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Sample records for intramolecular utilizando nbcl5

  1. A structurally-characterized NbCl5-NHC adduct.

    PubMed

    Bortoluzzi, Marco; Ferretti, Eleonora; Marchetti, Fabio; Pampaloni, Guido; Zacchini, Stefano

    2014-05-01

    The selective reactions of niobium pentachloride with two bulky NHC carbenes afforded NbCl5(NHC) complexes, bearing the highest oxidation state ever found for a metal centre in a transition metal halide-NHC adduct. The X-ray structure of 2a is the first one reported for a monodentate NHC-niobium species, and exhibits an abnormally long Nb-C bond. PMID:24658260

  2. Optical properties of NbCl5 and ZnMg intercalated graphite compounds

    NASA Astrophysics Data System (ADS)

    Jung, Eilho; Lee, Seokbae; Roh, Seulki; Meng, Xiuqing; Tongay, Sefaattin; Kang, Jihoon; Park, Tuson; Hwang, Jungseek

    2014-12-01

    We studied NbCl5 and ZnMg alloy intercalated graphite compounds using an optical spectroscopy technique. These intercalated metallic graphite samples were quite challenging to obtain optical reflectance spectra since they were not flat and quite thin. By using both a new method and an in situ gold evaporation technique we were able to obtain reliable reflectance spectra of our samples in the far and mid infrared range (80-7000 cm-1). We extracted the optical constants including the optical conductivity and the dielectric function from the measured reflectance spectra using a Kramers-Kronig analysis. We also extracted the dc conductivity and the plasma frequencies from the optical conductivity and dielectric functions. NbCl5 intercalated graphite samples show similar optical conductivity spectra as bare highly oriented pyrolytic graphite even though there are some differences in detail. ZnMg intercalated samples show significantly different optical conductivity spectra from the bare graphite. Optical spectroscopy is one of the most reliable experimental techniques to obtain the electronic band structures of materials. The obtained optical conductivities support the recent theoretically calculated electronic band structures of NbCl5 and ZnMg intercalated graphite compounds. Our results also provide important information of electronic structures and charge carrier properties of these two new intercalated materials for applications.

  3. Active low-valent niobium catalysts from NbCl5 and hydrosilanes for selective intermolecular cycloadditions.

    PubMed

    Satoh, Yasushi; Obora, Yasushi

    2011-10-21

    An active niobium catalyst was developed via a simple and nontoxic reduction method from NbCl(5)/hydrosilane and utilized for the selective [2 + 2 + 2] cycloaddition reaction of terminal alkynes and alkenes/α,ω-dienes, to give 1,3-cyclohexadiene derivatives in high yields with excellent chemo- and regioselectivity. PMID:21919436

  4. Allylic and Allenic Halide Synthesis via NbCl5- and NbBr5-Mediated Alkoxide Rearrangements

    PubMed Central

    Ravikumar, P. C.; Yao, Lihua; Fleming, Fraser F.

    2009-01-01

    Addition of NbCl5, or NbBr5, to a series of magnesium, lithium, or potassium allylic or propargylic alkoxides directly provides allylic or allenic halides. Halogenation formally occurs through a metalla-halo-[3,3] rearrangement although concerted, ionic, and direct displacement mechanisms appear to operate competitively. Transposition of the olefin is equally effective for allylic alkoxides prepared by nucleophilic addition, deprotonation, or reduction. Experimentally, the niobium pentahalide halogenations are rapid, afford essentially pure E-allylic or allenic halides after extraction, and are applicable to a range of aliphatic and aromatic alcohols, aldehydes, and ketones. PMID:19739606

  5. Allylic and allenic halide synthesis via NbCl(5)- and NbBr(5)-mediated alkoxide rearrangements.

    PubMed

    Ravikumar, P C; Yao, Lihua; Fleming, Fraser F

    2009-10-01

    Addition of NbCl(5) or NbBr(5) to a series of magnesium, lithium, or potassium allylic or propargylic alkoxides directly provides allylic or allenic halides. Halogenation formally occurs through a metalla-halo-[3,3] rearrangement, although concerted, ionic, and direct displacement mechanisms appear to operate competitively. Transposition of the olefin is equally effective for allylic alkoxides prepared by nucleophilic addition, deprotonation, or reduction. Experimentally, the niobium pentahalide halogenations are rapid, afford essentially pure (E)-allylic or -allenic halides after extraction, and are applicable to a range of aliphatic and aromatic alcohols, aldehydes, and ketones. PMID:19739606

  6. The solid state structure and reactivity of NbCl(5) x (N,N'-dicyclohexylurea) in solution: evidence for co-ordinated urea dehydration to the relevant carbodiimide.

    PubMed

    Aresta, Michele; Dibenedetto, Angela; Stufano, Paolo; Aresta, Brunella Maria; Maggi, Sabino; Pápai, Imre; Rokob, Tibor András; Gabriele, Bartolo

    2010-08-14

    NbCl(5) x (N,N'-dicyclohexylurea) 1a owns a distorted octahedral structure due to intramolecular NH...Cl bonding. The unit cell contains four units which are intermolecularly NH...Cl and NH...N bonded. An extended intramolecular network of H-bonding (N-H...Cl, CH...Cl, CH...N) causes the 3D self assembling of the units. Upon addition of base, the HCl release from 1a is observed with the transfer to Nb of the O-atom of the carbonylic function of the starting urea which is converted into the relevant carbodiimide CyN=C=NCy 4. The latter is quantitatively released by adding an excess of NEt(3) at 308 K (py and DBU are less efficient) with formation of the known NbOCl(3)(NEt(3))(2), isolated in quantitative yield. Increasing the temperature leads to a loss in selectivity as the formed DCC undergoes further reactions. At 350 K, the isocyanate CyN=C=O has been isolated in 60% yield besides a mixture of Nb-complexes. DFT calculations have been coupled to IR and NMR experiments for characterizing possible reaction intermediates and the behaviour of 1a. Several other MCl(x) species (ScCl(3), YCl(3), LaCl(3), TiCl(4), TaCl(5), AlCl(3), SnCl(4)) have been shown to be able to co-ordinate DCU but not all of them promote the conversion of urea into DCC. PMID:20544121

  7. Dynamics of the NbCl5-catalyzed cycloaddition of propylene oxide and CO2 : assessing the dual role of the nucleophilic Co-catalysts.

    PubMed

    D'Elia, Valerio; Ghani, Amylia A; Monassier, Antoine; Sofack-Kreutzer, Julien; Pelletier, Jeremie D A; Drees, Markus; Vummaleti, Sai V C; Poater, Albert; Cavallo, Luigi; Cokoja, Mirza; Basset, Jean-Marie; Kühn, Fritz E

    2014-09-01

    A mechanistic study on the synthesis of propylene carbonate (PC) from CO2 and propylene oxide (PO) catalyzed by NbCl5 and organic nucleophiles such as 4-dimethylaminopyridine (DMAP) or tetra-n-butylammonium bromide (NBu4 Br) is reported. A combination of in situ spectroscopic techniques and kinetic studies has been used to provide detailed insight into the reaction mechanism, the formation of intermediates, and interactions between the reaction partners. The results of DFT calculations support the experimental observations and allow us to propose a mechanism for this reaction. PMID:25056457

  8. Six- and eight-coordinate thio- and seleno-ether complexes of NbF5 and some comparisons with NbCl5 and NbBr5 adducts.

    PubMed

    Jura, Marek; Levason, William; Ratnani, Raju; Reid, Gillian; Webster, Michael

    2010-01-21

    The reaction of RS(CH(2))(2)SR (R = Me, Et or (i)Pr) with NbF(5) produces [NbF(4){RS(CH(2))(2)SR}(2)][NbF(6)] which contain distorted eight-coordinate (dodecahedral) cations and octahedral anions, whereas RSe(CH(2))(2)SeR (R = Me or Bu(n)) form six-coordinate [(NbF(5))(2)(mu-RSe(CH(2))(2)SeR)]. Et(2)S and Me(2)Se (L) also form six-coordinate [NbF(5)(L)], but Me(2)S forms both [NbF(5)(Me(2)S)] and an eight-coordinate cation in [NbF(4)(Me(2)S)(4)][NbF(6)]. MeS(CH(2))(2)SMe forms eight-coordinate cations in [NbX(4){MeS(CH(2))(2)SMe}(2)][NbX(6)] (X = Cl or Br), but other complexes of the heavier halides including [NbX(5)(L)] and [(NbX(5))(2)(mu-L-L)] (L-L = RSe(CH(2))(2)SeR; o-C(6)H(4)(CH(2)SMe)(2) and o-C(6)H(4)(CH(2)SeMe)(2)) contain six-coordinate niobium. The very unstable [NbCl(5)(Me(2)Te)] was characterised spectroscopically, but all other attempts to form telluroether complexes resulted in decomposition, and NbI(5) was reduced even by thioethers. The complexes have been characterised by multinuclear NMR ((1)H, (19)F, (93)Nb, (77)Se or (125)Te), IR and UV/visible spectroscopy, and X-ray crystal structures are reported for [NbF(4){RS(CH(2))(2)SR}(2)][NbF(6)] (R = Me, (i)Pr), [NbF(4)(Me(2)S)(4)][NbF(6)], [NbCl(5)(Me(2)Se)], [NbBr(5)(Me(2)S)], [(NbCl(5))(2){o-C(6)H(4)(CH(2)SMe)(2)}] and [(NbCl(5))(2){MeSe(CH(2))(2)SeMe}]. All the complexes are very moisture sensitive and the fluoride complexes decompose slowly with fluorination of the neutral ligand. PMID:20066233

  9. Intramolecular and nonlinear dynamics

    SciTech Connect

    Davis, M.J.

    1993-12-01

    Research in this program focuses on three interconnected areas. The first involves the study of intramolecular dynamics, particularly of highly excited systems. The second area involves the use of nonlinear dynamics as a tool for the study of molecular dynamics and complex kinetics. The third area is the study of the classical/quantum correspondence for highly excited systems, particularly systems exhibiting classical chaos.

  10. Carbon nanotube intramolecular junctions

    NASA Astrophysics Data System (ADS)

    Yao, Zhen; Postma, Henk W. Ch.; Balents, Leon; Dekker, Cees

    1999-11-01

    The ultimate device miniaturization would be to use individual molecules as functional devices. Single-wall carbon nanotubes (SWNTs) are promising candidates for achieving this: depending on their diameter and chirality, they are either one-dimensional metals or semiconductors. Single-electron transistors employing metallic nanotubes and field-effect transistors employing semiconducting nanotubes have been demonstrated. Intramolecular devices have also been proposed which should display a range of other device functions. For example, by introducing a pentagon and a heptagon into the hexagonal carbon lattice, two tube segments with different atomic and electronic structures can be seamlessly fused together to create intramolecular metal-metal, metal-semiconductor, or semiconductor-semiconductor junctions. Here we report electrical transport measurements on SWNTs with intramolecular junctions. We find that a metal-semiconductor junction behaves like a rectifying diode with nonlinear transport characteristics that are strongly asymmetric with respect to bias polarity. In the case of a metal-metal junction, the conductance appears to be strongly suppressed and it displays a power-law dependence on temperatures and applied voltage, consistent with tunnelling between the ends of two Luttinger liquids. Our results emphasize the need to consider screening and electron interactions when designing and modelling molecular devices. Realization of carbon-based molecular electronics will require future efforts in the controlled production of these intramolecular nanotube junctions.

  11. Intramolecular Aminoboration of Unfunctionalized Olefins.

    PubMed

    Yang, Chun-Hua; Zhang, Yu-Shi; Fan, Wen-Wen; Liu, Gong-Qing; Li, Yue-Ming

    2015-10-19

    A direct and catalyst-free method for the intramolecular aminoboration of unfunctionalized olefins is reported. In the presence of BCl3 (1 equiv) as the sole boron source, intramolecular aminoboration of sulfonamide derivatives of 4-penten-1-amines, 5-hexen-1-amines, and 2-allylanilines proceeded readily without the use of any catalyst. The boronic acids obtained after hydrolysis could be converted into the corresponding pinacol borates in a straightforward manner by treatment with pinacol under anhydrous conditions. PMID:26331979

  12. Materials Data on NbCl5 (SG:12) by Materials Project

    SciTech Connect

    Kristin Persson

    2014-11-02

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  13. Materials Data on NbCl5 (SG:14) by Materials Project

    DOE Data Explorer

    Kristin Persson

    2016-07-14

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  14. Intramolecular Hydrogen Bonding in Substituted Aminoalcohols.

    PubMed

    Lane, Joseph R; Schrøder, Sidsel D; Saunders, Graham C; Kjaergaard, Henrik G

    2016-08-18

    The qualifying features of a hydrogen bond can be contentious, particularly where the hydrogen bond is due to a constrained intramolecular interaction. Indeed there is disagreement within the literature whether it is even possible for an intramolecular hydrogen bond to form between functional groups on adjacent carbon atoms. This work considers the nature of the intramolecular interaction between the OH (donor) and NH2 (acceptor) groups of 2-aminoethanol, with varying substitution at the OH carbon. Gas-phase vibrational spectra of 1-amino-2-methyl-2-propanol (BMAE) and 1-amino-2,2-bis(trifluoromethyl)-2-ethanol (BFMAE) were recorded using Fourier transform infrared spectroscopy and compared to literature spectra of 2-aminoethanol (AE). Based on the experimental OH-stretching frequencies, the strength of the intramolecular hydrogen bond appears to increase from AE < BMAE ≪ BFMAE. Non-covalent interaction analysis shows evidence of an intramolecular hydrogen bond in all three molecules, with the order of the strength of interaction matching that of experiment. The experimental OH-stretching vibrational frequencies were found to correlate well with the calculated kinetic energy density, suggesting that this approach can be used to estimate the strength of an intramolecular hydrogen bond. PMID:27447952

  15. Intramolecular alpha–Glucosaminidation: Synthesis of Mycothiol

    PubMed Central

    Ajayi, Kehinde; Thakur, Vinay V.; Lapo, Robert C.; Knapp, Spencer

    2010-01-01

    A protected cyclitol aglycon was tethered to an (N-arylsulfonyl)glucosamine donor by a methylene linker; the exclusively alpha-selective intramolecular glycosyation reaction was then initiated by electrophilic activation of the thioglycoside donor portion. Further transformations of the glycosylation product to give the M. tuberculosis detoxifier mycothiol and its oxidized congener, the disulfide mycothione, are detailed. PMID:20443569

  16. Organocatalyzed Intramolecular Carbonyl-Ene Reactions.

    PubMed

    Dahlmann, Heidi A; McKinney, Amanda J; Santos, Maria P; Davis, Lindsey O

    2016-01-01

    An organocatalyzed intramolecular carbonyl-ene reaction was developed to produce carbocyclic and heterocyclic 5- and 6-membered rings from a citronellal-derived trifluoroketone and a variety of aldehydes. A phosphoramide derivative was found to promote the cyclization of the trifluoroketone, whereas a less acidic phosphoric acid proved to be a superior catalyst for the aldehyde substrates. PMID:27258238

  17. Aptamer switch probe based on intramolecular displacement.

    PubMed

    Tang, Zhiwen; Mallikaratchy, Prabodhika; Yang, Ronghua; Kim, Youngmi; Zhu, Zhi; Wang, Hui; Tan, Weihong

    2008-08-27

    A novel aptamer-based molecular probe design employing intramolecular signal transduction is demonstrated. The probe is composed of three elements: an aptamer, a short, partially cDNA sequence, and a PEG linker conjugating the aptamer with the short DNA strand. We have termed this aptamer probe an "aptamer switch probe", or ASP. The ASP design utilizes both a fluorophore and a quencher which are respectively modified at the two termini of the ASP. In the absence of the target molecule, the short DNA will hybridize with the aptamer, keeping the fluorophore and quencher in close proximity, thus switching off the fluorescence. However, when the ASP meets its target, the binding between the aptamer and the target molecule will disturb the intramolecular DNA hybridization, move the quencher away from the fluorophore, and, in effect, switch on the fluorescence. Both ATP and human alpha-thrombin aptamers were engineered to demonstrate this design, and both showed that fluorescence enhancement could be quantitatively mediated by the addition of various amounts of target molecules. Both of these ASPs presented excellent selectivity and prompt response toward their targets. With intrinsic advantages resulting from its intramolecular signal transduction architecture, the ASP design holds promising potential for future applications, such as biochip and in situ imaging, which require reusability, excellent stability, prompt response, and high sensitivity. PMID:18680291

  18. Femtosecond laser studies of ultrafast intramolecular processes

    SciTech Connect

    Hayden, C.

    1993-12-01

    The goal of this research is to better understand the detailed mechanisms of chemical reactions by observing, directly in time, the dynamics of fundamental chemical processes. In this work femtosecond laser pulses are used to initiate chemical processes and follow the progress of these processes in time. The authors are currently studying ultrafast internal conversion and subsequent intramolecular relaxation in unsaturated hydrocarbons. In addition, the authors are developing nonlinear optical techniques to prepare and monitor the time evolution of specific vibrational motions in ground electronic state molecules.

  19. Intramolecular energy transfer reactions in polymetallic

    SciTech Connect

    Petersen, J.

    1990-11-01

    This report is concerned with intramolecular, energy-transfer reactions. The concept of preparing synthetically a complex molecular species, capable of absorbing a photon at one metal center (antenna fragment), transferring that energy to a second metal center (reactive fragment) via a bridging ligand was first reported by our group in 1979. It is now apparent that a major emphasis in inorganic chemistry in the future will involve these types of molecular ensembles. Complexes discussed include Rh, Ru, and Cu complexes. 23 refs., 14 tabs.

  20. Solvent gating of intramolecular electron transfer

    SciTech Connect

    Miller, R.M. ); Spears, K.G.; Gong, J.H.; Wach, M. )

    1994-02-03

    The rates for ionic photodissociation of malachite green leucocyanide to form cyanide ion and a malachite green carbonium ion were measured as a function of solvent and temperature. The observed rates in mixtures of polar and nonpolar solvents all had an activation energy of about 1 kcal/mol for a wide range of dielectric constants. This dissociative intramolecular electron transfer (DIET) is unusual because it is the first example where solvent configurational entropy changes are required to enable a large amplitude molecular distortion leading to a nonadiabatic electron transfer and ionic dissociation. This solvent gated intramolecular electron-transfer mechanism is supported by analysis of the preexponential and activation energy trends in dipolar aprotic solven mixtures and alcohol solvents. The large amplitude motion is not separately measurable due to the slow gating rates, but viscosity effects on both the preexponential and the activation energy are analyzed to demonstrate consistency with a barrierless diffusion model having a structural dependence on electron-transfer rate. The rate has an inverse dependence on viscosity raised to the 0.53 power. 36 refs., 6 figs., 4 tabs.

  1. Quantitative Intramolecular Singlet Fission in Bipentacenes.

    PubMed

    Sanders, Samuel N; Kumarasamy, Elango; Pun, Andrew B; Trinh, M Tuan; Choi, Bonnie; Xia, Jianlong; Taffet, Elliot J; Low, Jonathan Z; Miller, John R; Roy, Xavier; Zhu, X-Y; Steigerwald, Michael L; Sfeir, Matthew Y; Campos, Luis M

    2015-07-22

    Singlet fission (SF) has the potential to significantly enhance the photocurrent in single-junction solar cells and thus raise the power conversion efficiency from the Shockley-Queisser limit of 33% to 44%. Until now, quantitative SF yield at room temperature has been observed only in crystalline solids or aggregates of oligoacenes. Here, we employ transient absorption spectroscopy, ultrafast photoluminescence spectroscopy, and triplet photosensitization to demonstrate intramolecular singlet fission (iSF) with triplet yields approaching 200% per absorbed photon in a series of bipentacenes. Crucially, in dilute solution of these systems, SF does not depend on intermolecular interactions. Instead, SF is an intrinsic property of the molecules, with both the fission rate and resulting triplet lifetime determined by the degree of electronic coupling between covalently linked pentacene molecules. We found that the triplet pair lifetime can be as short as 0.5 ns but can be extended up to 270 ns. PMID:26102432

  2. Ab initio of the intramolecular dynamics trifluoronitromethane

    SciTech Connect

    Roehrig, M.A.; McCarthy, W.J.; Kukolich, S.G.; Adamowicz, L.

    1993-12-31

    Several experimental studies of trifluoronitromethane have indicated that this molecule undergoes a low energy motion corresponding to an internal rotation of the CF{sub 3} relative to the NO{sub 2} group. Values for the V{sub 6} barrier have been obtained by electron diffraction and microwave spectroscopy to be 3 kcal/mol and 74 cal/mol respectively. A theoretical study of this molecule investigating this and possible other low energy motions is currently underway. Results from this study should reveal new information on the low barrier dynamics and shed some light on this large discrepancy on the V{sub 6} barriers. Preliminary calculations seem to indicate that a simple V{sub 6} barrier does not adequately describe the intramolecular dynamics of this molecule.

  3. Simple intramolecular model potentials for water

    SciTech Connect

    Dang, L.X.; Pettitt, B.M.

    1987-06-04

    An effective intramolecular potential is presented for use in conjunction with existing three-site models of water. Two commonly used internal geometries were fit to the same form yielding slightly different parametrizations. By including a Urey-Bradley-like term in an otherwise standard molecular mechanics form it was found that the experimental transition frequencies of water monomer can be reproduced accurately. Good qualitative agreements for spectral shifts were subsequently found for the models in condensed-phase applications. Harmonic analysis of clusters indicates good qualitative agreement with experimental environmental shifts in frequencies at low temperatures for these models. This model should be useful for a wide variety of applications including simulations of biopolymers and ionic solutions.

  4. Are intramolecular frustrated Lewis pairs also intramolecular catalysts? A theoretical study on H2 activation.

    PubMed

    Zeonjuk, Lei Liu; St Petkov, Petko; Heine, Thomas; Röschenthaler, Gerd-Volker; Eicher, Johannes; Vankova, Nina

    2015-04-28

    We investigate computationally a series of intramolecular frustrated Lewis pairs (FLPs), with the general formula Mes2PCHRCH2B(C6F5)2, that are known from the literature to either activate molecular hydrogen (FLPs with R = H (1) or Me (4)), or remain inert (FLPs with R = Ph (2) or SiMe3 (3)). The prototypical system Mes2PCH2CH2B(C6F5)2 (1) has been described in the literature (Grimme et al., Angew. Chem., Int. Ed., 2010; Rokob et al., J. Am. Chem. Soc., 2013) as an intramolecular reactant that triggers the reaction with H2 in a bimolecular concerted fashion. In the current study, we show that the concept of intramolecular H2 activation by linked FLPs is not able to explain the inertness of the derivative compounds 2 and 3 towards H2. To cope with this, we propose an alternative intermolecular mechanism for the investigated reaction, assuming stacking of two open-chain FLP conformers, and formation of a dimeric reactant with two Lewis acid–base domains, that can split up to two hydrogen molecules. Using quantum-chemical methods, we compute the reaction profiles describing these alternative mechanisms, and compare the derived predictions with earlier reported experimental results. We show that only the concept of intermolecular H2 activation could explain both the activity of the FLPs having small substituents in the bridging molecular region, and the inertness of the FLPs with a bulkier substitution, in a consistent way. Importantly, the intermolecular H2 activation driven by intramolecular FLPs indicates the key role of steric factors and noncovalent interactions for the design of metal-free systems that can efficiently split H2, and possibly serve as metal-free hydrogenation catalysts. PMID:25812167

  5. Intramolecular hydrogen bonds in sulfur-containing aminophenols

    NASA Astrophysics Data System (ADS)

    Belkov, M. V.; Harbachova, A. N.; Ksendzova, G. A.; Polozov, G. I.; Skornyakov, I. V.; Sorokin, V. L.; Tolstorozhev, G. B.; Shadyro, O. I.

    2010-07-01

    IR Fourier spectroscopy methods have been adopted to study intramolecular interactions that occur in CCl4 solutions of antiviral derivatives of aminophenol. Analysis of the IR spectra showed that intramolecular bonds O-H···N, O-H···O=C, N-H···O=S=O, and O-H···O=S=O can occur in these compounds depending on the substituent on the amino group. Not only the presence of intramolecular O-H···N, O-H···O=S=O, and N- H···O=S=O hydrogen bonds in 2-amino-4,6-di-tert-butylphenol derivatives containing a sulfonamide fragment but also conformational equilibrium among these types of intramolecular interactions are essential for the manifestation of high efficiency in suppressing HIV-infection in cell culture.

  6. Synchronous intramolecular cycloadditions of the polyene macrolactam polyketide heronamide C.

    PubMed

    Booth, Thomas J; Alt, Silke; Capon, Robert J; Wilkinson, Barrie

    2016-05-11

    A growing number of natural products appear to arise from biosynthetic pathways that involve pericyclic reactions. We show here that for the heronamides this can occur via two spontaneous pathways involving alternative thermal or photochemical intramolecular cycloadditions. PMID:27091090

  7. Exciton Correlations in Intramolecular Singlet Fission.

    PubMed

    Sanders, Samuel N; Kumarasamy, Elango; Pun, Andrew B; Appavoo, Kannatassen; Steigerwald, Michael L; Campos, Luis M; Sfeir, Matthew Y

    2016-06-15

    We have synthesized a series of asymmetric pentacene-tetracene heterodimers with a variable-length conjugated bridge that undergo fast and efficient intramolecular singlet fission (iSF). These compounds have distinct singlet and triplet energies, which allow us to study the spatial dynamics of excitons during the iSF process, including the significant role of exciton correlations in promoting triplet pair generation and recombination. We demonstrate that the primary photoexcitations in conjugated dimers are delocalized singlets that enable fast and efficient iSF. However, in these asymmetric dimers, the singlet becomes more localized on the lower energy unit as the length of the bridge is increased, slowing down iSF relative to analogous symmetric dimers. We resolve the recombination kinetics of the inequivalent triplets produced via iSF, and find that they primarily decay via concerted processes. By identifying different decay channels, including delayed fluorescence via triplet-triplet annihilation, we can separate transient species corresponding to both correlated triplet pairs and uncorrelated triplets. Recombination of the triplet pair proceeds rapidly despite our experimental and theoretical demonstration that individual triplets are highly localized and unable to be transported across the conjugated linker. In this class of compounds, the rate of formation and yield of uncorrelated triplets increases with bridge length. Overall, these constrained, asymmetric systems provide a unique platform to isolate and study transient species essential for singlet fission, which are otherwise difficult to observe in symmetric dimers or condensed phases. PMID:27183040

  8. Femtochemistry of Intramolecular Charge and Proton Transfer Reactions in Solution

    SciTech Connect

    Douhal, Abderrazzak; Sanz, Mikel; Carranza, Maria Angeles; Organero, Juan Angel; Tormo, Laura

    2005-03-17

    We report on the first observation of ultrafast intramolecular charge- and proton-transfer reactions in 4'-dimethylaminoflavonol (DAMF) in solution. Upon femtosecond excitation of a non-planar structure of DMAF in apolar medium, the intramolecular charge transfer (ICT) does not occur, and a slow (2 ps) proton motion takes place. However, in polar solvents, the ICT is very fast (100-200 fs) and the produced structure is stabilized that proton motion takes place in few or tens of ps.

  9. Intramolecular energy transfer in fullerene pyrazine dyads

    SciTech Connect

    Guldi, D.M.; Torres-Garcia, G.; Mattay, J.

    1998-11-26

    Excited-state properties of three different pyrazine derivatives 4--6 were probed by emission and transient absorption spectroscopy. They display emission maxima at 464 (4), 417 (5), and 515 nm (6) that are red-shifted with respect to their strong UV ground-state absorption and formed with overall quantum yields ({Phi}) of 0.156, 0.22, and 0.13, respectively. Once photoexcited, these triplet excited pyrazines undergo rapid intermolecular energy transfer to a monofunctionalized fullerene derivative (7) with bimolecular rate constants ranging from 3.64 {times} 10{sup 9} M{sup {minus}1} s{sup {minus}1} (6) to 1.1 {times} 10{sup 10} M{sup {minus}1} s{sup {minus}1} (4). The product of these bimolecular energy-transfer reactions is in all cases the fullerene triplet excited state. Functionalization of pristine C{sub 60} with the investigated pyrazine derivatives promotes the UV-vis absorption characteristics and, in turn, improves the light-harvesting efficiency of the resulting dyads 1--3 relative to pristine C{sub 60}. Photoexcitation of the pyrazine moieties in dyads 1--3 leads to the formation of their singlet excited states. In contrast to the pyrazine models, photoexcitation of dyad 1--3 is followed by rapid intramolecular deactivation processes of the latter via energy transfer to the fullerene ground state with half-lives between 37 and 100 ps. In turn, energy transfer transforms the short-lived and moderately redox-active singlet excited states of pyrazine into the highly reactive fullerene triplet excited state. The latter is found to produce effectively singlet oxygen ({sup 1}O{sub 2}) with quenching rate constants for 1--3 of (1--1.5) {times} 10{sup 9} M{sup {minus}1} s{sup {minus}1}. Similarly, reductive quenching of the triplet excited states in dyads 1--3 via electron transfer with diazabicyclooctane (DABCO) occurs with rate constants of 5.2--9.4 {times} 10{sup 7} M{sup {minus}1} s{sup {minus}1}.

  10. Silver-catalysed intramolecular hydroamination of alkynes with trichloroacetimidates.

    PubMed

    Wong, Valerie H L; Hor, T S Andy; Hii, King Kuok Mimi

    2013-10-18

    Silver(I) complexes catalyse the intramolecular addition of trichloroacetimidates to alkynes. In the absence of a ligand, the selectivity of the reaction is dependent upon the nature of the counter-anion and solvent. The introduction of non-chelating nitrogeneous ligands suppresses competitive Brønsted acid catalysis, improving the yield and selectivity of the reaction. PMID:23999555

  11. Intramolecular amide bonds stabilize pili on the surface of bacilli

    SciTech Connect

    Budzik, Jonathan M.; Poor, Catherine B.; Faull, Kym F.; Whitelegge, Julian P.; He, Chuan; Schneewind, Olaf

    2010-01-12

    Gram-positive bacteria elaborate pili and do so without the participation of folding chaperones or disulfide bond catalysts. Sortases, enzymes that cut pilin precursors, form covalent bonds that link pilin subunits and assemble pili on the bacterial surface. We determined the x-ray structure of BcpA, the major pilin subunit of Bacillus cereus. The BcpA precursor encompasses 2 Ig folds (CNA{sub 2} and CNA{sub 3}) and one jelly-roll domain (XNA) each of which synthesizes a single intramolecular amide bond. A fourth amide bond, derived from the Ig fold of CNA{sub 1}, is formed only after pilin subunits have been incorporated into pili. We report that the domains of pilin precursors have evolved to synthesize a discrete sequence of intramolecular amide bonds, thereby conferring structural stability and protease resistance to pili.

  12. Intramolecular Aminocyanation of Alkenes via N–CN Bond Cleavage**

    PubMed Central

    Pan, Zhongda; Pound, Sarah M.; Rondla, Naveen R.; Douglas, Christopher J.

    2014-01-01

    A metal-free, Lewis acid-promoted intramolecular aminocyanation of alkenes was developed. B(C6F5)3 activates N-sulfonyl cyanamides, leading an formal cleavage of the N-CN bonds in conjunction with vicinal addition of sulfonamide and nitrile groups across an alkene. This method enables atom-economical access to indolines and tetrahydroquinolines in excellent yields, and provides a complementary strategy for regioselective alkene difunctionalizations with sulfonamide and nitrile groups. Labeling experiments with 13C suggest a fully intramolecular cyclization pattern due to lack of label scrambling in double crossover experiments. Catalysis with Lewis acid is realized and the reaction can be conducted under air. PMID:24719371

  13. Stereodivergent Synthesis of Chromanones and Flavanones via Intramolecular Benzoin Reaction.

    PubMed

    Wen, Genfa; Su, Yingpeng; Zhang, Guoxiang; Lin, Qiqiao; Zhu, Yujin; Zhang, Qianqian; Fang, Xinqiang

    2016-08-19

    The strategy of stereodivergent reactions on racemic mixtures (stereodivergent RRM) was employed for the first time in intramolecular benzoin reactions and led to the rapid access of chromanones/flavanones with two consecutive stereocenters. The easily separable stereoisomers of the products were obtained with moderate to excellent enantioselectivities in a single step. Catechol type additives proved crucial in achieving the desired diastereo- and enantioselectivities. PMID:27490010

  14. Intramolecular interaction and dynamics of the cationic argon trimer

    SciTech Connect

    Ragnetti, F.; Zuhrt, C.; Zuelicke, L.

