxing; He, Lei; Gai, Zheng; Ivanov, Ilia; Wang, Min; Chiang, Long; Urbas, Augustine; Hu, Bin

    2013-10-02

    Traditionally, magneto-dielectric effects have been developed by combining ferroelectric and magnetic materials. Here, we show a magneto-dielectric effect from optically-generated intermolecular charge-transfer states in an organic semiconducting donor:acceptor (PVK:TCNB) system. We observe in magnetic field effects of photoluminescence that a magnetic field can change singlet/triplet population ratio in intermolecular charge-transfer states. Furthermore, our theoretical analysis and experimental evidence indicate that the singlets and triplets in charge-transfer states have stronger and weaker electrical polarizations, respectively. Therefore, the observed magneto-dielectric effect can be attributed to magnetically-dependent singlet/triplet ratio in intermolecular charge-transfer states. In principle, a magneto-dielectric effect can be generated through two different channels based on magneto-polarization and magneto-current effects when the singlet/triplet ratio in intermolecular charge-transfer states is changed by a magnetic field. We find, from the simulation of dielectric effects, that magneto-polarization and magneto-current effects play primary and secondary roles in the generation of magneto-dielectric effect.

  3. Applications and Analogies: Phototherapy and the Treatment of Hyperbilirubinemia: A Demonstration of Intra- versus Intermolecular Hydrogen Bonding.

    ERIC Educational Resources Information Center

    Wilbraham, Antony C.

    1984-01-01

    Background information and procedures are provided for a demonstration of intramolecular versus intermolecular hydrogen bonding. The demonstration is based on structural changes in bilirubin molecules which lead to changes in physical properties. A list of further investigations to try is included. (JN)

  4. Iodination of carbohydrate-derived 1,2-oxazines to enantiopure 5-iodo-3,6-dihydro-2H-1,2-oxazines and subsequent palladium-catalyzed cross-coupling reactions

    PubMed Central

    Medvecký, Michal; Linder, Igor; Schefzig, Luise

    2016-01-01

    Iodination of carbohydrate-derived 3,6-dihydro-2H-1,2-oxazines of type 3 using iodine and pyridine in DMF furnished 5-iodo-substituted 1,2-oxazine derivatives 4 with high efficacy. The alkenyl iodide moiety of 1,2-oxazine derivatives syn-4 and anti-4 was subsequently exploited for the introduction of new functionalities at the C-5 position by applying palladium-catalyzed carbon–carbon bond-forming reactions such as Sonogashira, Heck, or Suzuki coupling reactions as well as a cyanation reaction. These cross-coupling reactions led to a series of 5-alkynyl-, 5-alkenyl-, 5-aryl- and 5-cyano-substituted 1,2-oxazine derivatives being of considerable interest for further synthetic elaborations. This was exemplarily demonstrated by the hydrogenation of syn-21 and anti-24 and by a click reaction of a 5-alkynyl-substituted precursor. PMID:28144363

  5. Investigations of the Rg-BrCl (Rg=He, Ne, Ar, Kr, Xe) binary van der Waals complexes: ab initio intermolecular potential energy surfaces, vibrational states and predicted pure rotational transition frequencies.

    PubMed

    Li, Song; Zheng, Rui; Chen, Shan-Jun; Chen, Yan; Chen, Peng

    2017-03-05

    The intermolecular potential energy surfaces (PESs) of the ground electronic state for the Rg-BrCl (Rg=He, Ne, Ar, Kr, Xe) van der Waals complexes have been constructed by using the coupled-cluster method in combination with the augmented quadruple-zeta correlation-consistent basis sets supplemented with an additional set of bond functions. The features of the anisotropic PESs for these complexes are remarkably similar, which are characterized by three minima and two saddle points between them. The global minimum corresponds to a collinear Rg-Br-Cl configuration. Two local minima, correlate with an anti-linear Rg-Cl-Br geometry and a nearly T-shaped structure, can also be located on each PES. The quantum bound state calculations enable us to investigate intermolecular vibrational states and rotational energy levels of the complexes. The transition frequencies are predicted and are fitted to obtain their corresponding spectroscopic constants. In general, the periodic trends are observed for this complex family. Comparisons with available experimental data for the collinear isomer of Ar-BrCl demonstrate reliability of our theoretical predictions, and our results for the other two isomers of Ar-BrCl as well as for other members of the complex family are also anticipated to be trustable. Except for the collinear isomer of Ar-BrCl, the data presented in this paper would be beneficial to improve our knowledge for these experimentally unknown species.

  6. Investigations of the Rg-BrCl (Rg = He, Ne, Ar, Kr, Xe) binary van der Waals complexes: ab initio intermolecular potential energy surfaces, vibrational states and predicted pure rotational transition frequencies

    NASA Astrophysics Data System (ADS)

    Li, Song; Zheng, Rui; Chen, Shan-Jun; Chen, Yan; Chen, Peng

    2017-03-01

    The intermolecular potential energy surfaces (PESs) of the ground electronic state for the Rg-BrCl (Rg = He, Ne, Ar, Kr, Xe) van der Waals complexes have been constructed by using the coupled-cluster method in combination with the augmented quadruple-zeta correlation-consistent basis sets supplemented with an additional set of bond functions. The features of the anisotropic PESs for these complexes are remarkably similar, which are characterized by three minima and two saddle points between them. The global minimum corresponds to a collinear Rg-Br-Cl configuration. Two local minima, correlate with an anti-linear Rg-Cl-Br geometry and a nearly T-shaped structure, can also be located on each PES. The quantum bound state calculations enable us to investigate intermolecular vibrational states and rotational energy levels of the complexes. The transition frequencies are predicted and are fitted to obtain their corresponding spectroscopic constants. In general, the periodic trends are observed for this complex family. Comparisons with available experimental data for the collinear isomer of Ar-BrCl demonstrate reliability of our theoretical predictions, and our results for the other two isomers of Ar-BrCl as well as for other members of the complex family are also anticipated to be trustable. Except for the collinear isomer of Ar-BrCl, the data presented in this paper would be beneficial to improve our knowledge for these experimentally unknown species.

  7. Nonadiabatic Coupling

    NASA Astrophysics Data System (ADS)

    Kryachko, Eugene S.

    The general features of the nonadiabatic coupling and its relation to molecular properties are surveyed. Some consequences of the [`]equation of motion', formally expressing a [`]smoothness' of a given molecular property within the diabatic basis, are demonstrated. A particular emphasis is made on the relation between a [`]smoothness' of the electronic dipole moment and the generalized Mulliken-Hush formula for the diabatic electronic coupling.

  8. Synthesis of 3-iodoindoles by the Pd/Cu-catalyzed coupling of N,N-dialkyl-2-iodoanilines and terminal acetylenes, followed by electrophilic cyclization.

    PubMed

    Yue, Dawei; Yao, Tuanli; Larock, Richard C

    2006-01-06

    [reaction: see text] 3-Iodoindoles have been prepared in excellent yields by coupling terminal acetylenes with N,N-dialkyl-o-iodoanilines in the presence of a Pd/Cu catalyst, followed by an electrophilic cyclization of the resulting N,N-dialkyl-o-(1-alkynyl)anilines using I2 in CH2Cl2. Aryl-, vinylic-, alkyl-, and silyl-substituted terminal acetylenes undergo this process to produce excellent yields of 3-iodoindoles. The reactivity of the carbon-nitrogen bond cleavage during cyclization follows the following order: Me > n-Bu, Me > Ph, and cyclohexyl > Me. Subsequent palladium-catalyzed Sonogashira, Suzuki, and Heck reactions of the resulting 3-iodoindoles proceed smoothly in good yields.

  9. Intermolecularly-induced conformational disorder in ferrocene, 1-bromoferrocene and 1,1‧-dibromoferrocene

    NASA Astrophysics Data System (ADS)

    Silva, Patrícia A.; Maria, Teresa M. R.; Nunes, Cláudio M.; Eusébio, Maria Ermelinda S.; Fausto, Rui

    2014-12-01

    Conformational preferences for isolated molecules of ferrocene, 1-bromoferrocene and 1,1‧-dibromoferrocene were obtained by combined use of matrix-isolation infrared spectroscopy and quantum chemical calculations. Monomeric ferrocene and 1-dibromoferrocene were found to exist in a low temperature argon matrix (T = 15 K) exclusively in the eclipsed configuration, which corresponds to their most stable conformation in gas phase. On the other hand, for the neat compounds in crystalline phase, intermolecular interactions induce conformational disorder, leading to presence in the room temperature polymorphic forms of monomeric units with the staggered (or nearly staggered) conformation. 1,1‧-Dibromoferrocene exists in both gas phase and low temperature argon matrix in two conformers of C2 symmetry (C2-I and C2-II), with eclipsed cyclopentadienyl moieties and Br atoms opposed to H atoms. The populations of the two conformers trapped in the as-deposited matrix were found to correspond to those estimated from theory for the room temperature equilibrium gas phase. By increasing the temperature of the matrix (up to 35 K), the gas phase lower energy form (C2-I) converted to the C2-II form. Besides allowing the precise structural and spectroscopic characterization of the two forms, these studies also revealed that the C2-II conformer (having a largest dipole moment) is stabilized in the matrix media, thus becoming more stable than the C2-I form under these conditions. Very interestingly, the room temperature stable polymorph of the compound (Tfus = 325.4 ± 0.1 K) is composed by 1,1‧-dibromoferrocene units exhibiting the C2v symmetry eclipsed conformation with opposed bromine atoms, which for the isolated molecule corresponds to the highest energy conformation along the ring torsional coordinate and is the transition state structure between the two symmetry equivalent C2-II minima. Differential scanning calorimetry, polarized light thermomicroscopy and infrared

  10. Improving activity of minicellulosomes by integration of intra- and intermolecular synergies

    PubMed Central

    2013-01-01

    Background Complete hydrolysis of cellulose to glucose requires the synergistic action of three general types of glycoside hydrolases; endoglucanases, exoglucanases, and cellobiases. Cellulases that are found in Nature vary considerably in their modular diversity and architecture. They include: non-complexed enzymes with single catalytic domains, independent single peptide chains incorporating multiple catalytic modules, and complexed, scaffolded structures, such as the cellulosome. The discovery of the latter two enzyme architectures has led to a generally held hypothesis that these systems take advantage of intramolecular and intermolecular proximity synergies, respectively, to enhance cellulose degradation. We use domain engineering to exploit both of these concepts to improve cellulase activity relative to the activity of mixtures of the separate catalytic domains. Results We show that engineered minicellulosomes can achieve high levels of cellulose conversion on crystalline cellulose by taking advantage of three types of synergism; (1) a complementary synergy produced by interaction of endo- and exo-cellulases, (2) an intramolecular synergy of multiple catalytic modules in a single gene product (this type of synergism being introduced for the first time to minicellulosomes targeting crystalline cellulose), and (3) an intermolecular proximity synergy from the assembly of these cellulases into larger multi-molecular structures called minicellulosomes. The binary minicellulosome constructed in this study consists of an artificial multicatalytic cellulase (CBM4-Ig-GH9-X11-X12-GH8-Doc) and one cellulase with a single catalytic domain (a modified Cel48S with the structure CBM4-Ig-GH48-Doc), connected by a non-catalytic scaffoldin protein. The high level endo-exo synergy and intramolecular synergies within the artificial multifunctional cellulase have been combined with an additional proximity-dependent synergy produced by incorporation into a minicellulosome

  11. Role of amino acid insertions on intermolecular forces between arginine peptide condensed DNA helices: implications for protamine-DNA packaging in sperm.

    PubMed

    DeRouchey, Jason E; Rau, Donald C

    2011-12-09

    In spermatogenesis, chromatin histones are replaced by arginine-rich protamines to densely compact DNA in sperm heads. Tight packaging is considered necessary to protect the DNA from damage. To better understand the nature of the forces condensing protamine-DNA assemblies and their dependence on amino acid content, the effect of neutral and negatively charged amino acids on DNA-DNA intermolecular forces was studied using model peptides containing six arginines. We have previously observed that the neutral amino acids in salmon protamine decrease the net attraction between protamine-DNA helices compared with the equivalent homo-arginine peptide. Using osmotic stress coupled with x-ray scattering, we have investigated the component attractive and repulsive forces that determine the net attraction and equilibrium interhelical distance as a function of the chemistry, position, and number of the amino acid inserted. Neutral amino acids inserted into hexa-arginine increase the short range repulsion while only slightly affecting longer range attraction. The amino acid content alone of salmon protamine is enough to rationalize the forces that package DNA in sperm heads. Inserting a negatively charged amino acid into hexa-arginine dramatically weakens the net attraction. Both of these observations have biological implications for protamine-DNA packaging in sperm heads.

  12. Calculation of intermolecular potentials for H2sbnd H2 and H2sbnd O2 dimers ab initio and prediction of second virial coefficients

    NASA Astrophysics Data System (ADS)

    Pham Van, Tat; Deiters, Ulrich K.

    2015-08-01

    The intermolecular interaction potentials of the dimers H2sbnd H2 and H2sbnd O2 were calculated from quantum mechanics, using coupled-cluster theory CCSD(T) and correlation-consistent basis sets aug-cc-pVmZ (m = 2, 3); the results were extrapolated to the basis set limit aug-cc-pV23Z. The interaction energies were corrected for the basis set superposition error with the counterpoise scheme. For comparison also Møller-Plesset perturbation theory (at levels 2-4) with the basis sets aug-cc-pVTZ were considered, but the results proved inferior. The quantum mechanical results were used to construct analytical pair potential functions. From these functions the second virial coefficients of hydrogen and the cross virial coefficients of the hydrogen-oxygen system were obtained by integration; in both cases corrections for quantum effects were included. The results agree well with experimental data, if available, or with empirical correlations.

  13. Combining docking-based comparative intermolecular contacts analysis and k-nearest neighbor correlation for the discovery of new check point kinase 1 inhibitors

    NASA Astrophysics Data System (ADS)

    Jaradat, Nour Jamal; Khanfar, Mohammad A.; Habash, Maha; Taha, Mutasem Omar

    2015-06-01

    Check point kinase 1 (Chk1) is an important protein in G2 phase checkpoint arrest required by cancer cells to maintain cell cycle and to prevent cell death. Therefore, Chk1 inhibitors should have potential as anti-cancer therapeutics. Docking-based comparative intermolecular contacts analysis (dbCICA) is a new three-dimensional quantitative structure activity relationship method that depends on the quality and number of contact points between docked ligands and binding pocket amino acid residues. In this presented work we implemented a novel combination of k-nearest neighbor/genetic function algorithm modeling coupled with dbCICA to select critical ligand-Chk1 contacts capable of explaining anti-Chk1 bioactivity among a long list of inhibitors. The finest set of contacts were translated into two valid pharmacophore hypotheses that were used as 3D search queries to screen the National Cancer Institute's structural database for new Chk1 inhibitors. Three potent Chk1 inhibitors were discovered with IC50 values ranging from 2.4 to 69.7 µM.

  14. Structural analysis of intermolecular interactions in the kinesin adaptor complex fasciculation and elongation protein zeta 1/ short coiled-coil protein (FEZ1/SCOCO).