    1996-12-31

    For the simplest cationic argon cluster, Ar{sub 3}{sup +}, the topographical characteristics of the ground-state potential energy surface (PES), the mode coupling and the claswsical intramolecular dynamics are studied; PES data have been obtained by the diatomics-in-molecules approach of Kuntz et al. The results show that Ar{sub 3}{sup +} s a rather floppy system with rapid vibrational energy redistribution and early onset of classical chaos.

  15. Intramolecular vibrational dephasing obeys a power law at intermediate times

    PubMed Central

    Gruebele, M.

    1998-01-01

    Experimental intramolecular vibrational dephasing transients for several large organic molecules are reanalyzed. Fits to the experimental data, as well as full numerical quantum calculations with a factorized potential surface for all active degrees of freedom of fluorene indicate that power law decays, not exponentials, occur at intermediate times. The results support a proposal that power law decays describe vibrational dephasing dynamics in large molecules at intermediate times because of the local nature of energy flow. PMID:9600900

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

    PubMed

    Nagy, Peter I

    2014-01-01

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

  17. Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

    PubMed Central

    Nagy, Peter I.

    2014-01-01

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

  18. Mechanism of intramolecular transformations of nickel phosphanido hydride complexes.

    PubMed

    Latypov, Shamil K; Polyancev, Fedor M; Ganushevich, Yulia S; Miluykov, Vasily A; Sinyashin, Oleg G

    2016-02-01

    In solution, nickel phosphanido hydride complexes ([NiH{P(Ar)(H)}(dtbpe)], Ar = Dmp, Mes*) undergo a degenerate intramolecular exchange, with the Ni-H and P-H hydrogens and both halves of the dtbpe moiety interchanging. This intramolecular rearrangement was shown to occur in three steps: first, the hydride proton migrates to phosphorus, then the P-Aryl moiety rotates around the P-Ni bond, and finally the back migration of one proton to Ni completes the process. Both migration and rotation were determined to be characterized by high barriers (on the NMR time scale) and to depend on the type of aryl group at the terminal phosphorus. Compared to that observed for the Ni complexes, the same isomeric preference, but with a slower rate of intramolecular rearrangement, is predicted for the corresponding Pt complexes. An opposite isomeric preference, however, is expected for the corresponding Pd complexes. Thus, it is likely that some of the catalytic reactions of Pd and Pt complexes are driven by the relative thermodynamic stabilities of their main forms. PMID:26407302

  19. Catalytic Intramolecular Ketone Alkylation with Olefins by Dual Activation.

    PubMed

    Lim, Hee Nam; Dong, Guangbin

    2015-12-01

    Two complementary methods for catalytic intramolecular ketone alkylation reactions with unactivated olefins, resulting in Conia-ene-type reactions, are reported. The transformations are enabled by dual activation of both the ketone and the olefin and are atom-economical as stoichiometric oxidants or reductants are not required. Assisted by Kool's aniline catalyst, the reaction conditions can be both pH- and redox-neutral. A broad range of functional groups are thus tolerated. Whereas the rhodium catalysts are effective for the formation of five-membered rings, a ruthenium-based system that affords the six-membered ring products was also developed. PMID:26486569

  20. Intramolecular charge transfer in donor-acceptor molecules

    SciTech Connect

    Slama-Schwok, A.; Blanchard-Desce, M.; Lehn, J.M. )

    1990-05-17

    The photophysical properties of donor-acceptor molecules, push-pull polyenes and carotenoids, have been studied by absorption and fluorescence spectroscopy. The compounds bear various acceptor and donor groups, linked together by chains of different length and structure. The position of the absorption and fluorescence maxima and their variation in solvents of increasing polarity are in agreement with long-distance intramolecular charge-transfer processes, the linker acting as a molecular wire. The effects of the linker length and structure and of the nature of acceptor and donor are presented.

  1. Intramolecular Fluorescence Correlation Spectroscopy in a Feedback Tracking Microscope

    NASA Astrophysics Data System (ADS)

    McHale, Kevin; Mabuchi, Hideo

    2010-07-01

    We derive the statistics of the signals generated by shape fluctuations of large molecules studied by feedback tracking microscopy. We account for the influence of intramolecular dynamics on the response of the tracking system, and derive a general expression for the fluorescence autocorrelation function that applies when those dynamics are linear. We show that tracking provides enhanced sensitivity to translational diffusion, molecular size, heterogeneity and long time-scale decays in comparison to traditional fluorescence correlation spectroscopy. We demonstrate our approach by using a three-dimensional tracking microscope to study genomic $\\lambda$-phage DNA molecules with various fluorescence label configurations.

  2. C1-Cx revisited: intramolecular synergism in a cellulase.

    PubMed Central

    Din, N; Damude, H G; Gilkes, N R; Miller, R C; Warren, R A; Kilburn, D G

    1994-01-01

    Endoglucanase A (CenA) from the bacterium Cellulomonas fimi is composed of a catalytic domain and a nonhydrolytic cellulose-binding domain that can function independently. The individual domains interact synergistically in the disruption and hydrolysis of cellulose fibers. This intramolecular synergism is distinct from the well-known intermolecular synergism between individual cellulases. The catalytic domain corresponds to the hydrolytic Cx system and the cellulose-binding domain corresponds to the nonhydrolytic C1 system postulated by Reese et al. [Reese, E. T., Sui, R. G. H. & Levinson, H. S. (1950) J. Bacteriol. 59, 485-497] to be required for the hydrolysis of cellulose. PMID:7972069

  3. Effects of Intramolecular Distance between Amyloidogenic Domains on Amyloid Aggregation

    PubMed Central

    Ko, Ahra; Kim, Jin Ryoun

    2012-01-01

    Peptide/protein aggregation is implicated in many amyloid diseases. Some amyloidogenic peptides/proteins, such as those implicated in Alzheimer’s and Parkinson’s diseases, contain multiple amyloidogenic domains connected by “linker” sequences displaying high propensities to form turn structures. Recent studies have demonstrated the importance of physicochemical properties of each amino acid contained in the polypeptide sequences in amyloid aggregation. However, effects on aggregation related to the intramolecular distance between amyloidogenic domains, which may be determined by a linker length, have yet to be examined. In the study presented here, we created peptides containing two copies of KFFE, a simple four-residue amyloidogenic domain, connected by GS-rich linker sequences with different lengths yet similar physicochemical properties. Our experimental results indicate that aggregation occurred most rapidly when KFFE domains were connected by a linker of an intermediate length. Our experimental findings were consistent with estimated entropic contribution of a linker length toward formation of (partially) structured intermediates on the aggregation pathway. Moreover, inclusion of a relatively short linker was found to inhibit formation of aggregates with mature fibril morphology. When the results are assimilated, our study demonstrates that intramolecular distance between amyloidogenic domains is an important yet overlooked factor affecting amyloid aggregation. PMID:23202890

  4. Intermediate State Dependence of Intramolecular Vibrations in Photoactive Yellow Protein

    NASA Astrophysics Data System (ADS)

    Deng, Yanting; Xu, Mengyang; Niessen, Katherine; Schmidt, Marius; Markelz, Andrea

    Photoactive proteins provide a testbed for the role of long-range collective motions in protein function. Long-range intramolecular vibrations of the protein scaffold may provide efficient energy relaxation, enhancement of chromophore vibrations that promote structural transitions and assistance in electron energy transfer. Photoactive yellow protein (PYP) is a cytoplasmic photocycling protein associated with the negative phototactic response to blue light in halohodospira halophile. We measure the intramolecular vibrations of PYP using crystal anisotropy terahertz microscopy (CATM) as a function of photoexcitation. Room temperature CATM measurements are performed in the dark and with continuous illumination at 488 nm, which is found to result in an approximately 20% steady photoexcited state (pB). We find a decrease in anisotropic absorption in frequency range 20-60 cm-1 with photoexcitation. This result may be due to an increase in sample disorder associated with the structural change in pB state. We compare the measured and calculated spectra using molecular dynamics and normal mode/quasiharmonic analysis to identify the nature of the motions giving rise to the resonant absorption bands.

  5. Synthesis and intramolecular cyclization of methylenediphosphorus bisalkylamides containing one or two 4-coordinate phosphorus atoms

    SciTech Connect

    Novikova, Z.S.; Monin, E.A.; Kabachnik, M.M.; Lutsenko, I.F.

    1987-10-10

    We have previously reported on the synthesis of methylenediphosphorus bisalkylamides containing two 3-coordinate phosphorus atoms and their intramolecular cyclization into 1,2,4-azadiphosphetidines. In this work we have synthesized methylenediphosphorus bisalkylamides containing one or two 4-coordinate phosphorus atoms and have studied their intramolecular cyclization. The bisalkylamides were characterized in ether solution by their /sup 31/ NMR spectra.

  6. Direct Observation of Cascade of Photoinduced Ultrafast Intramolecular Charge Transfer Dynamics in Diphenyl Acetylene Derivatives: Via Solvation and Intramolecular Relaxation.

    PubMed

    Karunakaran, Venugopal; Das, Suresh

    2016-07-21

    Interaction of light with electron donor-acceptor π-conjugated systems leading to intramolecular charge transfer (ICT) plays an essential role in transformation of light energy. Here the cascade of photoinduced ICT processes is directly observed by investigating the excited state relaxation dynamics of cyano and mono/di methoxy substituted diphenyl acetylene derivatives using femtosecond pump-probe spectroscopy and nanosecond laser flash photolysis. The femtosecond transient absorption spectra of the chromophores upon ultrafast excitation reveal the dynamics of intermediates involved in transition from initially populated Frank-Condon state to local excited state (LE). It also provides the dynamic details of the transition from the LE to the charge transfer state yielding the formation of the radical ions. Finally, the charge transfer state decays to the triplet state by geminate charge recombination. The latter dynamics are observed in the nanosecond transient absorption spectra. It is found that excited state relaxation pathways are controlled by different stages of solvation and intramolecular relaxation depending on the solvent polarity. The twisted ICT state is more stabilized (978 ps) in acetonitrile than cyclohexane where major components of transient absorption originate from the S1 state. PMID:27347705

  7. Intramolecular strain coordinates kinesin stepping behavior along microtubules

    PubMed Central

    Yildiz, Ahmet; Tomishige, Michio; Gennerich, Arne; Vale, Ronald D.

    2008-01-01

    SUMMARY Kinesin advances 8 nm along a microtubule per ATP hydrolyzed, but the mechanism responsible for coordinating the enzymatic cycles of kinesin’s two identical motor domains remains unresolved. Here, we have tested whether such coordination is mediated by intramolecular tension generated by the “neck linkers”, mechanical elements that span between the motor domains. When tension is reduced by extending the neck linkers with artificial peptides, the coupling between ATP hydrolysis and forward stepping is impaired and motor’s velocity decreases as a consequence. However, speed recovers to nearly normal levels when external tension is applied by an optical trap. Remarkably, external load also induces bidirectional stepping of an immotile kinesin that lacks its mechanical element (neck linker) and fuel (ATP). Our results indicate that the kinesin motor domain senses and responds to strain in a manner that facilitates its plus-end-directed stepping and communication between its two motor domains. PMID:18805095

  8. Intramolecular dynamics of structure of alkaline phosphatase from Escherichia coli

    NASA Astrophysics Data System (ADS)

    Mazhul, Vladimir M.; Mjakinnik, Igor V.; Volkova, Alena N.

    1995-01-01

    The luminescent analysis with nano- and millisecond time resolution of intramolecular dynamics of Escherichia coli alkaline phosphatase was carried out. The effect of pH within the range 7.2 - 9.0, thermal inactivation, limited proteolysis by trypsin, binding of pyrophosphate, interconversion of enzyme and apoenzyme, the replacement of Zn2+ and Mg2+ in the active site by Cd2+ and Ni2+ on the spectral and kinetic parameters of luminescence was investigated. The essential changes of the level of nano- and millisecond dynamics of protein structure were found to correlate with the shift of enzymatic activity. The importance of small- and large-scale flexibility of protein structure for the act of enzymatic catalysis realization was shown.

  9. Universal prediction of intramolecular hydrogen bonds in organic crystals.

    PubMed

    Galek, Peter T A; Fábián, László; Allen, Frank H

    2010-04-01

    A complete exploration of intramolecular hydrogen bonds (IHBs) has been undertaken using a combination of statistical analyses of the Cambridge Structural Database and computation of ab initio interaction energies for prototypical hydrogen-bonded fragments. Notable correlations have been revealed between computed energies, hydrogen-bond geometries, donor and acceptor chemistry, and frequencies of occurrence. Significantly, we find that 95% of all observed IHBs correspond to the five-, six- or seven-membered rings. Our method to predict a propensity for hydrogen-bond occurrence in a crystal has been adapted for such IHBs, applying topological and chemical descriptors derived from our findings. In contrast to intermolecular hydrogen bonding, it is found that IHBs can be predicted across the complete chemical landscape from a single optimized probability model, which is presented. Predictivity of 85% has been obtained for generic organic structures, which can exceed 90% for discrete classes of IHB. PMID:20305358

  10. Gold‐Catalyzed Intramolecular Cyclizations of Cyclopropenes with Propargylic Esters

    PubMed Central

    Zhu, Peng‐Long

    2015-01-01

    Abstract Homogeneous gold catalysts are interesting as they can act as potent carbophilic Lewis acids to activate the π bonds of alkynes, allenes, and alkenes. Many impressive applications for the formation of C−C or C−heteroatom bonds have been found due to the excellent functional group compatibility of these catalysts and the air and moisture tolerance of their reactions. Here, we have developed gold‐catalyzed novel intramolecular cycloisomerizations of nitrogen or oxygen‐tethered cyclopropenes with propargylic esters. The reaction proceeded through different pathways according to different substituent styles, affording 5‐azaspiro[2.5]oct‐7‐enes and bicyclo[4.1.0]heptanes. PMID:27308208

  11. Sequence and intramolecular distance scoring analyses of microbial rhodopsins

    PubMed Central

    Asano, Miki; Ide, Shunta; Kamata, Atsushi; Takahasi, Kiyohiro; Okada, Tetsuji

    2016-01-01

    Recent accumulation of sequence and structural data, in conjunction with systematical classification into a set of families, has significantly advanced our understanding of diverse and specific protein functions. Analysis and interpretation of protein family data requires comprehensive sequence and structural alignments. Here, we present a simple scheme for analyzing a set of experimental structures of a given protein or family of proteins, using microbial rhodopsins as an example. For a data set comprised of around a dozen highly similar structures to each other (overall pairwise root-mean-squared deviation < 2.3 Å), intramolecular distance scoring analysis yielded valuable information with respect to structural properties, such as differences in the relative variability of transmembrane helices. Furthermore, a comparison with recent results for G protein-coupled receptors demonstrates how the results of the present analysis can be interpreted and effectively utilized for structural characterization of diverse protein families in general. PMID:26998236

  12. Solvent reorganizational red-edge effect in intramolecular electron transfer.

    PubMed Central

    Demchenko, A P; Sytnik, A I

    1991-01-01

    Polar solvents are characterized by statistical distributions of solute-solvent interaction energies that result in inhomogeneous broadening of the solute electronic spectra. This allows photoselection of the high interaction energy part of the distribution by excitation at the red (long-wavelength) edge of the absorption bands. We observe that intramolecular electron transfer in the bianthryl molecule from the locally excited (LE) to the charge-transfer (CT) state, which requires solvent relaxation and does not occur in vitrified polar solutions, is dramatically facilitated in low-temperature propylene glycol glass by the red-edge excitation. This allows one to obtain spectroscopically the pure CT form and observe its dependence upon the relaxational properties of the solvent. A qualitative potential model of this effect is presented. PMID:11607224

  13. Estimating the energy of intramolecular hydrogen bonds in chitosan oligomers

    NASA Astrophysics Data System (ADS)

    Mikhailov, G. P.; Lazarev, V. V.

    2016-07-01

    The effect the number of chitosan monomer units CTS n ( n = 1-5), the protonation of chitosan dimers, and the interaction between CTS n ( n = 1-3) and acetate ions have on the energy of intramolecular hydrogen bonds is investigated by means of QTAIM analysis and solving the vibrational problem within the cluster-continuum model. It is established that the number of H-bonds in CTS n is 2 n - 1 and the total energy of H-bonds grows by ~20 kJ/mol. It is concluded that the hydrogen bonds between CTS and acetate ions play a major role in the stabilization of polyelectrolyte complexes in dilute acetic acid solutions of CTS.

  14. Intramolecular diffusion controls aggregation of the PAPf39 peptide.

    PubMed

    Srivastava, Kinshuk R; French, Kinsley C; Tzul, Franco O; Makhatadze, George I; Lapidus, Lisa J

    2016-09-01

    The 39-residue fragment of human prostatic acidic phosphatase (PAP) is found in high concentrations in semen and easily form fibrils. Previous work has shown that fibrillization is accelerated with a deletion of the first 8, mostly charged residues and it was hypothesized that fibrillization depended on the dynamics of these peptides. To test this hypothesis we have measured the intramolecular diffusion of the full length and 8-residue deletion peptides at two different pHs and found a correlation with fibrillization lag time. These results can be explained by a simple kinetic model of the early stages of aggregation in which oligomerization is controlled by the rate of peptide reconfiguration. PMID:27393931

  15. Intramolecular Long-Distance Electron Transfer in Organic Molecules

    NASA Astrophysics Data System (ADS)

    Closs, Gerhard L.; Miller, John R.

    1988-04-01

    Intramolecular long-distance electron transfer (ET) has been actively studied in recent years in order to test existing theories in a quantitative way and to provide the necessary constants for predicting ET rates from simple structural parameters. Theoretical predictions of an ``inverted region,'' where increasing the driving force of the reaction will decrease its rate, have begun to be experimentally confirmed. A predicted nonlinear dependence of ET rates on the polarity of the solvent has also been confirmed. This work has implications for the design of efficient photochemical charge-separation devices. Other studies have been directed toward determining the distance dependence of ET reactions. Model studies on different series of compounds give similar distance dependences. When different stereochemical structures are compared, it becomes apparent that geometrical factors must be taken into account. Finally, the mechanism of coupling between donor and acceptor in weakly interacting systems has become of major importance. The theoretical and experimental evidence favors a model in which coupling is provided by the interaction with the orbitals of the intervening molecular fragments, although more experimental evidence is needed. Studies on intramolecular ET in organic model compounds have established that current theories give an adequate description of the process. The separation of electronic from nuclear coordinates is only a convenient approximation applied to many models, but in long-distance ET it works remarkably well. It is particularly gratifying to see Marcus' ideas finally confirmed after three decades of skepticism. By obtaining the numbers for quantitative correlations between rates and distances, these experiments have shown that saturated hydrocarbon fragments can ``conduct'' electrons over tens of angstroms. A dramatic demonstration of this fact has recently been obtained by tunneling electron microscopy on Langmuir-Blodgett films, showing in a

  16. Structural studies of photoinduced intramolecular electron transfer in cyclopentadienylnickelnitrosyl

    SciTech Connect

    Chen, L.X.; Bowman, M.K.; Wang, Zhiyu; Norris, J.R. |; Montano, P.A. |

    1994-03-01

    A structural study based on EXAFS, FTIR, and optical absorption spectroscopies has been conducted on a photogenerated, metastable state of cyclopentadienylnickelnitrosyl (CpNiNO) produced by a reversible photochemical reaction. The photogenerated, metastable state with distinctively different EXAFS, IR, and optical absorption spectra from those of the ground state molecules was created by irradiating the sample with the 365 nm line of a mercury lamp at 20K . At the same temperature, the reverse reaction was induced by irradiation with the 313 nm line from the mercury lamp. Based on the analysis of the EXAFS data, the photogenerated, metastable state of CpNiNO has undergone considerable nuclear rearrangements compared to its ground state. The nuclear movement is characterized by a 0.12{angstrom} elongation of Ni-N bond and by a bending of Ni-N-O. A shift of the N-O stretching frequency from 1824 to 1387 cm{sup {minus}1} was observed in the photoinduced reaction with 365 nm light, implying that a NO{sup {minus}} like species results from intramolecular electron transfer from Ni to NO. The changes in the absorption spectra for the same reaction showed reduced absorption of the 385 nm band and a newly generated broad band near IR region. Temperature dependence of the Debye-Waller factor of CpNiNO was in good agreement with the diatomic harmonic oscillator for the Ni-N bond, but deviated for the Ni-O and the Ni-C bonds. Based on the structures obtained from EXAFS, ZINDO calculations for both the ground state and the photogenerated, metastable state of CpNiNO reproduced the general features of the observed absorption spectra and qualitatively explained the wavelength dependence of the reaction. The calculated partial charges on each atom in the ground state and the photogenerated, metastable state of CpNiNO are consistent with intramolecular electron transfer upon photoexcitation by 365 nm light.

  17. Vibrational spectroscopy and intramolecular energy transfer in isocyanic acid (HNCO)

    SciTech Connect

    Coffey, M.J.; Berghout, H.L.; Woods, E. III; Crim, F.F.

    1999-06-01

    Room temperature photoacoustic spectra in the region of the first through the fourth overtones (2{nu}{sub 1} to 5{nu}{sub 1}) and free-jet action spectra of the second through the fourth overtones (3{nu}{sub 1} to 5{nu}{sub 1}) of the N{endash}H stretching vibration permit analysis of the vibrational and rotational structure of HNCO. The analysis identifies the strong intramolecular couplings that control the early stages of intramolecular vibrational energy redistribution (IVR) and gives the interaction matrix elements between the zero-order N{endash}H stretching states and the other zero-order states with which they interact. The experimentally determined couplings and zero-order state separations are consistent with {ital ab initio} calculations of East, Johnson, and Allen [J. Chem. Phys. {bold 98}, 1299 (1993)], and comparison with the calculation identifies the coupled states and likely interactions. The states most strongly coupled to the pure N{endash}H stretching zero-order states are ones with a quantum of N{endash}H stretching excitation ({nu}{sub 1}) replaced by different combinations of N{endash}C{endash}O asymmetric or symmetric stretching excitation ({nu}{sub 2} or {nu}{sub 3}) and {ital trans}-bending excitation ({nu}{sub 4}). The two strongest couplings of the n{nu}{sub 1} state are to the states (n{minus}1){nu}{sub 1}+{nu}{sub 2}+{nu}{sub 4} and (n{minus}1){nu}{sub 1}+{nu}{sub 3}+2{nu}{sub 4}, and sequential couplings through a series of low order resonances potentially play a role. The analysis shows that if the pure N{endash}H stretch zero-order state were excited, energy would initially flow out of that mode into the strongly coupled mode in 100 fs to 700 fs, depending on the level of initial excitation. {copyright} {ital 1999 American Institute of Physics.}

  18. Synthesis of 2-Cyclopentenone Derivatives via Palladium-Catalyzed Intramolecular Carbonyl α-Alkenylation.

    PubMed

    Chen, Panpan; Meng, Yinggao; Wang, Han; Han, Feipeng; Wang, Yulong; Song, Chuanjun; Chang, Junbiao

    2016-08-01

    2-Cyclopentenone derivatives have been efficiently synthesized from 5-bromo-5-hexen-2-ones via palladium-catalyzed intramolecular carbonyl α-alkenylation followed by double-bond migration under mild reaction conditions. PMID:27463262

  19. Light induced catalytic intramolecular hydrofunctionalization of allylphenols mediated by porphyrin rhodium(iii) complexes.

    PubMed

    Liu, Xu; Wang, Zikuan; Fu, Xuefeng

    2016-09-14

    Catalytic intramolecular hydrofunctionalization of allylphenols to heterocyclic compounds mediated by rhodium(iii) porphyrin complexes was described. The Wacker-type intermediate β-heterocyclic alkyl rhodium complex was independently synthesized and crystallized. PMID:27482840

  20. Intramolecular Hydrogen-Bonding Effects on the Fluorescence of PRODAN Derivatives.

    PubMed

    Alty, Isaac G; Cheek, Douglas W; Chen, Tao; Smith, David B; Walhout, Emma Q; Abelt, Christopher J

    2016-05-26

    The effects of intramolecular hydrogen-bonding on the fluorescence behavior of three derivatives of 6-propionyl-2-dimethylaminonaphthalene are reported. The H-bonding effects are revealed through comparisons with corresponding reference compounds in which the H-bond-donating hydroxyl groups are replaced with methoxy groups. In toluene, intramolecular H bonding gives rise to a dramatic increase in the fluorescence intensity but only a slight red shift in the position. This behavior is attributed to decreased efficiency in intersystem crossing due to an increase in the energy of the n → π* triplet state. The intramolecular H bond does not induce quenching in acetonitrile; however, in the presence of a very small concentration of methanol, a dual intramolecular, intermolecular H-bonding arrangement does lead to partial quenching as revealed by preferential solvation studies. PMID:27127907

  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. Thiol dependent intramolecular locking of Orai1 channels.

    PubMed

    Alansary, Dalia; Schmidt, Barbara; Dörr, Kathrin; Bogeski, Ivan; Rieger, Heiko; Kless, Achim; Niemeyer, Barbara A

    2016-01-01

    Store-operated Ca(2+) entry mediated by STIM1-gated Orai1 channels is essential to activate immune cells and its inhibition or gain-of-function can lead to immune dysfunction and other pathologies. Reactive oxygen species interacting with cysteine residues can alter protein function. Pretreatment of the Ca(2+) selective Orai1 with the oxidant H2O2 reduces ICRAC with C195, distant to the pore, being its major redox sensor. However, the mechanism of inhibition remained elusive. Here we combine experimental and theoretical approaches and show that oxidation of Orai1 leads to reduced subunit interaction, slows diffusion and that either oxidized C195 or its oxidomimetic mutation C195D located at the exit of transmembrane helix 3 virtually eliminates channel activation by intramolecular interaction with S239 of transmembrane helix 4, thereby locking the channel in a closed conformation. Our results demonstrate a novel mechanistic model for ROS-mediated inhibition of Orai1 and identify a candidate residue for pharmaceutical intervention. PMID:27624281

  3. Catalytic, Enantioselective, Intramolecular Carbosulfenylation of Olefins. Preparative and Stereochemical Aspects

    PubMed Central

    Denmark, Scott E.; Jaunet, Alex

    2014-01-01

    The first catalytic, enantioselective, intramolecular carbosulfenylation of isolated alkenes with aromatic nucleophiles is described. The combination of N-phenylsulfenylphthalimide, a chiral selenophosphoramide derived from BINAM, and ethanesulfonic acid as a co-catalytic Brønsted acid induced an efficient and selective cyclofunctionalization of various alkenes (aliphatic and aromatic) tethered to a 3,4-methylenedioxyphenyl ring. Under these conditions, 6-phenylthio-5,6,7,8-tetrahydronaphthalenes are formed diastereospecifically in good yields (50–92%) and high enantioselectivities (71:29 – 97:3 er). E-Alkenes reacted much more rapidly and with much higher selectivity than Z-alkenes, whereas electron rich alkenes reacted more rapidly but with comparable selectivity to electron-neutral alkenes and electron deficient alkenes. The Brønsted acid played a critical role in effecting reproducible enantioselectivity. A model for the origin of enantioselectivity and the dependence of rate and selectivity on alkene structure is proposed along with a rationale for the site selectivity in reactions with mono-activated arene nucleophiles. PMID:24328051

  4. 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

  5. Chirally selective, intramolecular interaction observed in an aminoacyl adenylate anhydride

    NASA Astrophysics Data System (ADS)

    Lacey, James C.; Hall, Leo M.; Mullins, Dail W.; Watkins, Charles L.

    1985-06-01

    All earthly creatures use only L-amino acids in template directed protein synthesis. The reason for this exclusive use of the L-isomer is not yet apparent, although recent experiments by Usher and his colleagues have shown some stereoselctivity in the aminoacylation of di- and polynucleotides [1 3]. We have separately reported on intramolecular interactions between hydrophobic amino acid side chains and the adenine ring in aminoacyl adenylates [4]. There was a preferential association of Phe > Leu = Ile > Val with the adenine in these studies, but we made no attempts to address the question of D, L selectivity. Recently, in1H NMR studies of N-acetylphenylalanyl adenylate anhydride, we noticed evidence that both D- and L-isomers of the amino acid were present and, furthermore, that one isomer seemed to be associating with the adenine ring more strongly than the other. Using HPLC, we have separated the two diastereoisomers and have enzymatically determined that the isomer which associates more strongly is the biologically important one, the L-isomer. We present those studies here and discuss the evolutionary significance of this finding.

  6. Intramolecular Hydrogen Bonding in Benzoxazines: When Structural Design Becomes Functional.

    PubMed

    Froimowicz, Pablo; Zhang, Kan; Ishida, Hatsuo

    2016-02-18

    The future evolution of benzoxazines and polybenzoxazines as advanced molecular, structural, functional, engineering, and newly commercial materials depends to a great extent on a deeper and more fundamental understanding at the molecular level. In this contribution, the field of benzoxazines is briefly introduced along with a more detailed review of ortho-amide-functional benzoxazines, which are the main subjects of this article. Provided in this article are the detailed and solid scientific evidences of intramolecular five-membered-ring hydrogen bonding, which is supposed to be responsible for the unique and characteristic features exhibited by this ever-growing family of ortho-functionalized benzoxazines. One-dimensional (1D) (1)H NMR spectroscopy was used to study various concentrations of benzoxazines in various solvents with different hydrogen-bonding capability and at various temperatures to investigate in detail the nature of hydrogen bonding in both ortho-amide-functionalized benzoxazine and its para counterpart. These materials were further investigated by two-dimensional (2D) (1)H-(1)H nuclear Overhauser effect spectroscopy (NOESY) to verify and support the conclusions derived during the 1D (1)H NMR experiments. Only highly purified single-crystal benzoxazine samples have been used for this study to avoid additional interactions caused by any impurities. PMID:26797690

  7. Intramolecular phenotypic capacitance in a modular RNA molecule

    PubMed Central

    Hayden, Eric J.; Bendixsen, Devin P.; Wagner, Andreas

    2015-01-01

    Phenotypic capacitance refers to the ability of a genome to accumulate mutations that are conditionally hidden and only reveal phenotype-altering effects after certain environmental or genetic changes. Capacitance has important implications for the evolution of novel forms and functions, but experimentally studied mechanisms behind capacitance are mostly limited to complex, multicomponent systems often involving several interacting protein molecules. Here we demonstrate phenotypic capacitance within a much simpler system, an individual RNA molecule with catalytic activity (ribozyme). This naturally occurring RNA molecule has a modular structure, where a scaffold module acts as an intramolecular chaperone that facilitates folding of a second catalytic module. Previous studies have shown that the scaffold module is not absolutely required for activity, but dramatically decreases the concentration of magnesium ions required for the formation of an active site. Here, we use an experimental perturbation of magnesium ion concentration that disrupts the folding of certain genetic variants of this ribozyme and use in vitro selection followed by deep sequencing to identify genotypes with altered phenotypes (catalytic activity). We identify multiple conditional mutations that alter the wild-type ribozyme phenotype under a stressful environmental condition of low magnesium ion concentration, but preserve the phenotype under more relaxed conditions. This conditional buffering is confined to the scaffold module, but controls the catalytic phenotype, demonstrating how modularity can enable phenotypic capacitance within a single macromolecule. RNA’s ancient role in life suggests that phenotypic capacitance may have influenced evolution since life’s origins. PMID:26401020

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

    PubMed

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

    2016-01-01

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

  9. Intramolecular phenotypic capacitance in a modular RNA molecule.

    PubMed

    Hayden, Eric J; Bendixsen, Devin P; Wagner, Andreas

    2015-10-01

    Phenotypic capacitance refers to the ability of a genome to accumulate mutations that are conditionally hidden and only reveal phenotype-altering effects after certain environmental or genetic changes. Capacitance has important implications for the evolution of novel forms and functions, but experimentally studied mechanisms behind capacitance are mostly limited to complex, multicomponent systems often involving several interacting protein molecules. Here we demonstrate phenotypic capacitance within a much simpler system, an individual RNA molecule with catalytic activity (ribozyme). This naturally occurring RNA molecule has a modular structure, where a scaffold module acts as an intramolecular chaperone that facilitates folding of a second catalytic module. Previous studies have shown that the scaffold module is not absolutely required for activity, but dramatically decreases the concentration of magnesium ions required for the formation of an active site. Here, we use an experimental perturbation of magnesium ion concentration that disrupts the folding of certain genetic variants of this ribozyme and use in vitro selection followed by deep sequencing to identify genotypes with altered phenotypes (catalytic activity). We identify multiple conditional mutations that alter the wild-type ribozyme phenotype under a stressful environmental condition of low magnesium ion concentration, but preserve the phenotype under more relaxed conditions. This conditional buffering is confined to the scaffold module, but controls the catalytic phenotype, demonstrating how modularity can enable phenotypic capacitance within a single macromolecule. RNA's ancient role in life suggests that phenotypic capacitance may have influenced evolution since life's origins. PMID:26401020

  10. Intramolecular Hydrogen Bonds in Low-Molecular-Weight Polyethylene Glycol.

    PubMed

    Kozlowska, Mariana; Goclon, Jakub; Rodziewicz, Pawel

    2016-04-18

    We used static DFT calculations to analyze, in detail, the intramolecular hydrogen bonds formed in low-molecular-weight polyethylene glycol (PEG) with two to five repeat subunits. Both red-shifted O-H⋅⋅⋅O and blue-shifting C-H⋅⋅⋅O hydrogen bonds, which control the structural flexibility of PEG, were detected. To estimate the strength of these hydrogen bonds, the quantum theory of atoms in molecules was used. Car-Parrinello molecular dynamics simulations were used to mimic the structural rearrangements and hydrogen-bond breaking/formation in the PEG molecule at 300 K. The time evolution of the H⋅⋅⋅O bond length and valence angles of the formed hydrogen bonds were fully analyzed. The characteristic hydrogen-bonding patterns of low-molecular-weight PEG were described with an estimation of their lifetime. The theoretical results obtained, in particular the presence of weak C-H⋅⋅⋅O hydrogen bonds, could serve as an explanation of the PEG structural stability in the experimental investigation. PMID:26864943

  11. Intramolecular electronic energy transfer in bichromophoric molecular macrocyclic systems

    NASA Astrophysics Data System (ADS)

    Speiser, Shammai

    1993-01-01

    The structures and spectral properties of several bichromophoric molecules, suitable for optical data processing, are presented. The bichromophoric molecules are composed of an aromatic ring connected by two methylene chains to an (alpha) -diketone moiety. Both the absorption and emission spectra of these compounds can be attributed to a superposition of the individual spectra of the separate chromophores. The critical transfer radia for electronic energy transfer from the aromatic (donor) chromophore to the (alpha) -diketone (acceptor) chromophore was calculated from the spectral overlap between the fluorescence spectrum of the aromatic ring with the absorption spectrum of the (alpha) -diketone chromophore. The results show that this series of molecules is well suited for a mechanistic study of short-range intramolecular electronic energy transfer (intra-EET). The temperature and the molecular structure dependence of the intra-EET efficiency in this series was measured and analyzed for both singlet-singlet and triplet-triplet routes. The results show that the transfer efficiency is strongly temperature and structure dependent, indicating that exchange interaction is responsible for intra-EET between close chromophores in a bichromophoric molecule. The relative contributions of interchromophoric distance and that of the relative orientation of the two chromophores to exchange interaction are discussed.

  12. Intramolecular Interactions That Induce Helical Rearrangement upon Rhodopsin Activation

    PubMed Central

    Yamazaki, Yoichi; Nagata, Tomoko; Terakita, Akihisa; Kandori, Hideki; Shichida, Yoshinori; Imamoto, Yasushi

    2014-01-01

    Rhodopsin undergoes rearrangements of its transmembrane helices after photon absorption to transfer a light signal to the G-protein transducin. To investigate the mechanism by which rhodopsin adopts the transducin-activating conformation, the local environmental changes in the transmembrane region were probed using the cysteine S-H group, whose stretching frequency is well isolated from the other protein vibrational modes. The S-H stretching modes of cysteine residues introduced into Helix III, which contains several key residues for the helical movements, and of native cysteine residues were measured by Fourier transform infrared spectroscopy. This method was applied to metarhodopsin IIa, a precursor of the transducin-activating state in which the intramolecular interactions are likely to produce a state ready for helical movements. No environmental change was observed near the ionic lock between Arg-135 in Helix III and Glu-247 in Helix VI that maintains the inactive conformation. Rather, the cysteine residues that showed environmental changes were located around the chromophore, Ala-164, His-211, and Phe-261. These findings imply that the hydrogen bond between Helix III and Helix V involving Glu-122 and His-211 and the hydrophobic packing between Helix III and Helix VI involving Gly-121, Leu-125, Phe-261, and Trp-265 are altered before the helical rearrangement leading toward the active conformation. PMID:24692562

  13. Intramolecular Alkene Aminocarbonylation Using Concerted Cycloadditions of Amino-Isocyanates.

    PubMed

    Ivanovich, Ryan A; Clavette, Christian; Vincent-Rocan, Jean-François; Roveda, Jean-Grégoire; Gorelsky, Serge I; Beauchemin, André M

    2016-06-01

    The ubiquity of nitrogen heterocycles in biologically active molecules challenges synthetic chemists to develop a variety of tools for their construction. While developing metal-free hydroamination reactions of hydrazine derivatives, it was discovered that carbazates and semicarbazides can also lead to alkene aminocarbonylation products if nitrogen-substituted isocyanates (N-isocyanates) are formed in situ as reactive intermediates. At first this reaction required high temperatures (150-200 °C), and issues included competing hydroamination and N-isocyanate dimerization pathways. Herein, improved conditions for concerted intramolecular alkene aminocarbonylation with N-isocyanates are reported. The use of βN-benzyl carbazate precursors allows the effective minimization of N-isocyanate dimerization. Diminished dimerization leads to higher yields of alkene aminocarbonylation products, to reactivity at lower temperatures, and to an improved scope for a reaction sequence involving alkene aminocarbonylation followed by 1,2-migration of the benzyl group. Furthermore, fine-tuning of the blocking (masking) group on the N-isocyanate precursor, and reaction conditions relying on base catalysis for N-isocyanate formation from simpler precursors resulted in room temperature reactivity, consequently minimizing the competing hydroamination pathway. Collectively, this work highlights that controlled reactivity of aminoisocyanates is possible, and provides a broadly applicable alkene aminocarbonylation approach to heterocycles possessing the β-aminocarbonyl motif. PMID:27112602

  14. Asymmetric Intramolecular Alkylation of Chiral Aromatic Imines via Catalytic C-H Bond Activation

    SciTech Connect

    Watzke, Anja; Wilson, Rebecca; O'Malley, Steven; Bergman, Robert; Ellman, Jonathan

    2007-04-16

    The asymmetric intramolecular alkylation of chiral aromatic aldimines, in which differentially substituted alkenes are tethered meta to the imine, was investigated. High enantioselectivities were obtained for imines prepared from aminoindane derivatives, which function as directing groups for the rhodium-catalyzed C-H bond activation. Initial demonstration of catalytic asymmetric intramolecular alkylation also was achieved by employing a sterically hindered achiral imine substrate and catalytic amounts of a chiral amine.

  15. Intramolecular hydrogen bond in biologically active o-carbonyl hydroquinones.

    PubMed

    Martínez-Cifuentes, Maximiliano; Weiss-López, Boris E; Santos, Leonardo S; Araya-Maturana, Ramiro

    2014-01-01

    Intramolecular hydrogen bonds (IHBs) play a central role in the molecular structure, chemical reactivity and interactions of biologically active molecules. Here, we study the IHBs of seven related o-carbonyl hydroquinones and one structurally-related aromatic lactone, some of which have shown anticancer and antioxidant activity. Experimental NMR data were correlated with theoretical calculations at the DFT and ab initio levels. Natural bond orbital (NBO) and molecular electrostatic potential (MEP) calculations were used to study the electronic characteristics of these IHB. As expected, our results show that NBO calculations are better than MEP to describe the strength of the IHBs. NBO energies (∆Eij(2)) show that the main contributions to energy stabilization correspond to LP-->σ* interactions for IHBs, O1…O2-H2 and the delocalization LP-->π* for O2-C2=Cα(β). For the O1…O2-H2 interaction, the values of ∆Eij(2) can be attributed to the difference in the overlap ability between orbitals i and j (Fij), instead of the energy difference between them. The large energy for the LP O2-->π* C2=Cα(β) interaction in the compounds 9-Hydroxy-5-oxo-4,8, 8-trimethyl-l,9(8H)-anthracenecarbolactone (VIII) and 9,10-dihydroxy-4,4-dimethylanthracen-1(4H)-one (VII) (55.49 and 60.70 kcal/mol, respectively) when compared with the remaining molecules (all less than 50 kcal/mol), suggests that the IHBs in VIII and VII are strongly resonance assisted. PMID:24995921

  16. Intramolecular Charge-Assisted Hydrogen Bond Strength in Pseudochair Carboxyphosphate

    PubMed Central

    2015-01-01

    Carboxyphosphate, a suspected intermediate in ATP-dependent carboxylases, has not been isolated nor observed directly by experiment. Consequently, little is known concerning its structure, stability, and ionization state. Recently, carboxyphosphate as either a monoanion or dianion has been shown computationally to adopt a novel pseudochair conformation featuring an intramolecular charge-assisted hydrogen bond (CAHB). In this work, additive and subtractive correction schemes to the commonly employed open–closed method are used to estimate the strength of the CAHB. Truhlar’s Minnesota M06-2X functional with Dunning’s aug-cc-pVTZ basis set has been used for geometry optimization, energy evaluation, and frequency analysis. The CHARMM force field has been used to approximate the Pauli repulsive terms in the closed and open forms of carboxyphosphate. From our additive correction scheme, differential Pauli repulsion contributions between the pseudochair (closed) and open conformations of carboxyphosphate are found to be significant in determining the CAHB strength. The additive correction modifies the CAHB prediction (ΔEclosed–open) of −14 kcal/mol for the monoanion and −12 kcal/mol for the dianion to −22.9 and −18.4 kcal/mol, respectively. Results from the subtractive technique reinforce those from our additive procedure, where the predicted CAHB strength ranges from −17.8 to −25.4 kcal/mol for the monoanion and from −15.7 to −20.9 kcal/mol for the dianion. Ultimately, we find that the CAHB in carboxyphosphate meets the criteria for short-strong hydrogen bonds. However, carboxyphosphate has a unique energy profile that does not result in the symmetric double-well behavior of low-barrier hydrogen bonds. These findings provide deeper insight into the pseudochair conformation of carboxyphosphate, and lead to an improved mechanistic understanding of this intermediate in ATP-dependent carboxylases. PMID:25405523

  17. Mean-Field Theory of Intra-Molecular Charge Ordering in (TTM--TTP)I3

    NASA Astrophysics Data System (ADS)

    Omori, Yukiko; Tsuchiizu, Masahisa; Suzumura, Yoshikazu

    2011-02-01

    We examine an intra-molecular charge-ordered (ICO) state in the multi-orbital molecular compound (TTM--TTP)I3 on the basis of an effective two-orbital model derived from ab initio calculations. Representing the model in terms of the fragment molecular-orbital (MO) picture, the ICO state is described as the charge disproportionation on the left and right fragment MOs. By applying the mean-field theory, the phase diagram of the ground state is obtained as a function of the inter-molecular Coulomb repulsion and the intra-molecular transfer integral. The ICO state is stabilized by large inter-fragment Coulomb interactions, and the small intra-molecular transfer energy between two fragment MOs. Furthermore, we examine the finite-temperature phase diagram. The relevance to the experimental observations in the molecular compound of (TTM--TTP)I3 is also discussed.

  18. Laser-Induced Dynamical Chirality and Intramolecular Energy Flow in the CH Chromophore

    SciTech Connect

    Thanopulos, Ioannis

    2007-11-29

    We review the quantum dynamics of intramolecular energy flow during and after coherent infrared multiphoton excitation of the CH organic chromophore. The understanding of the underlying dynamics is of central importance for a wide range of systems in molecular physics, chemistry and biology, due to the experimentally supported assumption that the chromophore dynamics is weakly-dependent on a specific environment, in particular on sub-picosecond time scale. The excitation process due to the interaction with the laser field is studied by computationally monitoring the wave packet motion in the configuration sub-space relevant to femtosecond dynamics, using global analytical potential energy and electric dipole functions previously developed. The features of the intramolecular vibrational energy redistribution and the related dynamical time scales are investigated. In particular, we discuss the generation of dynamical chirality in methane istopomers, the corresponding stereomutation and racemization phenomena on the femtosecond time scale, and their relation to intramolecular vibrational energy redistribution.

  19. Investigating the Disordered States of Two Proteins Using Intramolecular Contact Formation

    NASA Astrophysics Data System (ADS)

    Singh, Vijay; Kopka, Michaela; Chen, Yujie; Wedemeyer, William; Lapidus, Lisa

    2007-03-01

    Using the quenching of the triplet state of tryptophan by cysteine, we investigate the unfolded states of two structurally similar but sequentially non-homologous proteins, the IgG binding domain of proteins L and G, under a range of denaturing conditions. These proteins show remarkably similar dynamics of intramolecular diffusion marked by a decrease in contact formation at denaturant conditions that favor folding. A reaction limited rate and the diffusion limited rate are obtained by measuring the viscosity dependence of the intramolecular contact rate. To further investigate the polymer dynamics of the unfolded state under folding conditions, we modeled the proteins as a worm-like chain with excluded volume using Szabo, Schulten and Schulten (SSS) theory to estimate the effective persistence length and intramolecular diffusion constant at various concentrations of GdnHCl. The results reveal an unfolded state under folding conditions that is significantly more compact and less diffusive than the fully denatured state.

  20. Intramolecular circuits connected to N electrodes using a scattering matrix approach

    NASA Astrophysics Data System (ADS)

    Ami, S.; Joachim, C.

    2002-04-01

    The scattering matrix technique is extended to describe the electronic transport characteristics of intramolecular circuits driven in a ballistic or a tunnel transport regime. The circuit is assumed to be connected by N electrodes. As a working example, the electronic properties of a T-node circuit are presented leading to the design of an OR logic gate working in a ballistic regime. In the tunnel regime, only the ``node'' Kirchhoff law of circuit remains valid at the nodes of an intramolecular tunnel circuit and the electronic characteristics of the branches composing the circuit are mutually independent. It results in a difficult design of a logic OR intramolecular gate of high performance and stability, pointing out the urge for new architectures to implement complex logic functions inside a single molecule.

  1. Photophysics of 2-(4'-amino-2'-hydroxyphenyl)-1H-imidazo-[4,5-c]pyridine and its analogues: intramolecular proton transfer versus intramolecular charge transfer.

    PubMed

    Behera, Santosh Kumar; Karak, Ananda; Krishnamoorthy, G

    2015-02-12

    Photophysical characteristics of 2-(4'-amino-2'-hydroxyphenyl)-1H-imidazo-[4,5-c]pyridine (AHPIP-c) have been studied in various aprotic and protic solvents using UV-visible, steady state fluorescence and time-resolved fluorescence spectroscopic techniques. To comprehend the competition between the intramolecular charge transfer (ICT) and the excited state intramolecular proton transfer (ESIPT) processes, the photophysical properties of 2-(4'-amino-2'-methoxyphenyl)-1H-imidazo-[4,5-c]pyridine (AMPIP-c) and 2-(4'-aminophenyl)-1H-imidazo-[4,5-c]pyridine (APIP-c) were also investigated. Though APIP-c displays twisted ICT (TICT) emission in protic solvents, AHPIP-c exhibits normal and tautomer emissions in aprotic as well as in protic solvents due to ESIPT. However, the methoxy derivative, AMPIP-c, emits weak TICT fluorescence in methanol. PMID:25337987

  2. A novel non-fluorescent excited state intramolecular proton transfer phenomenon induced by intramolecular hydrogen bonds: an experimental and theoretical investigation

    PubMed Central

    Yin, Hang; Li, Hui; Xia, Guomin; Ruan, Chengyan; Shi, Ying; Wang, Hongming; Jin, Mingxing; Ding, Dajun

    2016-01-01

    Two molecules, 1-hydroxypyrene-2-carbaldehyde (HP) and 1-methoxypyrene-2-carbaldehyde (MP) were explored. We investigated their photophysical properties, using experimental transient absorption and theoretical density functional theory/time-dependent density functional theory (DFT/TDDFT). HP and MP have similar geometric conformations but exhibit entirely different photophysical properties upon excitation into the S1 state. In contrast to traditional excited state intramolecular proton transfer (ESIPT) in molecules that exhibit either single or dual fluorescence, HP has an unusual non-fluorescent property. Specifically, the ultrafast ESIPT process occurs in 158 fs and is followed by an intersystem crossing (ISC) component of 11.38 ps. In contrast to HP, MP undergoes only an 8 ps timescale process, which was attributed to interactions between solute and solvent. We concluded that this difference arises from intramolecular hydrogen bonds (IMHBs), which induce drastic structural alterntion upon excitation. PMID:26790961

  3. TD-DFT study on electron transfer mobility and intramolecular hydrogen bond of substituted indigo derivatives

    NASA Astrophysics Data System (ADS)

    Ma, Chi; Li, Hui; Yang, Yonggang; Li, Donglin; Liu, Yufang

    2015-10-01

    The density functional theory (DFT) and time-dependent density functional theory (TDDFT) method were carried out to investigate the ground and excited states of indigo and its derivative molecules. The results demonstrate that the intramolecular hydrogen bond I is weakened and the intramolecular hydrogen bond II is strengthened upon photo-excitation to the S1 state. In the absorption spectra, the substitution at R4R4, of indigo causes a significant redshift. In addition, the halogen substitution obviously increases the electron transfer mobility of indigo. It is proved that the halogen substitution may be a new method to design high performance organic semiconductors.

  4. Intramolecular Dehydrogenative Coupling of 2,3-Diaryl Acrylic Compounds: Access to Substituted Phenanthrenes.

    PubMed

    Gupta, Vijay; Rao, V U Bhaskara; Das, Tamal; Vanka, Kumar; Singh, Ravi P

    2016-07-01

    A simple, facile, and environmentally benign intramolecular dehydrogenative coupling of various 1,2-diarylethylenes for the synthesis of phenanthrenes in excellent yield has been described. This new methodology uses ceric ammonium nitrate (CAN) as a promoter at room temperature and has been extended to intermolecular synthesis of biaryl compounds. The electron transfer from methoxyarene to cerium leads to cationic radical formation, which further proceeds to intramolecular coupling. Preliminary mechanistic investigation by EPR spectroscopy and density functional theory calculation suggested a similar view. PMID:27232691

  5. Bond formations by intermolecular and intramolecular trappings of acylketenes and their applications in natural product synthesis†

    PubMed Central

    Reber, Keith P.; Tilley, S. David

    2011-01-01

    The reactive intermediates known as acylketenes exhibit a rich chemistry and have been extensively utilized for many types of inter- and intramolecular bond-forming reactions within the field of organic synthesis. Characteristic reactions of acylketenes include cycloadditions, carbon–carbon bond-forming reactions, and nucleophilic capture with alcohols or amines to give β-keto acid derivatives. In particular, the intramolecular capture of acylketene intermediates with pendant nucleophiles represents a powerful method for forming both medium-sized rings and macrocycles, often in high yield. This tutorial review examines the history, generation, and reactivity of acylketenes with a special focus on their applications in the synthesis of natural products. PMID:19847338

  6. Intra-molecular enantiomerism in R-(+)-Limonene as evidenced by the differential bond polarizabilities

    NASA Astrophysics Data System (ADS)

    Shen, Hongxia; Wu, Guozhen; Wang, Peijie

    2014-07-01

    We propose an algorithm to obtain the differential bond polarizabilities from the Raman and Raman optical activity (ROA) spectral intensities. The signs of the differential bond polarizabilities of R-Limonene demonstrate that there is intra-molecular enantiomerism in its six membered ring structure. That is, the signs of the differential bond polarizabilities around the six membered ring are inversed under an intra-molecular mirror reflection. This is similar to what happens in the right and left handed chiral isomers under a mirror conversion.

  7. Reversible Tuning of Interfacial and Intramolecular Charge Transfer in Individual MnPc Molecules.

    PubMed

    Zhong, Jian-Qiang; Wang, Zhunzhun; Zhang, Jia Lin; Wright, Christopher A; Yuan, Kaidi; Gu, Chengding; Tadich, Anton; Qi, Dongchen; Li, He Xing; Lai, Min; Wu, Kai; Xu, Guo Qin; Hu, Wenping; Li, Zhenyu; Chen, Wei

    2015-12-01

    The reversible selective hydrogenation and dehydrogenation of individual manganese phthalocyanine (MnPc) molecules has been investigated using photoelectron spectroscopy (PES), low-temperature scanning tunneling microscopy (LT-STM), synchrotron-based near edge X-ray absorption fine structure (NEXAFS) measurements, and supported by density functional theory (DFT) calculations. It is shown conclusively that interfacial and intramolecular charge transfer arises during the hydrogenation process. The electronic energetics upon hydrogenation is identified, enabling a greater understanding of interfacial and intramolecular charge transportation in the field of single-molecule electronics. PMID:26528623

  8. Application of the intramolecular vinylogous Morita-Baylis-Hillman reaction toward the synthesis of the spinosyn A tricyclic nucleus.

    PubMed

    Mergott, Dustin J; Frank, Scott A; Roush, William R

    2002-09-01

    [reaction: see text] A concise synthesis of the spinosyn A tricyclic nucleus 27 has been developed by a route featuring a one-pot tandem intramolecular Diels-Alder reaction and intramolecular vinylogous Morita-Baylis-Hillman cyclization in which five stereocenters in tricycle 10 are set with excellent selectivity. PMID:12201741

  9. Inter- and intramolecular annulation strategies to a cyclopentanone building block containing an all-carbon quaternary stereogenic center.

    PubMed

    Penrose, Stephen D; Stott, Andrew J; Breccia, Perla; Haughan, Alan F; Bürli, Roland W; Jarvis, Rebecca E; Dominguez, Celia

    2015-03-20

    Synthesis of (S)-2-methyl-3-fluorophenyl cyclopentanone methyl ester (1S)-1 has been achieved by both inter- and intramolecular alkylation reactions on multigram scale, using chiral pool reagents. The intramolecular variant is a novel example of a chiral bis-electrophile reacting with a carbon nucleophile to form an enantiomerically pure all-carbon quaternary center. PMID:25720587

  10. Using Open-Ended Questions to Diagnose Students' Understanding of Inter- and Intramolecular Forces

    ERIC Educational Resources Information Center

    Rompayom, Patcharee; Tambunchong, Chinda; Wongyounoi, Somson; Dechsri, Precharn

    2011-01-01

    The purpose of this study was to investigate Grade 10 Thai students about their understanding on inter- and intramolecular forces. Sixty four students were elicited by administered open-ended questions after finishing normal instruction on chemical bonding topics. The instrument was in a set of open-ended questions which contained a number of…

  11. Assembly of the Isoindolinone Core of Muironolide A by Asymmetric Intramolecular Diels-Alder Cycloaddition

    PubMed Central

    Flores, Beatris; Molinski, Tadeusz F.

    2011-01-01

    The hexahydro-1H-isoindolin-1-one core of muironolide A was prepared by asymmetric intramolecular Diels Alder cycloaddition using a variant of the MacMillan organocatalyst which sets the C4,C5 and C11 stereocenters. PMID:21751773

  12. Homoallylic amines by reductive inter- and intramolecular coupling of allenes and nitriles

    PubMed Central

    Manojlovic, Marija D

    2011-01-01

    Summary The one-pot hydrozirconation of allenes and nitriles followed by an in situ transmetalation of the allylzirconocene with dimethylzinc or zinc chloride provides functionalized homoallylic amines. An intramolecular version of this process leads to 3-aminotetrahydrofurans and 3-aminotetrahydropyrans. PMID:21804878

  13. Intramolecular glycosylation under neutral conditions for synthesis of 1,4-linked disaccharides.

    PubMed

    Laursen, J B; Petersen, L; Jensen, K J

    2001-03-01

    [structure: see text]. A new method for intramolecular glycosylation, in which the donor and acceptor were linked via a 3,5-dinitrosalicylic acid derivative, was developed. Simply dissolving the tethered glycoside in CH3NO2 and warming to 40-60 degrees C led to formation of 1,4-linked disaccharides under neutral, hence, exceptionally mild, conditions. PMID:11259037

  14. Enantioselective Carbocycle Formation through Intramolecular Pd-Catalyzed Allyl–Aryl Cross-Coupling

    PubMed Central

    2015-01-01

    Aryl electrophiles containing tethered allylboronate units undergo efficient intramolecular coupling in the presence of a chiral palladium catalyst to give enantioenriched carbocyclic products. The reaction is found to be quite general, affording 5, 6, and 7-membered carbocyclic products as single regioisomers and with moderate enantioselectivities. Examination of differential coupling partners points to rapid allyl-equilibration as a key stereodefining feature. PMID:25105510

  15. Intramolecular reorganization energy in zinc phthalocyanine and its fluorinated derivatives: a joint experimental and theoretical study.

    PubMed

    da Silva Filho, Demetrio A; Coropceanu, Veaceslav; Gruhn, Nadine E; de Oliveira Neto, Pedro Henrique; Brédas, Jean-Luc

    2013-07-11

    We report a high-resolution gas-phase UPS spectrum of zinc phthalocyanine (ZnPc) together with a detailed analysis of the vibronic structure of the first ionization band, showing that presents the lowest value of the intramolecular reorganization energy experimentally reported for a molecular organic semiconductor. PMID:23722445

  16. Stereochemically Rich Polycyclic Amines from the Kinetic Resolution of Indolines through Intramolecular Povarov Reactions.

    PubMed

    Min, Chang; Seidel, Daniel

    2016-07-25

    Under control of a chiral Brønsted acid catalyst, racemic indolines undergo intramolecular Povarov reactions with achiral aromatic aldehydes bearing a pendent dienophile. One enantiomer of the indoline reacts preferentially, resulting in the highly enantio- and diastereoselective formation of polycyclic heterocycles with four stereogenic centers. This kinetic resolution approach exploits the differential formation/reactivity of diastereomeric ion pairs. PMID:27346876

  17. Deciphering DNA-based asymmetric catalysis through intramolecular Friedel-Crafts alkylations.

    PubMed

    Park, Soyoung; Ikehata, Keiichi; Watabe, Ryo; Hidaka, Yuta; Rajendran, Arivazhagan; Sugiyama, Hiroshi

    2012-10-28

    We describe asymmetric intramolecular Friedel-Crafts alkylations with a DNA-based hybrid catalyst and propose a plausible binding model. This study shows promise for studying relationships between the helical chirality of DNA and enantioselectivity of the chemical reaction. PMID:22986468

  18. Usnic Acid and the Intramolecular Hydrogen Bond: A Computational Experiment for the Organic Laboratory

    ERIC Educational Resources Information Center

    Green, Thomas K.; Lane, Charles A.

    2006-01-01

    A computational experiment is described for the organic chemistry laboratory that allows students to estimate the relative strengths of the intramolecular hydrogen bonds of usnic and isousnic acids, two related lichen secondary metabolites. Students first extract and purify usnic acid from common lichens and obtain [superscript 1]H NMR and IR…

  19. Nickel-Catalyzed Intramolecular C-O Bond Formation: Synthesis of Cyclic Enol Ethers.

    PubMed

    Han, Seo-Jung; Doi, Ryohei; Stoltz, Brian M

    2016-06-20

    An efficient and exceptionally mild intramolecular nickel-catalyzed carbon-oxygen bond-forming reaction between vinyl halides and primary, secondary, and tertiary alcohols has been achieved. Zinc powder was found to be an essential additive for obtaining high catalyst turnover and yields. This operationally simple method allows direct access to cyclic vinyl ethers in high yields in a single step. PMID:27159831

  20. Solvent-induced reversible solid-state colour change of an intramolecular charge-transfer complex.

    PubMed

    Li, Ping; Maier, Josef M; Hwang, Jungwun; Smith, Mark D; Krause, Jeanette A; Mullis, Brian T; Strickland, Sharon M S; Shimizu, Ken D

    2015-10-11

    A dynamic intramolecular charge-transfer (CT) complex was designed that displayed reversible colour changes in the solid-state when treated with different organic solvents. The origins of the dichromatism were shown to be due to solvent-inclusion, which induced changes in the relative orientations of the donor pyrene and acceptor naphthalenediimide units. PMID:26299357

  1. Conversion of oxazolidinediones to isoindoloisoquinolinones via intramolecular Friedel–Crafts reaction.

    PubMed

    Min, Ji-Young; Kim, Guncheol

    2014-02-01

    Treatment of oxazolidinediones with TiCl4 in CH2Cl2 resulted in conversion to isoindoloisoquinolinones via intramolecular Friedel–Crafts reaction with extrusion of CO2 in the transformation. The alkaloid nuevamine has been synthesized under these conditions in a regiospecific manner. PMID:24400908

  2. Palladium-catalyzed synthesis of dibenzophosphole oxides via intramolecular dehydrogenative cyclization.

    PubMed

    Kuninobu, Yoichiro; Yoshida, Takuya; Takai, Kazuhiko

    2011-09-16

    Dibenzophosphole oxides were obtained from secondary hydrophosphine oxides with a biphenyl group by dehydrogenation via phosphine-hydrogen and carbon-hydrogen bond cleavage in the presence of a catalytic amount of palladium(II) acetate, Pd(OAc)(2). By using this reaction, a ladder-type dibenzophosphole oxide could also be synthesized by double intramolecular dehydrogenative cyclization. PMID:21819045

  3. Organocatalytic Enantioselective Intramolecular Oxa-Michael Reaction of Enols: Synthesis of Chiral Isochromenes.

    PubMed

    Parhi, Biswajit; Gurjar, Jitendra; Pramanik, Suman; Midya, Abhisek; Ghorai, Prasanta

    2016-06-01

    An unprecedented enantioselective intramolecular oxa-Michael reaction of enols has been described. A squaramide-containing tertiary amine based bifunctional organocatalyst efficiently activates the o-homoformyl chalcones to provide the chiral isochromenes in moderate yields and good to excellent enantioselectivities. Further, late-stage functionalizations of the vinyl ether moiety of the chiral isochromene products have also been exemplified. PMID:27176883

  4. Construction of erythrinane skeleton via Pd(0)-catalyzed intramolecular dearomatization of para-aminophenols.

    PubMed

    Xu, Ren-Qi; Gu, Qing; Wu, Wen-Ting; Zhao, Zhuo-An; You, Shu-Li

    2014-11-01

    A novel Pd(0)-catalyzed intramolecular arylative dearomatization of para-aminophenol derivatives is described. In the presence of 1.25 mol % [Pd(C3H5)Cl]2 and 3.75 mol % RuPhos, the arylative dearomatization reaction proceeds smoothly for a broad range of substrates, offering an efficient synthetic route to erythrinane derivatives in excellent yields. PMID:25308898

  5. Intramolecular σ-bond metathesis between carbon-carbon and silicon-silicon bonds.

    PubMed

    Ishida, Naoki; Ikemoto, Wataru; Murakami, Masahiro

    2012-06-15

    An intramolecular σ-bond metathesis between carbon-carbon and silicon-silicon bonds took place on treatment of a disilane tethered to a cyclobutanone with a palladium(0) catalyst, furnishing a silaindane skeleton as well as an acylsilane functionality at once. PMID:22651103

  6. Palladium-catalyzed intramolecular C-H arylation of arenes using tosylates and mesylates as electrophiles.

    PubMed

    Nervig, Christine S; Waller, Peter J; Kalyani, Dipannita

    2012-09-21

    This paper describes a method for the palladium catalyzed intramolecular C-H arylation using tosylates and mesylates as electrophiles. The transformation is efficient for the synthesis of various heterocyclic motifs including furans, carbazoles, indoles, and lactams. Additionally, a protocol for the one-pot sequential tosylation/arylation of phenol derivatives is presented. PMID:22974229

  7. Gold(I)-Catalyzed Inter- and Intramolecular Additions of Carbonyl Compounds to Allenenes

    PubMed Central

    2016-01-01

    The gold(I)-catalyzed intramolecular reaction of allenes with oxoalkenes leads to bicyclo[6.3.0]undecane ring systems, although in the case of terminally disubstituted allenes, seven-membered rings are formed. The related intermolecular addition of aldehydes to allenenes also gives seven-membered rings. PMID:26918852

  8. Gas-phase intramolecular elimination reaction studies of steviol glycosides in positive electrospray and tandem mass spectrometry.