    PubMed

    Alborghetti, Marcos Rodrigo; Furlan, Ariane da Silva; da Silva, Júlio César; Sforça, Maurício Luís; Honorato, Rodrigo Vargas; Granato, Daniela Campos; dos Santos Migueleti, Deivid Lucas; Neves, Jorge L; de Oliveira, Paulo Sergio Lopes; Paes-Leme, Adriana Franco; Zeri, Ana Carolina de Mattos; de Torriani, Iris Concepcion Linares; Kobarg, Jörg

    2013-01-01

    Cytoskeleton and protein trafficking processes, including vesicle transport to synapses, are key processes in neuronal differentiation and axon outgrowth. The human protein FEZ1 (fasciculation and elongation protein zeta 1 / UNC-76, in C. elegans), SCOCO (short coiled-coil protein / UNC-69) and kinesins (e.g. kinesin heavy chain / UNC116) are involved in these processes. Exploiting the feature of FEZ1 protein as a bivalent adapter of transport mediated by kinesins and FEZ1 protein interaction with SCOCO (proteins involved in the same path of axonal growth), we investigated the structural aspects of intermolecular interactions involved in this complex formation by NMR (Nuclear Magnetic Resonance), cross-linking coupled with mass spectrometry (MS), SAXS (Small Angle X-ray Scattering) and molecular modelling. The topology of homodimerization was accessed through NMR (Nuclear Magnetic Resonance) studies of the region involved in this process, corresponding to FEZ1 (92-194). Through studies involving the protein in its monomeric configuration (reduced) and dimeric state, we propose that homodimerization occurs with FEZ1 chains oriented in an anti-parallel topology. We demonstrate that the interaction interface of FEZ1 and SCOCO defined by MS and computational modelling is in accordance with that previously demonstrated for UNC-76 and UNC-69. SAXS and literature data support a heterotetrameric complex model. These data provide details about the interaction interfaces probably involved in the transport machinery assembly and open perspectives to understand and interfere in this assembly and its involvement in neuronal differentiation and axon outgrowth.

  15. Structural Analysis of Intermolecular Interactions in the Kinesin Adaptor Complex Fasciculation and Elongation Protein Zeta 1/ Short Coiled-Coil Protein (FEZ1/SCOCO)

    PubMed Central

    da Silva, Júlio César; Sforça, Maurício Luís; Honorato, Rodrigo Vargas; Granato, Daniela Campos; dos Santos Migueleti, Deivid Lucas; Neves, Jorge L.; de Oliveira, Paulo Sergio Lopes; Paes-Leme, Adriana Franco; Zeri, Ana Carolina de Mattos; de Torriani, Iris Concepcion Linares; Kobarg, Jörg

    2013-01-01

    Cytoskeleton and protein trafficking processes, including vesicle transport to synapses, are key processes in neuronal differentiation and axon outgrowth. The human protein FEZ1 (fasciculation and elongation protein zeta 1 / UNC-76, in C. elegans), SCOCO (short coiled-coil protein / UNC-69) and kinesins (e.g. kinesin heavy chain / UNC116) are involved in these processes. Exploiting the feature of FEZ1 protein as a bivalent adapter of transport mediated by kinesins and FEZ1 protein interaction with SCOCO (proteins involved in the same path of axonal growth), we investigated the structural aspects of intermolecular interactions involved in this complex formation by NMR (Nuclear Magnetic Resonance), cross-linking coupled with mass spectrometry (MS), SAXS (Small Angle X-ray Scattering) and molecular modelling. The topology of homodimerization was accessed through NMR (Nuclear Magnetic Resonance) studies of the region involved in this process, corresponding to FEZ1 (92-194). Through studies involving the protein in its monomeric configuration (reduced) and dimeric state, we propose that homodimerization occurs with FEZ1 chains oriented in an anti-parallel topology. We demonstrate that the interaction interface of FEZ1 and SCOCO defined by MS and computational modelling is in accordance with that previously demonstrated for UNC-76 and UNC-69. SAXS and literature data support a heterotetrameric complex model. These data provide details about the interaction interfaces probably involved in the transport machinery assembly and open perspectives to understand and interfere in this assembly and its involvement in neuronal differentiation and axon outgrowth. PMID:24116125

  16. Combining docking-based comparative intermolecular contacts analysis and k-nearest neighbor correlation for the discovery of new check point kinase 1 inhibitors.

    PubMed

    Jaradat, Nour Jamal; Khanfar, Mohammad A; Habash, Maha; Taha, Mutasem Omar

    2015-06-01

    Check point kinase 1 (Chk1) is an important protein in G2 phase checkpoint arrest required by cancer cells to maintain cell cycle and to prevent cell death. Therefore, Chk1 inhibitors should have potential as anti-cancer therapeutics. Docking-based comparative intermolecular contacts analysis (dbCICA) is a new three-dimensional quantitative structure activity relationship method that depends on the quality and number of contact points between docked ligands and binding pocket amino acid residues. In this presented work we implemented a novel combination of k-nearest neighbor/genetic function algorithm modeling coupled with dbCICA to select critical ligand-Chk1 contacts capable of explaining anti-Chk1 bioactivity among a long list of inhibitors. The finest set of contacts were translated into two valid pharmacophore hypotheses that were used as 3D search queries to screen the National Cancer Institute's structural database for new Chk1 inhibitors. Three potent Chk1 inhibitors were discovered with IC50 values ranging from 2.4 to 69.7 µM.

  17. Rh(I)–Bisphosphine-Catalyzed Asymmetric, Intermolecular Hydroheteroarylation of α-Substituted Acrylate Derivatives

    PubMed Central

    2015-01-01

    Asymmetric hydroheteroarylation of alkenes represents a convenient entry to elaborated heterocyclic motifs. While chiral acids are known to mediate asymmetric addition of electron-rich heteroarenes to Michael acceptors, very few methods exploit transition metals to catalyze alkylation of heterocycles with olefins via a C–H activation, migratory insertion sequence. Herein, we describe the development of an asymmetric, intermolecular hydroheteroarylation reaction of α-substituted acrylates with benzoxazoles. The reaction provides 2-substitued benzoxazoles in moderate to excellent yields and good to excellent enantioselectivities. Notably, a series of mechanistic studies appears to contradict a pathway involving enantioselective protonation of a Rh(I)–enolate, despite the fact that such a mechanism is invoked almost unanimously in the related addition of aryl boronic acids to methacrylate derivatives. Evidence suggests instead that migratory insertion or beta-hydride elimination is enantiodetermining and that isomerization of a Rh(I)–enolate to a Rh(I)–heterobenzyl species insulates the resultant α-stereocenter from epimerization. A bulky ligand, CTH-(R)-Xylyl-P-Phos, is crucial for reactivity and enantioselectivity, as it likely discourages undesired ligation of benzoxazole substrates or intermediates to on- or off-cycle rhodium complexes and attenuates coordination-promoted product epimerization. PMID:25545834

  18. Crystallographic Structure, Intermolecular Packing Energetics, Crystal Morphology and Surface Chemistry of Salmeterol Xinafoate (Form I).

    PubMed

    Moldovan, Alexandru A; Rosbottom, Ian; Ramachandran, Vasuki; Pask, Christopher M; Olomukhoro, Oboroghene; Roberts, Kevin J

    2017-03-01

    Single crystals of salmeterol xinafoate (form I), prepared from slow cooled supersaturated propan-2-ol solutions, crystallize in a triclinic P1¯ symmetry with 2 closely related independent salt pairs within the asymmetric unit, with an approximately double-unit cell volume compared with the previously published crystal structure. Synthonic analysis of the bulk intermolecular packing confirms the similarity in packing energetics between the 2 salt pairs. The strongest synthons, as expected, are dominated by coulombic interactions. Morphologic prediction reveals a plate-like morphology, dominated by the {001}, {010}, and {100} surfaces, consistent with experimentally grown crystals. Although surface chemistry of the slow-growing {001} face comprises large sterically hindering phenyl groups, although weaker coulombic interactions still prevail from the alcohol group present on the phenyl and hydroxymethyl groups. The surface chemistry of the faster growing {010} and {100} faces are dominated by the significantly stronger cation/anion interactions occurring between the carboxylate and protonated secondary ammonium ion groups. The importance of understanding the cohesive and adhesive nature of the crystal surfaces of an active pharmaceutical ingredient, with respect to their interaction with other active pharmaceutical ingredient crystals and how that may affect formulation design, is highlighted.

  19. Intermolecular interactions and solvent diffusion in ordered nanostructures formed by self-assembly of block copolymers

    NASA Astrophysics Data System (ADS)

    Gu, Zhiyong

    Hydrogels formed by Poloxamer poly(ethylene oxide)-poly(propylene oxide) (PEO-PPO) block copolymers find various pharmaceutical and biomedical applications. A variety of ordered structures can be exhibited by Poloxamer block copolymers in selective solvents such as water, for example, micellar cubic phase, hexagonal phase, lamellar phase, etc. We are interested in the thermodynamic and transport properties of water in such hydrogels that have an ordered (lyotropic liquid crystalline) structure. We have investigated the time evolution of water loss from Poloxamer gel films under a driving force of known water vapor pressure in the air in contact with the film. The experimental data on the drying process have been fitted to the diffusion equation for water in the film, under a boundary condition that includes the water concentration in the gel at infinite time; the water diffusion coefficient and other parameters have thus been obtained. The water chemical potential and osmotic pressure in the gel have been obtained from osmotic stress measurements. The osmotic pressure (force), together with data on the corresponding lyotropic liquid crystal spacing (distance) that we obtained from Small Angle X-Ray Scattering (SAXS) measurements, have been analyzed to provide information on the prevailing intermolecular (inter-assembly) forces in the gel. The forces in the gel reveal interactions that occur at two levels, that of the PEO coil and that of the PEO segment.

  20. Organocatalytic asymmetric assembly reactions for the syntheses of carbohydrate derivatives by intermolecular Michael-Henry reactions

    PubMed Central

    Uehara, Hisatoshi; Imashiro, Ritsuo; Hernández-Torres, Gloria; Barbas, Carlos F.

    2010-01-01

    Given the significance of carbohydrates in life, medicine, and industry, the development of simple and efficient de novo methods to synthesize carbohydrates are highly desirable. Organocatalytic asymmetric assembly reactions are powerful tools to rapidly construct molecules with stereochemical complexity from simple precursors. Here, we present a simple and robust methodology for the asymmetric synthesis of pyranose derivatives with talo- and manno- configurations from simple achiral precursors through organocatalytic asymmetric intermolecular Michael–Henry reaction sequences. In this process, (tert-butyldimethylsilyloxy)acetaldehyde 1 was successfully utilized in two ways: as a donor in a highly selective anti-Michael reaction and as an acceptor in a consecutive Henry reaction. Varied nitroolefins served as Michael acceptors and varied aldehydes substituted for 1 as Henry acceptors providing for the construction of a wide range of carbohydrates with up to 5 stereocenters. In these reactions, a catalyst-controlled Michael reaction followed by a substrate-controlled Henry reaction provided 3,4-dideoxytalose derivatives 6 in a highly stereoselective manner. The Henry reaction was affected by addition of a simple base such as triethylamine: A complex chiral base was not necessary. 3,4-Dideoxymannose derivatives 7 were produced by simply changing the base from triethylamine to 1,8-diazabicyclo[5.4.0]undec-7-ene. Extension of this methodology to a syn-Michael initiated sequence was also successful. A mechanistic discussion is provided to explain the unusual substrate-induced stereoselectivity of the Henry reaction. PMID:20639468

  1. Phase behavior, intermolecular interaction, and solid state characterization of amorphous solid dispersion of Febuxostat.

    PubMed

    Kini, Ashwini; Patel, Sarsvatkumar B

    2017-02-01

    The aim of this work was to prepare and characterize the amorphous molecular dispersion of Febuxostat (FXT) using PVP K30, HPMC-AS, Soluplus®, and PVP VA64. The solid dispersions were prepared by solvent evaporation technique. Their physical properties were studied by differential scanning calorimetry, powder X-ray diffraction, Fourier transformation infrared spectroscopy, and compared to that of same physical mixtures. The success of physicochemical stability of the dispersions is often revealed as glass transition temperature (Tg) versus composition (w) dependencies. The shape of the Tg versus composition was mathematically modeled using the Gordon-Taylor equation, Couchman-Karasz equation, Brekner-Schneider-Cantow equation, and a three-parameter BCKV equation. In this work, different types of Tg patterns obtained for FXT-polymer binary mixtures are analyzed in terms of the above equations and relations between their prime fitting parameters are presented. The theoretical values and modeled parameters were compared using various results obtained by thermal analysis. The influence of important physicochemical phenomena and properties of the mixtures on the shape of the Tg versus composition patterns are also illustrated. The interaction between drug and polymers and the model parameters were analyzed, aiming to assess the state of mixing and intermolecular interactions.

  2. An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidase

    SciTech Connect

    Wong, Jaslyn E. M. M.; Midtgaard, Søren Roi; Gysel, Kira; Thygesen, Mikkel B.; Sørensen, Kasper K.; Jensen, Knud J.; Stougaard, Jens; Thirup, Søren; Blaise, Mickaël

    2015-03-01

    The crystal and solution structures of the T. thermophilus NlpC/P60 d, l-endopeptidase as well as the co-crystal structure of its N-terminal LysM domains bound to chitohexaose allow a proposal to be made regarding how the enzyme recognizes peptidoglycan. LysM domains, which are frequently present as repetitive entities in both bacterial and plant proteins, are known to interact with carbohydrates containing N-acetylglucosamine (GlcNAc) moieties, such as chitin and peptidoglycan. In bacteria, the functional significance of the involvement of multiple LysM domains in substrate binding has so far lacked support from high-resolution structures of ligand-bound complexes. Here, a structural study of the Thermus thermophilus NlpC/P60 endopeptidase containing two LysM domains is presented. The crystal structure and small-angle X-ray scattering solution studies of this endopeptidase revealed the presence of a homodimer. The structure of the two LysM domains co-crystallized with N-acetyl-chitohexaose revealed a new intermolecular binding mode that may explain the differential interaction between LysM domains and short or long chitin oligomers. By combining the structural information with the three-dimensional model of peptidoglycan, a model suggesting how protein dimerization enhances the recognition of peptidoglycan is proposed.

  3. Hydrogen versus fluorine: effects on molecular structure and intermolecular interactions in a platinum isocyanate complex.

    PubMed

    Raven, William; Joschko, Thomas; Kalf, Irmgard; Englert, Ulli

    2016-03-01

    At the molecular level, the enantiomerically pure square-planar organoplatinum complex (SP-4-4)-(R)-[2-(1-aminoethyl)-5-fluorophenyl-κ(2)C(1),N][(R)-1-(4-fluorophenyl)ethylamine-κN](isocyanato-κN)platinum(II), [Pt(C8H9FN)(NCO)(C8H10FN)], and its congener without fluorine substituents on the aryl rings adopt the same structure within error. The similarities between the compounds extend to the most relevant intermolecular interactions, i.e. N-H...O and N-H...N hydrogen bonds link neighbouring molecules into chains along the shortest lattice parameter in each structure. Differences between the crystal structures of the fluoro-substituted and parent complex become obvious with respect to secondary interactions perpendicular to the classical hydrogen bonds; the fluorinated compound features short C-H...F contacts with an F...H distance of ca 2.6 Å. The fluorine substitution is also reflected in reduced backbonding from the metal cation to the isocyanate ligand.