    PubMed

    Upreti, Mani; Clos, John F; Somayajula, Kasi V; Milanowski, Dennis J; Mocek, Ulla; Dubois, Grant E; Prakash, Indra

    2009-01-01

    This paper reports the first study of the gas-phase intramolecular elimination reaction of steviol glycosides in positive electrospray mass spectrometry. The observed glycosylated product ions are proposed to be formed via an intramolecular elimination of sugar units from the parent molecule ion. It was further proven by MS/MS studies and deuterium labeling experiments with one of the steviol glycosides, rebaudioside A. These mass spectrometric results confirmed that the new glycosylated product ions observed are most likely formed by the combination of glucose moieties (Glu) II-IV and Glu I via a gas-phase intramolecular elimination reaction. PMID:19174590

  9. Conformational stability and intramolecular hydrogen bonding in 1,2-ethanediol and 1,4-butanediol.

    PubMed

    Das, Prasanta; Das, Puspendu K; Arunan, E

    2015-04-23

    The gas-phase infrared spectra of 1,2-ED and 1,4-BD have been recorded at three different temperatures using a multipass gas cell of 6 m optical path length. DFT calculation has also been carried out using 6-311++G** and aug-cc-pVDZ basis sets to look for the existence of intramolecular hydrogen bonding in them from the red shift and infrared absorption intensity enhancement of the bonded O-H band compared to that of the free O-H band. Equilibrium population analysis with 10 conformers of 1,2-ED and 1,4-BD at experimental temperatures were carried out for the reconstruction of the observed vibrational spectra at that temperature using standard statistical relationships. The most abundant conformer at experimental temperatures was identified. In 1,2-ED a red shift of 45 cm(-1) in the intramolecularly interacting O-H stretching vibrational band position and no significant intensity enhancement compared to that of the free O-H have been observed. On the contrary, in one of the hydrogen-bonded conformers of 1,4-BD, a 124 cm(-1) red shift in the O-H stretching frequency and a 8.5 times intensity enhancement for the "bonded" O-H compared to that of the "free" O-H is seen. On the basis of this comparative study, we have concluded that strong intramolecular hydrogen bonding exists in 1,4-BD. But there appears to be weak intramolecular hydrogen bonding in 1,2-ED at temperatures of 303, 313, and 323 K in the gas phase. We have found that most stable hydrogen-bonded conformers of 1,4-BD are less populated than some of the non-hydrogen-bonded conformers. Even for the 1,4-BD, the relative population of the g'GG'Gt conformer, which has a strong intramolecular hydrogen bond, is less than what is predicted. Perhaps the intramolecular hydrogen bond plays a less significant role in the relative stability of the various conformers than what has been predicted from calculations and prevails in the literature. PMID:25839224

  10. Evidence for excited-state intramolecular proton transfer in 4-chlorosalicylic acid from combined experimental and computational studies: Quantum chemical treatment of the intramolecular hydrogen bonding interaction

    NASA Astrophysics Data System (ADS)

    Paul, Bijan Kumar; Guchhait, Nikhil

    2012-07-01

    The photophysical study of a pharmaceutically important chlorine substituted derivative of salicylic acid viz., 4-chlorosalicylic acid (4ClSA) has been carried out by steady-state absorption, emission and time-resolved emission spectroscopy. A large Stokes shifted emission band with negligible solvent polarity dependence marks the spectroscopic signature of excited-state intramolecular proton transfer (ESIPT) reaction in 4ClSA. Theoretical calculation by ab initio and Density Functional Theory methods yields results consistent with experimental findings. Theoretical potential energy surfaces predict the occurrence of proton transfer in S1-state. Geometrical and energetic criteria, Atoms-In-Molecule topological parameters, Natural Bond Orbital population analysis have been exploited to evaluate the intramolecular hydrogen bond (IMHB) interaction and to explore its directional nature. The inter-correlation between aromaticity and resonance assisted H-bond is also discussed in this context. Our results unveil that the quantum chemical treatment is a more accurate tool to assess hydrogen bonding interaction in comparison to geometrical criteria.

  11. Inequivalence of substitution pairs in hydroxynaphthaldehyde: A theoretical measurement by intramolecular hydrogen bond strength, aromaticity, and excited-state intramolecular proton transfer reaction.

    PubMed

    Mahanta, Subrata; Paul, Bijan Kumar; Balia Singh, Rupashree; Guchhait, Nikhil

    2011-01-15

    The inequivalence of substitution pair positions of naphthalene ring has been investigated by a theoretical measurement of hydrogen bond strength, aromaticity, and excited state intramolecular proton transfer (ESIPT) reaction as the tools in three substituted naphthalene compounds viz 1-hydroxy-2-naphthaldehyde (HN12), 2-hydroxy-1-naphthaldehyde (HN21), and 2-hydroxy-3-naphthaldehyde (HN23). The difference in intramolecular hydrogen bond (IMHB) strength clearly reflects the inequivalence of substitution pairs where the calculated IMHB strength is found to be greater for HN12 and HN21 than HN23. The H-bonding interactions have been explored by calculation of electron density ρ(r) and Laplacian ∇(2) ρ(r) at the bond critical point using atoms in molecule method and by calculation of interaction between σ* of OH with lone pair of carbonyl oxygen atom using NBO analysis. The ground and excited state potential energy surfaces (PESs) for the proton transfer reaction at HF (6-31G**) and DFT (B3LYP/6-31G**) levels are similar for HN12, HN21 and different for HN23. The computed aromaticity of the two rings of naphthalene moiety at B3LYP/6-31G** method also predicts similarity between HN12 and HN21, but different for HN23. PMID:20623648

  12. Enantioselective Intramolecular Hydroarylation of Alkenes via Directed C-H Bond Activation

    SciTech Connect

    Harada, Hitoshi; Thalji, Reema; Bergman, Robert; Ellman, Jonathan

    2008-05-22

    Highly enantioselective catalytic intramolecular ortho-alkylation of aromatic imines containing alkenyl groups tethered at the meta position relative to the imine directing group has been achieved using [RhCl(coe){sub 2}]{sub 2} and chiral phosphoramidite ligands. Cyclization of substrates containing 1,1- and 1,2-disubstituted as well as trisubstituted alkenes were achieved with enantioselectivities >90% ee for each substrate class. Cyclization of substrates with Z-alkene isomers proceeded much more efficiently than substrates with E-alkene isomers. This further enabled the highly stereoselective intramolecular alkylation of certain substrates containing Z/E-alkene mixtures via a Rh-catalyzed alkene isomerization with preferential cyclization of the Z-isomer.

  13. Intramolecular hydrogen bonds in crystals of thiophosphorylbenzopyrane derivatives X-ray and FT-IR studies

    NASA Astrophysics Data System (ADS)

    Rybarczyk-Pirek, Agnieszka J.; Dubis, Alina T.; Grabowski, Sławomir J.; Nawrot-Modranka, Jolanta

    2006-01-01

    The crystal structures of two new benzopyrane derivatives are analyzed and compared with previous X-ray investigations on related compounds. A particular attention is focused on intramolecular interactions. For the chromone derivatives ( 1 and 3) only one kind of interaction is possible, i.e., N-H⋯O, whereas for the coumarine derivatives ( 2 and 4) two types of intramolecular hydrogen bonding are observed - N-H⋯O and O-H⋯N. Two types of H-bond for coumarine derivatives are the result of the existence of two tautomeric forms - enamine and iminoenol. Combined spectroscopic, NMR and IR measurements confirm such tautomeric equilibrium in solution. The influence of the additional intermolecular hydrogen bonds on the stabilization of tautomeric forms in crystals is also discussed here.

  14. Internal Stark effect mediates intramolecular excited-state proton transfer in 3-hydroxyflavone derivatives

    NASA Astrophysics Data System (ADS)

    Klymchenko, Andriy S.; Demchenko, Alexander P.

    2002-12-01

    Internal Stark effect in electronic spectra is the effect that is observed when the electronic bands shift udner the influence of promixal charges. In order to study the possible involvement of this effect in modulating the intramolecular proton transfer reactions in the excited state, we designed and studied several derivatives of 3-hydroxyflavone. They include the species containing neutral and positively charged substituents in 6 position of chromone ring. These compounds were studied in solvents of different polarities. In these experiments the shifts of both normal and tautomer flurosence bands are clearly observed in a manner predicted by Stark effect theory. In addition, a dramatic effect of suppression by introduced charge of intramolecular excited-state proton transfer was observed.

  15. Design of Small Intramolecular Singlet Fission Chromophores: An Azaborine Candidate and General Small Size Effects.

    PubMed

    Zeng, Tao; Goel, Prateek

    2016-04-01

    We report the first attempt to design small intramolecular singlet fission chromophores, with the aid of quantum chemistry and explicitly simulating the time evolution of state populations using quantum dynamics method. We start with three previously proposed azaborine-substituted intermolecular singlet fission chromophores. Through analyzing their frontier orbital amplitudes, we select a BN-substituted azulene as the building block. Covalently connecting two such monomers and tuning their relative configuration, we examine three dimers. One dimer is found to be an eminent candidate: the triplet-pair state is quickly formed within 1 ps, and the two triplets are ready to be disentangled. We elucidate the general small size effects in intramolecular singlet fission and focus on specific aspects which should be taken care of when manipulating the fission rate through steric hindrance. PMID:27007577

  16. Intramolecular symmetry-adapted perturbation theory with a single-determinant wavefunction

    NASA Astrophysics Data System (ADS)

    Pastorczak, Ewa; Prlj, Antonio; Gonthier, Jérôme F.; Corminboeuf, Clémence

    2015-12-01

    We introduce an intramolecular energy decomposition scheme for analyzing non-covalent interactions within molecules in the spirit of symmetry-adapted perturbation theory (SAPT). The proposed intra-SAPT approach is based upon the Chemical Hamiltonian of Mayer [Int. J. Quantum Chem. 23(2), 341-363 (1983)] and the recently introduced zeroth-order wavefunction [J. F. Gonthier and C. Corminboeuf, J. Chem. Phys. 140(15), 154107 (2014)]. The scheme decomposes the interaction energy between weakly bound fragments located within the same molecule into physically meaningful components, i.e., electrostatic-exchange, induction, and dispersion. Here, we discuss the key steps of the approach and demonstrate that a single-determinant wavefunction can already deliver a detailed and insightful description of a wide range of intramolecular non-covalent phenomena such as hydrogen bonds, dihydrogen contacts, and π - π stacking interactions. Intra-SAPT is also used to shed the light on competing intra- and intermolecular interactions.

  17. Broadband Tunable Microlasers Based on Controlled Intramolecular Charge-Transfer Process in Organic Supramolecular Microcrystals.

    PubMed

    Dong, Haiyun; Wei, Yanhui; Zhang, Wei; Wei, Cong; Zhang, Chunhuan; Yao, Jiannian; Zhao, Yong Sheng

    2016-02-01

    Wavelength tunable micro/nanolasers are indispensable components for various photonic devices. Here, we report broadband tunable microlasers built by incorporating a highly polarized organic intramolecular charge-transfer (ICT) compound with a supramolecular host. The spatial confinement of the ICT dye generates an optimized energy level system that favors controlled population distribution between the locally excited (LE) state and the twisted intramolecular charge-transfer (TICT) state, which is beneficial for significantly broadening the tailorable gain region. As a result, we realized a wide tuning of lasing wavelength in the organic supramolecular microcrystals based on temperature-controlled population transfer from the LE to TICT state. The results will provide a useful enlightenment for the rational design of miniaturized lasers with desired performances. PMID:26756966

  18. Intramolecular Crystal Nucleation Favored by Polymer Crystallization: Monte Carlo Simulation Evidence.

    PubMed

    Zhang, Rong; Zha, Liyun; Hu, Wenbing

    2016-07-14

    We performed dynamic Monte Carlo simulations of half-half binary blends of symmetric (double and mutual) crystallizable polymers. We separately enhanced the driving forces for polymer-uniform and polymer-staggered crystals. Under parallel enhancements, polymer-uniform crystals exhibit faster nucleation and growth, with more chain folding and less lamellar thickening, than those in polymer-staggered crystals. We attributed the results to intramolecular crystal nucleation, ruined by enhanced polymer-staggered crystallization. Our observations provide direct molecular-level evidence to support the fact that intramolecular crystal nucleation is favored by polymer crystallization in quiescent solutions and melt, which yields chain folding for the characteristic β-sheet or lamellar morphology of macromolecular crystals. PMID:27300471

  19. Impact of Stereospecific Intramolecular Hydrogen Bonding on Cell Permeability and Physicochemical Properties

    PubMed Central

    2014-01-01

    Profiling of eight stereoisomeric T. cruzi growth inhibitors revealed vastly different in vitro properties such as solubility, lipophilicity, pKa, and cell permeability for two sets of four stereoisomers. Using computational chemistry and NMR spectroscopy, we identified the formation of an intramolecular NH→NR3 hydrogen bond in the set of stereoisomers displaying lower solubility, higher lipophilicity, and higher cell permeability. The intramolecular hydrogen bond resulted in a significant pKa difference that accounts for the other structure–property relationships. Application of this knowledge could be of particular value to maintain the delicate balance of size, solubility, and lipophilicity required for cell penetration and oral administration for chemical probes or therapeutics with properties at, or beyond, Lipinski’s rule of 5. PMID:24524242

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

    PubMed

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

    2016-07-13

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

  1. Design Principles of Electronic Couplings for Intramolecular Singlet Fission in Covalently-Linked Systems.

    PubMed

    Ito, Soichi; Nagami, Takanori; Nakano, Masayoshi

    2016-08-11

    We theoretically investigate the singlet fission in three types of covalently-linked systems, that is, ortho-, meta- and para-linked pentacene dimers, where these are shown to have significantly different singlet fission rates. Each molecule is composed of two chromophores (pentacenes), which are active sites for singlet fission, and covalent bridges linking them. We clarify the origin of the difference in the electronic couplings in these systems, which are found to well support a recent experimental observation. It is also found that the next-nearest-neighbor interaction is indispensable for intramolecular singlet fission in these systems. On the basis of these results, we present design principles for efficient intramolecular singlet fission in covalently-linked systems and demonstrate the performance by using several novel conjugated linkers. PMID:27448100

  2. Identification of intramolecular hydrogen bonds as the origin of malfunctioning of multitopic receptors

    NASA Astrophysics Data System (ADS)

    Dolenský, Bohumil; Konvalinka, Roman; Jakubek, Milan; Král, Vladimír

    2013-03-01

    Several trisamides of N,N-bis(2-aminoethyl)ethane-1,2-amine are prepared as potential saccharide receptors. Surprisingly low or even nil affinity to n-octyl-glucose is found by 1H NMR titration, and explained as a consequence of intramolecular hydrogen bonds of trisamides, (Rsbnd COsbnd NHsbnd C2H4)3N. The hydrogen bonds are identified by combination of 1H NMR and infrared spectra, and 1H NMR temperature coefficients. Results demonstrate that even small molecule can has a rather strong secondary structure, which can cause their malfunctioning in certain applications. Results also point out that the amide temperature coefficients should not be used as the only parameter for the consideration a hydrogen bond is intermolecular or intramolecular, particularly, in the case of furcated hydrogen bonds, and in the cases were a couple of signals are averaged.

  3. Intramolecular hydrogen bonding and calixarene-like structures in p-cresol/formaldehyde resins

    NASA Astrophysics Data System (ADS)

    Opaprakasit, P.; Scaroni, A.; Painter, P.

    2001-08-01

    The nature of the strong hydrogen bonds found in p-cresol/formaldehyde (PCF) resins, compared to ordinary phenolic compounds, is studied. The evidence from FTIR spectroscopy indicates that this strong interaction is due to intramolecular hydrogen bonding from "calixarene-like" structures. The formation of this structure in PCF is enabled by its "linear" (all- ortho-linkage) structure, which is not present in branched resins. Additionally, a transition is observed at around 175 to 200°C where the intramolecular hydrogen bonded structure is lost. This structure cannot be recovered upon cooling or annealing due to restrictions on conformational rotations that are coupled to a new pattern of intermolecular hydrogen bonding. However, the structure is reformed by dissolving the resin in solution and casting new films.

  4. Intramolecular symmetry-adapted perturbation theory with a single-determinant wavefunction

    SciTech Connect

    Pastorczak, Ewa; Prlj, Antonio; Corminboeuf, Clémence; Gonthier, Jérôme F.

    2015-12-14

    We introduce an intramolecular energy decomposition scheme for analyzing non-covalent interactions within molecules in the spirit of symmetry-adapted perturbation theory (SAPT). The proposed intra-SAPT approach is based upon the Chemical Hamiltonian of Mayer [Int. J. Quantum Chem. 23(2), 341–363 (1983)] and the recently introduced zeroth-order wavefunction [J. F. Gonthier and C. Corminboeuf, J. Chem. Phys. 140(15), 154107 (2014)]. The scheme decomposes the interaction energy between weakly bound fragments located within the same molecule into physically meaningful components, i.e., electrostatic-exchange, induction, and dispersion. Here, we discuss the key steps of the approach and demonstrate that a single-determinant wavefunction can already deliver a detailed and insightful description of a wide range of intramolecular non-covalent phenomena such as hydrogen bonds, dihydrogen contacts, and π − π stacking interactions. Intra-SAPT is also used to shed the light on competing intra- and intermolecular interactions.

  5. Intramolecular cycloaddition in 6,6-spiroepoxycyclohexa-2,4-dienone: simple aromatics to (+/-)-platencin.

    PubMed

    Singh, Vishwakarma; Sahu, Bharat Chandra; Bansal, Varsha; Mobin, Shaikh M

    2010-10-01

    A formal total synthesis of platencin from a simple aromatic precursor is described. Transformation of the aromatic compound into reactive spiroepoxycyclohexa-2,4-dienone and intramolecular cycloaddition are the key features of our methodology. 2-Hydroxymethyl-6-(3-hydroxy-hex-5-enyl)-phenol was oxidized with NaIO(4) to give a dimer that, upon a retro-Diels-Alder reaction, generated the spiroepoxycyclohexa-2,4-dienone that underwent intramolecular Diels-Alder reaction to give a tricyclic adduct having a core structure of platencin and appropriately disposed functional groups in a single step. Reduction of the double bond present in the ethano-bridge, manipulation of the oxirane ring and introduction of a double bond in the six-membered ring furnished a tricyclic intermediate which has already been converted into platencin. PMID:20683538

  6. Intramolecular complex formation and triplet energy transfer in polynorbornenes incorporating benzophenone

    SciTech Connect

    Fossum, R.D.; Fox, M.A.

    1997-02-12

    The photophysical properties of homopolymers (2) and block copolymers (3) prepared by ring-opening metathesis polymerization of norbornenes substituted with benzophenone, naphthalene, and phenanthrene groups (1) have been investigated. When benzophenone is attached to this polynorbornene backbone, its excited state behavior differs from that observed for monomeric benzophenone. A new intramolecular excited state complex can be observed in the transient absorption and emission measurements of the benzophenone-substituted homopolymer. In copolymers bearing benzophenone and naphthalene or phenanthrene substituent blocks, triplet energy transfer from the sensitizer (benzophenone) to the arene is observed. This energy transfer dominates over the intramolecular complexation that characterizes group interactions in the homopolymer. 41 refs., 14 figs., 7 tabs.

  7. Intramolecular nitrone dipolar cycloadditions: control of regioselectivity and synthesis of naturally-occurring spirocyclic alkaloids.

    PubMed

    Hodges, Alastair J; Adams, Joseph P; Bond, Andrew D; Holmes, Andrew B; Press, Neil J; Roughley, Stephen D; Ryan, John H; Saubern, Simon; Smith, Catherine J; Turnbull, Michael D; Newton, Annabella F

    2012-12-01

    The intramolecular nitrone dipolar cycloaddition of in situ-generated nitrones such as compound 26 has been used for the synthesis of cyclic isoxazolidines 27 and 29. The regioselectivity of the intramolecular cycloaddition depends on the nature of the terminal substituent on the dipolarophile. The influence of the substituent on the regioselectivity of the cycloaddition has been examined using several model systems and two methods of nitrone formation. These studies demonstrated that the cyano-substituent plays a special role in favouring the formation of the 6,6,5-ring fused adduct 27 under thermodynamically controlled conditions. The utility of the cyclo-adduct 57 (see Scheme 12) as a precursor for the naturally occurring histrionicotoxins is illustrated by the synthesis of three "unsymmetrical" (i.e. with each side chain bearing different functional groups) members of the histrionicotoxin family HTX-259A, HTX-285C and HTX-285E (2, 3 and 4 respectively). PMID:23051904

  8. EVAPORATION: a new vapour pressure estimation methodfor organic molecules including non-additivity and intramolecular interactions

    NASA Astrophysics Data System (ADS)

    Compernolle, S.; Ceulemans, K.; Müller, J.-F.

    2011-09-01

    We present EVAPORATION (Estimation of VApour Pressure of ORganics, Accounting for Temperature, Intramolecular, and Non-additivity effects), a method to predict (subcooled) liquid pure compound vapour pressure p0 of organic molecules that requires only molecular structure as input. The method is applicable to zero-, mono- and polyfunctional molecules. A simple formula to describe log10p0(T) is employed, that takes into account both a wide temperature dependence and the non-additivity of functional groups. In order to match the recent data on functionalised diacids an empirical modification to the method was introduced. Contributions due to carbon skeleton, functional groups, and intramolecular interaction between groups are included. Molecules typically originating from oxidation of biogenic molecules are within the scope of this method: aldehydes, ketones, alcohols, ethers, esters, nitrates, acids, peroxides, hydroperoxides, peroxy acyl nitrates and peracids. Therefore the method is especially suited to describe compounds forming secondary organic aerosol (SOA).

  9. Theoretical Investigation of Intramolecular Hydrogen Shift Reactions in 3-Methyltetrahydrofuran (3-MTHF) Oxidation.

    PubMed

    Parab, Prajakta R; Sakade, Naoki; Sakai, Yasuyuki; Fernandes, Ravi; Heufer, K Alexander

    2015-11-01

    3-Methyltetrahydrofuran (3-MTHF) is proposed to be a promising fuel component among the cyclic oxygenated species. To have detailed insight of its combustion kinetics, intramolecular hydrogen shift reactions for the ROO to QOOH reaction class are studied for eight ROO isomers of 3-MTHF. Rate constants of all possible reaction paths that involve formation of cyclic transition states are computed by employing the CBS-QB3 composite method. A Pitzer-Gwinn-like approximation has been applied for the internal rotations in reactants, products, and transition states for the accurate treatment of hindered rotors. Calculated relative barrier heights highlight that the most favorable reaction channel proceeds via a six membered transition state, which is consistent with the computed rate constants. Comparing total rate constants in ROO isomers of 3-MTHF with the corresponding isomers of methylcyclopentane depicts faster kinetics in 3-MTHF than methylcyclopentane reflecting the effect of ring oxygen on the intramolecular hydrogen shift reactions. PMID:26444499

  10. Molecular Orbital Study of the Formation of Intramolecular Hydrogen Bonding of a Ligand Molecule in a Protein Aromatic Hydrophobic Pocket.

    PubMed

    Koseki, Jun; Gouda, Hiroaki; Hirono, Shuichi

    2016-01-01

    The natural product argadin is a cyclopentapeptide chitinase inhibitor that binds to chitinase B (ChiB) from the pathogenic bacteria Serratia marcescens. N(ω)-Acetyl-L-arginine and L-aminoadipic acid of argadin form intramolecular ionic hydrogen bonds in the aromatic hydrophobic pocket of ChiB. We performed ab initio molecular orbital and density functional theory calculations to elucidate the role of this intramolecular hydrogen bonding on intermolecular interactions between argadin and ChiB. We found that argadin accrues large stabilization energies from the van der Waals dispersion interactions, such as CH-π, π-π, and π-lone pair interactions, in the aromatic hydrophobic pocket of ChiB, although intramolecular hydrogen bonding within argadin might result in loss of entropy. The intramolecular ionic hydrogen bonding formation canceled local molecular charges and provided good van der Waals interactions with surrounding aromatic residues. PMID:27373666

  11. Copper-catalyzed intramolecular N-arylation of quinazolinones: facile convergent approach to (-)-circumdatins H and J.

    PubMed

    Kshirsagar, Umesh A; Argade, Narshinha P

    2010-08-20

    A copper-catalyzed intramolecular N-arylation of a quinazolinone nucleus that furnished the central benzodiazepine core unit has been demonstrated to accomplish an efficient convergent total synthesis of (-)-circumdatins H and J. PMID:20669978

  12. Indium-Mediated Intramolecular Reaction of N-(2-Iodobenzoyl)azabenzonorbornadienes: A General Access to Dihydrobenzo[c]phenanthridinones.

    PubMed

    Liu, Yang; Lei, Kang; Liu, Na; Sun, Dong-Wei; Hua, Xue-Wen; Li, Ya-Juan; Xu, Xiao-Hua

    2016-07-01

    An efficient synthesis of dihydrobenzo[c]phenanthridinones was achieved by utilizing an indium(0)-mediated intramolecular cyclization reaction under ligand- and base-free conditions. A variety of functional groups were tolerated in the present protocol. PMID:27243934

  13. Intramolecular transport of small-molecule cargo in a nanoscale device operated by light.

    PubMed

    Chen, Jiawen; Wezenberg, Sander J; Feringa, Ben L

    2016-05-21

    An intramolecular cargo transport device, based on a light-driven molecular motor, is presented. Detailed UV-vis and (1)H NMR studies demonstrate that the gripper attached to the upper half of the molecular motor is able to pick up an acetyl group from one side of the lower stator and, after a photochemical Z-E isomerization, drop it on the opposite side. PMID:27068214

  14. Stable Blue Phosphorescence Iridium(III) Cyclometalated Complexes Prompted by Intramolecular Hydrogen Bond in Ancillary Ligand.

    PubMed

    Yi, Seungjun; Kim, Jin-Hyoung; Cho, Yang-Jin; Lee, Jiwon; Choi, Tae-Sup; Cho, Dae Won; Pac, Chyongjin; Han, Won-Sik; Son, Ho-Jin; Kang, Sang Ook

    2016-04-01

    Improvement of the stability of blue phosphorescent dopant material is one of the key factors for real application of organic light-emitting diodes (OLEDs). In this study, we found that the intramolecular hydrogen bonding in an ancillary ligand from a heteroleptic Ir(III) complex can play an important role in the stability of blue phosphorescence. To rationalize the role of intramolecular hydrogen bonding, a series of Ir(III) complexes is designed and prepared: Ir(dfppy)2(pic-OH) (1a), Ir(dfppy)2(pic-OMe) (1b), Ir(ppy)2(pic-OH) (2a), and Ir(ppy)2(pic-OMe) (2b). The emission lifetime of Ir(dfppy)2(pic-OH) (1a) (τem = 3.19 μs) in dichloromethane solution was found to be significantly longer than that of Ir(dfppy)2(pic-OMe) (1b) (τem = 0.94 μs), because of a substantial difference in the nonradiative decay rate (knr = 0.28 × 10(5) s(-1) for (1a) vs 2.99 × 10(5) s(-1) for (1b)). These results were attributed to the intramolecular OH···O═C hydrogen bond of the 3-hydroxy-picolinato ligand. Finally, device lifetime was significantly improved when 1a was used as the dopant compared to FIrpic, a well-known blue dopant. Device III (1a as dopant) achieved an operational lifetime of 34.3 h for an initial luminance of 400 nits compared to that of device IV (FIrpic as dopant), a value of 20.1 h, indicating that the intramolecular hydrogen bond in ancillary ligand is playing an important role in device stability. PMID:26991672

  15. A Concomitant Allylic Azide Rearrangement/Intramolecular Azide–Alkyne Cycloaddition Sequence

    PubMed Central

    2015-01-01

    An intramolecular Huisgen cycloaddition of an interconverting set of isomeric allylic azides with alkynes affords substituted triazoles in high yield. The stereoisomeric vinyl-substituted triazoloxazines formed depend on the rate of cycloaddition of the different allylic azide precursors when the reaction is carried out under thermal conditions. In contrast, dimerized macrocyclic products were obtained when the reaction was done using copper(I)-catalyzed conditions, demonstrating the ability to control the reaction products through changing conditions. PMID:24635056

  16. Intramolecular electron transfer reactions in meso-(4-nitrophenyl)-substituted subporphyrins.

    PubMed

    Copley, Graeme; Oh, Juwon; Yoshida, Kota; Shimizu, Daiki; Kim, Dongho; Osuka, Atsuhiro

    2016-01-25

    A2B-type meso-(4-nitrophenyl)-substituted subporphyrins have been synthesized and shown to undergo very fast photoinduced intramolecular charge separation (CS) and charge recombination (CR) between the subporphyrin core and the meso-4-nitrophenyl group in CH2Cl2 as probed by femtosecond time-resolved transient absorption spectroscopy. Red-shifted emissions were detected from charge-separated states as a rare case for porphyrinoids. PMID:26645430

  17. Ruthenium Catalyzed Intramolecular C-S Coupling Reactions: Synthetic Scope and Mechanistic Insight.

    PubMed

    Sharma, Shivani; Pathare, Ramdas S; Maurya, Antim K; Gopal, Kandasamy; Roy, Tapta Kanchan; Sawant, Devesh M; Pardasani, Ram T

    2016-02-01

    A ruthenium catalyzed intramolecular C-S coupling reaction of N-arylthioureas for the synthesis of 2-aminobenzothiazoles has been developed. Kinetic, isotope labeling, and computational studies reveal the involvement of an electrophilic ruthenation pathway instead of a direct C-H activation. Stereoelectronic effect of meta-substituents on the N-arylthiourea dictates the final regioselective outcome of the reaction. PMID:26761401

  18. A Chiral Thiourea as a Template for Enantioselective Intramolecular [2 + 2] Photocycloaddition Reactions

    PubMed Central

    2016-01-01

    A chiral (1R,2R)-diaminocyclohexane-derived bisthiourea was found to exhibit a significant asymmetric induction in the intramolecular [2 + 2] photocycloaddition of 2,3-dihydropyridone-5-carboxylates. Under optimized conditions, the reaction was performed with visible light employing 10 mol % of thioxanthone as triplet sensitizer. Due to the different electronic properties of its carbonyl oxygen atoms, a directed binding of the substrate to the template is possible, which in turn enables an efficient enantioface differentiation. PMID:27258626

  19. Utilising tetraphenylethene as a dual activator for intramolecular charge transfer and aggregation induced emission.

    PubMed

    Zhang, Guo-Feng; Aldred, Matthew P; Gong, Wen-Liang; Li, Chong; Zhu, Ming-Qiang

    2012-08-11

    We report a simple design and synthesis of a donor-acceptor tetraphenylethene-naphthalimide (TPE-NI) dyad, in which TPE acts both as an electron-donor for intramolecular charge transfer (ICT) and activator for aggregation induced emission (AIE). Strong solvent-dependent photoluminescence covering almost the whole visible spectrum and AIE in its nanoparticle state compared to its solution state are demonstrated. PMID:22745935

  20. An intramolecular inverse electron demand Diels–Alder approach to annulated α-carbolines

    PubMed Central

    Ma, Zhiyuan; Ni, Feng; Woo, Grace H C; Lo, Sie-Mun; Roveto, Philip M; Schaus, Scott E

    2012-01-01

    Summary Intramolecular inverse electron demand cycloadditions of isatin-derived 1,2,4-triazines with acetylenic dienophiles tethered by amidations or transesterifications proceed in excellent yields to produce lactam- or lactone-fused α-carbolines. Beginning with various isatins and alkynyl dienophiles, a pilot-scale library of eighty-eight α-carbolines was prepared by using this robust methodology for biological evaluation. PMID:23015831

  1. A near infrared colorimetric and fluorometric probe for organophosphorus nerve agent mimics by intramolecular amidation.