  4. Application of atomic force microscopy for characteristics of single intermolecular interactions.

    PubMed

    Safenkova, I V; Zherdev, A V; Dzantievf, B B

    2012-12-01

    Atomic force microscopy (AFM) can be used to make measurements in vacuum, air, and water. The method is able to gather information about intermolecular interaction forces at the level of single molecules. This review encompasses experimental and theoretical data on the characterization of ligand-receptor interactions by AFM. The advantage of AFM in comparison with other methods developed for the characterization of single molecular interactions is its ability to estimate not only rupture forces, but also thermodynamic and kinetic parameters of the rupture of a complex. The specific features of force spectroscopy applied to ligand-receptor interactions are examined in this review from the stage of the modification of the substrate and the cantilever up to the processing and interpretation of the data. We show the specificities of the statistical analysis of the array of data based on the results of AFM measurements, and we discuss transformation of data into thermodynamic and kinetic parameters (kinetic dissociation constant, Gibbs free energy, enthalpy, and entropy). Particular attention is paid to the study of polyvalent interactions, where the definition of the constants is hampered due to the complex stoichiometry of the reactions.

  5. Modeling and simulation of magnetic resonance imaging based on intermolecular multiple quantum coherences

    NASA Astrophysics Data System (ADS)

    Cai, Congbo; Dong, Jiyang; Cai, Shuhui; Cheng, En; Chen, Zhong

    2006-11-01

    Intermolecular multiple quantum coherences (iMQCs) have many potential applications since they can provide interaction information between different molecules within the range of dipolar correlation distance, and can provide new contrast in magnetic resonance imaging (MRI). Because of the non-localized property of dipolar field, and the non-linear property of the Bloch equations incorporating the dipolar field term, the evolution behavior of iMQC is difficult to deduce strictly in many cases. In such cases, simulation studies are very important. Simulation results can not only give a guide to optimize experimental conditions, but also help analyze unexpected experimental results. Based on our product operator matrix and the K-space method for dipolar field calculation, the MRI simulation software was constructed, running on Windows operation system. The non-linear Bloch equations are calculated by a fifth-order Cash-Karp Runge-Kutta formulism. Computational time can be efficiently reduced by separating the effects of chemical shifts and strong gradient field. Using this software, simulation of different kinds of complex MRI sequences can be done conveniently and quickly on general personal computers. Some examples were given. The results were discussed.

  6. Intermolecular Interactions in the TMEM16A Dimer Controlling Channel Activity

    PubMed Central

    Scudieri, Paolo; Musante, Ilaria; Gianotti, Ambra; Moran, Oscar; Galietta, Luis J. V.

    2016-01-01

    TMEM16A and TMEM16B are plasma membrane proteins with Ca2+-dependent Cl− channel function. By replacing the carboxy-terminus of TMEM16A with the equivalent region of TMEM16B, we obtained channels with potentiation of channel activity. Progressive shortening of the chimeric region restricted the “activating domain” to a short sequence close to the last transmembrane domain and led to TMEM16A channels with high activity at very low intracellular Ca2+ concentrations. To elucidate the molecular mechanism underlying this effect, we carried out experiments based on double chimeras, Forster resonance energy transfer, and intermolecular cross-linking. We also modeled TMEM16A structure using the Nectria haematococca TMEM16 protein as template. Our results indicate that the enhanced activity in chimeric channels is due to altered interaction between the carboxy-terminus and the first intracellular loop in the TMEM16A homo-dimer. Mimicking this perturbation with a small molecule could be the basis for a pharmacological stimulation of TMEM16A-dependent Cl− transport. PMID:27929144

  7. Intermolecular forces in spread phospholipid monolayers at oil/water interfaces.

    PubMed

    Mingins, James; Pethica, Brian A

    2004-08-31

    The lateral intermolecular forces between phospholipids are of particular relevance to the behavior of biomembranes, and have been approached via studies of monolayer isotherms at aqueous interfaces, mostly restricted to air/water (A/W) systems. For thermodynamic properties, the oil/water (O/W) interface has major advantages but is experimentally more difficult and less studied. A comprehensive reanalysis of the available thermodynamic data on spread monolayers of phosphatidyl cholines (PC) and phosphatidyl ethanolamines (PE) at O/W interfaces is conducted to identify the secure key features that will underpin further development of molecular models. Relevant recourse is made to isotherms of single-chain molecules and of mixed monolayers to identify the contributions of chain-chain interactions and interionic forces. The emphasis is on the properties of the phase transitions for a range of oil phases. Apparent published discrepancies in thermodynamic properties are resolved and substantial agreement emerges on the main features of these phospholipid monolayer systems. In compression to low areas, the forces between the zwitterions of like phospholipids are repulsive. The molecular model for phospholipid headgroup interactions developed by Stigter et al. accounts well for the virial coefficients in expanded phospholipid O/W monolayers. Inclusion of the changes in configuration and orientation of the zwitterion headgroups on compression, which are indicated by the surface potentials in the phase transition region, and inclusion of the energy of chain demixing from the oil phase will be required for molecular modeling of the phase transitions.

  8. Keto-enol tautomerization and intermolecular proton transfer in photoionized cyclopentanone dimer in the gas phase

    SciTech Connect

    Ghosh, Arup K.; Chatterjee, Piyali; Chakraborty, Tapas

    2014-07-28

    Time-of-flight mass spectra of cyclopentanone and its clusters cooled in a supersonic jet expansion have been measured following 4-, 3-, and 2-photon ionizations by the 2nd, 3rd, and 4th harmonic wavelengths, respectively, of a Q-switched Nd:YAG laser. The mass spectra reveal signatures of energetically favored keto to enol tautomerization of the molecular ion leading to intermolecular proton transfer, and this observation is found sharply dependent on the ionization wavelengths used. Electronic structure calculation predicts that in spite of the energetic preference, keto-enol conversion barrier of isolated molecular ion is high. However, the barrier is significantly reduced in a CH⋯O hydrogen-bonded dimer of the molecule. The transition states associated with tautomeric conversion of both cyclopentanone monomer and dimer cations have been identified by means of intrinsic reaction co-ordinate calculation. In a supersonic jet expansion, although a weakly bound dimer is readily generated, the corresponding cation and also the protonated counterpart are observed only for ionization by 532 nm. For other two ionization wavelengths, these species do not register in the mass spectra, where the competing reaction channels via α-cleavage of the ring become dominant. In contrast to the report of a recent study, we notice that the intact molecular ion largely survives fragmentations when ionized from the 2-photon resonant 3p Rydberg state as intermediate using nanosecond laser pulses, and the corresponding resonant 3-photon ionization spectrum has been recorded probing the intact molecular ion.

  9. Intermolecular potentials and the accurate prediction of the thermodynamic properties of water

    NASA Astrophysics Data System (ADS)

    Shvab, I.; Sadus, Richard J.

    2013-11-01

    The ability of intermolecular potentials to correctly predict the thermodynamic properties of liquid water at a density of 0.998 g/cm3 for a wide range of temperatures (298-650 K) and pressures (0.1-700 MPa) is investigated. Molecular dynamics simulations are reported for the pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, and Joule-Thomson coefficient of liquid water using the non-polarizable SPC/E and TIP4P/2005 potentials. The results are compared with both experiment data and results obtained from the ab initio-based Matsuoka-Clementi-Yoshimine non-additive (MCYna) [J. Li, Z. Zhou, and R. J. Sadus, J. Chem. Phys. 127, 154509 (2007)] potential, which includes polarization contributions. The data clearly indicate that both the SPC/E and TIP4P/2005 potentials are only in qualitative agreement with experiment, whereas the polarizable MCYna potential predicts some properties within experimental uncertainty. This highlights the importance of polarizability for the accurate prediction of the thermodynamic properties of water, particularly at temperatures beyond 298 K.

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

    PubMed

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

    2014-03-01

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

  11. Photophysical and computational investigation of the intermolecular interactions of pyrene with phenothiazine and promazine

    NASA Astrophysics Data System (ADS)

    Güloğlu, Pınar; Acar, Nursel

    2016-10-01

    The intermolecular interactions between the pyrene (Py) (as acceptor) and phenothiazine (Pheno), promazine (Prom) (as donors) were investigated using UV/Vis absorption and fluorescence spectroscopy. Fluorescence quenching rate constants for Py-Pheno and Py-Prom systems have been calculated approximately 1010 M-1 s-1, indicating diffusion controlled processes. A computational investigation has also been carried out in gas phase at ωB97XD/6-31G(d,p) level. Time-dependent density functional theory (TDDFT) was used to calculate the electronic transitions of molecules at B3LYP/6-311++G(d,p) level. Total electronic energies, complexation energies, free energy differences, excitation wavelengths, and HOMO-LUMO energy gaps are discussed in gas phase. Analyses of first excited singlet states have indicated charge transfers transitions between Py and Pheno, Prom through π-π stacking in gas phase at 433 nm and 466 nm, respectively. Due to its charge transfer character, Py-Pheno and Py-Prom systems seem to be appropriate models to investigate and design photosensitive materials.

  12. Inter-molecular β-sheet structure facilitates lung-targeting siRNA delivery

    PubMed Central

    Zhou, Jihan; Li, Dong; Wen, Hao; Zheng, Shuquan; Su, Cuicui; Yi, Fan; Wang, Jue; Liang, Zicai; Tang, Tao; Zhou, Demin; Zhang, Li-He; Liang, Dehai; Du, Quan

    2016-01-01

    Size-dependent passive targeting based on the characteristics of tissues is a basic mechanism of drug delivery. While the nanometer-sized particles are efficiently captured by the liver and spleen, the micron-sized particles are most likely entrapped within the lung owing to its unique capillary structure and physiological features. To exploit this property in lung-targeting siRNA delivery, we designed and studied a multi-domain peptide named K-β, which was able to form inter-molecular β-sheet structures. Results showed that K-β peptides and siRNAs formed stable complex particles of 60 nm when mixed together. A critical property of such particles was that, after being intravenously injected into mice, they further associated into loose and micron-sized aggregates, and thus effectively entrapped within the capillaries of the lung, leading to a passive accumulation and gene-silencing. The large size aggregates can dissociate or break down by the shear stress generated by blood flow, alleviating the pulmonary embolism. Besides the lung, siRNA enrichment and targeted gene silencing were also observed in the liver. This drug delivery strategy, together with the low toxicity, biodegradability, and programmability of peptide carriers, show great potentials in vivo applications. PMID:26955887

  13. Resolution enhancement in MR spectroscopy of red bone marrow fat via intermolecular double-quantum coherences

    NASA Astrophysics Data System (ADS)

    Bao, Jianfeng; Cui, Xiaohong; Huang, Yuqing; Zhong, Jianhui; Chen, Zhong

    2015-08-01

    High-resolution 1H magnetic resonance spectroscopy (MRS) is generally inaccessible in red bone marrow (RBM) tissues using conventional MRS techniques. This is because signal from these tissues suffers from severe inhomogeneity in the main static B0 field originated from the intrinsic honeycomb structures in trabecular bone. One way to reduce effects of B0 field inhomogeneity is by using the intermolecular double quantum coherence (iDQC) technique, which has been shown in other systems to obtain signals insensitive to B0 field inhomogeneity. In the present study, we employed an iDQC approach to enhance the spectral resolution of RBM. The feasibility and performance of this method for achieving high resolution MRS was verified by experiments on phantoms and pig vertebral bone samples. Unsaturated fatty acid peaks which overlap in the conventional MRS were well resolved and identified in the iDQC spectrum. Quantitative comparison of fractions of three types of fatty acids was performed between iDQC spectra on the in situ RMB and conventional MRS on the extracted fat from the same RBM. Observations of unsaturated fatty acids with iDQC MRS may provide valuable information and may hold potential in diagnosis of diseases such as obesity, diabetes, and leukemia.

  14. In Vivo Noninvasive Detection of Brown Adipose Tissue through Intermolecular Zero-Quantum MRI

    PubMed Central

    Branca, Rosa T.; Zhang, Le; Warren, Warren S.; Auerbach, Edward; Khanna, Arjun; Degan, Simone; Ugurbil, Kamil; Maronpot, Robert

    2013-01-01

    The recent discovery of active Brown Adipose Tissue (BAT) in adult humans has opened new avenues for obesity research and treatment, as reduced BAT activity seem to be implicated in human energy imbalance, diabetes, and hypertension. However, clinical applications are currently limited by the lack of non-invasive tools for measuring mass and function of this tissue in humans. Here we present a new magnetic resonance imaging method based on the normally invisible intermolecular multiple-quantum coherence 1H MR signal. This method, which doesn’t require special hardware modifications, can be used to overcome partial volume effect, the major limitation of MR-based approaches that are currently being investigated for the detection of BAT in humans. With this method we can exploit the characteristic cellular structure of BAT to selectively image it, even when (as in humans) it is intimately mixed with other tissues. We demonstrate and validate this method in mice using PET scans and histology. We compare this methodology with conventional 1H MR fat fraction methods. Finally, we investigate its feasibility for the detection of BAT in humans. PMID:24040203

  15. On the influence of the intermolecular potential on the wetting properties of water on silica surfaces

    NASA Astrophysics Data System (ADS)

    Pafong, E.; Geske, J.; Drossel, B.

    2016-09-01

    We study the wetting properties of water on silica surfaces using molecular dynamics (MD) simulations. To describe the intermolecular interaction between water and silica atoms, two types of interaction potential models are used: the standard BródkA and Zerda (BZ) model and the Gulmen and Thompson (GT) model. We perform an in-depth analysis of the influence of the choice of the potential on the arrangement of the water molecules in partially filled pores and on top of silica slabs. We find that at moderate pore filling ratios, the GT silica surface is completely wetted by water molecules, which agrees well with experimental findings, while the commonly used BZ surface is less hydrophilic and is only partially wetted. We interpret our simulation results using an analytical calculation of the phase diagram of water in partially filled pores. Moreover, an evaluation of the contact angle of the water droplet on top of the silica slab reveals that the interaction becomes more hydrophilic with increasing slab thickness and saturates around 2.5-3 nm, in agreement with the experimentally found value. Our analysis also shows that the hydroaffinity of the surface is mainly determined by the electrostatic interaction, but the van der Waals interaction nevertheless is strong enough that it can turn a hydrophobic surface into a hydrophilic surface.

  16. A heuristic approach to evaluate peri interactions versus intermolecular interactions in an overcrowded naphthalene

    PubMed Central

    Row, Tayur N. Guru

    2017-01-01

    Octachloronaphthalene (OCN), a serious environmental pollutant, has been investigated by charge density analysis to unravel several unexplored factors responsible for steric overcrowding. The topological features of the enigmatic peri interactions contributing to steric overcrowding are qualified and quantified from experimental and theoretical charge-density studies. A new facet in the fundamental understanding of peri interactions is revealed by NCI (non-covalent interaction) analysis. The potential role of these interactions in deforming the molecular geometry and subsequent effect on aromaticity are substantiated from NICS (Nuclear Independent Chemical Shift) and QTAIM (Quantum Theory of Atoms in Molecules) calculations. The eye-catching dissimilarity in the out-of-plane twisting of OCN renders the molecule in an asymmetric geometry in the crystalline phase compared with symmetric geometry in the optimized solvated phase. This is uniquely characterized by their molecular electrostatic potential (MESP), respectively, and is explained in terms of conflict between two opposing forces – peri interactions, and symbiotic intermolecular Cl⋯Cl and Cl⋯π contacts. PMID:28250940

  17. Intermolecular potentials and the accurate prediction of the thermodynamic properties of water.

    PubMed

    Shvab, I; Sadus, Richard J

    2013-11-21

    The ability of intermolecular potentials to correctly predict the thermodynamic properties of liquid water at a density of 0.998 g∕cm(3) for a wide range of temperatures (298-650 K) and pressures (0.1-700 MPa) is investigated. Molecular dynamics simulations are reported for the pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, and Joule-Thomson coefficient of liquid water using the non-polarizable SPC∕E and TIP4P∕2005 potentials. The results are compared with both experiment data and results obtained from the ab initio-based Matsuoka-Clementi-Yoshimine non-additive (MCYna) [J. Li, Z. Zhou, and R. J. Sadus, J. Chem. Phys. 127, 154509 (2007)] potential, which includes polarization contributions. The data clearly indicate that both the SPC∕E and TIP4P∕2005 potentials are only in qualitative agreement with experiment, whereas the polarizable MCYna potential predicts some properties within experimental uncertainty. This highlights the importance of polarizability for the accurate prediction of the thermodynamic properties of water, particularly at temperatures beyond 298 K.

  18. On the intermolecular Coulombic decay of singly and doubly ionized states of water dimer.

    PubMed

    Stoychev, Spas D; Kuleff, Alexander I; Cederbaum, Lorenz S

    2010-10-21

    A semiquantitative study of the intermolecular Coulombic decay (ICD) of singly and doubly ionized water dimer has been carried out with the help of ab initio computed ionization spectra and potential energy curves (PECs). These PECs are particular cuts through the (H(2)O)(2), (H(2)O)(2) (+), and (H(2)O)(2) (++) hypersurfaces along the distance between the two oxygen atoms. A comparison with the recently published experimental data for the ICD in singly ionized water dimers [T. Jahnke, H. Sann, T. Havermeier et al., Nat. Phys. 6, 139 (2010)] and in large water clusters [M. Mucke, M. Braune, S. Barth et al., Nat. Phys. 6, 143 (2010)] shows that such a simplified description in which the internal degrees of freedom of the water molecules are frozen gives surprisingly useful results. Other possible decay channels of the singly ionized water dimer are also investigated and the influence of the H-atom participating in the hydrogen bond on the spectra of the proton-donor and proton-acceptor molecules in the dimer is discussed. Importantly, the decay processes of one-site dicationic states of water dimer are discussed and an estimate of the ICD-electron spectra is made. More than 33% of the dications produced by Auger decay are found to undergo ICD. The qualitative results show that the ICD following Auger decay in water is also expected to be an additional source of low-energy electrons proven to be extremely important for causing damages to living tissues.

  19. Intermolecular electron transfer from naphthalene derivatives in the higher triplet excited states.

    PubMed

    Sakamoto, Masanori; Cai, Xichen; Hara, Michihiro; Fujitsuka, Mamoru; Majima, Tetsuro

    2004-08-11

    Intermolecular electron transfer (ELT) from a series of naphthalene derivatives (NpD) in the higher triplet excited states (T(n)) to carbon tetrachloride (CCl(4)) in Ar-saturated acetonitrile was observed using the two-color two-laser flash photolysis method. The ELT efficiency depended on the driving force of ELT. Since the ELT from the T(n) state occurred competitively with the internal conversion (IC, T(n) --> T(1)) and the triplet energy transfer (ENT), the ELT became apparent only when sufficient free energy change of ELT was attained. On the other hand, ELT from the T(1) state was not observed, although ELT from the T(1) state with sufficiently long lifetime has a slightly exothermic driving force. The fast ELT from the T(n) state and lack of the reactivity of the T(1) state were explained well by the "sticky" dissociative electron-transfer model based on one-electron reductive attachment to CCl(4) leading to the C-Cl bond cleavage.

  20. Intermolecular Interactions in the TMEM16A Dimer Controlling Channel Activity

    NASA Astrophysics Data System (ADS)

    Scudieri, Paolo; Musante, Ilaria; Gianotti, Ambra; Moran, Oscar; Galietta, Luis J. V.

    2016-12-01

    TMEM16A and TMEM16B are plasma membrane proteins with Ca2+-dependent Cl‑ channel function. By replacing the carboxy-terminus of TMEM16A with the equivalent region of TMEM16B, we obtained channels with potentiation of channel activity. Progressive shortening of the chimeric region restricted the “activating domain” to a short sequence close to the last transmembrane domain and led to TMEM16A channels with high activity at very low intracellular Ca2+ concentrations. To elucidate the molecular mechanism underlying this effect, we carried out experiments based on double chimeras, Forster resonance energy transfer, and intermolecular cross-linking. We also modeled TMEM16A structure using the Nectria haematococca TMEM16 protein as template. Our results indicate that the enhanced activity in chimeric channels is due to altered interaction between the carboxy-terminus and the first intracellular loop in the TMEM16A homo-dimer. Mimicking this perturbation with a small molecule could be the basis for a pharmacological stimulation of TMEM16A-dependent Cl‑ transport.

  1. Chemical Dynamics Simulations of Intermolecular Energy Transfer: Azulene + N2 Collisions.

    PubMed

    Kim, Hyunsik; Paul, Amit K; Pratihar, Subha; Hase, William L

    2016-07-14

    Chemical dynamics simulations were performed to investigate collisional energy transfer from highly vibrationally excited azulene (Az*) in a N2 bath. The intermolecular potential between Az and N2, used for the simulations, was determined from MP2/6-31+G* ab initio calculations. Az* is prepared with an 87.5 kcal/mol excitation energy by using quantum microcanonical sampling, including its 95.7 kcal/mol zero-point energy. The average energy of Az* versus time, obtained from the simulations, shows different rates of Az* deactivation depending on the N2 bath density. Using the N2 bath density and Lennard-Jones collision number, the average energy transfer per collision ⟨ΔEc⟩ was obtained for Az* as it is collisionally relaxed. By comparing ⟨ΔEc⟩ versus the bath density, the single collision limiting density was found for energy transfer. The resulting ⟨ΔEc⟩, for an 87.5 kcal/mol excitation energy, is 0.30 ± 0.01 and 0.32 ± 0.01 kcal/mol for harmonic and anharmonic Az potentials, respectively. For comparison, the experimental value is 0.57 ± 0.11 kcal/mol. During Az* relaxation there is no appreciable energy transfer to Az translation and rotation, and the energy transfer is to the N2 bath.

  2. Structure and polarization properties of water: molecular dynamics with a nonadditive intermolecular potential.

    PubMed

    Shvab, I; Sadus, Richard J

    2012-05-01

    The temperature and density dependence of the structure and polarization properties of bulk water were systematically investigated using the ab initio MCYna potential [Li et al., J. Chem. Phys. 127, 154509 (2007)], which includes nonadditive contributions to intermolecular interactions. Molecular dynamics simulations were conducted for isochores of 1, 0.8, and 0.6 g/cm^{3} and temperatures from 278 to 750 K. Special attention was paid to the structural change of water in the range from the normal boiling point to supercritical temperatures. At temperatures below the normal boiling temperature, water exhibits a tetrahedral structure along the 0.8 and 0.6 g/cm^{3} isochores. A significant collapse of the hydrogen bonding network was observed at temperatures of 450, 550, and 650 K. The MCYna potential was able to successfully reproduce the experimental dielectric constant. The dielectric constant and average dipole moments decrease with increasing temperature and decreasing density due to weakened polarization. A comparison is also made with SPC-based models.

  3. Anti-plasticizing effect of amorphous indomethacin induced by specific intermolecular interactions with PVA copolymer.

    PubMed

    Ueda, Hiroshi; Aikawa, Shohei; Kashima, Yousuke; Kikuchi, Junko; Ida, Yasuo; Tanino, Tadatsugu; Kadota, Kazunori; Tozuka, Yuichi

    2014-09-01

    The mechanism of how poly(vinyl alcohol-co-acrylic acid-co-methyl methacrylate) (PVA copolymer) stabilizes an amorphous drug was investigated. Solid dispersions of PVA copolymer, poly(vinyl pyrrolidone) (PVP), and poly(vinyl pyrrolidone-co-vinyl acetate) (PVPVA) with indomethacin (IMC) were prepared. The glass transition temperature (Tg)-proportion profiles were evaluated by differential scanning calorimetry (DSC). General Tg profiles decreasing with the IMC ratio were observed for IMC-PVP and IMC-PVPVA samples. An interesting antiplasticizing effect of IMC on PVA copolymer was observed; Tg increased up to 20% IMC ratio. Further addition of IMC caused moderate reduction with positive deviation from theoretical values. Specific hydrophilic and hydrophobic interactions between IMC and PVA copolymer were revealed by infrared spectra. The indole amide of IMC played an important role in hydrogen bonding with PVA copolymer, but not with PVP and PVPVA. X-ray diffraction findings and the endotherm on DSC profiles suggested that PVA copolymer could form a semicrystalline structure and a possibility of correlation of the crystallographic nature with its low hygroscopicity was suggested. PVA copolymer was able to prevent crystallization of amorphous IMC through both low hygroscopicity and the formation of a specific intermolecular interaction compared with that with PVP and PVPVA.

  4. Solubility Challenges in High Concentration Monoclonal Antibody Formulations: Relationship with Amino Acid Sequence and Intermolecular Interactions.

    PubMed

    Pindrus, Mariya; Shire, Steven J; Kelley, Robert F; Demeule, Barthélemy; Wong, Rita; Xu, Yiren; Yadav, Sandeep

    2015-11-02

    The purpose of this work was to elucidate the molecular interactions leading to monoclonal antibody self-association and precipitation and utilize biophysical measurements to predict solubility behavior at high protein concentration. Two monoclonal antibodies (mAb-G and mAb-R) binding to overlapping epitopes were investigated. Precipitation of mAb-G solutions was most prominent at high ionic strength conditions and demonstrated strong dependence on ionic strength, as well as slight dependence on solution pH. At similar conditions no precipitation was observed for mAb-R solutions. Intermolecular interactions (interaction parameter, kD) related well with high concentration solubility behavior of both antibodies. Upon increasing buffer ionic strength, interactions of mAb-R tended to weaken, while those of mAb-G became more attractive. To investigate the role of amino acid sequence on precipitation behavior, mutants were designed by substituting the CDR of mAb-R into the mAb-G framework (GM-1) or deleting two hydrophobic residues in the CDR of mAb-G (GM-2). No precipitation was observed at high ionic strength for either mutant. The molecular interactions of mutants were similar in magnitude to those of mAb-R. The results suggest that presence of hydrophobic groups in the CDR of mAb-G may be responsible for compromising its solubility at high ionic strength conditions since deleting these residues mitigated the solubility issue.

  5. Intermolecular Interactions in the TMEM16A Dimer Controlling Channel Activity.

    PubMed

    Scudieri, Paolo; Musante, Ilaria; Gianotti, Ambra; Moran, Oscar; Galietta, Luis J V

    2016-12-08

    TMEM16A and TMEM16B are plasma membrane proteins with Ca(2+)-dependent Cl(-) channel function. By replacing the carboxy-terminus of TMEM16A with the equivalent region of TMEM16B, we obtained channels with potentiation of channel activity. Progressive shortening of the chimeric region restricted the "activating domain" to a short sequence close to the last transmembrane domain and led to TMEM16A channels with high activity at very low intracellular Ca(2+) concentrations. To elucidate the molecular mechanism underlying this effect, we carried out experiments based on double chimeras, Forster resonance energy transfer, and intermolecular cross-linking. We also modeled TMEM16A structure using the Nectria haematococca TMEM16 protein as template. Our results indicate that the enhanced activity in chimeric channels is due to altered interaction between the carboxy-terminus and the first intracellular loop in the TMEM16A homo-dimer. Mimicking this perturbation with a small molecule could be the basis for a pharmacological stimulation of TMEM16A-dependent Cl(-) transport.

  6. Intermolecular proton-transfer in acetic acid clusters induced by vacuum-ultraviolet photoionization

    NASA Astrophysics Data System (ADS)

    Ohta, Keisuke; Matsuda, Yoshiyuki; Mikami, Naohiko; Fujii, Asuka

    2009-11-01

    Infrared (IR) spectroscopy based on vacuum-ultraviolet one-photon ionization detection was carried out to investigate geometric structures of neutral and cationic clusters of acetic acid: (CH3COOH)2, CH3COOH-CH3OH, and CH3COOH-H2O. All the neutral clusters have cyclic-type intermolecular structures, in which acetic acid and solvent molecules act as both hydrogen donors and acceptors, and two hydrogen-bonds are formed. On the other hand, (CH3COOH)2+ and (CH3COOH-CH3OH)+ form proton-transferred structures, where the acetic acid moiety donates the proton to the counter molecule. (CH3COOH-H2O)+ has a non-proton-transferred structure, where CH3COOH+ and H2O are hydrogen-bonded. The origin of these structural differences among the cluster cations is discussed with the relative sizes of the proton affinities of the cluster components and the potential energy curves along the proton-transfer coordinate.

  7. Intermolecular and intramolecular hydrogen bonds involving fluorine atoms: implications for recognition, selectivity, and chemical properties.

    PubMed

    Dalvit, Claudio; Vulpetti, Anna

    2012-02-06

    A correlation between 19F NMR isotropic chemical shift and close intermolecular F⋅⋅⋅H-X contacts (with X=N or O) has been identified upon analysis of the X-ray crystal structures of fluorinated molecules listed in the Cambridge Structural Database (CSD). An optimal F⋅⋅⋅X distance involving primary and shielded secondary fluorine atoms in hydrogen-bond formation along with a correlation between F⋅⋅⋅H distance and F⋅⋅⋅H-X angle were also derived from the analysis. The hydrogen bonds involving fluorine are relevant, not only for the recognition mechanism and stabilization of a preferred conformation, but also for improvement in the permeability of the molecules, as shown with examples taken from a proprietary database. Results of an analysis of the small number of fluorine-containing natural products listed in the Protein Data Bank (PDB) appear to strengthen the derived correlation between 19F NMR isotropic chemical shift and interactions involving fluorine (also known as the "rule of shielding") and provides a hypothesis for the recognition mechanism and catalytic activity of specific enzymes. Novel chemical scaffolds, based on the rule of shielding, have been designed for recognizing distinct structural motifs present in proteins. It is envisaged that this approach could find useful applications in drug design for the efficient optimization of chemical fragments or promising compounds by increasing potency and selectivity against the desired biomolecular target.