    PubMed

    Hu, Xiao-Xiao; Su, Yue-Ting; Ma, Yun-Wei; Zhan, Xin-Qi; Zheng, Hong; Jiang, Yun-Bao

    2015-10-21

    A near infrared probe for sensitive colorimetric and fluorimetric detection of nerve agent mimics, DCP and DCNP, was reported based on the activation of a carboxylic acid group by the mimics to conduct an intramolecular amidation reaction in the heptamethine chromophore, where its absorption or excitation maximum wavelength could be greatly red-shifted by attenuating the electron-donating ability of the amine group in the bridgehead site of heptamethine cyanine. PMID:26323249

  2. Synthesis of an ABCD-Type Phthalocyanine by Intramolecular Cyclization Reaction.

    PubMed

    Chow, Sun Y S; Ng, Dennis K P

    2016-07-01

    Unsymmetrical phthalocyanines with a low symmetry can exhibit unique and intriguing properties that can facilitate their applications in certain disciplines. The synthesis of these compounds, however, has posed a great difficulty. A novel and unprecedented approach for phthalocyanine synthesis is reported that involves intramolecular cyclization of prelinked tetrakisphthalonitriles. By using this strategy, the first ABCD-type phthalocyanine has been prepared in 7.2% yield. PMID:27309120

  3. Synthesis of carbazoles by copper-catalyzed intramolecular C-H/N-H coupling.

    PubMed

    Takamatsu, Kazutaka; Hirano, Koji; Satoh, Tetsuya; Miura, Masahiro

    2014-06-01

    A Cu-catalyzed intramolecular C-H amination for the synthesis of carbazoles has been developed. The key to success is the installation of the picolinamide-based directing group, which is spontaneously removed after the coupling event. The Cu catalysis proceeded smoothly under Pd- and I(III)-free conditions, and its mild oxidation aptitude enables the rapid and concise construction of heteroatom-incorporated carbazole core π-systems. PMID:24813821

  4. Auger electron spectroscopy as a tool for measuring intramolecular charges of adsorbed molecules

    NASA Astrophysics Data System (ADS)

    Magkoev, T. T.

    A way for the determination of the values of intramolecular charges of adsorbed molecules of some binary dielectrics, based on Auger electron spectroscopy (AES), is proposed. These values can be obtained from the coverage dependences of the ratios of intensities of anion KL 23L 23 and KL 1L 1 Auger transitions, which are sensitive to the amount of charge at the 2p-orbitals. As an example, MgO adsorbed on Mo(110) is presented.

  5. Auger electron spectroscopy as a tool for measuring intramolecular charges of adsorbed molecules

    NASA Astrophysics Data System (ADS)

    Magkoev, T. T.

    1993-10-01

    A way for the determination of the values of intramolecular charges of adsorbed molecules of some binary dielectrics, based on Auger electron spectroscopy (AES), is proposed. These values can be obtained from the coverage dependences of the ratios of intensities of anion KL 23L 23 and KL 1L 1 Auger transitions, which are sensitive to the amount of charge at the 2p-orbitals. As an example, MgO adsorbed on Mo(110) is presented.

  6. An Iridium(I) N-Heterocyclic Carbene Complex Catalyzes Asymmetric Intramolecular Allylic Amination Reactions.

    PubMed

    Ye, Ke-Yin; Cheng, Qiang; Zhuo, Chun-Xiang; Dai, Li-Xin; You, Shu-Li

    2016-07-01

    A chiral iridium(I) N-heterocyclic carbene complex was reported for the first time as the catalyst in the highly enantioselective intramolecular allylic amination reaction. The current method provides facile access to biologically important enantioenriched indolopiperazinones and piperazinones in good yields (74-91 %) and excellent enantioselectivities (92-99 % ee). Preliminary mechanistic investigations reveal that the C-H activation occurs at the position ortho to the N-aryl group of the ligand. PMID:27162135

  7. Vibrationally highly excited molecules and intramolecular mode coupling through high-overtone spectroscopy

    SciTech Connect

    Wong, J.S.; Moore, C.B.

    1981-08-01

    High overtone spectra of organic molecules can be interpreted using the local mode model for absorptions by the inequivalent C-H bonds. The spectra can be assigned using either observed C-H bond lengths or isolated fundamental frequencies. The spectra of trihalomethanes indicate that the dominant intramolecular mode coupling for the C-H stretching overtones is Fermi resonance with combination states with one less C-H stretching quantum plus two quanta of the C-H bending vibrations.

  8. Characterization of intramolecular hydrogen bonds by atomic charges and charge fluxes.

    PubMed

    Baranović, Goran; Biliškov, Nikola; Vojta, Danijela

    2012-08-16

    The electronic charge redistribution and the infrared intensities of the two types of intramolecular hydrogen bonds, O-H···O and O-H···π, of o-hydroxy- and o-ethynylphenol, respectively, together with a set of related intermolecular hydrogen bond complexes are described in terms of atomic charges and charge fluxes derived from atomic polar tensors calculated at the B3LYP/cc-pVTZ level of theory. The polarizable continuum model shows that both the atomic charges and charge fluxes are strongly dependent on solvent. It is shown that their values for the OH bond in an intramolecular hydrogen bond are not much different from those for the "free" OH bond, but the changes are toward the values found for an intermolecular hydrogen bond. The intermolecular hydrogen bond is characterized not only by the decreased atomic charge but also by the enlarged charge flux term of the same sign producing thus an enormous increase in IR intensity. The overall behavior of the charges and fluxes of the hydrogen atom in OH and ≡CH bonds agree well with the observed spectroscopic characteristics of inter- and intramolecular hydrogen bonding. The main reason for the differences between the two types of the hydrogen bond lies in the molecular structure because favorable linear proton donor-acceptor arrangement is not possible to achieve within a small molecule. The calculated intensities (in vacuo and in polarizable continuum) are only in qualitative agreement with the measured data. PMID:22809455

  9. Regulation of interleukin-4 signaling by extracellular reduction of intramolecular disulfides

    SciTech Connect

    Curbo, Sophie; Gaudin, Raphael; Carlsten, Mattias; Malmberg, Karl-Johan; Troye-Blomberg, Marita; Ahlborg, Niklas; Karlsson, Anna; Johansson, Magnus; Lundberg, Mathias

    2009-12-25

    Interleukin-4 (IL-4) contains three structurally important intramolecular disulfides that are required for the bioactivity of the cytokine. We show that the cell surface of HeLa cells and endotoxin-activated monocytes can reduce IL-4 intramolecular disulfides in the extracellular space and inhibit binding of IL-4 to the IL-4R{alpha} receptor. IL-4 disulfides were in vitro reduced by thioredoxin 1 (Trx1) and protein disulfide isomerase (PDI). Reduction of IL-4 disulfides by the cell surface of HeLa cells was inhibited by auranofin, an inhibitor of thioredoxin reductase that is an electron donor to both Trx1 and PDI. Both Trx1 and PDI have been shown to be located at the cell surface and our data suggests that these enzymes are involved in catalyzing reduction of IL-4 disulfides. The pro-drug N-acetylcysteine (NAC) that promotes T-helper type 1 responses was also shown to mediate the reduction of IL-4 disulfides. Our data provides evidence for a novel redox dependent pathway for regulation of cytokine activity by extracellular reduction of intramolecular disulfides at the cell surface by members of the thioredoxin enzyme family.

  10. Bridge- and Solvent-Mediated Intramolecular Electronic Communications in Ubiquinone-Based Biomolecular Wires

    NASA Astrophysics Data System (ADS)

    Liu, Xiao-Yuan; Ma, Wei; Zhou, Hao; Cao, Xiao-Ming; Long, Yi-Tao

    2015-05-01

    Intramolecular electronic communications of molecular wires play a crucial role for developing molecular devices. In the present work, we describe different degrees of intramolecular electronic communications in the redox processes of three ubiquinone-based biomolecular wires (Bis-CoQ0s) evaluated by electrochemistry and Density Functional Theory (DFT) methods in different solvents. We found that the bridges linkers have a significant effect on the electronic communications between the two peripheral ubiquinone moieties and solvents effects are limited and mostly depend on the nature of solvents. The DFT calculations for the first time indicate the intensity of the electronic communications during the redox processes rely on the molecular orbital elements VL for electron transfer (half of the energy splitting of the LUMO and LUMO+1), which is could be affected by the bridges linkers. The DFT calculations also demonstrates the effect of solvents on the latter two-electron transfer of Bis-CoQ0s is more significant than the former two electrons transfer as the observed electrochemical behaviors of three Bis-CoQ0s. In addition, the electrochemistry and theoretical calculations reveal the intramolecular electronic communications vary in the four-electron redox processes of three Bis-CoQ0s.

  11. Molecular dynamics of excited state intramolecular proton transfer: 3-hydroxyflavone in solution

    SciTech Connect

    Bellucci, Michael A.; Coker, David F.

    2012-05-21

    The ultrafast enol-keto photoisomerization in the lowest singlet excited state of 3-hydroxyflavone is investigated using classical molecular dynamics in conjunction with empirical valence bond (EVB) potentials for the description of intramolecular interactions, and a molecular mechanics and variable partial charge model, dependent on transferring proton position, for the description of solute-solvent interactions. A parallel multi-level genetic program was used to accurately fit the EVB potential energy surfaces to high level ab initio data. We have studied the excited state intramolecular proton transfer (ESIPT) reaction in three different solvent environments: methylcyclohexane, acetonitrile, and methanol. The effects of the environment on the proton transfer time and the underlying mechanisms responsible for the varied time scales of the ESIPT reaction rates are analyzed. We find that simulations with our EVB potential energy surfaces accurately reproduce experimentally determined reaction rates, fluorescence spectra, and vibrational frequency spectra in all three solvents. Furthermore, we find that the ultrafast ESIPT process results from a combination of ballistic transfer, and intramolecular vibrational redistribution, which leads to the excitation of a set of low frequency promoting vibrational modes. From this set of promoting modes, we find that an O-O in plane bend and a C-H out of plane bend are present in all three solvents, indicating that they are fundamental to the ultrafast proton transfer. Analysis of the slow proton transfer trajectories reveals a solvent mediated proton transfer mechanism, which is diffusion limited.

  12. An intramolecular disulfide bond designed in myoglobin fine-tunes both protein structure and peroxidase activity.

    PubMed

    Wu, Lei-Bin; Yuan, Hong; Zhou, Hu; Gao, Shu-Qin; Nie, Chang-Ming; Tan, Xiangshi; Wen, Ge-Bo; Lin, Ying-Wu

    2016-06-15

    Disulfide bond plays crucial roles in stabilization of protein structure and in fine-tuning protein functions. To explore an approach for rational heme protein design, we herein rationally introduced a pair of cysteines (F46C/M55C) into the scaffold of myoglobin (Mb), mimicking those in native neuroglobin. Molecular modeling suggested that it is possible for Cys46 and Cys55 to form an intramolecular disulfide bond, which was confirmed experimentally by ESI-MS analysis, DTNB reaction and CD spectrum. Moreover, it was shown that the spontaneously formed disulfide bond of Cys46-Cys55 fine-tunes not only the heme active site structure, but also the protein functions. The substitution of Phe46 with Ser46 in F46S Mb destabilizes the protein while facilitates H2O2 activation. Remarkably, the formation of an intramolecular disulfide bond of Cys46-Cys55 in F46C/M55C Mb improves the protein stability and regulates the heme site to be more favorable for substrate binding, resulting in enhanced peroxidase activity. This study provides valuable information of structure-function relationship for heme proteins regulated by an intramolecular disulfide bond, and also suggests that construction of such a covalent bond is useful for design of functional heme proteins. PMID:27117233

  13. Understanding the mechanism of the intramolecular stetter reaction. A DFT study.

    PubMed

    Domingo, Luis R; Zaragozá, Ramón J; Saéz, Jose A; Arnó, Manuel

    2012-01-01

    The mechanism of the N-heterocyclic carbene (NHC)-catalyzed intramolecular Stetter reaction of salicylaldehyde 1 to yield chromanone 3 has been theoretically studied at the B3LYP/6-31G** level. This NHC-catalyzed reaction takes place through six elementary steps, which involve: (i) formation of the Breslow intermediate IN2; (ii) an intramolecular Michael-Type addition in IN2 to form the new C-C s bond; and (iii) extrusion of the NHC catalyst from the Michael adduct to yield chromanone 3. Analysis of the relative free energies in toluene indicates that while formation of Breslow intermediate IN2 involves the rate-determining step of the catalytic process, the intramolecular Michael-type addition is the stereoselectivity determining step responsible for the configuration of the stereogenic carbon a to the carbonyl of chromanone 3. An ELF analysis at TSs and intermediates involved in the Michael-type addition allows for the characterization of the electronic changes along the C-C bond-formation. PMID:22301721

  14. Bridge- and Solvent-Mediated Intramolecular Electronic Communications in Ubiquinone-Based Biomolecular Wires

    PubMed Central

    Liu, Xiao-Yuan; Ma, Wei; Zhou, Hao; Cao, Xiao-Ming; Long, Yi-Tao

    2015-01-01

    Intramolecular electronic communications of molecular wires play a crucial role for developing molecular devices. In the present work, we describe different degrees of intramolecular electronic communications in the redox processes of three ubiquinone-based biomolecular wires (Bis-CoQ0s) evaluated by electrochemistry and Density Functional Theory (DFT) methods in different solvents. We found that the bridges linkers have a significant effect on the electronic communications between the two peripheral ubiquinone moieties and solvents effects are limited and mostly depend on the nature of solvents. The DFT calculations for the first time indicate the intensity of the electronic communications during the redox processes rely on the molecular orbital elements VL for electron transfer (half of the energy splitting of the LUMO and LUMO+1), which is could be affected by the bridges linkers. The DFT calculations also demonstrates the effect of solvents on the latter two-electron transfer of Bis-CoQ0s is more significant than the former two electrons transfer as the observed electrochemical behaviors of three Bis-CoQ0s. In addition, the electrochemistry and theoretical calculations reveal the intramolecular electronic communications vary in the four-electron redox processes of three Bis-CoQ0s. PMID:25996306

  15. The interplay between inter- and intra-molecular dynamics in a series of alkylcitrates

    SciTech Connect

    Kipnusu, Wycliffe Kiprop; Kossack, Wilhelm; Iacob, Ciprian; Zeigermann, Philipp; Jasiurkowska, Malgorzata; Sangoro, Joshua R; Valiullin, Rustem; Kremer, Friedrich

    2013-01-01

    The inter- and intra-molecular dynamics in a series of glass-forming alkylcitrates is studied by a combination of Broadband Dielectric Spectroscopy (BDS), Pulsed Field Gradient Nuclear Magnetic Resonance (PFG NMR), Fourier-Transform Infrared (FTIR) spectroscopy and Differential Scanning Calorimetry (DSC). Analyzing the temperature dependencies of specific IR absorption bands in terms of their spectral position and the corresponding oscillator strengths enables one to unravel the intramolecular dynamics of specific molecular moieties and to compare them with the (primarily dielectrically) determined intermolecular dynamics. With decreasing temperature, the IR band positions of carbonyls (part of the core units) and H-bonded moieties of citrates show a red shift with a kink at the calorimetric glass transition temperature (Tg) while other moieties, whose dynamics are decoupled from those of the core units, exhibit a blue shift with nominal changes at Tg. The oscillator strength of all units in citrates depicts stronger temperature dependencies above Tg and in some, the ester linkage and H-bonded units show a change of slope at a temperature where structural and faster secondary relaxations merge. By that, a wealth of novel information is obtained proving the fundamental importance of intramolecular mobility in the process of glass formation, beyond coarse-grained descriptions.

  16. Conformational analysis and intramolecular hydrogen bonding of cis-3-aminoindan-1-ol: a quantum chemical study.

    PubMed

    Kheffache, Djaffar; Guemmour, Hind; Dekhira, Azzedine; Benaboura, Ahmed; Ouamerali, Ourida

    2013-11-01

    In the present work, we carried out a conformational analysis of cis-3-aminoindan-1-ol and evaluated the role of the intramolecular hydrogen bond in the stabilization of various conformers using quantum mechanical DFT (B3LYP) and MP2 methods. On the basis of relative energies, we have found nine conformational minima, which can interchange through the ring-puckering and the internal rotation of the OH and NH2 groups on the five-membered ring. The intramolecular hydrogen bonds such as OH∙∙∙∙π, NH∙∙∙∙π, NH∙∙∙∙OH and HN∙∙∙∙HO are expected to be of critical importance for the conformational stabilities. The intramolecular interactions of the minima have been analyzed by calculation of electron density (ρ) and Laplacian (ρ) at the bond critical points (BCPs) using atoms-in-molecule (AIM) theory. The existence or absence of OH∙∙∙∙π and NH∙∙∙∙π in cis-3-aminoindan-1-ol remains unclear since the geometrical investigation has not been confirmed by topological criteria. The results of theoretical calculations demonstrate that this compound exists predominantly in one ring-puckering form stabilized by strong hydrogen bond HN∙∙∙∙HO Interaction. PMID:24026578

  17. 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

  18. Intramolecular stable isotope distributions detect plant metabolic responses on century time scales

    NASA Astrophysics Data System (ADS)

    Schleucher, Jürgen; Ehlers, Ina; Augusti, Angela; Betson, Tatiana

    2014-05-01

    Plants respond to environmental changes on a vast range of time scales, and plant gas exchanges constitute important feedback mechanisms in the global C cycle. Responses on time scales of decades to centuries are most important for climate models, for prediction of crop productivity, and for adaptation to climate change. Unfortunately, responses on these timescale are least understood. We argue that the knowledge gap on intermediate time scales is due to a lack of adequate methods that can bridge between short-term manipulative experiments (e.g. FACE) and paleo research. Manipulative experiments in plant ecophysiology give information on metabolism on time scales up to years. However, this information cannot be linked to results from retrospective studies in paleo research, because little metabolic information can be derived from paleo archives. Stable isotopes are prominent tools in plant ecophysiology, biogeochemistry and in paleo research, but in all applications to date, isotope ratios of whole molecules are measured. However, it is well established that stable isotope abundance varies among intramolecular groups of biochemical metabolites, that is each so-called "isotopomer" has a distinct abundance. This intramolecular variation carries information on metabolic regulation, which can even be traced to individual enzymes (Schleucher et al., Plant, Cell Environ 1999). Here, we apply intramolecular isotope distributions to study the metabolic response of plants to increasing atmospheric [CO2] during the past century. Greenhouse experiments show that the deuterium abundance among the two positions in the C6H2 group of photosynthetic glucose depends on [CO2] during growth. This is observed for all plants using C3 photosynthesis, and reflects the metabolic flux ratio between photorespiration and photosynthesis. Photorespiration is a major C flux that limits assimilation in C3 plants, which encompass the overwhelming fraction of terrestrial photosynthesis and the

  19. High resolution photoelectron spectroscopy and femtosecond intramolecular dynamics using supersonic molecular beams

    SciTech Connect

    Niu, B.

    1992-09-01

    High resolution He I[alpha] photoelectron spectroscopy of formaldehyde and ketene and their deuterated compounds, are reported. The combination of a (H2CO) double-pass high-resolution electron-energy analyzer and effective rotational cooling of the sample by supersonic expansion enable the spectroscopy of these molecular cations. The vibrational autocorrelation functions are calculated from the high-resolution photoelectron spectra, shedding light on the ultrafast intramolecular dynamics of the molecular cations. This study reveals much more vibrational structural detail in the first electronic excited state of H2CO cations. The first electronic excited state of H2CO cations may have nonplanar equilibrium geometry. Strong isotope effects on vibronic (vibrational) coupling are observed in the second electronic excited state of H2CO. Vibrational autocorrelation functions are calculated for all four observed electronic states of H2CO. The correlation function of the first electronic excited state of H2CO shows a slow decay rate on the femtosecond time scale. The ultrafast decay of the H2CO cations in the third electronic excited state implies that dissociation and intramolecular processes are the main decay pathways. The present spectra of the ground states of ketene cations have more fine structure than before. The AIEs of the first and fifth excited states are determined unambiguously more accurately. The doublet-like fine structures present in the lint excited state of ketene implies the excitation of a soft'' mode not observed before. The vibrational autocorrelation functions are calculated for 4 of the 6 observed electronic states. The dynamics of the ground states of the cations are characterized by a wave packet oscillating with small amplitude around the minimum on the upper PES. The decay dynamics of the first and the fifth excited states of ketene are characterized by ultra-fast intramolecular processes like predissociation.

  20. High resolution photoelectron spectroscopy and femtosecond intramolecular dynamics using supersonic molecular beams

    SciTech Connect

    Niu, B.

    1992-09-01

    High resolution He I{alpha} photoelectron spectroscopy of formaldehyde and ketene and their deuterated compounds, are reported. The combination of a (H2CO) double-pass high-resolution electron-energy analyzer and effective rotational cooling of the sample by supersonic expansion enable the spectroscopy of these molecular cations. The vibrational autocorrelation functions are calculated from the high-resolution photoelectron spectra, shedding light on the ultrafast intramolecular dynamics of the molecular cations. This study reveals much more vibrational structural detail in the first electronic excited state of H2CO cations. The first electronic excited state of H2CO cations may have nonplanar equilibrium geometry. Strong isotope effects on vibronic (vibrational) coupling are observed in the second electronic excited state of H2CO. Vibrational autocorrelation functions are calculated for all four observed electronic states of H2CO. The correlation function of the first electronic excited state of H2CO shows a slow decay rate on the femtosecond time scale. The ultrafast decay of the H2CO cations in the third electronic excited state implies that dissociation and intramolecular processes are the main decay pathways. The present spectra of the ground states of ketene cations have more fine structure than before. The AIEs of the first and fifth excited states are determined unambiguously more accurately. The doublet-like fine structures present in the lint excited state of ketene implies the excitation of a ``soft`` mode not observed before. The vibrational autocorrelation functions are calculated for 4 of the 6 observed electronic states. The dynamics of the ground states of the cations are characterized by a wave packet oscillating with small amplitude around the minimum on the upper PES. The decay dynamics of the first and the fifth excited states of ketene are characterized by ultra-fast intramolecular processes like predissociation.

  1. Vapor-liquid equilibria for copolymer+solvent systems: Effect of intramolecular repulsion

    SciTech Connect

    Gupta, R.B.; Prausnitz, J.M.

    1995-03-01

    Role of intramolecular interactions in blend miscibility is well documented for polymer+copolymer mixtures. Some copolymer+polymer mixtures are miscible although their corresponding homopolymers are not miscible; for example, over a range of acrylonitrile content, styrene/acrylonitrile copolymers are miscible with poly(methyl methacrylate) but neither polystyrene nor polyacrylonitrile is miscible with poly(methyl methacrylate). Similarly, over a composition range, butadiene/acrylonitrile copolymers are miscible with poly(vinyl chloride) while none of the binary combinations of the homopolymers [polybutadiene, polyacrylonitrile, and poly(vinyl chloride)] are miscible. This behavior has been attributed to ``intramolecular repulsion`` between unlike copolymer segments. We have observed similar behavior in vapor-liquid equilibria (VLE) of copolymer+solvent systems. We find that acrylonitrile/butadiene copolymers have higher affinity for acetonitrile solvent than do polyacrylonitrile or polybutadiene. We attribute this non-intuitive behavior to ``intramolecular repulsion`` between unlike segments of the copolymer. This repulsive interaction is weakened when acetonitrile molecules are in the vicinity of unlike copolymer segments, favoring copolymer+solvent miscibility. We find similar behavior when acetonitrile is replaced by methyl ethyl ketone. To best knowledge, this effect has not been reported previously for VLE. We have obtained VLE data for mixtures containing a solvent and a copolymer as a function of copolymer composition. It appears that, at a given solvent partial pressure, there may be copolymer composition that yields maximum absorption of the solvent. This highly non-ideal VLE phase behavior may be useful for optimum design of a membrane for a separation process.

  2. Conformational analysis and intramolecular interactions in monosubstituted phenylboranes and phenylboronic acids

    PubMed Central

    Silla, Josué M; Cormanich, Rodrigo A; Rittner, Roberto

    2013-01-01

    Summary A 1 TS J F,H(O) coupling pathway, dictated by a hydrogen bond, in some 2-fluorobenzoic acids has been observed, while such an interaction does not occur in 2-fluorophenol. Thus, this work reports the conformational analysis of 2-fluorophenylboronic acid (1), in order to evaluate a possible intramolecular OH∙∙∙F hydrogen bond in comparison to an nF→pB interaction, which mimics the quantum nF→σ*OH hydrogen bond that would be expected in 2-fluorophenol. 2-Fluorophenylborane (3), which does not experience hydrogen bonding, was used to verify whether nF→pB interaction governs the conformational equilibrium in 1 due to a predominant OH∙∙∙F hydrogen bond or to other effects. A series of 2-X-phenylboranes (X = Cl, Br, NH2, PH2, OH and SH) were further computationally analyzed to search for electron donors to boron, capable of influencing the conformational equilibrium. Overall, the intramolecular OH∙∙∙F hydrogen bond in 1 is quite stabilizing and dictates the 1 h J F,H(O) coupling constant. Moreover, electron donation to the empty p orbital of boron (for noncoplanar BH2 moiety relative to the phenyl ring) is also significantly stabilizing for the NH2 and PH2 derivatives, but not enough to make the corresponding conformers appreciably populated, because of steric effects and the loss of πCC→pB resonance. Thus, the results found earlier for 2-fluorophenol about the lack of intramolecular hydrogen bonding are now corroborated. PMID:23843904

  3. Path-integral calculation of the second virial coefficient including intramolecular flexibility effects

    SciTech Connect

    Garberoglio, Giovanni; Jankowski, Piotr; Szalewicz, Krzysztof; Harvey, Allan H.

    2014-07-28

    We present a path-integral Monte Carlo procedure for the fully quantum calculation of the second molecular virial coefficient accounting for intramolecular flexibility. This method is applied to molecular hydrogen (H{sub 2}) and deuterium (D{sub 2}) in the temperature range 15–2000 K, showing that the effect of molecular flexibility is not negligible. Our results are in good agreement with experimental data, as well as with virials given by recent empirical equations of state, although some discrepancies are observed for H{sub 2} between 100 and 200 K.

  4. Low Band Gap Coplanar Conjugated Molecules Featuring Dynamic Intramolecular Lewis Acid-Base Coordination.

    PubMed

    Zhu, Congzhi; Guo, Zi-Hao; Mu, Anthony U; Liu, Yi; Wheeler, Steven E; Fang, Lei

    2016-05-20

    Ladder-type conjugated molecules with a low band gap and low LUMO level were synthesized through an N-directed borylation reaction of pyrazine-derived donor-acceptor-donor precursors. The intramolecular boron-nitrogen coordination bonds played a key role in rendering the rigid and coplanar conformation of these molecules and their corresponding electronic structures. Experimental investigation and theoretical simulation revealed the dynamic nature of such coordination, which allowed for active manipulation of the optical properties of these molecules by using competing Lewis basic solvents. PMID:27096728

  5. Oligo(p-phenylene-ethynylene)s with backbone conformation controlled by competitive intramolecular hydrogen bonds.

    PubMed

    Hu, Wei; Yan, Qifan; Zhao, Dahui

    2011-06-14

    A series of conjugated oligo(p-phenylene-ethynylene) (OPE) molecules with backbone conformations (that is, the relative orientations of the contained phenylene units) controlled by competitive intramolecular hydrogen bonds to be either co-planar or random were synthesised and studied. In these oligomers, carboxylate and amido substituents were attached to alternate phenylene units in the OPE backbone. These functional groups were able to form intramolecular hydrogen bonds between neighbouring phenylene units. Thereby, all phenylene units in the backbone were confined in a co-planar conformation. This planarised structure featured a more extended effective conjugation length than that of regular OPEs with phenylene units adopting random orientation due to a low rotational-energy barrier. However, if a tri(ethylene glycol) (Tg) side chain was appended to the amido group, it enabled another type of intramolecular hydrogen bond, formed by the Tg chain folding back and the contained ether oxygen atom competing with the ester carbonyl group as the hydrogen-bond acceptor. The outcome of this competition was proven to depend on the length of the alkylene linker joining the ether oxygen atom to the amido group. Specifically, if the Tg chain folded back to form a five-membered cyclic structure, this hydrogen-bonding motif was sufficiently robust to overrule the hydrogen bonds between adjacent phenylene units. Consequently, the oligomers assumed non-planar conformations. However, if the side chain formed a six-membered ring by hydrogen bonding with the amido NH group, such a motif was much less stable and yielded in the competition with the ester carbonyl group from the adjacent phenylene unit. Thus, the hydrogen bonds between the phenylene units remained, and the co-planar conformation was manifested. In our system, the hydrogen bonds formed by the back-folded Tg chain and amido NH group relied on a single oxygen atom as the hydrogen-bond acceptor. The additional oxygen

  6. Transition from direct tunneling to field emission in carbon nanotube intramolecular junctions

    NASA Astrophysics Data System (ADS)

    Chiu, Po-Wen; Roth, Siegmar

    2008-01-01

    Transport measurements through metal-semiconductor carbon nanotube intramolecular junctions were carried out at high gate voltages in which regime the influence of Schottky barrier to charge transport is weak. The I-Vds curves exhibit an inflection point in the form of ln(I /Vds2)-1/Vds, showing a transition of transport mechanism from direct tunneling to field emission. The findings are interpreted in terms of quantum tunneling through a rectanglelike barrier at the junction, with a barrier width of ˜4nm, in good agreement with that observed on pentagon-heptagon defects at nanotube junctions via scanning tunneling spectroscopy.

  7. Solvent-tuned intramolecular charge-recombination rates in a conjugated donor-acceptor molecule

    NASA Technical Reports Server (NTRS)

    Khundkar, Lutfur R.; Stiegman, A. E.; Perry, Joseph W.

    1990-01-01

    The nonradiative charge-recombination rates from the charge-transfer state of a new conjugated donor-acceptor molecule (p-cyano-p-prime-methylthiodiphenylacetylene) can be tuned over almost an order of magnitude by varying the polarity of the solvent. These measurements of intramolecular recombination show a turnover of rates as a function of emission energy, consistent with the 'normal' and 'inverted' behavior of Marcus theory. Steady-state spectra and time-resolved measurements make it possible to quantitatively compare thermal and optical electron-transfer rates as a function of driving force and demonstrate their correspondence.

  8. Size measuring techniques as tool to monitor pea proteins intramolecular crosslinking by transglutaminase treatment.

    PubMed

    Djoullah, Attaf; Krechiche, Ghali; Husson, Florence; Saurel, Rémi

    2016-01-01

    In this work, techniques for monitoring the intramolecular transglutaminase cross-links of pea proteins, based on protein size determination, were developed. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis profiles of transglutaminase-treated low concentration (0.01% w/w) pea albumin samples, compared to the untreated one (control), showed a higher electrophoretic migration of the major albumin fraction band (26 kDa), reflecting a decrease in protein size. This protein size decrease was confirmed, after DEAE column purification, by dynamic light scattering (DLS) where the hydrodynamic radius of treated samples appears to be reduced compared to the control one. PMID:26212961

  9. Application of time-resolved resonance Raman spectroscopy to intramolecular electron transfer

    SciTech Connect

    Schoonover, J.R.; Strouse, G.F.; Chen, P.; Bates, D.; Meyer, T.J. )

    1993-06-09

    Time-resolved resonance Raman spectroscopy has been applied for the first time to the study of intramolecular electron transfer in a chromophore-quencher complex, based on a metal-to-ligand charge-transfer (MLCT) excited state. These measurements allow for (1) the identification of redox sites that are reached following excitation and (2) the inferring of structural information in short-lived intermediates. This technique is a more sensitive probe than transient absorption as shown by its application to the redox-separated complex shown below involving a pyridinium acceptor and a phenothiazine donor.

  10. Stereoselection in Intramolecular Diels-Alder Reactions of 2-Cyano-1-azadienes: Indolizidine and Quinolizidine Synthesis.