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

  9. Effects of intermolecular interactions on the stability of carbon nanotube–gold nanoparticle conjugates in solution

    PubMed Central

    Konczak, Lukasz; Narkiewicz-Michalek, Jolanta; Pastorin, Giorgia; Panczyk, Tomasz

    2016-01-01

    This work deals with the role of intermolecular interactions in the stability of a carbon nanotube (CNT) capped by functionalized gold nanoparticles (AuNPs). The importance of such a system is due to its potential application as a pH-controlled drug carrier. Our preliminary experimental studies showed that fabrication of such a nanobottle/nanocontainer is feasible and it is possible to encapsulate the anticancer drug cisplatin inside the inner space of a CNT and seal its ends by functionalized AuNPs. The expected behavior, that is, detachment of AuNPs at acidic pH and the release of cisplatin, was, however, not observed. On the other hand, our theoretical studies of chemically identical system led to the conclusion that the release of cisplatin at acidic pH should be observed. Therefore, in this work, a deeper theoretical analysis of various factors that could be responsible for the disagreement between experimental and theoretical results were performed. The study found that the major factor is a large dispersion interaction component acting between CNT and AuNP in solution in the case of the experimental system. This factor can be controlled to some extent by tuning the system size or the ratio between AuNP diameter and CNT diameter. Thus, such kind of a pH-sensitive drug carrier is still of great interest, but its structural parameters need to be properly adjusted. PMID:27853368

  10. Sensitivity of predicted gas hydrate occupancies on treatment of intermolecular interactions.

    PubMed

    Thomas, Caroline; Picaud, Sylvain; Ballenegger, Vincent; Mousis, Olivier

    2010-03-14

    The sensitivity of gas hydrate occupancies predicted on the basis of van der Waals-Platteeuw theory is investigated, as a function of the intermolecular guest-water interaction potential model, and of the number of water molecules taken into account. Simple analytical correction terms that account for the interactions with the water molecules beyond the cutoff distance are introduced, and shown to improve significantly the convergence rate, and hence the efficiency of the computation of the Langmuir constants. The predicted cage occupancies in pure methane and pure carbon dioxide clathrates, calculated using different recent guest-water pair potentials models derived from ab initio calculations, can vary significantly depending on the model. That sensitivity becomes especially strong in the case of multiple guest clathrates. It is shown that the abundances of coenclathrated molecules in multiple guest clathrate hydrates potentially formed on the surface of Mars can vary by more than two orders of magnitude depending on the model. These results underline the strong need for experimental data on pure and multiple guest clathrate hydrates, in particular in the temperature and pressure range that are relevant in extreme environment conditions, to discriminate among the theoretical models.

  11. Intermolecular potentials and the accurate prediction of the thermodynamic properties of water

    SciTech Connect

    Shvab, I.; Sadus, Richard J.

    2013-11-21

    The ability of intermolecular potentials to correctly predict the thermodynamic properties of liquid water at a density of 0.998 g/cm{sup 3} for a wide range of temperatures (298–650 K) and pressures (0.1–700 MPa) is investigated. Molecular dynamics simulations are reported for the pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, and Joule-Thomson coefficient of liquid water using the non-polarizable SPC/E and TIP4P/2005 potentials. The results are compared with both experiment data and results obtained from the ab initio-based Matsuoka-Clementi-Yoshimine non-additive (MCYna) [J. Li, Z. Zhou, and R. J. Sadus, J. Chem. Phys. 127, 154509 (2007)] potential, which includes polarization contributions. The data clearly indicate that both the SPC/E and TIP4P/2005 potentials are only in qualitative agreement with experiment, whereas the polarizable MCYna potential predicts some properties within experimental uncertainty. This highlights the importance of polarizability for the accurate prediction of the thermodynamic properties of water, particularly at temperatures beyond 298 K.

  12. Inter-molecular β-sheet structure facilitates lung-targeting siRNA delivery

    NASA Astrophysics Data System (ADS)

    Zhou, Jihan; Li, Dong; Wen, Hao; Zheng, Shuquan; Su, Cuicui; Yi, Fan; Wang, Jue; Liang, Zicai; Tang, Tao; Zhou, Demin; Zhang, Li-He; Liang, Dehai; Du, Quan

    2016-03-01

    Size-dependent passive targeting based on the characteristics of tissues is a basic mechanism of drug delivery. While the nanometer-sized particles are efficiently captured by the liver and spleen, the micron-sized particles are most likely entrapped within the lung owing to its unique capillary structure and physiological features. To exploit this property in lung-targeting siRNA delivery, we designed and studied a multi-domain peptide named K-β, which was able to form inter-molecular β-sheet structures. Results showed that K-β peptides and siRNAs formed stable complex particles of 60 nm when mixed together. A critical property of such particles was that, after being intravenously injected into mice, they further associated into loose and micron-sized aggregates, and thus effectively entrapped within the capillaries of the lung, leading to a passive accumulation and gene-silencing. The large size aggregates can dissociate or break down by the shear stress generated by blood flow, alleviating the pulmonary embolism. Besides the lung, siRNA enrichment and targeted gene silencing were also observed in the liver. This drug delivery strategy, together with the low toxicity, biodegradability, and programmability of peptide carriers, show great potentials in vivo applications.

  13. FLEXIBLE COUPLING

    DOEpatents

    Babelay, E.F.

    1962-02-13

    A flexible shaft coupling for operation at speeds in excess of 14,000 rpm is designed which requires no lubrication. A driving sleeve member and a driven sleeve member are placed in concentric spaced relationship. A torque force is transmitted to the driven member from the driving member through a plurality of nylon balls symmetrically disposed between the spaced sleeves. The balls extend into races and recesses within the respective sleeve members. The sleeve members have a suitable clearance therebetween and the balls have a suitable radial clearance during operation of the coupling to provide a relatively loose coupling. These clearances accommodate for both parallel and/or angular misalignments and avoid metal-tometal contact between the sleeve members during operation. Thus, no lubrication is needed, and a minimum of vibrations is transmitted between the sleeve members. (AEC)

  14. Prosthesis coupling

    NASA Technical Reports Server (NTRS)

    Reswick, J. B.; Mooney, V.; Bright, C. W.; Owens, L. J. (Inventor)

    1979-01-01

    A coupling for use in an apparatus for connecting a prosthesis to the bone of a stump of an amputated limb is described which permits a bio-compatible carbon sleeve forming a part of the prosthesis connector to float so as to prevent disturbing the skin seal around the carbon sleeve. The coupling includes a flexible member interposed between a socket that is inserted within an intermedullary cavity of the bone and the sleeve. A lock pin is carried by the prosthesis and has a stem portion which is adapted to be coaxially disposed and slideably within the tubular female socket for securing the prosthesis to the stump. The skin around the percutaneous carbon sleeve is able to move as a result of the flexing coupling so as to reduce stresses caused by changes in the stump shape and/or movement between the bone and the flesh portion of the stump.

  15. The fragment spin difference scheme for triplet-triplet energy transfer coupling

    NASA Astrophysics Data System (ADS)

    You, Zhi-Qiang; Hsu, Chao-Ping

    2010-08-01

    To calculate the electronic couplings in both inter- and intramolecular triplet energy transfer (TET), we have developed the "fragment spin difference" (FSD) scheme. The FSD was a generalization from the "fragment charge difference" (FCD) method of Voityuk et al. [J. Chem. Phys. 117, 5607 (2002)] for electron transfer (ET) coupling. In FSD, the spin population difference was used in place of the charge difference in FCD. FSD is derived from the eigenstate energies and populations, and therefore the FSD couplings contain all contributions in the Hamiltonian as well as the potential overlap effect. In the present work, two series of molecules, all-trans-polyene oligomers and polycyclic aromatic hydrocarbons, were tested for intermolecular TET study. The TET coupling results are largely similar to those from the previously developed direct coupling scheme, with FSD being easier and more flexible in use. On the other hand, the Dexter's exchange integral value, a quantity that is often used as an approximate for the TET coupling, varies in a large range as compared to the corresponding TET coupling. To test the FSD for intramolecular TET, we have calculated the TET couplings between zinc(II)-porphyrin and free-base porphyrin separated by different numbers of p-phenyleneethynylene bridge units. Our estimated rate constants are consistent with experimentally measured TET rates. The FSD method can be used for both intermolecular and intramolecular TET, regardless of their symmetry. This general applicability is an improvement over most existing methodologies.

  16. From H2+ to the multidimensional potential of the intermolecular interaction Ar·HBr: A canonical approach

    NASA Astrophysics Data System (ADS)

    Walton, Jay R.; Rivera-Rivera, Luis A.; Lucchese, Robert R.; Bevan, John W.

    2015-10-01

    A proof-of-concept for the accurate generation of multidimensional intermolecular interaction potentials is demonstrated. The basis for evaluating this application is the available very accurate 3-D morphed potential of Ar·HBr. Starting from the well-defined potential of the simplest molecule, the diatomic H2+, a recently developed 1-D canonical potential is used with selected 2-D polyatomic data to generate the adiabatic intermolecular interaction potential in Ar·HBr, with HBr in the vibrational ground state. This represents the first application of canonical transformations to a higher vibrationally dimensional molecular system, in this case, Ar·HBr. Results indicate intrinsic bonding characteristics inherent to both systems.

  17. Weak intermolecular interactions in 11-chloro-2,3,4,5-tetrahydro-1H-cyclohepta[b]quinoline.

    PubMed

    Novaković, Sladjana B; Vitorović-Todorović, Maja D; Bogdanović, Goran A; Drakulić, Branko J

    2008-09-01

    The title compound, C(14)H(14)ClN, is a chloro analogue of tacrine, an acetylcholinesterase inhibitor. The compound comprises a seven-membered alicyclic ring whose CH donor groups are engaged in extensive intermolecular interactions. The important feature of this crystal structure is that, regardless of the presence of two typical hydrogen-bonding acceptors, viz. chlorine and nitrogen, the corresponding C-H...Cl and C-H...N interactions take no significant role in crystal stabilization. The molecules form dimers through pi-pi interactions with an interplanar distance between interacting pyridine rings of 3.576 (1) A. Within the dimers, the molecules are additionally interconnected by four C-H...pi interactions. The dimers arrange into regular columns via further intermolecular C-H...pi interactions.

  18. Intermolecular hydroamination of ethylene and 1-alkenes with cyclic ureas catalyzed by achiral and chiral gold(I) complexes.

    PubMed

    Zhang, Zhibin; Lee, Seong Du; Widenhoefer, Ross A

    2009-04-22

    Reaction of 1-methyl-imidazolidin-2-one (1) with 1-octene (10 equiv) catalyzed by a 1:1 mixture of (2b)AuCl [2b = 2-di-tert-butylphosphino-1,1'-binaphthyl] and AgSbF(6) in dioxane at 100 degrees C for 24 h led to isolation of 1-methyl-3-(octan-2-yl)imidazolidin-2-one in 96% yield as a single regioisomer. A range of unactivated 1-alkenes and ethylene underwent gold(I)-catalyzed intermolecular hydroamination at or below 100 degrees C in excellent yield with high regioselectivity. Reaction of 1-alkenes with substituted imidazolidin-2-ones catalyzed by chiral bis(gold) phosphine complexes led to enantioselective intermolecular hydroamination with up to 78% ee.

  19. Intermolecular hydrogen bonds in hetero-complexes of biologically active aromatic molecules probed by the methods of vibrational spectroscopy.

    PubMed

    Semenov, M A; Blyzniuk, Iu N; Bolbukh, T V; Shestopalova, A V; Evstigneev, M P; Maleev, V Ya

    2012-09-01

    By the methods of vibrational spectroscopy (Infrared and Raman) the investigation of the hetero-association of biologically active aromatic compounds: flavin-mononucleotide (FMN), ethidium bromide (EB) and proflavine (PRF) was performed in aqueous solutions. It was shown that between the functional groups (CO and NH(2)) the intermolecular hydrogen bonds are formed in the hetero-complexes FMN-EB and FMN-PRF, additionally stabilizing these structures. An estimation of the enthalpy of Н-bonding obtained from experimental shifts of carbonyl vibrational frequencies has shown that the H-bonds do not dominate in the magnitude of experimentally measured total enthalpy of the hetero-association reactions. The main stabilization is likely due to intermolecular interactions of the molecules in these complexes and their interaction with water environment.

  20. Gibb's energy and intermolecular free length of 'Borassus Flabellifier' (BF) and Adansonia digitata (AnD) aqueous binary mixture

    NASA Astrophysics Data System (ADS)

    Phadke, Sushil; Darshan Shrivastava, Bhakt; Ujle, S. K.; Mishra, Ashutosh; Dagaonkar, N.

    2014-09-01

    One of the potential driving forces behind a chemical reaction is favourable a new quantity known as the Gibbs free energy (G) of the system, which reflects the balance between these forces. Ultrasonic velocity and absorption measurements in liquids and liquid mixtures find extensive application to study the nature of intermolecular forces. Ultrasonic velocity measurements have been successfully employed to detect weak and strong molecular interactions present in binary and ternary liquid mixtures. After measuring the density and ultrasonic velocity of aqueous solution of 'Borassus Flabellifier' BF and Adansonia digitata And, we calculated Gibb's energy and intermolecular free length. The velocity of ultrasonic waves was measured, using a multi-frequency ultrasonic interferometer with a high degree of accuracy operating Model M-84 by M/s Mittal Enterprises, New Delhi, at a fixed frequency of 2MHz. Natural sample 'Borassus Flabellifier' BF fruit pulp and Adansonia digitata AnD powder was collected from Dhar, District of MP, India for this study.

  1. Intermolecular hydrogen bonds in hetero-complexes of biologically active aromatic molecules probed by the methods of vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Semenov, M. A.; Blyzniuk, Iu. N.; Bolbukh, T. V.; Shestopalova, A. V.; Evstigneev, M. P.; Maleev, V. Ya.

    2012-09-01

    By the methods of vibrational spectroscopy (Infrared and Raman) the investigation of the hetero-association of biologically active aromatic compounds: flavin-mononucleotide (FMN), ethidium bromide (EB) and proflavine (PRF) was performed in aqueous solutions. It was shown that between the functional groups (Cdbnd O and NH2) the intermolecular hydrogen bonds are formed in the hetero-complexes FMN-EB and FMN-PRF, additionally stabilizing these structures. An estimation of the enthalpy of Н-bonding obtained from experimental shifts of carbonyl vibrational frequencies has shown that the H-bonds do not dominate in the magnitude of experimentally measured total enthalpy of the hetero-association reactions. The main stabilization is likely due to intermolecular interactions of the molecules in these complexes and their interaction with water environment.

  2. Exciton dynamics reveal aggregates with intermolecular order at hidden interfaces in solution-cast organic semiconducting films.

    PubMed

    Wong, Cathy Y; Cotts, Benjamin L; Wu, Hao; Ginsberg, Naomi S

    2015-01-12

    Large-scale organic electronics manufacturing requires solution processing. For small-molecule organic semiconductors, solution processing results in crystalline domains with high charge mobility, but the interfaces between these domains impede charge transport, degrading device performance. Although understanding these interfaces is essential to improve device performance, their intermolecular and electronic structure is unknown: they are smaller than the diffraction limit, are hidden from surface probe techniques, and their nanoscale heterogeneity is not typically resolved using X-ray methods. Here we use transient absorption microscopy to isolate a unique signature of a hidden interface in a TIPS-pentacene thin film, exposing its exciton dynamics and intermolecular structure. Surprisingly, instead of finding an abrupt grain boundary, we reveal that the interface can be composed of nanoscale crystallites interleaved by a web of interfaces that compound decreases in charge mobility. Our novel approach provides critical missing information on interface morphology necessary to correlate solution-processing methods to optimal device performance.