    PubMed

    Tay, Gidget C; Sizemore, Nicholas; Rychnovsky, Scott D

    2016-07-01

    Progress toward understanding the scope and diastereoselectivity of intramolecular Diels-Alder reactions using 2-cyano-1-azadienes is described herein. The resulting cyanoenamine products are underutilized intermediates in organic synthesis. Assembly of the Diels-Alder precursors was achieved using an improved imine condensation/oxidative cyanation protocol. By this method, several highly substituted indolizidine and quinolizidine architectures were constructed. Quantum mechanical DFT calculations at the B3LYP/6-31+G(d) level of theory were performed for these cyclizations and provide insights into the origins of the observed diastereoselectivities. PMID:27295460

  11. Concise synthesis of calystegines B2 and B3via intramolecular Nozaki-Hiyama-Kishi reaction.

    PubMed

    Wang, Hong-Yao; Kato, Atsushi; Kinami, Kyoko; Li, Yi-Xian; Fleet, George W J; Yu, Chu-Yi

    2016-06-01

    The key step in the concise syntheses of calystegine B2 and its C-2 epimer calystegine B3 was the construction of cycloheptanone 8via an intramolecular Nozaki-Hiyama-Kishi (NHK) reaction of 9, an aldehyde containing a Z-vinyl iodide. Vinyl iodide 9 was obtained by the Stork olefination of aldehyde 10, derived from carbohydrate starting materials. Calystegines B2 (3) and B3 (4) were synthesized from d-xylose and l-arabinose derivatives respectively in 11 steps in excellent overall yields (27% and 19%). PMID:27161660

  12. Towards Uniform Iodine Catalysis: Intramolecular C-H Amination of Arenes under Visible Light.

    PubMed

    Martínez, Claudio; Bosnidou, Alexandra E; Allmendinger, Simon; Muñiz, Kilian

    2016-07-11

    A photochemical catalytic amination of arenes is presented. The reaction proceeds under benign iodine catalysis in the presence of visible light as the initiator and provides access to a range of differently substituted arylamines. A total of 29 examples demonstrate the broad applicability of this mild oxidation method. The scope of the reaction could further be expanded to silyl-tethered derivatives, which undergo intramolecular amination upon formation of seven-membered heterocycles. Cleavage of the silicon tether provides access to the corresponding 3-substituted anilines. PMID:27159628

  13. Temperature dependence of turnover in a Sc(OTf)3-catalyzed intramolecular Schmidt reaction

    PubMed Central

    Fehl, Charlie; Hirt, Erin E.; Li, Sze-Wan; Aubé, Jeffrey

    2015-01-01

    The intramolecular Schmidt reaction of ketones and tethered azides is an efficient method for the generation of amides and lactams. This reaction is catalyzed by Lewis acids, which tightly bind the strongly basic amide product and result in product inhibition. We report herein conditions to achieve a catalytic Schmidt reaction using substoichiometric amounts of the heat-stable Lewis acid Sc(OTf)3. This species was shown to effectively release products of the Schmidt reaction in a temperature-dependent fashion. Thus, heat was able to promote catalyst turnover. A brief substrate scope was conducted using these conditions. PMID:26085693

  14. Gold-Catalyzed Intramolecular Tandem Cyclization of Indole-Ynamides: Diastereoselective Synthesis of Spirocyclic Pyrrolidinoindolines.

    PubMed

    Zheng, Nan; Chang, Yuan-Yuan; Zhang, Li-Jie; Gong, Jian-Xian; Yang, Zhen

    2016-02-01

    A gold-catalyzed intramolecular tandem cyclization of indole-ynamide affords tetracyclic spirocyclic pyrrolidinoindoline bearing an all-carbon quaternary stereocentre in a single step; however, when the reaction was carried out in the presence of BF3 ⋅Et2 O, the corresponding tricyclic spirocyclic pyrrolidinoindoline-based enones are produced through a key 1,5-hydride shift. The developed chemistry provides a diastereoselective and straightforward entry to structurally diverse polycylic pyrrolidinoindolines from indole-ynamides in one-pot reactions under mild conditions. PMID:26374716

  15. Cyclic Triradicals Composed of Iminonitroxide-Gold(I) with Intramolecular Ferromagnetic Interactions.

    PubMed

    Suzuki, Shuich; Wada, Tomoyuki; Tanimoto, Ryu; Kozaki, Masatoshi; Shiomi, Daisuke; Sugisaki, Kenji; Sato, Kazunobu; Takui, Takeji; Miyake, Yota; Hosokoshi, Yuko; Okada, Keiji

    2016-08-26

    A triangular gold(iminonitroxide-2-ide) trimer complex (5) was prepared and investigated to determine its magnetic properties. The results showed that the metalloid triradical is highly stable, even in solution under aerated conditions. The intramolecular exchange interaction of 5 was found to be positive (Jintra /kB ≈+29 K), thus showing that 5 is in a quartet ground state. In addition, a silver sandwich complex (5-Ag(+) -5) was prepared and its electronic and magnetic properties were also clarified. PMID:27490798

  16. Au25 Clusters as Electron-Transfer Catalysts Induced the Intramolecular Cascade Reaction of 2-nitrobenzonitrile

    PubMed Central

    Chong, Hanbao; Li, Peng; Wang, Shuxin; Fu, Fangyu; Xiang, Ji; Zhu, Manzhou; Li, Yadong

    2013-01-01

    Design of atomically precise metal nanocluster catalysts is of great importance in understanding the essence of the catalytic reactions at the atomic level. Here, for the first time, Au25z nanoslusters were employed as electron transfer catalysts to induce an intramolecular cascade reaction at ambient conditions and gave rise to high conversion (87%) and selectivity (96%). Electron spin-resonance spectra indeed confirmed the consecutive electron transfer process and the formation of N radical. UV-vis absorption spectra also verified Au25z was intact after the catalytic circle. Our research may open up wide opportunities for extensive organic reactions catalyzed by Au25z. PMID:24225495

  17. Model studies of pyridoxal Schiff's bases. Coplanarity and intramolecular hydrogen bonding.

    PubMed

    Chang, C; Shieh, T L; Floss, H G

    1977-01-01

    The interactions between the pi cloud of the aromatic ring and the pi-electron pair of the imine double bond of aromatic oximes as model compounds of pyridoxal Schiff's bases have been studied by high-resolution carbon-13 magnetic resonance spectroscopy. The coplanarity and intramolecular hydrogen bonding have been determined by 13C-1H long range couplings. This detailed investigation of 13C-1H coupling also provides unambiguous proof of the existence of the "enol-imine" tautomers in chloroform and dimethyl sulfoxide solutions. The tautomerism between the "enol-imine" and "keto-enamine" is discussed. PMID:833823

  18. Aziridinyl Fluorophores Demonstrate Bright Fluorescence and Superior Photostability by Effectively Inhibiting Twisted Intramolecular Charge Transfer.

    PubMed

    Liu, Xiaogang; Qiao, Qinglong; Tian, Wenming; Liu, Wenjuan; Chen, Jie; Lang, Matthew J; Xu, Zhaochao

    2016-06-01

    Replacing conventional dialkylamino substituents with a three-membered aziridine ring in naphthalimide leads to significantly enhanced brightness and photostability by effectively suppressing twisted intramolecular charge transfer formation. This replacement is generalizable in other chemical families of fluorophores, such as coumarin, phthalimide, and nitrobenzoxadiazole dyes. In highly polar fluorophores, we show that aziridinyl dyes even outperform their azetidinyl analogues in aqueous solution. We also proposed one simple mechanism that can explain the vulnerability of quantum yield to hydrogen bond interactions in protonic solvents in various fluorophore families. Such knowledge is a critical step toward developing high-performance fluorophores for advanced fluorescence imaging. PMID:27203847

  19. Stereocontrolled synthesis of rosuvastatin calcium via iodine chloride-induced intramolecular cyclization.

    PubMed

    Xiong, Fangjun; Wang, Haifeng; Yan, Lingjie; Han, Sheng; Tao, Yuan; Wu, Yan; Chen, Fener

    2016-01-28

    A novel, stereoselective approach towards rosuvastatin calcium from the known (S)-homoallylic alcohol has been developed. The synthesis is highlighted by a regio- and stereocontrolled ICl-induced intramolecular cyclization of chiral homoallylic carbonate to deliver the C6-formyl statin side chain with a syn-1,3-diol moiety. An improved synthesis of the rosuvastatin pyrimidine core moiety is also included. Moreover, this methodology is useful in the asymmetric synthesis of structural variants of statins such as pitavastatin calcium and atorvastatin calcium and their related analogs. PMID:26659808

  20. Copper-catalyzed intramolecular cyclization of N-propargyl-adenine: synthesis of purine-fused tricyclics.

    PubMed

    Li, Ren-Long; Liang, Lei; Xie, Ming-Sheng; Qu, Gui-Rong; Niu, Hong-Ying; Guo, Hai-Ming

    2014-04-18

    A novel protocol to construct fluorescent purine-fused tricyclic products via intramolecular cyclization of N-propargyl-adenine has been developed. With CuBr as the catalyst, a series of purine-fused tricyclic products were obtained in good to excellent yields (19 examples, 75-89% yields). When R2 was a hydrogen atom in N-propargyl-adenines, the reactions only afforded the endocyclic double bond products. When R2 was an aryl group, the electron-donating groups favored the endocyclic double bond products, while the electron-withdrawing groups favored the exocyclic double bond products. PMID:24678722

  1. Efficient copper-catalyzed direct intramolecular aminotrifluoromethylation of unactivated alkenes with diverse nitrogen-based nucleophiles.

    PubMed

    Lin, Jin-Shun; Xiong, Ya-Ping; Ma, Can-Liang; Zhao, Li-Jiao; Tan, Bin; Liu, Xin-Yuan

    2014-01-27

    A mild, convenient, and step-economical intramolecular aminotrifluoromethylation of unactivated alkenes with a variety of electronically distinct, nitrogen-based nucleophiles in the presence of a simple copper salt catalyst, in the absence of extra ligands, is described. Many different nitrogen-based nucleophiles (e.g., basic primary aliphatic and aromatic amines, sulfonamides, carbamates, and ureas) can be employed in this new aminotrifluoromethylation reaction. The aminotrifluoromethylation process allows straightforward access to diversely substituted CF3-containing pyrrolidines or indolines, in good to excellent yields, through a direct difunctionalization strategy from the respective acyclic starting materials. Mechanistic studies were conducted and a plausible mechanism was proposed. PMID:24458913

  2. Negative resists for electron-beam lithography utilizing acid-catalyzed intramolecular dehydration of phenylcarbinol

    NASA Astrophysics Data System (ADS)

    Migitaka, Sonoko; Uchino, Shou-ichi; Ueno, Takumi; Yamamoto, Jiro; Kojima, Kyoko; Hashimoto, Michiaki; Shiraishi, Hiroshi

    1996-06-01

    Acid-catalyzed intramolecular dehydration of phenylcarbinol is used to design highly sensitive negative resists for electron beam lithography. Of the phenylcarbinol resists evaluated in this study, the resist composed of 1,3-bis(alpha-hydroxyisopropyl)benzene (Diol-1), m/p-cresol novolak resin, and diphenyliodonium triflate (DIT) shows the best lithographic performance in terms of sensitivity and resolution. Fine 0.25-micrometer line-and-space patterns were formed by using the resist containing Diol-1 with a dose of 3.6 (mu) C/cm2 in conjunction with a 50 kV electron beam exposure system.

  3. Anomalous ligand effect in gold(I)-catalyzed intramolecular hydroamination of alkynes.

    PubMed

    Gaggioli, Carlo Alberto; Ciancaleoni, Gianluca; Biasiolo, Luca; Bistoni, Giovanni; Zuccaccia, Daniele; Belpassi, Leonardo; Belanzoni, Paola; Tarantelli, Francesco

    2015-04-01

    We analyzed the ligand electronic effect in a gold(I)-catalyzed intramolecular alkyne hydroamination, through a DFT and charge-displacement function (CDF) study. We found that, in the presence of π-electron conjugation between the alkyne and the nucleophilic functionality, electron poor ligands modify the coordination mode and the geometric parameters of the substrate in such a way that, contrary to expectations, the activation barrier of the nucleophilic attack increases. This remarkable effect is due to the competition between alkyne activation and nucleophile deactivation. The general relevance of these findings is highlighted. PMID:25738820

  4. An O-to-N intramolecular acyl migration in C₁₉-diterpenoid alkaloids.

    PubMed

    Chen, Qi-Feng; Jian, Xi-Xian; Chen, Qiao-Hong; Wang, Feng-Peng

    2012-01-01

    The O-acyl group at C-1 of two C₁₉-diterpenoid alkaloids 2 and 5 was transferred to the secondary amine nitrogen to form amides 3 and 6 in the basic condition. This kind of O-to-N intramolecular acyl migration could be caused by the near distance between the nucleophilic nitrogen atom and the carbonyl group of the ester at C-1 in the C₁₉-diterpenoid alkaloids, which is consistent with the conformation of rings A and E in the C₁₉-diterpenoid alkaloids. PMID:22568819

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

    PubMed

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

    2014-12-01

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

  6. An intramolecular charge transfer fluorescent probe: Synthesis and selective fluorescent sensing of Ag +

    NASA Astrophysics Data System (ADS)

    Mu, Honglei; Gong, Rui; Ren, Lin; Zhong, Cheng; Sun, Yimin; Fu, Enqin

    2008-09-01

    An intramolecular charge transfer (ICT) fluorescent probe, in which the thiourea derivative moiety is linked to the fluorescent 4-(dimethylamino) benzamide, has been designed and synthesized. The ions-selective signaling behaviors of the probe were investigated. Upon the addition of Ag +, an overall emission enhancement of 14-fold was observed. Compound 1 displayed highly selective chelation enhanced fluorescence (CHEF) effect with Ag + over alkali, alkali earth metal ions and some transition metal ions in aqueous methanol solutions. The prominent selective and efficient fluorescent enhancing behavior could be utilized as a new chemosensing probe for the analysis of Ag + ion in aqueous environment.

  7. Intramolecular Folding in Human ILPR Fragment with Three C-Rich Repeats

    PubMed Central

    Dhakal, Soma; Lafontaine, Javonne L.; Yu, Zhongbo; Koirala, Deepak; Mao, Hanbin

    2012-01-01

    Enrichment of four tandem repeats of guanine (G) rich and cytosine (C) rich sequences in functionally important regions of human genome forebodes the biological implications of four-stranded DNA structures, such as G-quadruplex and i-motif, that can form in these sequences. However, there have been few reports on the intramolecular formation of non-B DNA structures in less than four tandem repeats of G or C rich sequences. Here, using mechanical unfolding at the single-molecule level, electrophoretic mobility shift assay (EMSA), circular dichroism (CD), and ultraviolet (UV) spectroscopy, we report an intramolecularly folded non-B DNA structure in three tandem cytosine rich repeats, 5'-TGTC4ACAC4TGTC4ACA (ILPR-I3), in the human insulin linked polymorphic region (ILPR). The thermal denaturation analyses of the sequences with systematic C to T mutations have suggested that the structure is linchpinned by a stack of hemiprotonated cytosine pairs between two terminal C4 tracts. Mechanical unfolding and Br2 footprinting experiments on a mixture of the ILPR-I3 and a 5′-C4TGT fragment have further indicated that the structure serves as a building block for intermolecular i-motif formation. The existence of such a conformation under acidic or neutral pH complies with the strand-by-strand folding pathway of ILPR i-motif structures. PMID:22761750

  8. Photodynamics of intramolecular proton transfer in polar and nonpolar biflavonoid solutions

    NASA Astrophysics Data System (ADS)

    Bondarev, S. L.; Knyukshto, V. N.; Tikhomirov, S. A.; Buganov, O. V.; Pyrko, A. N.

    2012-10-01

    Using methods of steady state luminescence and femtosecond spectroscopy, we have studied the mechanism of intramolecular proton transfer in synthesized 3,7-dihydroxy-2,8-di(4-methoxyphenyl)-4H,6H-pyrano[3,2- g]chromen-4,6-dion in polar and nonpolar solutions, films, and polycrystals at 293 and 77 K. In an excited singlet state, intramolecular proton transfer occurs in two stages. At the first stage, a tautomer with one transferred proton (OTP tautomer) is formed from the Franck-Condon state within τ1 = 0.6 ps. At the second stage, the second proton is transferred within τ2 = 3.1 ps and a tautomer with two transferred protons (TTP tautomer) is formed, which fluoresces in toluene at 293 K with a high quantum yield, Φ f = 0.66, and the fluorescence spectrum of which is characterized by a large Stokes shift, 9900 cm-1. At 293 K, polar solvents (dimethylformamide, dimethyl sulfoxide, ethanol, etc.) solvate the BFV molecule in the ground state, while, in the excited state, an OTP tautomer is mainly formed. In polar ethanol at 77 K, a dual fluorescence spectrum is observed, which is caused by the fluorescence emission of polysolvates with λ{max/ f } = 460 nm and TTP phototautomers at λ{max/ f }= 610 nm.

  9. A Direct Mechanism of Ultrafast Intramolecular Singlet Fission in Pentacene Dimers.

    PubMed

    Fuemmeler, Eric G; Sanders, Samuel N; Pun, Andrew B; Kumarasamy, Elango; Zeng, Tao; Miyata, Kiyoshi; Steigerwald, Michael L; Zhu, X-Y; Sfeir, Matthew Y; Campos, Luis M; Ananth, Nandini

    2016-05-25

    Interest in materials that undergo singlet fission (SF) has been catalyzed by the potential to exceed the Shockley-Queisser limit of solar power conversion efficiency. In conventional materials, the mechanism of SF is an intermolecular process (xSF), which is mediated by charge transfer (CT) states and depends sensitively on crystal packing or molecular collisions. In contrast, recently reported covalently coupled pentacenes yield ∼2 triplets per photon absorbed in individual molecules: the hallmark of intramolecular singlet fission (iSF). However, the mechanism of iSF is unclear. Here, using multireference electronic structure calculations and transient absorption spectroscopy, we establish that iSF can occur via a direct coupling mechanism that is independent of CT states. We show that a near-degeneracy in electronic state energies induced by vibronic coupling to intramolecular modes of the covalent dimer allows for strong mixing between the correlated triplet pair state and the local excitonic state, despite weak direct coupling. PMID:27280166

  10. Dynamic Kinetic Resolution Enabled by Intramolecular Benzoin Reaction: Synthetic Applications and Mechanistic Insights.

    PubMed

    Zhang, Guoxiang; Yang, Shuang; Zhang, Xiaoyan; Lin, Qiqiao; Das, Deb K; Liu, Jian; Fang, Xinqiang

    2016-06-29

    The highly enantio-, diastereo-, and regioselective dynamic kinetic resolution of β-ketoesters and 1,3-diketones was achieved via a chiral N-heterocyclic carbene catalyzed intramolecular cross-benzoin reaction. A variety of tetralone derivatives bearing two contiguous stereocenters and multiple functionalities were liberated in moderate to excellent yields and with high levels of stereoselectivity (>95% ee and >20:1 dr in most cases). In addition, the excellent regioselectivity control for aryl/alkyl 1,3-diketones, and the superior electronic differentiation of 1,3-diarylketones were highlighted. Moreover, a set of new mechanistic rationale that differs with the currently widely accepted understanding of intramolecular benzoin reactions was established to demonstrate the superior preference of benzoin over aldol transformation: (1) A coexistence of competitive aldol and benzoin reactions was detected, but a retro-aldol-irreversible benzoin process performs a vital role in the generation of predominant benzoin products. (2) The most essential role of an N-electron-withdrawing substituent in triazolium catalysts was revealed to be accelerating the rate of the benzoin transformation, rather than suppressing the aldol process through reducing the inherent basicity of the catalyst. PMID:27270409

  11. Intra-molecular Triplet Energy Transfer is a General Approach to Improve Organic Fluorophore Photostability

    PubMed Central

    Zheng, Qinsi; Jockusch, Steffen; Rodríguez-Calero, Gabriel G.; Zhou, Zhou; Zhao, Hong; Altman, Roger B.; Abruña, Héctor D.; Blanchard, Scott C.

    2015-01-01

    Bright, long-lasting and non-phototoxic organic fluorophores are essential to the continued advancement of biological imaging. Traditional approaches towards achieving photostability, such as the removal of molecular oxygen and the use of small-molecule additives in solution, suffer from potentially toxic side effects, particularly in the context of living cells. The direct conjugation of small-molecule triplet state quenchers, such as cyclooctatetraene (COT), to organic fluorophores has the potential to bypass these issues by restoring reactive fluorophore triplet states to the ground state through intra-molecular triplet energy transfer. Such methods have enabled marked improvement in cyanine fluorophore photostability spanning the visible spectrum. However, the generality of this strategy to chemically and structurally diverse fluorophore species has yet to be examined. Here, we show that the proximal linkage of COT increases the photon yield of a diverse range of organic fluorophores widely used in biological imaging applications, demonstrating that the intra-molecular triplet energy transfer mechanism is a potentially general approach for improving organic fluorophore performance and photostability. PMID:26700693

  12. A Direct Mechanism of Ultrafast Intramolecular Singlet Fission in Pentacene Dimers

    PubMed Central

    2016-01-01

    Interest in materials that undergo singlet fission (SF) has been catalyzed by the potential to exceed the Shockley–Queisser limit of solar power conversion efficiency. In conventional materials, the mechanism of SF is an intermolecular process (xSF), which is mediated by charge transfer (CT) states and depends sensitively on crystal packing or molecular collisions. In contrast, recently reported covalently coupled pentacenes yield ∼2 triplets per photon absorbed in individual molecules: the hallmark of intramolecular singlet fission (iSF). However, the mechanism of iSF is unclear. Here, using multireference electronic structure calculations and transient absorption spectroscopy, we establish that iSF can occur via a direct coupling mechanism that is independent of CT states. We show that a near-degeneracy in electronic state energies induced by vibronic coupling to intramolecular modes of the covalent dimer allows for strong mixing between the correlated triplet pair state and the local excitonic state, despite weak direct coupling. PMID:27280166

  13. A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization

    PubMed Central

    van der Velde, Jasper H. M.; Oelerich, Jens; Huang, Jingyi; Smit, Jochem H.; Aminian Jazi, Atieh; Galiani, Silvia; Kolmakov, Kirill; Guoridis, Giorgos; Eggeling, Christian; Herrmann, Andreas; Roelfes, Gerard; Cordes, Thorben

    2016-01-01

    Intramolecular photostabilization via triple-state quenching was recently revived as a tool to impart synthetic organic fluorophores with ‘self-healing' properties. To date, utilization of such fluorophore derivatives is rare due to their elaborate multi-step synthesis. Here we present a general strategy to covalently link a synthetic organic fluorophore simultaneously to a photostabilizer and biomolecular target via unnatural amino acids. The modular approach uses commercially available starting materials and simple chemical transformations. The resulting photostabilizer–dye conjugates are based on rhodamines, carbopyronines and cyanines with excellent photophysical properties, that is, high photostability and minimal signal fluctuations. Their versatile use is demonstrated by single-step labelling of DNA, antibodies and proteins, as well as applications in single-molecule and super-resolution fluorescence microscopy. We are convinced that the presented scaffolding strategy and the improved characteristics of the conjugates in applications will trigger the broader use of intramolecular photostabilization and help to emerge this approach as a new gold standard. PMID:26751640

  14. A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization.

    PubMed

    van der Velde, Jasper H M; Oelerich, Jens; Huang, Jingyi; Smit, Jochem H; Aminian Jazi, Atieh; Galiani, Silvia; Kolmakov, Kirill; Guoridis, Giorgos; Eggeling, Christian; Herrmann, Andreas; Roelfes, Gerard; Cordes, Thorben

    2016-01-01

    Intramolecular photostabilization via triple-state quenching was recently revived as a tool to impart synthetic organic fluorophores with 'self-healing' properties. To date, utilization of such fluorophore derivatives is rare due to their elaborate multi-step synthesis. Here we present a general strategy to covalently link a synthetic organic fluorophore simultaneously to a photostabilizer and biomolecular target via unnatural amino acids. The modular approach uses commercially available starting materials and simple chemical transformations. The resulting photostabilizer-dye conjugates are based on rhodamines, carbopyronines and cyanines with excellent photophysical properties, that is, high photostability and minimal signal fluctuations. Their versatile use is demonstrated by single-step labelling of DNA, antibodies and proteins, as well as applications in single-molecule and super-resolution fluorescence microscopy. We are convinced that the presented scaffolding strategy and the improved characteristics of the conjugates in applications will trigger the broader use of intramolecular photostabilization and help to emerge this approach as a new gold standard. PMID:26751640

  15. Intramolecular symmetry-adapted perturbation theory with a single-determinant wavefunction.

    PubMed

    Pastorczak, Ewa; Prlj, Antonio; Gonthier, Jérôme F; Corminboeuf, Clémence

    2015-12-14

    We introduce an intramolecular energy decomposition scheme for analyzing non-covalent interactions within molecules in the spirit of symmetry-adapted perturbation theory (SAPT). The proposed intra-SAPT approach is based upon the Chemical Hamiltonian of Mayer [Int. J. Quantum Chem. 23(2), 341-363 (1983)] and the recently introduced zeroth-order wavefunction [J. F. Gonthier and C. Corminboeuf, J. Chem. Phys. 140(15), 154107 (2014)]. The scheme decomposes the interaction energy between weakly bound fragments located within the same molecule into physically meaningful components, i.e., electrostatic-exchange, induction, and dispersion. Here, we discuss the key steps of the approach and demonstrate that a single-determinant wavefunction can already deliver a detailed and insightful description of a wide range of intramolecular non-covalent phenomena such as hydrogen bonds, dihydrogen contacts, and π - π stacking interactions. Intra-SAPT is also used to shed the light on competing intra- and intermolecular interactions. PMID:26671358

  16. A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization

    NASA Astrophysics Data System (ADS)

    van der Velde, Jasper H. M.; Oelerich, Jens; Huang, Jingyi; Smit, Jochem H.; Aminian Jazi, Atieh; Galiani, Silvia; Kolmakov, Kirill; Guoridis, Giorgos; Eggeling, Christian; Herrmann, Andreas; Roelfes, Gerard; Cordes, Thorben

    2016-01-01

    Intramolecular photostabilization via triple-state quenching was recently revived as a tool to impart synthetic organic fluorophores with `self-healing' properties. To date, utilization of such fluorophore derivatives is rare due to their elaborate multi-step synthesis. Here we present a general strategy to covalently link a synthetic organic fluorophore simultaneously to a photostabilizer and biomolecular target via unnatural amino acids. The modular approach uses commercially available starting materials and simple chemical transformations. The resulting photostabilizer-dye conjugates are based on rhodamines, carbopyronines and cyanines with excellent photophysical properties, that is, high photostability and minimal signal fluctuations. Their versatile use is demonstrated by single-step labelling of DNA, antibodies and proteins, as well as applications in single-molecule and super-resolution fluorescence microscopy. We are convinced that the presented scaffolding strategy and the improved characteristics of the conjugates in applications will trigger the broader use of intramolecular photostabilization and help to emerge this approach as a new gold standard.

  17. ALG-2 activates the MVB sorting function of ALIX through relieving its intramolecular interaction

    PubMed Central

    Sun, Sheng; Zhou, Xi; Corvera, Joe; Gallick, Gary E; Lin, Sue-Hwa; Kuang, Jian

    2015-01-01

    The modular adaptor protein ALIX is critically involved in endosomal sorting complexes required for transport (ESCRT)-mediated multivesicular body (MVB) sorting of activated epidermal growth factor receptor (EGFR); however, ALIX contains a default intramolecular interaction that renders ALIX unable to perform this ESCRT function. The ALIX partner protein ALG-2 is a calcium-binding protein that belongs to the calmodulin superfamily. Prompted by a defined biological function of calmodulin, we determined the role of ALG-2 in regulating ALIX involvement in MVB sorting of activated EGFR. Our results show that calcium-dependent ALG-2 interaction with ALIX completely relieves the intramolecular interaction of ALIX and promotes CHMP4-dependent ALIX association with the membrane. EGFR activation induces increased ALG-2 interaction with ALIX, and this increased interaction is responsible for increased ALIX association with the membrane. Functionally, inhibition of ALIX activation by ALG-2 inhibits MVB sorting of activated EGFR as effectively as inhibition of ALIX interaction with CHMP4 does; however, inhibition of ALIX activation by ALG-2 does not affect cytokinetic abscission or equine infectious anemia virus (EIAV) budding. These findings indicate that calcium-dependent ALG-2 interaction with ALIX is specifically responsible for generating functional ALIX that supports MVB sorting of ubiquitinated membrane receptors.

  18. Computational study of the rate constants and free energies of intramolecular radical addition to substituted anilines

    PubMed Central

    Seddiqzai, Meriam; Dahmen, Tobias; Sure, Rebecca

    2013-01-01

    Summary The intramolecular radical addition to aniline derivatives was investigated by DFT calculations. The computational methods were benchmarked by comparing the calculated values of the rate constant for the 5-exo cyclization of the hexenyl radical with the experimental values. The dispersion-corrected PW6B95-D3 functional provided very good results with deviations for the free activation barrier compared to the experimental values of only about 0.5 kcal mol−1 and was therefore employed in further calculations. Corrections for intramolecular London dispersion and solvation effects in the quantum chemical treatment are essential to obtain consistent and accurate theoretical data. For the investigated radical addition reaction it turned out that the polarity of the molecules is important and that a combination of electrophilic radicals with preferably nucleophilic arenes results in the highest rate constants. This is opposite to the Minisci reaction where the radical acts as nucleophile and the arene as electrophile. The substitution at the N-atom of the aniline is crucial. Methyl substitution leads to slower addition than phenyl substitution. Carbamates as substituents are suitable only when the radical center is not too electrophilic. No correlations between free reaction barriers and energies (ΔG ‡ and ΔG R) are found. Addition reactions leading to indanes or dihydrobenzofurans are too slow to be useful synthetically. PMID:24062821

  19. Flow Cytometry Enables Multiplexed Measurements of Genetically Encoded Intramolecular FRET Sensors Suitable for Screening.

    PubMed

    Doucette, Jaimee; Zhao, Ziyan; Geyer, Rory J; Barra, Melanie M; Balunas, Marcy J; Zweifach, Adam

    2016-07-01

    Genetically encoded sensors based on intramolecular FRET between CFP and YFP are used extensively in cell biology research. Flow cytometry has been shown to offer a means to measure CFP-YFP FRET; we suspected it would provide a unique way to conduct multiplexed measurements from cells expressing different FRET sensors, which is difficult to do with microscopy, and that this could be used for screening. We confirmed that flow cytometry accurately measures FRET signals using cells transiently transfected with an ERK activity reporter, comparing responses measured with imaging and cytometry. We created polyclonal long-term transfectant lines, each expressing a different intramolecular FRET sensor, and devised a way to bar-code four distinct populations of cells. We demonstrated the feasibility of multiplexed measurements and determined that robust multiplexed measurements can be conducted in plate format. To validate the suitability of the method for screening, we measured responses from a plate of bacterial extracts that in unrelated experiments we had determined contained the protein kinase C (PKC)-activating compound teleocidin A-1. The multiplexed assay correctly identifying the teleocidin A-1-containing well. We propose that multiplexed cytometric FRET measurements will be useful for analyzing cellular function and for screening compound collections. PMID:26908592

  20. Multiwall nanotubes with intramolecular junctions (CNx/C): Preparation, rectification, logic gates, and application

    NASA Astrophysics Data System (ADS)

    Hu, Ping'an; Xiao, Kai; Liu, Yunqi; Yu, Gui; Wang, Xianbao; Fu, Lei; Cui, Guanglei; Zhu, Daoben

    2004-06-01

    We prepared a large quantity of multiwall nanotubes with intramolecular junctions (CNx/C) by pyrolysis of iron phthalocyanine with or without an inlet of ammonia gas. The nanotubes consist of two sections, one section made of carbon nitride featuring bamboo-like structure and the other one made of carbon featuring empty hollow cylinder structure, and thus the intramolecular junctions were formed in the middle as a result of being doped or undoped with nitrogen. Nanodiode based on a single CNx/C junction shows reproducible rectifying behavior with a rectification ratio of 1.3×103 at ±2 V. In addition, the nanodiode demonstrated as a half-wave rectifier worked at an input sine wave of 1 kHz. Two CNx/C junctions were configured together to exhibit functions of OR and AND logic gates. Moreover, after substituting the wave-detection silicon diode in common transistor radio set with our nanodiode, the radio set still worked normally, representing an important step toward the potential application for nano-scale devices.