  3. Exciton dynamics reveal aggregates with intermolecular order at hidden interfaces in solution-cast organic semiconducting films

    NASA Astrophysics Data System (ADS)

    Wong, Cathy Y.; Cotts, Benjamin L.; Wu, Hao; Ginsberg, Naomi S.

    2015-01-01

    Large-scale organic electronics manufacturing requires solution processing. For small-molecule organic semiconductors, solution processing results in crystalline domains with high charge mobility, but the interfaces between these domains impede charge transport, degrading device performance. Although understanding these interfaces is essential to improve device performance, their intermolecular and electronic structure is unknown: they are smaller than the diffraction limit, are hidden from surface probe techniques, and their nanoscale heterogeneity is not typically resolved using X-ray methods. Here we use transient absorption microscopy to isolate a unique signature of a hidden interface in a TIPS-pentacene thin film, exposing its exciton dynamics and intermolecular structure. Surprisingly, instead of finding an abrupt grain boundary, we reveal that the interface can be composed of nanoscale crystallites interleaved by a web of interfaces that compound decreases in charge mobility. Our novel approach provides critical missing information on interface morphology necessary to correlate solution-processing methods to optimal device performance.

  4. Diastereoselective Synthesis of γ-Substituted 2-Butenolides via (CDC)-Rh-Catalyzed Intermolecular Hydroalkylation of Dienes with Silyloxyfurans.

    PubMed

    Goldfogel, Matthew J; Roberts, Courtney C; Manan, Rajith S; Meek, Simon J

    2017-01-06

    Catalytic intermolecular hydroalkylation of dienes with silyloxyfuran nucleophiles is reported. Reactions are catalyzed by 5 mol % of a (CDC)-Rh complex and proceed in up to 87% yield and 6:1 dr (syn/anti) to provide allylic butenolides bearing vicinal stereocenters. Reactions proceed with terminal aryl and alkyl dienes and with modified silyl enol ether nucleophiles including a thiophenone variant. Utility of the products is demonstrated in the synthesis of a polypropionate anti,syn-stereotriad.

  5. Crystallization force--a density functional theory concept for revealing intermolecular interactions and molecular packing in organic crystals.

    PubMed

    Li, Tonglei; Ayers, Paul W; Liu, Shubin; Swadley, Matthew J; Aubrey-Medendorp, Clare

    2009-01-01

    Organic molecules are prone to polymorphic formation in the solid state due to the rich diversity of functional groups that results in comparable intermolecular interactions, which can be greatly affected by the selection of solvent and other crystallization conditions. Intermolecular interactions are typically weak forces, such as van der Waals and stronger short-range ones including hydrogen bonding, that are believed to determine the packing of organic molecules during the crystal-growth process. A different packing of the same molecules leads to the formation of a new crystal structure. To disclose the underlying causes that drive the molecule to have various packing motifs in the solid state, an electronic concept or function within the framework of conceptual density functional theory has been developed, namely, crystallization force. The concept aims to describe the local change in electronic structure as a result of the self-assembly process of crystallization and may likely quantify the locality of intermolecular interactions that directs the molecular packing in a crystal. To assess the applicability of the concept, 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile, so-called ROY, which is known to have the largest number of solved polymorphs, has been examined. Electronic calculations were conducted on the seven available crystal structures as well as on the single molecule. The electronic structures were analyzed and crystallization force values were obtained. The results indicate that the crystallization forces are able to reveal intermolecular interactions in the crystals, in particular, the close contacts that are formed between molecules. Strong correlations exist between the total crystallization force and lattice energy of a crystal structure, further suggesting the underlying connection between the crystallization force and molecular packing.

  6. A terthiophene-containing alkynylplatinum terpyridine Pacman complex: controllable folding/unfolding modulated by weak intermolecular interactions.

    PubMed

    Cao, Yang; Wolf, Michael O; Patrick, Brian O

    2013-05-20

    Folded and unfolded solid-state structures of a bimetallic alkynylplatinum terpyridine complex with a flexible terthiophene linker have been obtained. Weak intermolecular interactions including π-π stacking and C-H···O and C-H···Cl interactions as well as Cl-π interactions stabilize the folded structure. In solution, folding is studied by electronic absorption spectroscopy and (1)H and NOESY NMR experiments.

  7. Highly regio- and enantioselective synthesis of N-substituted 2-pyridones: iridium-catalyzed intermolecular asymmetric allylic amination.

    PubMed

    Zhang, Xiao; Yang, Ze-Peng; Huang, Lin; You, Shu-Li

    2015-02-02

    The first iridium-catalyzed intermolecular asymmetric allylic amination reaction with 2-hydroxypyridines has been developed, thus providing a highly efficient synthesis of enantioenriched N-substituted 2-pyridone derivatives from readily available starting materials. This protocol features a good tolerance of functional groups in both the allylic carbonates and 2-hydroxypyridines, thereby delivering multifunctionalized heterocyclic products with up to 98% yield and 99% ee.

  8. Intramolecular 1,1-carboboration versus intermolecular FLP addition in reactions of boranes and bis(phenylethynyl)telluroether.

    PubMed

    Tsao, Fu An; Lough, Alan J; Stephan, Douglas W

    2015-03-11

    Reactions of boranes with Te(CCPh)2 proceed via initial intermolecular 1,1-carboboration followed by either an intramolecular carboboration or an FLP addition to a second molecule of the intermediate, yielding 1-bora-4-tellurocyclohexa-2,5-diene heterocycles or tricylic derivatives of 1,4-ditellurocyclohexa-2,5-diene, respectively. The latter species is also shown to convert to the former upon heating.

  9. Organophotocatalysis: Insights into the Mechanistic Aspects of Thiourea-Mediated Intermolecular [2+2] Photocycloadditions.

    PubMed

    Vallavoju, Nandini; Selvakumar, Sermadurai; Pemberton, Barry C; Jockusch, Steffen; Sibi, Mukund P; Sivaguru, Jayaraman

    2016-04-25

    Mechanistic investigations of the intermolecular [2+2] photocycloaddition of coumarin with tetramethylethylene mediated by thiourea catalysts reveal that the reaction is enabled by a combination of minimized aggregation, enhanced intersystem crossing, and altered excited-state lifetime(s). These results clarify how the excited-state reactivity can be manipulated through catalyst-substrate interactions and reveal a third mechanistic pathway for thiourea-mediated organo-photocatalysis.

  10. Energy of the quasi-free electron in H{sub 2}, D{sub 2}, and O{sub 2}: Probing intermolecular potentials within the local Wigner-Seitz model

    SciTech Connect

    Evans, C. M. Krynski, Kamil; Streeter, Zachary; Findley, G. L.

    2015-12-14

    We present for the first time the quasi-free electron energy V{sub 0}(ρ) for H{sub 2}, D{sub 2}, and O{sub 2} from gas to liquid densities, on noncritical isotherms and on a near critical isotherm in each fluid. These data illustrate the ability of field enhanced photoemission (FEP) to determine V{sub 0}(ρ) accurately in strongly absorbing fluids (e.g., O{sub 2}) and fluids with extremely low critical temperatures (e.g., H{sub 2} and D{sub 2}). We also show that the isotropic local Wigner-Seitz model for V{sub 0}(ρ) — when coupled with thermodynamic data for the fluid — can yield optimized parameters for intermolecular potentials, as well as zero kinetic energy electron scattering lengths.

  11. Comparative Study of the Intermolecular Dynamics and Physical Properties of Branched and Linear Alkyl Chain Imidazolium Ionic Liquids

    NASA Astrophysics Data System (ADS)

    Xue, Lianjie; Bardak, Fehmi; Tamas, George; Gurung, Eshan; Quitevis, Edward; Koh, Yung; Simon, Sindee

    2014-03-01

    The optical Kerr effect (OKE) spectra, densities, viscosities, and transition temperatures of 1-alkyl-3-methylimidazolium bis{(trifluoromethane)sulfonyl}amide ionic liquids (ILs) with branched alkyl chains, -Cn-3CH(CH3)2 (branched ILs), were measured and compared to those with linear alkyl chains, -Cn-1CH3 (linear ILs), for n = 3, 4, 5, 6 and 7. The results show that a branched IL has a higher viscosity and transition temperature Tg than the corresponding linear IL with the same n, whereas the densities of each branched/linear IL pair are the same within experimental error. For short alkyl chains (n =3 and 4) the intermolecular part of the OKE spectrum of the branched ILs tends to be narrower and lower in frequency than that of the linear ILs. This suggests that branching softens the intermolecular modes. For long alkyl chains (n =5-7), the difference between the intermolecular spectrum of the branched IL and that of the linear IL with the same n decreases, which indicates that the branching effect becomes smaller when the alkyl chains get longer. This work was supported by NSF grant CHE-1153077.

  12. Permutationally invariant fitting of intermolecular potential energy surfaces: A case study of the Ne-C2H2 system

    NASA Astrophysics Data System (ADS)

    Li, Jun; Guo, Hua

    2015-12-01

    The permutation invariant polynomial-neural network (PIP-NN) approach is extended to fit intermolecular potential energy surfaces (PESs). Specifically, three PESs were constructed for the Ne-C2H2 system. PES1 is a full nine-dimensional PIP-NN PES directly fitted to ˜42 000 ab initio points calculated at the level of CCSD(T)-F12a/cc-pCVTZ-F12, while the other two consist of the six-dimensional PES for C2H2 [H. Han, A. Li, and H. Guo, J. Chem. Phys. 141, 244312 (2014)] and an intermolecular PES represented in either the PIP (PES2) or PIP-NN (PES3) form. The comparison of fitting errors and their distributions, one-dimensional cuts and two-dimensional contour plots of the PESs, as well as classical trajectory collisional energy transfer dynamics calculations shows that the three PESs are very similar. We conclude that full-dimensional PESs for non-covalent interacting molecular systems can be constructed efficiently and accurately by the PIP-NN approach for both the constituent molecules and intermolecular parts.

  13. Synthesis, crystal structure and theoretical analysis of intermolecular interactions in two biologically active derivatives of 1,2,4-triazoles

    NASA Astrophysics Data System (ADS)

    Shukla, Rahul; Mohan, T. P.; Vishalakshi, B.; Chopra, Deepak

    2017-04-01

    In the present study, we have synthesized and structurally characterized two biologically active derivatives of 1,2,4 triazoles, namely 3-(4-fluoro-3-phenoxyphenyl)-1-(piperidin-1-ylmethyl)-1H-1,2,4-triazole-5(4H)-thione (TR) and 1-((3-(4-fluoro-3-phenoxyphenyl)-5-(methylthio)-1H-1,2,4-triazol-1-yl)methyl)piperidine (TR1) via single crystal X-ray diffraction. Both the structures show the presence of various intermolecular interactions in the crystalline solid such as Csbnd H…F, Csbnd H…S, Csbnd H…N, Csbnd H…O, Csbnd H … π, and π … π intermolecular interactions. The role of these interactions in molecular packing was analyzed, and the nature of these interactions was evaluated through computational procedures using PIXEL. Hirshfeld analysis further reveals that the contribution of H…F interactions was more prominent towards packing as compared to H…N/O intermolecular interactions.

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

    PubMed

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

    2011-07-21

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

  15. Intermolecular vibrations of the CO2-CS2 complex: Experiment and theory agree, but understanding remains challenging

    NASA Astrophysics Data System (ADS)

    Dehghany, M.; Rezaei, Mojtaba; Moazzen-Ahmadi, N.; McKellar, A. R. W.; Brown, James; Wang, Xiao-Gang; Carrington, Tucker

    2016-12-01

    The infrared spectrum of the cross-shaped van der Waals complex CO2-CS2 is observed in the region of the CO2 ν3 fundamental band (≈2350 cm-1) using a tuneable diode laser to probe a pulsed supersonic slit jet expansion. Two combination bands are assigned, corresponding to the intermolecular torsion and CO2 bend modes, and their positions and rotational structure agree extremely well (<0.1 cm-1) with calculations based on a recent ab initio intermolecular potential. The b-type torsional band is well-behaved, but the a-type CO2 bending band is highly unusual, with large shifts between the subband origins for Ka = 0, 2, and 4. The shifts may be rationalized as due to tunnelling effects and Ka-dependent perturbations from other intermolecular modes. But even though they are well predicted by our calculations, there is no simple qualitative explanation. The predicted low-lying planar slipped parallel isomer of CO2-CS2 is not observed.

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

    PubMed

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

    2014-12-11

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

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

    PubMed

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

    2013-04-08

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

  18. Intermolecular vibrational modes and orientational dynamics of cooperative hydrogen-bonding dimer of 7-azaindole in solution.

    PubMed

    Kato, Tatsuya; Shirota, Hideaki

    2011-04-28

    We observed the low-frequency Raman-active intermolecular vibrational modes of 7-azaindole in CCl(4) by femtosecond Raman-induced Kerr effect spectroscopy. To understand the dynamical aspects and vibrational modes of 7-azaindole in the solution, the ultrafast dynamics of 1-benzofuran in CCl(4) was also examined as a reference and ab initio quantum chemistry calculations were performed for 7-azaindole and 1-benzofuran. The cooperative hydrogen-bonding vibrational bands of 7-azaindole dimer in CCl(4) appeared at 89 cm(-1) and 105 cm(-1) represent the overlap of stagger and wheeling modes and the intermolecular stretching mode, respectively. They are almost independent of the concentration in the solution. We further found from the low-frequency differential Kerr spectra of the solutions with neat CCl(4) that the intermolecular motion in the low frequency region below 20 cm(-1) was less active in the case of 7-azaindole/CCl(4) than in the case of 1-benzofuran/CCl(4). The slow orientational relaxation time in 7-azaindole/CCl(4) is ~3.5 times that in 1-benzofuran/CCl(4) because of the nature of the dimerization of 7-azaindole.

  19. A mode-coupling theory of vibrational line broadening in near-critical fluids.

    PubMed

    Egorov, S A; Lawrence, C P; Skinner, J L

    2005-04-14

    We present a fully microscopic mode-coupling theory of near-critical line broadening. All the structural and dynamical input required by the theory is calculated directly from intermolecular potentials. We compute vibrational frequency time-correlation functions and line shapes as the critical point is approached along both the critical isochore and the liquid-gas coexistence curve. Theory is shown to be in good agreement with simulation.

  20. Concentration-dependent reversible self-oligomerization of serum albumins through intermolecular β-sheet formation.

    PubMed

    Bhattacharya, Arpan; Prajapati, Roopali; Chatterjee, Surajit; Mukherjee, Tushar Kanti

    2014-12-16

    Proteins inside a cell remain in highly crowded environments, and this often affects their structure and activity. However, most of the earlier studies involving serum albumins were performed under dilute conditions, which lack biological relevance. The effect of protein-protein interactions on the structure and properties of serum albumins at physiological conditions have not yet been explored. Here, we report for the first time the effect of protein-protein and protein-crowder interactions on the structure and stability of two homologous serum albumins, namely, human serum albumin (HSA) and bovine serum albumin (BSA), at physiological conditions by using spectroscopic techniques and scanning electron microscopy (SEM). Concentration-dependent self-oligomerization and subsequent structural alteration of serum albumins have been explored by means of fluorescence and circular dichroism spectroscopy at pH 7.4. The excitation wavelength (λex) dependence of the intrinsic fluorescence and the corresponding excitation spectra at each emission wavelength indicate the presence of various ground state oligomers of serum albumins in the concentration range 10-150 μM. Circular dichroism and thioflavin T binding assay revealed formation of intermolecular β-sheet rich interfaces at high protein concentration. Excellent correlations have been observed between β-sheet content of both the albumins and fluorescence enhancement of ThT with protein concentrations. SEM images at a concentration of 150 μM revealed large dispersed self-oligomeric states with sizes vary from 330 to 924 nm and 260 to 520 nm for BSA and HSA, respectively. The self-oligomerization of serum albumins is found to be a reversible process; upon dilution, these oligomers dissociate into a native monomeric state. It has also been observed that synthetic macromolecular crowder polyethylene glycol (PEG 200) stabilizes the self-associated state of both the albumins which is contrary to expectations that the

  1. Isolating the non-polar contributions to the intermolecular potential for water-alkane interactions

    NASA Astrophysics Data System (ADS)

    Ballal, Deepti; Venkataraman, Pradeep; Fouad, Wael A.; Cox, Kenneth R.; Chapman, Walter G.

    2014-08-01

    Intermolecular potential models for water and alkanes describe pure component properties fairly well, but fail to reproduce properties of water-alkane mixtures. Understanding interactions between water and non-polar molecules like alkanes is important not only for the hydrocarbon industry but has implications to biological processes as well. Although non-polar solutes in water have been widely studied, much less work has focused on water in non-polar solvents. In this study we calculate the solubility of water in different alkanes (methane to dodecane) at ambient conditions where the water content in alkanes is very low so that the non-polar water-alkane interactions determine solubility. Only the alkane-rich phase is simulated since the fugacity of water in the water rich phase is calculated from an accurate equation of state. Using the SPC/E model for water and TraPPE model for alkanes along with Lorentz-Berthelot mixing rules for the cross parameters produces a water solubility that is an order of magnitude lower than the experimental value. It is found that an effective water Lennard-Jones energy ɛW/k = 220 K is required to match the experimental water solubility in TraPPE alkanes. This number is much higher than used in most simulation water models (SPC/E—ɛW/k = 78.2 K). It is surprising that the interaction energy obtained here is also higher than the water-alkane interaction energy predicted by studies on solubility of alkanes in water. The reason for this high water-alkane interaction energy is not completely understood. Some factors that might contribute to the large interaction energy, such as polarizability of alkanes, octupole moment of methane, and clustering of water at low concentrations in alkanes, are examined. It is found that, though important, these factors do not completely explain the anomalously strong attraction between alkanes and water observed experimentally.

  2. Model intermolecular potentials and virial coefficients determined from the speed of sound

    NASA Astrophysics Data System (ADS)

    Trusler, J. P. M.; Wakeham, W. A.; Zarari, M. P.

    A simple procedure is given for determining model two- and three-body intermolecular potential energy functions from precise measurements of the speed of sound in the gas phase. The method is applied to the pure gases argon, methane and nitrogen and results are considered for propane and the mixture (methane + propane) obtained recently by similar methods. For the pair potential, the four-parameter model proposed by Maitland and Smith is used while the consequences of three-body forces were generally assumed to be represented adequately by the triple-dipole dispersion potential of Axilrod and Teller. The effect of including additional dispersion and exchange terms in the three-body potential was investigated for argon; each of these terms is significant but their effect on the third virial coefficient may be absorbed accurately in an effective triple-dipole potential. Three or, in some cases, all four of the parameters in the pair potential were optimized, together with the triple-dipole dispersion coefficient, in fits to the acoustic data. Ordinary second and third virial coefficients have been calculated from the model potential and the former are shown to be in excellent agreement with directly measured values. In the case of the third virial coefficient, some small discrepancies are noted; the resolution of these differences could have important implications for our understanding of many-body forces. The values of the dilute-gas viscosity predicted by the model pair potentials are examined also and, in the case of argon, found to be in good agreement with experimental values; for the other systems differences of several per cent were noted.

  3. Aggregation and other intermolecular interactions of biological buffers observed by capillary electrophoresis and UV photometry.

    PubMed

    Vespalec, R; Vlcková, M; Horáková, H

    2004-10-08

    Electrophoretic and photometric experiments strongly indicate that monovalent anions, which arise by deprotonation of the nitrogen atom in zwitterionic Good's buffers 3-(cyclohexylamino)-2-hydroxy-1-propanesulfonic acid (CAPSO) and 3-morpholinopropanesulfonic acid (MOPS), spontaneously aggregate. Cationic migration of sanguinarine (SA) and chelerythrine (CHE) in highly alkaline 1,3-bis[tris(hydroxymethyl)methylamino]propane (Bis-Tris-propane), in which the concentration of cations of both alkaloids is negligible, may be explained by the existence of an aggregate, which contains uncharged sanguinarine or chelerythrine and one monovalent cation of Bis-Tris-propane at least. Tendency of tris(hydroxymethyl)aminomethane (Tris), bis (2-hydroxyethyl)iminotris(hydroxymethyl)methane (Bis-Tris) and Bis-Tris-propane cations to ion pairing with synthetic cluster borane anions and with fused silica markedly rises up with the size and charge of these cations. The drop in mobility of cluster borane compounds sometimes exceeds 50% of their mobility found at identical pH and ionic strength in buffers with sodium cation. The electroosmosis drop approached 70% if background electrolyte contained Bis-Tris-propane cations instead of sodium cations. Nitrate, taken as a model inorganic ion, and four randomly chosen organic anions interacted markedly less with Tris, Bis-Tris and Bis-Tris-propane cations than cluster borane anions. 2-(N-morpholino)ethanesulfonic (MES) acid anions present in background electrolyte affect the ion pairing of Tris, Bis-Tris and Bis-Tris-propane cations with anionic analytes and, in this way influence also mobilites of these anionic analytes. Limited hydrophilicity at least one of interacting species appears to be the most probable cause of observed intermolecular interactions of biological buffers.

  4. Isolating the non-polar contributions to the intermolecular potential for water-alkane interactions.

    PubMed

    Ballal, Deepti; Venkataraman, Pradeep; Fouad, Wael A; Cox, Kenneth R; Chapman, Walter G

    2014-08-14

    Intermolecular potential models for water and alkanes describe pure component properties fairly well, but fail to reproduce properties of water-alkane mixtures. Understanding interactions between water and non-polar molecules like alkanes is important not only for the hydrocarbon industry but has implications to biological processes as well. Although non-polar solutes in water have been widely studied, much less work has focused on water in non-polar solvents. In this study we calculate the solubility of water in different alkanes (methane to dodecane) at ambient conditions where the water content in alkanes is very low so that the non-polar water-alkane interactions determine solubility. Only the alkane-rich phase is simulated since the fugacity of water in the water rich phase is calculated from an accurate equation of state. Using the SPC/E model for water and TraPPE model for alkanes along with Lorentz-Berthelot mixing rules for the cross parameters produces a water solubility that is an order of magnitude lower than the experimental value. It is found that an effective water Lennard-Jones energy ε(W)/k = 220 K is required to match the experimental water solubility in TraPPE alkanes. This number is much higher than used in most simulation water models (SPC/E-ε(W)/k = 78.2 K). It is surprising that the interaction energy obtained here is also higher than the water-alkane interaction energy predicted by studies on solubility of alkanes in water. The reason for this high water-alkane interaction energy is not completely understood. Some factors that might contribute to the large interaction energy, such as polarizability of alkanes, octupole moment of methane, and clustering of water at low concentrations in alkanes, are examined. It is found that, though important, these factors do not completely explain the anomalously strong attraction between alkanes and water observed experimentally.

  5. Photo-induced spin transition of Iron(III) compounds with pi-pi intermolecular interactions.

    PubMed

    Hayami, Shinya; Hiki, Kenji; Kawahara, Takayoshi; Maeda, Yonezo; Urakami, Daisuke; Inoue, Katsuya; Ohama, Mitsuo; Kawata, Satoshi; Sato, Osamu

    2009-01-01

    Iron(III) spin-crossover compounds [Fe(pap)(2)]ClO(4) (1), [Fe(pap)(2)]BF(4) (2), [Fe(pap)(2)]PF(6) (3), [Fe(qsal)(2)]NCS (4), and [Fe(qsal)(2)]NCSe (5) (Hpap=2-(2-pyridylmethyleneamino)phenol and Hqsal=2-[(8-quinolinylimino)methyl]phenol) were prepared and their spin-transition properties investigated by magnetic susceptibility and Mössbauer spectroscopy measurements. The iron(III) compounds exhibited spin transition with thermal hysteresis. Single crystals of the iron(III) compounds were obtained as suitable solvent adducts for X-ray analysis, and structures in high-spin (HS) and low-spin (LS) states were revealed. Light-induced excited-spin-state trapping (LIESST) effects of the iron(III) compounds were induced by light irradiation at 532 nm for 1-3 and at 800 nm for 4 and 5. The activation energy E(a) and the low-temperature tunneling rate k(HL)(T-->0) of iron(III) LIESST compound 1 were estimated to be 1079 cm(-1) and 2.4x10(-8) s(-1), respectively, by HS-->LS relaxation experiments. The Huang-Rhys factor S of 1 was also estimated to be 50, which was similar to that expected for iron(II) complexes. It is thought that the slow relaxation in iron(III) systems is achieved by the large structural distortion between HS and LS states. Introduction of strong intermolecular interactions, such as pi-pi stacking, can also play an important role in the relaxation behavior, because it can enhance the structural distortion of the LIESST complex.

  6. LINGO, an efficient holographic text based method to calculate biophysical properties and intermolecular similarities.

    PubMed

    Vidal, David; Thormann, Michael; Pons, Miquel

    2005-01-01

    SMILES strings are the most compact text based molecular representations. Implicitly they contain the information needed to compute all kinds of molecular structures and, thus, molecular properties derived from these structures. We show that this implicit information can be accessed directly at SMILES string level without the need to apply explicit time-consuming conversion of the SMILES strings into molecular graphs or 3D structures with subsequent 2D or 3D QSPR calculations. Our method is based on the fragmentation of SMILES strings into overlapping substrings of a defined size that we call LINGOs. The integral set of LINGOs derived from a given SMILES string, the LINGO profile, is a hologram of the SMILES representation of the molecule described. LINGO profiles provide input for QSPR models and the calculation of intermolecular similarities at very low computational cost. The octanol/water partition coefficient (LlogP) QSPR model achieved a correlation coefficient R2=0.93, a root-mean-square error RRMS=0.49 log units, a goodness of prediction correlation coefficient Q2=0.89 and a QRMS=0.61 log units. The intrinsic aqueous solubility (LlogS) QSPR model achieved correlation coefficient values of R2=0.91, Q2=0.82, and RRMS=0.60 and QRMS=0.89 log units. Integral Tanimoto coefficients computed from LINGO profiles provided sharp discrimination between random and bioisoster pairs extracted from Accelrys Bioster Database. Average similarities (LINGOsim) were 0.07 for the random pairs and 0.36 for the bioisosteric pairs.

  7. Intermolecular Interactions and Electrostatic Properties of the [beta]-Hydroquinone Apohost: Implications for Supramolecular Chemistry

    SciTech Connect

    Clausen, Henrik F.; Chen, Yu-Sheng; Jayatilaka, Dylan; Overgaard, Jacob; Koutsantonis, George A.; Spackman, Mark A.; Iversen, Bo B.

    2012-02-07

    The crystal structure of the {beta}-polymorph of hydroquinone ({beta}-HQ), the apohost of a large family of clathrates, is reported with a specific focus on intermolecular interactions and the electrostatic nature of its cavity. Hirshfeld surface analysis reveals subtle close contacts between two interconnecting HQ networks, and the local packing and related close contacts were examined by breakdown of the fingerprint plot. An experimental multipole model containing anisotropic thermal parameters for hydrogen atoms has been successfully refined against 15(2) K single microcrystal synchrotron X-ray diffraction data. The experimental electron density model has been compared with a theoretical electron density calculated with the molecule embedded in its own crystal field. Hirshfeld charges, interaction energies and the electrostatic potential calculated for both models are qualitatively in good agreement, but small differences in the electrostatic potential persist due to charge transfer from all hydrogen atoms to the oxygen atoms in the theoretical model. The electrostatic potential in the center of the cavity is positive, very shallow and highly symmetric, suggesting that the inclusion of polar molecules in the void will involve a balance between opposing effects. The electric field is by symmetry zero in the center of the cavity, increasing to a value of 0.0185 e/{angstrom}{sup 2} (0.27 V/{angstrom}) 1 {angstrom} along the 3-fold axis and 0.0105 e/{angstrom}{sup 2} (0.15 V/{angstrom}) 1 {angstrom} along the perpendicular direction. While these values are substantial in a macroscopic context, they are quite small for a molecular cavity and are not expected to strongly polarize a guest molecule.

  8. Conserved intermolecular salt bridge required for activation of protein kinases PKR, GCN2, and PERK.

    PubMed

    Dey, Madhusudan; Cao, Chune; Sicheri, Frank; Dever, Thomas E

    2007-03-02

    The protein kinases PKR, GCN2, and PERK phosphorylate translation initiation factor eIF2alpha to regulate general and genespecific protein synthesis under various cellular stress conditions. Recent x-ray crystallographic structures of PKR and GCN2 revealed distinct dimeric configurations of the kinase domains. Whereas PKR kinase domains dimerized in a back-to-back and parallel orientation, the GCN2 kinase domains displayed an antiparallel orientation. The dimerization interfaces on PKR and GCN2 were localized to overlapping surfaces on the N-terminal lobes of the kinase domains but utilized different intermolecular contacts. A key feature of the PKR dimerization interface is a salt bridge interaction between Arg(262) from one protomer and Asp(266) from the second protomer. Interestingly, these two residues are conserved in all eIF2alpha kinases, although in the GCN2 structure, the two residues are too remote to interact. To test the importance of this potential salt bridge interaction in PKR, GCN2, and PERK, the residues constituting the salt bridge were mutated either independently or together to residues with the opposite charge. Single mutations of the Asp (or Glu) and Arg residues blocked kinase function both in yeast cells and in vitro. However, for all three kinases, the double mutation designed to restore the salt bridge interaction with opposite polarity resulted in a functional kinase. Thus, the salt bridge interaction and dimer interface observed in the PKR structure is critical for the activity of all three eIF2alpha kinases. These results are consistent with the notion that the PKR structure represents the active state of the eIF2alpha kinase domain, whereas the GCN2 structure may represent an inactive state of the kinase.

  9. Rh-Catalyzed Intermolecular Reactions of α-Alkyl-α-Diazo Carbonyl Compounds with Selectivity over β-Hydride Migration.