  1. Aluminium-catalysed intramolecular hydroamination of aminoalkenes: computational perusal of alternative pathways for aminoalkene activation.

    PubMed

    Tobisch, Sven

    2015-07-21

    A comprehensive computational examination of alternatively plausible mechanistic pathways for the intramolecular hydroamination (HA) of aminoalkenes utilising a recently reported novel phenylene-diamine aluminium amido compound is presented. On the one hand, a proton-assisted concerted N-C/C-H bond-forming pathway to afford the cycloamine in a single step can be invoked, and, on the other, a stepwise σ-insertive pathway that involves a relatively fast, reversible migratory olefin 1,2-insertion step linked to a less rapid, irreversible Al-C alkyl bond protonolysis. The present study, which employs a sophisticated and reliable computational methodology, supports the prevailing mechanism to be a stepwise σ-insertive pathway. The predicted effective barrier for turnover-limiting aminolysis compares favourably with reported catalytic performance data. Non-competitive kinetic demands militates against the operation of the concerted proton-assisted pathway, which describes N-C bond-forming ring closure triggered by concomitant amino proton delivery at the C[double bond, length as m-dash]C linkage evolving through a six-centre transition state structure. The valuable insights into mechanistic intricacies of aluminium-mediated intramolecular HA reported herein will help guide the rational design of group 13 metal-based HA catalysts. PMID:25801632

  2. Solvent viscosity influence on the chemiexcitation efficiency of inter and intramolecular chemiluminescence systems.

    PubMed

    Khalid, Muhammad; Souza, Sergio P; Ciscato, Luiz F M L; Bartoloni, Fernando H; Baader, Wilhelm J

    2015-07-01

    The effects of the medium viscosity on the chemiexcitation quantum yields of the induced decomposition of 1,2-dioxetanes (highly efficient intramolecular CIEEL system) and the catalyzed decomposition of diphenoyl peroxide and a 1,2-dioxetanone derivative (model systems for the intermolecular CIEEL mechanism, despite their low efficiency) are compared in this work. Quantum yields of the rubrene catalyzed decomposition of diphenoyl peroxide and spiro-adamantyl-1,2-dioxetanone as well as the fluoride induced decomposition of a phenoxy-substituted 1,2-dioxetane derivative are shown to depend on the composition of the binary solvent mixture toluene/diphenyl ether, which possess similar polarity parameters but different viscosities. Correlations of the quantum yield data with the medium viscosity using the diffusional and the frictional (free-volume) models indicate that the induced 1,2-dioxetane decomposition indeed occurs by an entirely intramolecular process and the low efficiency of the intermolecular chemiluminescence systems (catalyzed decomposition of diphenoyl peroxide and 1,2-dioxetanone derivative) is not primarily due to the cage escape of radical ion species. PMID:26067192

  3. Intramolecular electron transfer in fullerene/ferrocene based donor-bridge-acceptor dyads

    SciTech Connect

    Guldi, D.M.; Maggini, M.; Scorrano, G.; Prato, M.

    1997-02-05

    A systematic steady-state fluorescence and time-resolved flash photolytic investigation of a series of covalently linked fullerene/ferrocene based donor-bridge-acceptor dyads is reported as a function of the nature of the spacer between the donor site (ferrocene) and acceptor site (fullerene) and the dielectric constant of the medium. The fluorescence of the investigated dyads 2, 3, 4, 5, and 6 in methylcyclohexane at 77 K were substantially quenched, relative to N-methylfulleropyrrolidine 1, indicating intramolecular quenching of the fullerene excited singlet state. Excitation of N-methylfulleropyrrolidine revealed the immediate formation of the excited singlet state, with {lambda}{sub max} around 886 nm. A rapid intersystem crossing ({tau}{sub 1/2} = 1.2 ps ) to the excited triplet state was observed with characteristic absorption around 705 nm. Picosecond resolved photolysis of dyads 2-6 in toluene showed light-induced formation of the excited singlet state which undergoes rapid intramolecular quenching. Nanosecond-resolved photolysis of dyads 3 and 4 in degassed benzonitrile revealed long-lived charge separated states with characteristic fullerene radical-anion bands at {lambda}{sub max} = 1055 nm. 30 refs., 5 figs., 3 tabs.

  4. Intramolecular proton transfer and tunnelling reactions of hydroxyphenylbenzoxazole derivatives in Xenon at 15 K

    NASA Astrophysics Data System (ADS)

    Walla, Peter J.; Nickel, Bernhard

    2005-06-01

    We investigated the site dependence and the tunnelling processes of the intramolecular proton and deuteron transfer in the triplet state of the compounds 2-(2‧-hydroxy-4‧-methylphenyl)benzoxazole (m-MeHBO) and 2-(2‧-hydroxy-3‧-methylphenyl)benzoxazoles (o-MeHBO) and their deuterio-oxy analogues in a solid xenon matrix. After singlet excitation there occurs an ultrafast intramolecular enol → keto proton transfer and subsequent intersystem crossing mainly to the keto triplet state. In the triplet state of m-MeHBO, the proton transfer back to the lower enol triplet state is governed by tunnelling processes. In o-MeHBO, however, the enol triplet state is higher and therefore normally no tunnel reaction can be observed. Because of the external heavy atom-effect in a xenon matrix, we were able to investigate the reverse enol-keto-tunnelling after exciting directly the enol triplet state of deuterated o-MeHBO. The time constants of the reverse enol-keto tautomerization are similar to those of the normal keto-enol tautomerization. In a xenon matrix, the observed site-selective phosphorescence spectra are very well-resolved vibrationally. This allowed the study of the tunnel rates in different well-defined sites. The vibrational energies obtained in the spectra are in good agreement with vibrational energies found in resonant Raman and IR spectra of 2-(2‧-hydroxyphenyl)benzoxazole (HBO).

  5. How To Reach Intense Luminescence for Compounds Capable of Excited-State Intramolecular Proton Transfer?

    PubMed

    Skonieczny, Kamil; Yoo, Jaeduk; Larsen, Jillian M; Espinoza, Eli M; Barbasiewicz, Michał; Vullev, Valentine I; Lee, Chang-Hee; Gryko, Daniel T

    2016-05-23

    Photoinduced intramolecular direct arylation allows structurally unique compounds containing phenanthro[9',10':4,5]imidazo[1,2-f]phenanthridine and imidazo[1,2-f]phenanthridine skeletons, which mediate excited-state intramolecular proton transfer (ESIPT), to be efficiently synthesized. The developed polycyclic aromatics demonstrate that the combination of five-membered ring structures with a rigid arrangement between a proton donor and a proton acceptor provides a means for attaining large fluorescence quantum yields, exceeding 0.5, even in protic solvents. Steady-state and time-resolved UV/Vis spectroscopy reveals that, upon photoexcitation, the prepared protic heteroaromatics undergo ESIPT, converting them efficiently into their excited-state keto tautomers, which have lifetimes ranging from about 5 to 10 ns. The rigidity of their structures, which suppresses nonradiative decay pathways, is believed to be the underlying reason for the nanosecond lifetimes of these singlet excited states and the observed high fluorescence quantum yields. Hydrogen bonding with protic solvents does not interfere with the excited-state dynamics and, as a result, there is no difference between the occurrences of ESIPT processes in MeOH versus cyclohexane. Acidic media has a more dramatic effect on suppressing ESIPT by protonating the proton acceptor. As a result, in the presence of an acid, a larger proportion of the fluorescence of ESIPT-capable compounds originates from their enol excited states. PMID:27062363

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

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

  7. Computational study of the rate constants and free energies of intramolecular radical addition to substituted anilines.

    PubMed

    Gansäuer, Andreas; Seddiqzai, Meriam; Dahmen, Tobias; Sure, Rebecca; Grimme, Stefan

    2013-01-01

    The intramolecular radical addition to aniline derivatives was investigated by DFT calculations. The computational methods were benchmarked by comparing the calculated values of the rate constant for the 5-exo cyclization of the hexenyl radical with the experimental values. The dispersion-corrected PW6B95-D3 functional provided very good results with deviations for the free activation barrier compared to the experimental values of only about 0.5 kcal mol(-1) and was therefore employed in further calculations. Corrections for intramolecular London dispersion and solvation effects in the quantum chemical treatment are essential to obtain consistent and accurate theoretical data. For the investigated radical addition reaction it turned out that the polarity of the molecules is important and that a combination of electrophilic radicals with preferably nucleophilic arenes results in the highest rate constants. This is opposite to the Minisci reaction where the radical acts as nucleophile and the arene as electrophile. The substitution at the N-atom of the aniline is crucial. Methyl substitution leads to slower addition than phenyl substitution. Carbamates as substituents are suitable only when the radical center is not too electrophilic. No correlations between free reaction barriers and energies (ΔG (‡) and ΔG R) are found. Addition reactions leading to indanes or dihydrobenzofurans are too slow to be useful synthetically. PMID:24062821

  8. IS1-mediated intramolecular rearrangements: formation of excised transposon circles and replicative deletions.

    PubMed Central

    Turlan, C; Chandler, M

    1995-01-01

    A system is described which permits visualization and analysis of a number of molecular species associated with transposition activity of the bacterial insertion sequence, IS1, in vivo. The technique involves induction of an IS1 transposase gene carried by a plasmid which also includes an IS1-based transposable element. It is, in principle, applicable to the identification of transposition intermediates as well as unstable transposition products and those which are not detectable by genetic means. Thirteen novel molecular species were detected after 4 h of induction. Five major species were characterized, based on their behaviour as a function of time, on their hybridization patterns and on the nucleotide sequences of the transposon-backbone junctions. All result from intramolecular IS1 transposition events. The two reciprocal partner products of IS1-mediated deletions, the intramolecular equivalent of co-integrates generated by intermolecular transposition, have been identified. Both carry a single copy of the transposable element and present complementary distributions of deletion endpoints. These results establish, by direct physical means, that adjacent IS1-mediated deletions are accompanied by duplication of the element. A second type of molecule identified was an excised circular copy of the transposon, raising the possibility that IS1 is capable of following an intermolecular transposition pathway, via excised transposon circles, leading to direct insertion. Images PMID:7489730

  9. The role of intramolecular self-destruction of reactive metabolic intermediates in determining toxicity.

    PubMed

    Svennebring, Andreas

    2016-04-01

    When reactive centers are formed in chemical conversions, intermolecular reactions tend to dominate over intramolecular alternatives whenever both alternatives are possible. Hence, when reactive metabolites are formed from xenobiotics, intramolecular quenching by moieties adjacent to a toxicophore may play an important role in reducing toxicity related to reactive intermediates. The phenomenon is likely to be particularly noticeable for toxicophores that are readily associated with a type of toxicity that is rarely caused by other structural motives. In two demonstrative investigations, it is concluded that nitrobenzenes for which the expected nitrosyl metabolite is likely to react with adjacent groups are less toxic than what is rationally expected, and that among aryl amine drugs allowing for the immediate quenching of the corresponding N-aryl hydroxylamine metabolite, the typical erythrocyte toxicity often seen with aryl amines is absent. The deliberate introduction of effective quenching groups nearby a toxicophoric moiety may present a potential strategy for reducing toxicity in the design of drugs and other man-made xenobiotics. PMID:26542997

  10. Characteristics of Intramolecular Charge Transfer by J-Aggregates in Merocyanine Dye LB Films.

    PubMed

    Yang, Chang Heon; Kwon, Young-Soo; Shin, Hoon-Kyu

    2016-06-01

    In this study, for the development of future molecular electronic devices, we have investigated the characteristics of the aggregates of Langmuir-Blodgett films. The characteristics of intramolecular charge transfer by J-aggregates in merocyanine dye LB films have been studied experimentally by using UV irradiation and heat treatment. In addition to intramolecular charge transfer, we also studied the conjugation and energy changes of the molecules. In case a dye is thinned by LB method, the alkyl chain is often displaced in order to form a mono-molecular film with ease. Since the molecular association form is often made by self-organization of molecules themselves, in case the dye and the alkyl chain are strongly bonded by the covalent bond, it may be said that the properties of the LB film to be built up are almost determined at the time of synthesis of film-forming molecules. Meanwhile, since, in case LB film is fabricated by the diffusion absorption method, the cohesive force between the water-soluble dye and the surface-active mono-molecular film is electrostatic, the dye molecule can move relatively freely on the air/water interface, which may be regarded as a two-dimensional crystal growth process. PMID:27427711

  11. Rate of intramolecular reduction of oxyferryl iron in horse heart myoglobin

    SciTech Connect

    Fenwick, C.; Marmor, S.; Govindaraju, K.; English, A.M. ); Wishart, J.F.; Sun, J. )

    1994-04-06

    Like heme peroxidases and other heme enzymes, myoglobin forms oxyferryl (Fe[sup IV][triple bond]O) on reaction with peroxides. We have recently observed slow intramolecular electron transfer (ET) to the oxyferryl heme of cytochrome c peroxidase (CCP) from a[sub 5]Ru[sup II] (a[sub 5]Ru = pentaammineruthenium) bound at His60 and proposed a large reorganizational energy ([lambda]) for oxyferryl heme. An obvious test of this large postulated [lambda] is to directly compare intramolecular ET rates between oxyferryl and a[sub 5]Ru centers in myoglobin with the corresponding rates in zinc-substituted sperm whale (SWMb) and recombinant human myoglobins (RHMb). Since the oxyferryl heme of horse heart myoglobin (HHMb) is significantly more stable than that of SWMb, the former protein was chosen for this study. A a[sub 5]Ru group was attached to the surface His48 of HHMb, and rates of ET over the 12.7-angstrom distance between the a[sub 5]Ru center and the ferric and oxyferryl hemes were measured by pulse radiolysis at Brookhaven National Laboratory. HHMb (0.5-10 [mu]M) solutions were prepared in N[sub 2]O-saturated sodium phosphate buffer at pH 7.0 (40 mM) containing 12 mM HCOONa to generate CO[sub 2][sup .[minus

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

    SciTech Connect

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

    2013-11-28

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

  13. Intramolecular cyclopropanation and C-H insertion reactions with metal carbenoids generated from cyclopropenes.

    PubMed

    Archambeau, Alexis; Miege, Frédéric; Meyer, Christophe; Cossy, Janine

    2015-04-21

    Activation of unsaturated carbon-carbon bonds by means of transition metal catalysts is an exceptionally active research field in organic synthesis. In this context, due to their high ring strain, cyclopropenes constitute an interesting class of substrates that displays a versatile reactivity in the presence of transition metal catalysts. Metal complexes of vinyl carbenes are involved as key intermediates in a wide variety of transition metal-catalyzed ring-opening reactions of cyclopropenes. Most of the reported transformations rely on intermolecular or intramolecular addition of nucleophiles to these latter reactive species. This Account focuses specifically on the reactivity of carbenoids resulting from the ring-opening of cyclopropenes in cyclopropanation and C-H insertion reactions, which are arguably two of the most representative transformations of metal complexes of carbenes. Compared with the more conventional α-diazo carbonyl compounds, the use of cyclopropenes as precursors of metal carbenoids in intramolecular cyclopropanation or C-H insertion reactions has been largely underexploited. One of the challenges is to devise appropriately substituted and readily available cyclopropenes that would not only undergo regioselective ring-opening under mild conditions but also trigger the subsequent desired transformations with a high level of chemoselectivity and stereoselectivity. These goals were met by considering several substrates derived from the readily available 3,3-dimethylcyclopropenylcarbinols or 3,3-dimethylcyclopropenylcarbinyl amines. In the case of 1,6-cyclopropene-enes, highly efficient and diastereoselective gold(I)-catalyzed ring-opening/intramolecular cyclopropanations were developed as a route to diversely substituted heterocycles and carbocycles possessing a bicyclo[4.1.0]heptane framework. The use of rhodium(II) catalysts enabled us to widen the scope of this transformation for the synthesis of medium-sized heterocyclic scaffolds

  14. Medium-Ring Effects on the Endo/Exo Selectivity of the Organocatalytic Intramolecular Diels-Alder Reaction.

    PubMed

    Hooper, Joel F; James, Natalie C; Bozkurt, Esra; Aviyente, Viktorya; White, Jonathan M; Holland, Mareike C; Gilmour, Ryan; Holmes, Andrew B; Houk, K N

    2015-12-18

    The intramolecular Diels-Alder reaction has been used as a powerful method to access the tricyclic core of the eunicellin natural products from a number of 9-membered-ring precursors. The endo/exo selectivity of this reaction can be controlled through a remarkable organocatalytic approach, employing MacMillan's imidazolidinone catalysts, although the mechanistic origin of this selectivity remains unclear. We present a combined experimental and density functional theory investigation, providing insight into the effects of medium-ring constraints on the organocatalyzed intramolecular Diels-Alder reaction to form the isobenzofuran core of the eunicellins. PMID:26560246

  15. Intramolecular Conjugate Ene Reaction of γ-Difluoromethyl- and γ-Trifluoromethyl-α,β-Unsaturated γ-Butyrolactones.

    PubMed

    Srimontree, Watchara; Masusai, Chonticha; Soorukram, Darunee; Kuhakarn, Chutima; Reutrakul, Vichai; Pohmakotr, Manat

    2015-11-01

    A general synthetic strategy to cis-fused bicyclic γ-butyrolactones via the retro-Diels-Alder reaction/intramolecular conjugate ene cascade (RDA/ICE) reaction under the flash-vacuum pyrolysis of maleic anhydride adducts is developed. The reaction gave high yields of products with high stereoselectivity. The existence of the difluoromethyl or trifluoromethyl group at the γ-position of the in situ-generated homoalkenyl- or homoalkynyl-α,β-unsaturated γ-butyrolactones was found to accelerate the rate of the intramolecular conjugate ene reaction leading to γ-difluoromethylated and γ-trifluoromethylated cis-fused bicyclic γ-butyrolactones. PMID:26417837

  16. Regulation of ASPP2 Interaction with p53 Core Domain by an Intramolecular Autoinhibitory Mechanism

    PubMed Central

    Rotem-Bamberger, Shahar; Katz, Chen; Friedler, Assaf

    2013-01-01

    ASPP2 is a key protein in regulating apoptosis both in p53-dependent and-independent pathways. The C-terminal part of ASPP2 contains four ankyrin repeats and an SH3 domain (Ank-SH3) that mediate the interactions of ASPP2 with apoptosis related proteins such as p53, Bcl-2 and the p65 subunit of NFκB. p53 core domain (p53CD) binds the n-src loop and the RT loop of ASPP2 SH3. ASPP2 contains a disordered proline rich domain (ASPP2 Pro) that forms an intramolecular autoinhibitory interaction with the Ank-SH3 domains. Here we show how this intramolecular interaction affects the intermolecular interactions of ASPP2 with p53, Bcl-2 and NFkB. We used biophysical methods to obtain better understanding of the relationship between ASPP2 and its partners for getting a comprehensive view on ASPP2 pathways. Fluorescence anisotropy competition experiments revealed that both ASPP2 Pro and p53CD competed for binding the n-src loop of the ASPP2 SH3, indicating regulation of p53CD binding to this loop by ASPP2 Pro. Peptides derived from the ASPP2-binding interface of Bcl-2 did not compete with p53CD or NFkB peptides for binding the ASPP2 n-src loop. However, p53CD displaced the NFκB peptide (residues 303–332) from its complex with ASPP2 Ank-SH3, indicating that NFκB 303–332 and p53CD bind a partly overlapping site in ASPP2 SH3, mostly in the RT loop. These results are in agreement with previous docking studies, which showed that ASPP2 Ank-SH3 binds Bcl-2 and NFκB mostly via distinct sites from p53. However they show some overlap between the binding sites of p53CD and NFkB in ASPP2 Ank-SH3. Our results provide experimental evidence that the intramolecular interaction in ASPP2 regulates its binding to p53CD and that ASPP2 Ank-SH3 binds Bcl-2 and NFκB via distinct sites. PMID:23472201

  17. Computational mechanistic elucidation of the intramolecular aminoalkene hydroamination catalysed by iminoanilide alkaline-earth compounds.

    PubMed

    Tobisch, Sven

    2015-04-27

    A comprehensive computational exploration of plausible alternative mechanistic pathways for the intramolecular hydroamination (HA) of aminoalkenes by a recently reported class of kinetically stabilised iminoanilide alkaline-earth silylamido compounds [{N^N}Ae{N(SiMe3)2}⋅(thf)n] ({N^N} = iminoanilide; Ae = Ca, Sr, Ba) is presented. On the one hand, a proton-assisted concerted N-C/C-H bond-forming pathway to afford the cycloamine in a single step can be invoked and on the other hand, a stepwise σ-insertive pathway that involves a fast, reversible migratory olefin 1,2-insertion step linked to a less rapid, irreversible metal-C azacycle tether σ-bond aminolysis. Notably, these alternative mechanistic avenues are equally consistent with reported key experimental features. The present study, which employs a thoroughly benchmarked and reliable DFT methodology, supports the prevailing mechanism to be a stepwise σ-insertive pathway that sees an initial conversion of the {N^N}Ae silylamido into the catalytically competent {N^N}Ae amidoalkene compound and involves thereafter facile and reversible insertive N-C bond-forming ring closure, linked to irreversible intramolecular Ae-C tether σ-bond aminolysis at the transient {N^N}Ae alkyl intermediate. Turnover-limiting protonolysis accounts for the substantial primary kinetic isotope effect observed; its DFT-derived barrier satisfactorily matches the empirically determined Eyring parameter and predicts the decrease in rate observed across the series Ca>Sr>Ba correctly. Non-competitive kinetic demands militate against the operation of the concerted proton-assisted pathway, which describes N-C bond-forming ring closure triggered by concomitant amino proton delivery at the C=C linkage evolving through a multi-centre TS structure. Valuable insights into the catalytic structure-activity relationships are unveiled by a detailed comparison of [{N^N}Ae(NHR)] catalysts. Moreover, the intriguingly opposite trends in reactivity

  18. Palladium-Catalyzed Synthesis of Phenanthridine/Benzoxazine-Fused Quinazolinones by Intramolecular C-H Bond Activation.

    PubMed

    Gupta, Puneet K; Yadav, Nisha; Jaiswal, Subodh; Asad, Mohd; Kant, Ruchir; Hajela, Kanchan

    2015-09-14

    A highly efficient synthesis of phenanthridine/benzoxazine-fused quinazolinones by ligand-free palladium-catalyzed intramolecular C-H bond activation under mild conditions has been developed. The C-C coupling provides the corresponding N-fused polycyclic heterocycles in good to excellent yields and with wide functional group tolerance. PMID:26230355

  19. Do fluorescence and transient absorption probe the same intramolecular charge transfer state of 4-(dimethylamino)benzonitrile?

    SciTech Connect

    Gustavsson, Thomas; Fujiwara, Takashige; Lim, Edward C.

    2009-07-21

    We present here the results of time-resolved absorption and emission experiments for 4-(dimethylamino)benzonitrile in solution, which suggest that the fluorescent intramolecular charge transfer (ICT) state may differ from the twisted ICT (TICT) state observed in transient absorption.

  20. Intramolecular 1,3-dipolar cycloaddition reactions in the synthesis of complex annelated quinolines, α-carbolines and coumarins.

    PubMed

    Majumder, Swarup; Borah, Pallabi; Bhuyan, Pulak J

    2012-05-01

    In this study, we report the synthesis of several novel dihydroisoxazole-, tetrahydroisoxazole- and dihydropyrazole-fused pyrido[2,3-b]quinolines, α-carbolines, and pyrido[2,3-c]coumarins, respectively, from simple precursors and by exploring intramolecular 1,3-dipolar cycloaddition reactions involving nitrile oxides, nitrones, and nitrile imines as 1,3-dipoles. PMID:22374452

  1. Organocatalytic Synthesis of Fused Bicyclic 2,3-Dihydro-1,3,4-oxadiazoles through an Intramolecular Cascade Cyclization.

    PubMed

    Fugard, Alison J; Thompson, Bethany K; Slawin, Alexandra M Z; Taylor, James E; Smith, Andrew D

    2015-12-01

    Hydrazone-carboxylic acids undergo intramolecular cyclization in the presence of pivaloyl chloride, iPr(2)NEt, and catalytic DABCO to form a range of substituted fused tricyclic 2,3-dihydro-1,3,4-oxadiazoles in high yields. PMID:26598296

  2. Brønsted acid cocatalysis in photocatalytic intramolecular coupling of tertiary amines: efficient synthesis of 2-arylindols.

    PubMed

    Yuan, Xiaoqian; Wu, Xinxin; Dong, Shupeng; Wu, Guibing; Ye, Jinxing

    2016-08-21

    We report herein a highly efficient intramolecular coupling reaction of tertiary amines and ketones (α,β-unsaturated ketones) by using a Brønsted acid as a cocatalyst, affording 2-arylindols in good to excellent yields (up to 92%) under visible light irradiation at room temperature. PMID:27431277

  3. Asymmetric Synthesis of (-)-Incarvillateine Employing an Intramolecular Alkylation via Rh-Catalyzed Olefinic C-H Bond Activation

    SciTech Connect

    Tsai, Andy; Bergman, Robert; Ellman, Jonathan

    2008-02-18

    An asymmetric total synthesis of (-)-incarvillateine, a natural product having potent analgesic properties, has been achieved in 11 steps and 15.4% overall yield. The key step is a rhodium-catalyzed intramolecular alkylation of an olefinic C-H bond to set two stereocenters. Additionally, this transformation produces an exocyclic, tetrasubstituted alkene through which the bicyclic piperidine moiety can readily be accessed.

  4. Visible Light-Induced Radical Rearrangement to Construct C-C Bonds via an Intramolecular Aryl Migration/Desulfonylation Process.

    PubMed

    Li, Yuyuan; Hu, Bei; Dong, Wuheng; Xie, Xiaomin; Wan, Jun; Zhang, Zhaoguo

    2016-08-19

    A highly efficient intramolecular selective aryl migration/desulfonylation of 2-bromo-N-aryl-N-(arenesulfonyl)amide via visible light-induced photoredox catalysis has been accomplished. This approach allows for the construction of a variety of multisubstituted N,2-diarylacetamide under mild reaction conditions. PMID:27351977

  5. Palladium-catalyzed regioselective intramolecular coupling of o-carborane with aromatics via direct cage B-H activation.

    PubMed

    Quan, Yangjian; Xie, Zuowei

    2015-03-18

    Palladium-catalyzed intramolecular coupling of o-carborane with aromatics via direct cage B-H bond activation has been achieved, leading to the synthesis of a series of o-carborane-functionalized aromatics in high yields with excellent regioselectivity. In addition, the site selectivity can also be tuned by the substituents on cage carbon atom. PMID:25747772

  6. Application of an intramolecular dipolar cycloaddition to an asymmetric synthesis of the fully oxygenated tricyclic core of the stemofoline alkaloids

    PubMed Central

    Carra, Ryan J.; Epperson, Matthew T.; Gin, David Y.

    2008-01-01

    An intramolecular non-stabilized azomethine ylide dipolar cycloaddition was applied toward the first non-racemic synthesis of the fully-oxygenated bridged pyrrolizidine core (45) of (+)-stemofoline (1) in eleven steps from a commercially available starting material. PMID:18443655

  7. Enantioselective Intramolecular C-H Insertion of Donor and Donor/Donor Carbenes by a Nondiazo Approach.

    PubMed

    Zhu, Dong; Ma, Jun; Luo, Kui; Fu, Hongguang; Zhang, Li; Zhu, Shifa

    2016-07-11

    The first enantioselective intramolecular C-H insertion and cyclopropanation reactions of donor- and donor/donor-carbenes by a nondiazo approach are reported. The reactions were conducted in a one-pot manner without slow addition and provided the desired dihydroindole, dihydrobenzofuran, tetrahydrofuran, and tetrahydropyrrole derivatives with up to 99 % ee and 100 % atom efficiency. PMID:27265896

  8. The role of the angle of pretwist of some molecules forming twisted intramolecular charge transfer (TICT) states in polymer matrices

    NASA Astrophysics Data System (ADS)

    Al-Hassan, Khader A.; Azumi, Tohru; Rettig, Wolfgang

    1993-04-01

    It is shown that the relative intensity of the twisted intramolecular charge transfer band of ester and benzonitrile derivatives of dialkylaniline in non-hydrogen-bonding polymers increases with increasing size of the donor (dialkylamino) group and is sensitive to both the local polarity and local free volume of polymer sites.

  9. Enhancement of chemical stability and crystallinity in porphyrin-containing covalent organic frameworks by intramolecular hydrogen bonds.

    PubMed

    Kandambeth, Sharath; Shinde, Digambar Balaji; Panda, Manas K; Lukose, Binit; Heine, Thomas; Banerjee, Rahul

    2013-12-01

    A strong bond: A strategy based on intramolecular hydrogen-binding interactions in 2D covalent organic frameworks (COFs) is shown to improve the crystallinity, porosity, and chemical stability of the material. The concept is validated by removing the hydrogen-bonding interaction in the methoxy analog which showed a lower stability and crystallinity. PMID:24127339

  10. Functional analysis of propeptide as an intramolecular chaperone for in vivo folding of subtilisin nattokinase.

    PubMed

    Jia, Yan; Liu, Hui; Bao, Wei; Weng, Meizhi; Chen, Wei; Cai, Yongjun; Zheng, Zhongliang; Zou, Guolin

    2010-12-01

    Here, we show that during in vivo folding of the precursor, the propeptide of subtilisin nattokinase functions as an intramolecular chaperone (IMC) that organises the in vivo folding of the subtilisin domain. Two residues belonging to β-strands formed by conserved regions of the IMC are crucial for the folding of the subtilisin domain through direct interactions. An identical protease can fold into different conformations in vivo due to the action of a mutated IMC, resulting in different kinetic parameters. Some interfacial changes involving conserved regions, even those induced by the subtilisin domain, blocked subtilisin folding and altered its conformation. Insight into the interaction between the subtilisin and IMC domains is provided by a three-dimensional structural model. PMID:21074529

  11. Intramolecular charge ordering in the multi molecular orbital system (TTM-TTP)I3

    NASA Astrophysics Data System (ADS)

    Bonnet, Marie-Laure; Robert, Vincent; Tsuchiizu, Masahisa; Omori, Yukiko; Suzumura, Yoshikazu

    2010-06-01

    Starting from the structure of the (TTM-TTP)I3 molecular-based material, we examine the characteristics of frontier molecular orbitals using ab initio (CASSCF/CASPT2) configurations interaction calculations. It is shown that the singly occupied and second-highest-occupied molecular orbitals are close to each other, i.e., this compound should be regarded as a two-orbital system. By dividing virtually the [TTM-TTP] molecule into three fragments, an effective model is constructed to rationalize the origin of this picture. In order to investigate the low-temperature, symmetry breaking experimentally observed in the crystal, the electronic distribution in a pair of [TTM-TTP] molecules is analyzed from CASPT2 calculations. Our inspection supports and explains the speculated intramolecular charge ordering which is likely to give rise to low-energy magnetic properties.

  12. All intermediates of the arsenate reductase mechanism, including an intramolecular dynamic disulfide cascade

    PubMed Central

    Messens, Joris; Martins, José C.; Van Belle, Karolien; Brosens, Elke; Desmyter, Aline; De Gieter, Marjan; Wieruszeski, Jean-Michel; Willem, Rudolph; Wyns, Lode; Zegers, Ingrid

    2002-01-01

    The mechanism of pI258 arsenate reductase (ArsC) catalyzed arsenate reduction, involving its P-loop structural motif and three redox active cysteines, has been unraveled. All essential intermediates are visualized with x-ray crystallography, and NMR is used to map dynamic regions in a key disulfide intermediate. Steady-state kinetics of ArsC mutants gives a view of the crucial residues for catalysis. ArsC combines a phosphatase-like nucleophilic displacement reaction with a unique intramolecular disulfide bond cascade. Within this cascade, the formation of a disulfide bond triggers a reversible “conformational switch” that transfers the oxidative equivalents to the surface of the protein, while releasing the reduced substrate. PMID:12072565

  13. Detailed theoretical investigation of excited-state intramolecular proton transfer mechanism of a new chromophore II

    NASA Astrophysics Data System (ADS)

    Cui, Yanling; Li, Yafei; Dai, Yumei; Verpoort, Francis; Song, Peng; Xia, Lixin

    2016-02-01

    In the present work, TDDFT has been used to investigate the excited state intramolecular proton transfer (ESIPT) mechanism of a new chromophore II [Sensors and Actuators B: Chemical. 202 (2014) 1190]. The calculated absorption and fluorescence spectra agree well with experimental results. In addition, two types of II configurations are found in the first excited state (S1), which can be ascribed to the ESIPT reaction. Based on analysis of the calculated infrared (IR) spectra of O-H stretching vibration as well as the hydrogen bonding energies, the strengthening of the hydrogen bond in the S1 state has been confirmed. The frontier molecular orbitals (MOs), Hirshfeld charge distribution and the Natural bond orbital (NBO) have also been analyzed, which displays the tendency of the ESIPT process. Finally, potential energy curves of the S0 and S1 states were constructed, demonstrating that the ESIPT reaction can be facilitated based on the photo-excitation.