    PubMed

    DeAngelis, Andrew; Panish, Robert; Fox, Joseph M

    2016-01-19

    Rh-carbenes derived from α-diazocarbonyl compounds have found broad utility across a remarkable range of reactivity, including cyclopropanation, cyclopropenation, C-H insertions, heteroatom-hydrogen insertions, and ylide forming reactions. However, in contrast to α-aryl or α-vinyl-α-diazocarbonyl compounds, the utility of α-alkyl-α-diazocarbonyl compounds had been moderated by the propensity of such compounds to undergo intramolecular β-hydride migration to give alkene products. Especially challenging had been intermolecular reactions involving α-alkyl-α-diazocarbonyl compounds. This Account discusses the historical context and prior limitations of Rh-catalyzed reactions involving α-alkyl-α-diazocarbonyl compounds. Early studies demonstrated that ligand and temperature effects could influence chemoselectivity over β-hydride migration. However, effects were modest and conflicting conclusions had been drawn about the influence of sterically demanding ligands on β-hydride migration. More recent advances have led to a more detailed understanding of the reaction conditions that can promote intermolecular reactivity in preference to β-hydride migration. In particular, the use of bulky carboxylate ligands and low reaction temperatures have been key to enabling intermolecular cyclopropenation, cyclopropanation, carbonyl ylide formation/dipolar cycloaddition, indole C-H functionalization, and intramolecular bicyclobutanation with high chemoselectivity over β-hydride migration. Cyclic α-diazocarbonyl compounds have been shown to be particularly resilient toward β-hydride migration and are the first class of compounds that can engage in intermolecular reactivity in the presence of tertiary β-hydrogens. DFT calculations were used to propose that for cyclic α-diazocarbonyl compounds, ring constraints relieve steric interaction for intermolecular reactions and thereby accelerate the rate of intermolecular reactivity relative to intramolecular

  10. Intermolecular hydroamination of vinylarenes by iminoanilide alkaline-earth catalysts: a computational scrutiny of mechanistic pathways.

    PubMed

    Tobisch, Sven

    2014-07-14

    A thorough computational exploration of the mechanistic intricacies of the intermolecular hydroamination (HA) of vinylarenes by a recently reported class of kinetically stabilised iminoanilide [{N^N}Ae{N(SiMe3)2}⋅(THF)n] alkaline-earth amido compounds (Ae = Ca, Sr, Ba) is presented. Two distinct mechanistic pathways for catalytic HA mediated by alkaline-earth and rare-earth compounds have emerged over the years that account equally well for the specific features of the process. On one hand, a concerted proton-assisted pathway to deliver the amine product in a single step can be invoked and, on the other, a stepwise σ-insertive pathway that comprises a rapid, reversible migratory olefin insertion step linked to a less facile, irreversible Ae-C alkyl bond aminolysis. The results of the study presented herein, which employed a heavily benchmarked and reliable DFT methodology, supports a stepwise σ-insertive pathway that involves fast and reversible migratory C=C bond insertion into the polar Ae-N pyrrolido σ bond. This proceeds with strict 2,1 regioselectivity via a highly polarised four-centre transition state (TS) structure, linked to irreversible intramolecular Ae-C bond aminolysis of the alkaline-earth alkyl intermediate as the energetically favourable mechanism. Turnover-limiting aminolysis is consistent with the significant KIE measured; the DFT-derived effective barrier matches the Eyring parameter empirically determined for the best-performing {N^N}Ba(NR2) catalyst gratifyingly well. It also predicts the observed trend in reactivity (Ca

  11. Probing Intramolecular versus Intermolecular CO2 Adsorption on Amine-Grafted SBA-15.

    PubMed

    Yoo, Chun-Jae; Lee, Li-Chen; Jones, Christopher W

    2015-12-15

    A mesoporous silica SBA-15 is modified with an array of amine-containing organosilanes including (i) propylamine, SiCH2CH2CH2NH2 (MONO), (ii) propylethylenediamine, SiCH2CH2CH2NHCH2CH2NH2 (DI), (iii) propyldiethylenetriamine, SiCH2CH2CH2NHCH2CH2NHCH2CH2NH2 (TRI), and (iv) propyltriethylenetetramine, SiCH2CH2CH2NHCH2CH2N(CH2CH2NH2)2 (TREN) and the low loading silane adsorbents (∼0.45 mmol silane/g) are evaluated for their CO2 adsorption properties, with a focus on gaining insight into the propensity for intramolecular vs intermolecular CO2 adsorption. Adsorption isotherms at low CO2 coverages are measured while simultaneously recording the heat evolved via a Tian-Calvet calorimeter. The results are compared on a silane molecule efficiency basis (mol CO2 adsorbed/mol silane) to assess the potential for intramolecular CO2 adsorption, employing two amine groups in a single silane molecule. As the number of amines in the silane molecule increases (MONO < DI < TREN ∼ TRI), the silane molecule efficiency is enhanced owing to the ability to intramolecularly capture CO2. Analysis of the CO2 uptake for samples with the surface silanols removed by capping demonstrates that cooperative uptake due to amine-CO2-silanol interactions is also possible over these adsorbents and is the primary mode of sorption for the MONO material at the studied low silane loading. As the propensity for intramolecular CO2 capture increases due to the presence of multiple amines in a single silane molecule (MONO < DI < TREN ∼ TRI), the measured heat of adsorption also increases. This study of various amine-containing silanes at low coverage is the first to provide significant, direct evidence for intramolecular CO2 capture in a single silane molecule. Furthermore, it provides evidence for the relative heats of adsorption for physisorption on a silanol laden surface (ca. 37 kJ/mol), a silanol-capped surface (ca. 25 kJ/mol), via amine-CO2-silanol interactions (ca. 46 kJ/mol), and via amine-CO2

  12. Tubular Coupling

    NASA Technical Reports Server (NTRS)

    Rosenbaum, Bernard J. (Inventor)

    2000-01-01

    A system for coupling a vascular overflow graft or cannula to a heart pump. A pump pipe outlet is provided with an external tapered surface which receives the end of a compressible connula. An annular compression ring with a tapered internal bore surface is arranged about the cannula with the tapered internal surface in a facing relationship to the external tapered surface. The angle of inclination of the tapered surfaces is converging such that the spacing between the tapered surfaces decreases from one end of the external tapered surface to the other end thereby providing a clamping action of the tapered surface on a cannula which increases as a function of the length of cannula segment between the tapered surfaces. The annular compression ring is disposed within a tubular locking nut which threadedly couples to the pump and provides a compression force for urging the annular ring onto the cannula between the tapered surfaces. The nut has a threaded connection to the pump body. The threaded coupling to the pump body provides a compression force for the annular ring. The annular ring has an annular enclosure space in which excess cannula material from the compression between the tapered surfaces to "bunch up" in the space and serve as an enlarged annular ring segment to assist holding the cannula in place. The clamped cannula provides a seamless joint connection to the pump pipe outlet where the clamping force is uniformly applied to the cannula because of self alignment of the tapered surfaces. The nut can be easily disconnected to replace the pump if necessary.

  13. Phosphorus as a simultaneous electron-pair acceptor in intermolecular P···N pnicogen bonds and electron-pair donor to Lewis acids.

    PubMed

    Del Bene, Janet E; Alkorta, Ibon; Sánchez-Sanz, Goar; Elguero, José

    2013-04-11

    Ab initio MP2/aug'-cc-pVTZ calculations have been performed to investigate the structures and energies of binary complexes LA:PH2F and LA:PH3 and of ternary complexes LA:H2FP:NFH2 and LA:H3P:NH3 in which the pnicogen-bonded P atom also acts as an electron-pair donor to a Lewis acid (LA), for LA = BH3, NCH, ClH, FH, FCl, and HLi. Hydrogen bonds, halogen bonds, and dative covalent bonds are found at P in some cases, depending on the nature of the Lewis acid. HLi forms a lithium bond with P only in the binary complex HLi:PH3. The binding energies of ternary complexes exhibit a classical synergistic effect, although the computed cooperativity may be overestimated due to neglect of the interaction of the Lewis acid with NH2F or NH3 in some cases. The hydrogen-bonding Lewis acids appear to have little effect on the strength of the P···N bond, while the remaining Lewis acids strengthen the pnicogen bond. (31)P absolute chemical shieldings increase in LA:H2FP:NFH2 complexes relative to the corresponding LA:PH2F complexes as the positive charge on P decreases, while chemical shieldings decrease in LA:H3P:NH3 relative to the corresponding LA:PH3 complexes as the positive charge increases. Absolute values of (1p)J(P-N) spin-spin coupling constants in complexes LA:H2FP:NFH2 decrease as the P-N distance decreases. It appears that this behavior is associated with the presence of a second intermolecular interaction, whether electron-donation by P or hydrogen bond formation at P-F.

  14. Collecting high-order interactions in an effective pairwise intermolecular potential using the hydrated ion concept: The hydration of Cf{sup 3+}

    SciTech Connect

    Galbis, Elsa; Pappalardo, Rafael R.; Marcos, Enrique Sánchez; Hernández-Cobos, Jorge

    2014-06-07

    This work proposes a new methodology to build interaction potentials between a highly charged metal cation and water molecules. These potentials, which can be used in classical computer simulations, have been fitted to reproduce quantum mechanical interaction energies (MP2 and BP86) for a wide range of [M(H{sub 2}O){sub n}]{sup m+}(H{sub 2}O){sub ℓ} clusters (n going from 6 to 10 and ℓ from 0 to 18). A flexible and polarizable water shell model (Mobile Charge Density of Harmonic Oscillator) has been coupled to the cation-water potential. The simultaneous consideration of poly-hydrated clusters and the polarizability of the interacting particles allows the inclusion of the most important many-body effects in the new polarizable potential. Applications have been centered on the californium, Cf(III) the heaviest actinoid experimentally studied in solution. Two different strategies to select a set of about 2000 structures which are used for the potential building were checked. Monte Carlo simulations of Cf(III)+500 H{sub 2}O for three of the intermolecular potentials predict an aquaion structure with coordination number close to 8 and average R{sub Cf−−O} in the range 2.43–2.48 Å, whereas the fourth one is closer to 9 with R{sub Cf−−O} = 2.54 Å. Simulated EXAFS spectra derived from the structural Monte Carlo distribution compares fairly well with the available experimental spectrum for the simulations bearing 8 water molecules. An angular distribution similar to that of a square antiprism is found for the octa-coordination.

  15. Collecting high-order interactions in an effective pairwise intermolecular potential using the hydrated ion concept: The hydration of Cf3+

    NASA Astrophysics Data System (ADS)

    Galbis, Elsa; Hernández-Cobos, Jorge; Pappalardo, Rafael R.; Marcos, Enrique Sánchez

    2014-06-01

    This work proposes a new methodology to build interaction potentials between a highly charged metal cation and water molecules. These potentials, which can be used in classical computer simulations, have been fitted to reproduce quantum mechanical interaction energies (MP2 and BP86) for a wide range of [M(H2O)n]m+(H2O)ℓ clusters (n going from 6 to 10 and ℓ from 0 to 18). A flexible and polarizable water shell model (Mobile Charge Density of Harmonic Oscillator) has been coupled to the cation-water potential. The simultaneous consideration of poly-hydrated clusters and the polarizability of the interacting particles allows the inclusion of the most important many-body effects in the new polarizable potential. Applications have been centered on the californium, Cf(III) the heaviest actinoid experimentally studied in solution. Two different strategies to select a set of about 2000 structures which are used for the potential building were checked. Monte Carlo simulations of Cf(III)+500 H2O for three of the intermolecular potentials predict an aquaion structure with coordination number close to 8 and average R_{{Cf-O}} in the range 2.43-2.48 Å, whereas the fourth one is closer to 9 with R_{{Cf-O}} = 2.54 Å. Simulated EXAFS spectra derived from the structural Monte Carlo distribution compares fairly well with the available experimental spectrum for the simulations bearing 8 water molecules. An angular distribution similar to that of a square antiprism is found for the octa-coordination.

  16. Successive copper(I)-catalyzed cross-couplings in one pot: a novel and efficient starting point for synthesis of carbapenems.

    PubMed

    Jiang, Biao; Tian, Hua; Huang, Zuo-Gang; Xu, Min

    2008-07-03

    An efficient approach for synthesizing a series of 2-sulfide carbapenems has been developed using two successive Cu(I)-catalyzed cross-couplings in a single pot. The method involves highly selective intramolecular coupling of lactam and dihaloalkene using 2,2'-bipyridine as a ligand, followed by intermolecular C-S formation in the presence of another ligand (1,10-phenanthroline, PPh 3) and mercaptan.

  17. Intermolecular decarboxylative direct C-3 arylation of indoles with benzoic acids.

    PubMed

    Cornella, Josep; Lu, Pengfei; Larrosa, Igor

    2009-12-03

    A palladium catalyzed C-H activation of indoles and a silver catalyzed decarboxylative C-C activation of ortho substituted benzoic acids are synergistically combined to synthesize indoles arylated exclusively in the C-3 position. This novel decarboxylative C-H arylation methodology is compatible with electron-donating and -withdrawing substituents in both coupling partners.

  18. Intermolecular interactions in aqueous solutions of gallic acid at 296-306 K according to spectrofluorimetry and densimetry data

    NASA Astrophysics Data System (ADS)

    Grigoryan, K. R.; Sargsyan, L. S.

    2015-12-01

    Features of intermolecular interactions in aqueous solutions of gallic acid (GA) are studied by means of densimetry and fluorescence spectroscopy (intrinsic fluorescence, 2D spectra, and excitation/ emission matrix fluorescence spectra, 3D) at 296.15, 301.15, and 306.15 K in the concentration range of 5.88 × 10-4-5.88 × 10-2 mol L-1. It is shown by analyzing the concentration and temperature dependences of the apparent molar volumes and fluorescence parameters of GA that the equilibrium between nonassociated and associated species in the solution and the hydration of these species undergo changes.

  19. Rh-Catalyzed Intermolecular Reactions of α-Alkyl-α-Diazo Carbonyl Compounds with Selectivity over β-Hydride Migration

    PubMed Central

    DeAngelis, Andrew; Panish, Robert; Fox, Joseph M.

    2016-01-01

    CONSPECTUS Rh-carbenes derived from α-diazocarbonyl compounds have found broad utility across a remarkable range of reactivity, including cyclopropanation, cyclopropenation, C–H insertions, heteroatom–H insertions, and ylide forming reactions. However, in contrast to α-aryl or α-vinyl-α-diazocarbonyl compounds, the utility of α-alkyl-α-diazocarbonyl compounds had been moderated by the propensity of such compounds to undergo intramolecular β-hydride migration to give alkene products. Especially challenging had been intermolecular reactions involving α-alkyl-α-diazocarbonyl compounds. PMID:26689221

  20. Cascade intermolecular Michael addition-intramolecular azide/internal alkyne 1,3-dipolar cycloaddition reaction in one pot.

    PubMed

    Arigela, Rajesh K; Mandadapu, Anil K; Sharma, Sudhir K; Kumar, Brijesh; Kundu, Bijoy

    2012-04-06

    A rapid one-pot protocol for the synthesis of indole-based polyheterocycles via a sequential Lewis acid catalyzed intermolecular Michael addition and an intramolecular azide/internal alkyne 1,3-dipolar cycloaddition reaction has been described. The generality of the method has been demonstrated by treating a series of aromatic/aliphatic 2-alkynyl indoles with substituted (E)-1-azido-2-(2-nitrovinyl)benzenes to furnish annulated tetracyclic indolo[2,3-c][1,2,3]triazolo[1,5-a][1]benzazepines in good yields.