  14. Intramolecular hydrogen bonds: ab initio Car Parrinello simulations of arylamide torsions

    NASA Astrophysics Data System (ADS)

    Doerksen, Robert J.; Chen, Bin; Klein, Michael L.

    2003-10-01

    Gas-phase, room temperature Car-Parrinello molecular dynamics simulations using the HCTH density functional are reported for the arylamides acetanilide ( 1) and ortho-methylthioacetanilide ( 2). The simulations show that in 1, rotation around the ring-amide bond is relatively unrestricted. By contrast, in 2 the methylthio side chain encourages the amide to be directed with N-H pointing toward S, not to flip by 360°, and furthermore to remain close to coplanar with the benzene ring. Because of an intramolecular N-H⋯S hydrogen bond, the N-H stretch frequency of 2 is red-shifted by ˜78 cm -1 compared to that of 1.

  15. Uncovering Intramolecular π-Type Hydrogen Bonds in Solution by NMR Spectroscopy and DFT Calculations.

    PubMed

    Mastrorilli, Piero; Gallo, Vito; Todisco, Stefano; Latronico, Mario; Saielli, Giacomo

    2016-06-01

    Reaction between the phosphinito bridged diplatinum species [(PHCy2 )Pt(μ-PCy2 ){κ(2) P,O-μ-P(O)Cy2 }Pt(PHCy2 )](Pt-Pt) (1), and (trimethylsilyl)acetylene at 273 K affords the σ-acetylide complex [(PHCy2 )(η(1) -Me3 SiC≡C)Pt(μ-PCy2 )Pt(PHCy2 ){κP-P(OH)Cy2 }](Pt-Pt) (2) featuring an intramolecular π-type hydrogen bond. Scalar and dipolar couplings involving the POH proton were detected by 2D NMR experiments. Relativistic DFT calculations of the geometry, relative energy, and NMR properties of model systems of 2 confirmed the structural assignment and allowed the energy of the π-type hydrogen bond to be estimated (ca. 22 kJ mol(-1) ). PMID:27097847

  16. 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.

  17. Intramolecular vibrational redistribution of CH 2I 2 dissolved in supercritical Xe

    NASA Astrophysics Data System (ADS)

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

    2003-03-01

    Intramolecular vibrational energy redistribution (IVR) of CH 2I 2 in supercritical Xe has been studied. The first overtone of the C-H stretching mode was excited with a near infrared laser pulse and the transient UV absorption near 390 nm was monitored. Signals showed a rise and decay profile, which gave the IVR and VET (intermolecular vibrational energy transfer) rates, respectively. Solvent density dependence of each rate was obtained by tuning the pressure at a constant temperature. The IVR rate in supercritical Xe increased with increasing solvent density and asymptotically reached a limiting value. This result suggests that the IVR process of CH 2I 2 in condensed phase is a solvent-assisted process.

  18. Vibrational Signatures of Conformer-Specific Intramolecular Interactions in Protonated Tryptophan.

    PubMed

    Pereverzev, Aleksandr Y; Cheng, Xiaolu; Nagornova, Natalia S; Reese, Diana L; Steele, Ryan P; Boyarkin, Oleg V

    2016-07-21

    Because of both experimental and computational challenges, protonated tryptophan has remained the last aromatic amino acid for which the intrinsic structures of low-energy conformers have not been unambiguously solved. The IR-IR-UV hole-burning spectroscopy technique has been applied to overcome the limitations of the commonly used IR-UV double resonance technique and to measure conformer-specific vibrational spectra of TrpH(+), cooled to T = 10 K. Anharmonic ab initio vibrational spectroscopy simulations unambiguously assign the dominant conformers to the two lowest-energy geometries from benchmark coupled-cluster structure computations. The match between experimental and ab initio spectra provides an unbiased validation of the calculated structures of the two experimentally observed conformers of this benchmark ion. Furthermore, the vibrational spectra provide conformer-specific signatures of the stabilizing interactions, including hydrogen bonding and an intramolecular cation-π interaction. PMID:27351636

  19. Intramolecular charge transfer of push-pull pyridinium salts in the singlet manifold.

    PubMed

    Carlotti, Benedetta; Consiglio, Giuseppe; Elisei, Fausto; Fortuna, Cosimo G; Mazzucato, Ugo; Spalletti, Anna

    2014-05-22

    The solvent effect on the photophysical and photochemical properties of the iodides of three trans (E) isomers of 2-D-vinyl,1-methylpyridinium, where D is a donor group (4-dimethylaminophenyl, 3,4,5-trimethoxyphenyl and 1-pyrenyl), was studied by stationary and transient absorption techniques. The results obtained allowed the negative solvatochromism and relaxation pathways of the excited states in the singlet manifold to be reasonably interpreted. Resorting to ultrafast absorption techniques and DFT calculations allowed information on the excited state dynamics and the role of the solvent-controlled intramolecular charge transfer (ICT) processes to be obtained. The structure-dependent excited state dynamics in nonpolar solvents, where the ICT is slower than solvent rearrangement, and in polar solvents, where an opposite situation is operative, was thus explained. The push-pull character of the three compounds, particularly the anilino-derivative, suggests their potential application in optoelectronics. PMID:24779555

  20. High Yield Ultrafast Intramolecular Singlet Exciton Fission in a Quinoidal Bithiophene.

    PubMed

    Varnavski, Oleg; Abeyasinghe, Neranga; Aragó, Juan; Serrano-Pérez, Juan J; Ortí, Enrique; López Navarrete, Juan T; Takimiya, Kazuo; Casanova, David; Casado, Juan; Goodson, Theodore

    2015-04-16

    We report the process of singlet exciton fission with high-yield upon photoexcitation of a quinoidal thiophene molecule. Efficient ultrafast triplet photogeneration and its yield are determined by photoinduced triplet-triplet absorption, flash photolysis triplet lifetime measurements, as well as by femtosecond time-resolved transient absorption and fluorescence methods. These experiments show that optically excited quinoidal bithiophene molecule undergoes ultrafast formation of the triplet-like state with the lifetime ∼57 μs. CASPT2 and RAS-SF calculations have been performed to support the experimental findings. To date, high singlet fission rates have been reported for crystalline and polycrystalline materials, whereas for covalently linked dimers and small oligomers it was found to be relatively small. In this contribution, we show an unprecedented quantum yield of intramolecular singlet exciton fission of ∼180% for a quinoidal bithiophene system. PMID:26263138

  1. Solution-based intramolecular singlet fission in cross-conjugated pentacene dimers.

    PubMed

    Zirzlmeier, Johannes; Casillas, Rubén; Reddy, S Rajagopala; Coto, Pedro B; Lehnherr, Dan; Chernick, Erin T; Papadopoulos, Ilias; Thoss, Michael; Tykwinski, Rik R; Guldi, Dirk M

    2016-05-21

    We show unambiguous and compelling evidence by means of pump-probe experiments, which are complemented by calculations using ab initio multireference perturbation theory, for intramolecular singlet fission (SF) within two synthetically tailored pentacene dimers with cross-conjugation, namely XC1 and XC2. The two pentacene dimers differ in terms of electronic interactions as evidenced by perturbation of the ground state absorption spectra stemming from stronger through-bond contributions in XC1 as confirmed by theory. Multiwavelength analysis, on one hand, and global analysis, on the other hand, confirm that the rapid singlet excited state decay and triplet excited state growth relate to SF. SF rate constants and quantum yields increase with solvent polarity. For example, XC2 reveals triplet quantum yields and rate constants as high as 162 ± 10% and (0.7 ± 0.1) × 10(12) s(-1), respectively, in room temperature solutions. PMID:27122097

  2. Intermolecular and intramolecular reorientations in nonchiral smectic liquid-crystalline phases studied by broadband dielectric spectroscopy

    PubMed

    Schacht; Zugenmaier; Buivydas; Komitov; Stebler; Lagerwall; Gouda; Horii

    2000-04-01

    Molecular dynamics has been studied by broadband dielectric relaxation spectroscopy in the Sm-A, Sm-B, and Sm-E phases (Sm denotes smectic) of a homologous series of nonchiral stilbenes. An assignment of modes is presented based on their dependence on temperature and molecular length, and, as far as they obey the Arrhenius law, their activation energy has been determined. In general, reorientations of entire molecules around their short axis are active, whereas reorientations of entire molecules around their long axis are locked out in the Sm-E phase of shorter homologs, yet intramolecular reorientations of polar sites have been established. Strong evidence is presented for an interdependence of reorientations of entire molecules around the short and long axes within the biaxial Sm-E phase of longer homologs. PMID:11088173

  3. Shape of the proton potential in an intramolecular hydrogen-bonded system. Part II

    NASA Astrophysics Data System (ADS)

    Wojciechowski, Grzegorz; Ratajczak-Sitarz, Małgorzata; Katrusiak, Andrzej; Brzezinski, Bogumil

    2002-06-01

    The crystals of 5,5'-dibromo-3-diethylaminomethyl-2,2'-biphenol N-oxide were studied by X-ray and FT-IR spectroscopy. Within this molecule two short OHO intramolecular hydrogen bonds are formed. The NO⋯H +⋯O - bond between the OH and the N-oxide groups is very strong, of 2.419(7) Å between the oxygen atoms. The proton potential of this hydrogen bond is flat, broad and has probably no barrier—consequently it could not be located from X-ray diffraction data. The other hydrogen bond formed between two hydroxyl groups appears asymmetrical from FT-IR spectra, and shows also relatively limited proton polarizability. The molecular conformation is non-planar, due to strong overcrowding effect between the oxygen atoms involved in the hydrogen bonds.

  4. Shape of the proton potential in an intramolecular hydrogen-bonded system

    NASA Astrophysics Data System (ADS)

    Wojciechowski, Grzegorz; Brzezinski, Bogumil

    2001-09-01

    5,5'-dibromo-3-diethylaminomethyl-2,2'-biphenol N-oxide was studied by IR and NMR spectroscopy in chloroform and acetonitrile solutions. Two intramolecular hydrogen bonds are present in these molecules. The NO⋯H +⋯O - bond formed between the OH and the N-oxide groups is very strong. The proton potential is flat and broad and has probably no barrier. This hydrogen bond shows only slight proton polarizability. The other hydrogen bond formed between two hydroxyl groups OH⋯O -⇌ -O⋯HO is weaker and show large proton polarizability. The proton motions in both hydrogen bonds are not coupled and therefore these hydrogen bonds are not cooperative.

  5. Ultrafast twisting dynamics of thioflavin-T: spectroscopy of the twisted intramolecular charge-transfer state.

    PubMed

    Ghosh, Rajib; Palit, Dipak K

    2014-12-15

    Understanding the excited-state properties of thioflavin-T (ThT) has been of immense importance, because of its efficient amyloid-sensing ability related to neurodegenerative disorders. The excited-state dynamics of ThT is studied by using sub-pico- and nanosecond time-resolved transient absorption techniques as well as density functional theory (DFT)/time-dependent DFT calculations. Barrierless twisting around the central C-C bond between two aromatic moieties is the dominant process that contributes to the ultrafast dynamics of the S1 state. The spectroscopic properties of the intramolecular charge-transfer state are characterized for the first time. The energetics of the S0 and S1 states has also been correlated with the experimentally observed spectroscopic parameters and structural dynamics. A longer-lived transient state populated with a very low yield has been characterized as the triplet state. PMID:25251013

  6. Mapping the intramolecular contributions to the inelastic electron tunneling signal of a molecular junction

    NASA Astrophysics Data System (ADS)

    Foti, Giuseppe; Vázquez, Héctor

    2016-07-01

    We present a quantitative analysis of the intramolecular origin of the inelastic electron tunneling signal of a molecular junction. We use density-functional theory to study a representative conjugated molecule with a low degree of symmetry and calculate, for all modes, the different contributions that give rise to the vibrational spectrum. These local contributions involve products of scattering states with electron-phonon matrix elements and thus encode information on both the vibrational modes and the electronic structure. We separate these intra- and interatomic terms and draw a pattern of addition or cancellation of these partial contributions throughout the inelastic spectrum. This allows for a quantitative relation between the degree of symmetry of each vibrational mode, its inelastic signal, and the locality of selection rules.

  7. Raman spectroscopy in hot compressed hydrogen and nitrogen - implications for the intramolecular potential

    SciTech Connect

    Goncharov, A F; Crowhurst, J C

    2005-09-19

    Raman measurements of molecular hydrogen (H{sub 2} and D{sub 2}) and nitrogen (N{sub 2}) have been made under simultaneous conditions of high temperature and high static pressure. Measurements have been made on H{sub 2} and D{sub 2} to 50 GPa and 1600 K, and on N{sub 2} to 50 GPa and 2000 K. In all three materials the familiar molecular stretching mode (vibron) is accompanied in the high-temperature Raman spectra by one or more lower-frequency peaks due to transitions from excited vibrational states. We find that the frequency differences between these bands decreases with pressure, implying that the anharmonicity of the corresponding part of the intramolecular potential also decreases. This is accompanied by an increase in the measured linewidths of the bands that is consistent with a decrease of the depth of the potential and an approaching molecular dissociation.

  8. A highly sensitive and selective fluorescent probe for fluoride anions based on intramolecular charge transfer.

    PubMed

    Liu, Jingkai; Xu, Zhenghe; Liu, Caiyun; Xu, Lirong; Wang, Zhongpeng; Zhu, Baocun

    2016-08-01

    Currently, there is a great need to develop methods for the selective detection of fluoride anions (F(-) ) owing to their toxicity in the environment and biological function in living systems. In this study, we developed a new fluorescent probe (probe 1) employing a Si-O bond as a highly selective recognition receptor for detecting F(-) via intramolecular charge transfer. Probe 1 could detect F(-) quantitatively using the turn-on fluorescence spectroscopy method with excellent sensitivity in the range of 4-38 μM and a detection limit of 0.26 μM; the detection time was < 17 min. We anticipate that probe 1 would be used widely to monitor F(-) in the environment. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26467672

  9. Intramolecular energy- and electron-transfer reactions in polymetallic complexes. Annual report

    SciTech Connect

    Peterson, J.D.

    1991-12-01

    The complexes (tpy)Ru(II)(tpp)Co(III)(PPhEt{sub 2})H{sub 2}{sup 3+}, (NC){sub 3}Fe(II)(tpp)Co(III)(PPhEt{sub 2})H{sub 2} and (NC){sub 3}Fe(II)(tpp)Co(III)(PPh{sub 3})H{sub 2} (where tpp = 2,3,5,6-tetrakis(2{prime}-pyridyl)pyrazine), were prepared and their photochemistry studied. Reasons for the low quantum yields for H{sub 2} production are discussed briefly. A series of FeRuRh complexes is being prepared. Plans for the coming year on intramolecular energy transfer and charge separation are discussed.

  10. Rational Design for Rotaxane Synthesis through Intramolecular Slippage: Control of Activation Energy by Rigid Axle Length.

    PubMed

    Masai, Hiroshi; Terao, Jun; Fujihara, Tetsuaki; Tsuji, Yasushi

    2016-05-01

    We describe a new concept for rotaxane synthesis through intramolecular slippage using π-conjugated molecules as rigid axles linked with organic soluble and flexible permethylated α-cyclodextrins (PM α-CDs) as macrocycles. Through hydrophilic-hydrophobic interactions and flipping of PM α-CDs, successful quantitative conversion into rotaxanes was achieved without covalent bond formation. The rotaxanes had high activation barrier for their de-threading, so that they were kinetically isolated and derivatized even under conditions unfavorable for maintaining the rotaxane structures. (1) H NMR spectroscopy experiments clearly revealed that the restricted motion of the linked macrocycle with the rigid axle made it possible to control the kinetic stability by adjusting the length of the rigid axle in the precursor structure rather than the steric bulkiness of the stopper unit. PMID:27027800

  11. Solution-state structure of an intramolecular G-quadruplex with propeller, diagonal and edgewise loops

    PubMed Central

    Marušič, Maja; Šket, Primož; Bauer, Lubos; Viglasky, Viktor; Plavec, Janez

    2012-01-01

    We herein report on the formation and high-resolution NMR solution-state structure determination of a G-quadruplex adopted by d[G3ATG3ACACAG4ACG3] comprised of four G-tracts with the third one consisting of four guanines that are intervened with non-G streches of different lengths. A single intramolecular antiparallel (3+1) G-quadruplex exhibits three stacked G-quartets connected with propeller, diagonal and edgewise loops of different lengths. The propeller and edgewise loops are well structured, whereas the longer diagonal loop is more flexible. To the best of our knowledge, this is the first high-resolution G-quadruplex structure where all of the three main loop types are present. PMID:22532609

  12. Intramolecular Force Contrast and Dynamic Current-Distance Measurements at Room Temperature.

    PubMed

    Huber, F; Matencio, S; Weymouth, A J; Ocal, C; Barrena, E; Giessibl, F J

    2015-08-01

    Scanning probe microscopy can be used to probe the internal atomic structure of flat organic molecules. This technique requires an unreactive tip and has, until now, been demonstrated only at liquid helium and liquid nitrogen temperatures. We demonstrate intramolecular and intermolecular force contrast at room temperature on PTCDA molecules adsorbed on a Ag/Si(111)-(√[3]×√[3]) surface. The oscillating force sensor allows us to dynamically measure the vertical decay constant of the tunneling current. The precision of this method is increased by quantifying the transimpedance of the current to voltage converter and accounting for the tip oscillation. This measurement yields a clear contrast between neighboring molecules, which we attribute to the different charge states. PMID:26296122

  13. Intramolecular Force Contrast and Dynamic Current-Distance Measurements at Room Temperature

    NASA Astrophysics Data System (ADS)

    Huber, F.; Matencio, S.; Weymouth, A. J.; Ocal, C.; Barrena, E.; Giessibl, F. J.

    2015-08-01

    Scanning probe microscopy can be used to probe the internal atomic structure of flat organic molecules. This technique requires an unreactive tip and has, until now, been demonstrated only at liquid helium and liquid nitrogen temperatures. We demonstrate intramolecular and intermolecular force contrast at room temperature on PTCDA molecules adsorbed on a Ag /Si (111 )-(√{3 }×√{3 }) surface. The oscillating force sensor allows us to dynamically measure the vertical decay constant of the tunneling current. The precision of this method is increased by quantifying the transimpedance of the current to voltage converter and accounting for the tip oscillation. This measurement yields a clear contrast between neighboring molecules, which we attribute to the different charge states.

  14. Crystalline CO2-based polycarbonates prepared from racemic catalyst through intramolecularly interlocked assembly

    PubMed Central

    Liu, Ye; Ren, Wei-Min; Zhang, Wei-Ping; Zhao, Rong-Rong; Lu, Xiao-Bing

    2015-01-01

    The crystalline stereocomplexed polycarbonates can be prepared by mixing enantiopure polymers with opposite configuration, which derived from the asymmetric copolymerization with CO2 using enantiopure catalyst or/and chiral epoxides. Herein, we develop a powerful strategy for producing crystalline intramolecular stereocomplexed polycarbonates from racemic catalysts, which possess similar thermal stability and crystalline behaviour in comparison with the stereocomplexes by mixing opposite enantiopure polymers. Living polymer chains shuttle between catalyst molecules with different configurations to produce diastereomeric active species which is suggested to be responsible for the formation of isotactic multiblock polycarbonates in racemic bimetallic cobalt catalyst-mediated stereoselective copolymerization of CO2 and meso-epoxides. Solid-state NMR spectroscopy study suggests that the interaction in the carbonyl and methine regions is responsible for the strong crystallization capacity and compact package structure in the crystalline polycarbonates. PMID:26469884

  15. Origins of stereoselectivity in intramolecular aldol reactions catalyzed by cinchona amines.

    PubMed

    Lam, Yu-Hong; Houk, K N

    2015-02-11

    The intramolecular aldol condensation of 4-substituted heptane-2,6-diones leads to chiral cyclohexenones. The origins of the enantioselectivities of this reaction, disclosed by List et al. using a cinchona alkaloid-derived primary amine (cinchona amine) organocatalyst, have been determined with dispersion-corrected density functional theory (DFT). The stereocontrol hinges on the chair preference of the substrate-enamine intermediate and the conformational preferences of a hydrogen-bonded nine-membered aldol transition state containing eight heavy atoms. The conformations of the hydrogen-bonded ring in the various stereoisomeric transition structures have been analyzed in detail and shown to closely resemble the conformers of cyclooctane. A model of stereoselectivity is proposed for the cinchona amine catalysis of this reaction. The inclusion of Grimme's dispersion corrections in the DFT calculations (B3LYP-D3(BJ)) substantially improves the agreement of the computed energetics and experiment, attesting to the importance of dispersion effects in stereoselectivity. PMID:25629689

  16. Total synthesis of Elisabethin A: intramolecular Diels-Alder reaction under biomimetic conditions.

    PubMed

    Heckrodt, Thilo J; Mulzer, Johann

    2003-04-23

    We describe the first total synthesis of the marine diterpenoid elisabethin A. The synthesis uses (S)-hydroxy-2-methyl-propionate as the chiral starting material, which is elaborated into a dienyl-iodide and added to an aryl acetic acid ester via enolate alkylation. The hydroquinoid system is oxidized to the quinone which serves as the dienophile in a highly stereocontrolled intramolecular Diels-Alder addition. This IMDA reaction, which to our knowledge is the first one to employ a terminal (Z)-diene, proceeds under biomimetic conditions (water, ferrichloride as the oxidant, room temperature) with high yield and stereoselectivity. The Diels-Alder adduct is transformed into the natural product via a three-step sequence including selective hydrogenation, base-catalyzed epimerization of the cis- into the trans-decalin system and O-demethylation. PMID:12696865

  17. Computational design of effective, bioinspired HOCl antioxidants: the role of intramolecular Cl+ and H+ shifts.

    PubMed

    Karton, Amir; O'Reilly, Robert J; Pattison, David I; Davies, Michael J; Radom, Leo

    2012-11-21

    The enzyme myeloperoxidase generates significant amounts of hypochlorous acid (HOCl) at sites of inflammation to inflict oxidative damage upon invading pathogens. However, excessive production of this potent oxidant is associated with numerous inflammatory diseases. Recent kinetic measurements suggest that the endogenous antioxidant carnosine is an effective HOCl scavenger. On the basis of computational modeling, we suggest a possible mechanism for this antioxidant activity. We find that a unique structural relationship between three adjacent functional groups (imidazole, carboxylic acid, and terminal amine) enables an intramolecular chlorine transfer to occur. In particular, two sequential proton shifts are coupled with a Cl(+) shift converting the kinetically favored product (chlorinated at the imidazole nitrogen) into the thermodynamically favored product (chlorinated at the terminal amine) effectively trapping the chlorine. We proceed to design systems that share similar structural features to those of carnosine but with even greater HOCl-scavenging capabilities. PMID:23148773

  18. Phosphine-Catalyzed Enantioselective Intramolecular [3+2] Annulations To Generate Fused Ring Systems

    PubMed Central

    2015-01-01

    Substantial progress has been described in the development of asymmetric variants of the phosphine-catalyzed intermolecular [3+2] annulation of allenes with alkenes; however, there have not been corresponding advances for the intramolecular process, which can generate a higher level of complexity (an additional ring and stereocenter(s)). In this study, we describe the application of chiral phosphepine catalysts to address this challenge, thereby providing access to useful scaffolds that are found in bioactive compounds, including diquinane and quinolin-2-one derivatives, with very good stereoselectivity. The products of the [3+2] annulation can be readily transformed into structures that are even more stereochemically rich. Mechanistic studies are consistent with β addition of the phosphepine to the allene being the turnover-limiting step of the catalytic cycle, followed by a concerted [3+2] cycloaddition to the pendant olefin. PMID:25815702

  19. Unusual NHC-Iridium(I) Complexes and Their Use in the Intramolecular Hydroamination of Unactivated Aminoalkenes.

    PubMed

    Sipos, Gellért; Ou, Arnold; Skelton, Brian W; Falivene, Laura; Cavallo, Luigi; Dorta, Reto

    2016-05-10

    N-heterocyclic carbene (NHC) ligands with naphthyl side chains were employed for the synthesis of unsaturated, yet isolable [(NHC)Ir(cod)](+) (cod=1,5-cyclooctadiene) complexes. These compounds are stabilised by an interaction of the aromatic wingtip that leads to a sideways tilt of the NHC-Ir bond. Detailed studies show how the tilting of such N-heterocyclic carbenes affects the electronic shielding properties of the carbene carbon atom and how this is reflected by significant upfield shifts in the (13) C NMR signals. When employed in the intramolecular hydroamination, these [(NHC)Ir(cod)](+) species show very high catalytic activity under mild reaction conditions. An enantiopure version of the catalyst system produces pyrrolidines with excellent enantioselectivities. PMID:27059164

  20. Theoretical study of γ-aminobutyric acid conformers: Intramolecular interactions and ionization energies

    NASA Astrophysics Data System (ADS)

    Wang, Ke-Dong; Wang, Mei-Ting; Meng, Ju

    2014-10-01

    Allowing for all combinations of internal single-bond rotamers, 1,296 unique trial structures of γ-Aminobutyric acid (GABA) are obtained. All of these structures are optimized at the M06-2X level of theory and a total of 68 local minimal conformers are found. The nine low-lying conformers are used for further studies. According to the calculated relative Gibbs free energies at M06-2X level of theory, we find that the dispersion is important for the relative energy of GABA. The intramolecular hydrogen bonds and hyperconjugative interaction and their effects on the conformational stability are studied. The results show that both of them have great influence on the conformers. The vertical ionization energies (VIE) are calculated and match the experimental data well. The results show that the neutral GABA in the gas phase is a multi-conformer system and at least four conformations exist.

  1. Online Measurement of the Intramolecular Isotopic Composition of Acetate in Natural Porewater Samples

    NASA Astrophysics Data System (ADS)

    Thomas, R. B.; Arthur, M. A.; Freeman, K. H.

    2006-12-01

    Carbon dioxide and methane are traditionally considered to be the dominant end products of anaerobic metabolism while acetate is thought to be a rapidly consumed intermediate. However, in some settings, recent evidence has grown to suggest that, at least transiently, acetate can be a major metabolic end product. In natural systems, isotopic mass balances can be used to partition the flow of carbon to methane, CO2, and acetate. However, these isotopic estimates require intramolecular measurements of acetate in addition to isotopic measurements of the gaseous species, CO2 and CH4. In practice, the intramolecular isotopic composition of acetate is rarely measured because the analysis is technically challenging and traditionally requires prior separation and offline pyrolysis of purified acetate. As a result of these technical challenges, acetate methyl carbon is usually assumed to be a few permil depleted relative to the carbon isotopic composition of bulk organic matter. In environments where acetate may be produced by autotrophic acetogens this assumption can be devastatingly false. This work describes the use of an online method for the analysis of the intramolecular carbon isotopic composition of dissolved acetate from dilute surface water samples with a detection limit of injected sample down to 500uM. Preconcentration of samples via lyophilization has resulted in detection limits as low as 30uM. In 2002, at Penn State, Dias et al. (Organic Geochemistry Vol. 33, p161-168) reported a technique to examine the intramolecular isotopic composition of acetate from oil-prone source rocks using SPME extraction with an online GC-pyrolysis-IRMS. We have adapted the Dias method to be used with direct injection of dilute natural water samples. Briefly, this procedure protonates acetate with a .1M addition of oxalic acid and vaporizes the sample in the GC inlet at low temperatures. This prevents oxalic acid decomposition and provides sufficient separation of acetate from

  2. Effect of. gamma. -cyclodextrin on the intramolecular charge transfer processes in aminocoumarin laser dyes

    SciTech Connect

    Nag, A.; Chakrabarty, T.; Bhattacharyya, K. )

    1990-05-17

    Steady-state and time-resolved studies on the emission properties of three 7-(diethylamino)coumarin laser dyes (I-III) in aqueous {gamma}-cyclodextrin ({gamma}-CD) solutions are reported. On addition of {gamma}-CD, fluorescence maxima of all the three dyes shift to higher energy, with a huge enhancement of the yield of intramolecular charge transfer (ICT) emission for the flexible ones (I and II) and a very slight enhancement for the rigid analogue III. The results are explained in terms of the concept of polarity-dependent twisted ICT rates. It is proposed that twisted ICT, the main nonradiative process in the excited ICT states of these dyes, is severely restricted inside the {gamma}-cyclodextrin cavity because of the reduced polarity. This is responsible for the enhancement of fluorescence from the ICT state.

  3. Theoretical investigation of intramolecular vibrational energy redistribution in HFCO and DFCO induced by an external field.

    PubMed

    Pasin, Gauthier; Iung, Christophe; Gatti, Fabien; Richter, Falk; Léonard, Céline; Meyer, Hans-Dieter

    2008-10-14

    The present paper is devoted to a full quantum mechanical study of the intramolecular vibrational energy redistribution in HFCO and DFCO. In contrast to our previous studies [Pasin et al., J. Chem. Phys. 124, 194304 (2006) and 126, 024302 (2007)], the dynamics is now performed in the presence of an external time-dependent field. This more closely reflects the experimental conditions. A six-dimensional dipole surface is computed. The multiconfiguration time-dependent Hartree method is exploited to propagate the corresponding six-dimensional wave packets. Special emphasis is placed on the excitation of the out-of-plane bending vibration and on the dissociation of the molecule. In the case of DFCO, we predict that it is possible to excite the out-of-plane bending mode of vibration and to drive the dissociation to DF+CO with only one laser pulse with a fixed frequency and without excitation of an electronic state. PMID:19045144

  4. Dynamics of intramolecular spin exchange interaction of a nitronyl nitroxide diradical in solution and on surfaces.

    PubMed

    Lloveras, V; Badetti, E; Veciana, J; Vidal-Gancedo, J

    2016-03-01

    In this paper we report the study of the dynamics of a thermally modulated intramolecular spin exchange interaction of a novel diradical nitronyl nitroxide-substituted disulfide in solution and when it is grafted on a gold surface. The structure of this diradical was designed to have flexible chains leading to intramolecular collisions and hence spin exchange interaction, and with an appropriate binding group to be grafted on the gold surface to study its behavior on the surface. In solution, this diradical shows a strong spin exchange interaction between both radicals which is modulated by temperature, but also gold nanoparticles (AuNPs) functionalized with this diradical permit investigation of such a phenomenon in surface-grafted radicals. The spin-labelled AuNP synthesis was optimized to obtain high coverage of spin labels to lead to high spin exchange interaction. The obtained AuNPs were studied by Electron Paramagnetic Resonance (EPR), UV-Vis, and IR spectroscopies, HR-TEM microscopy, Cyclic Voltammetry (CV), Energy Dispersive X-ray analysis (EDX) and Thermogravimetric Analysis (TGA). This inorganic-organic hybrid material also showed dipolar interactions between its radicals which were confirmed by the appearance in the EPR spectra of an |Δms| = 2 transition at half-field. This signal gives direct evidence of the presence of a high-spin state and permitted us to study the nature of the magnetic coupling between the spins which was found to be antiferromagnetic. Self-Assembled Monolayers (SAMs) of these radicals on the Au (111) substrate were also prepared and studied by contact angle, X-Ray Photoelectron Spectroscopy (XPS), Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS), Cyclic Voltammetry and EPR. The magnetic as well as the electrochemical properties of the hybrid surfaces were studied and compared with the properties of this diradical in solution. Analogies between the properties of AuNPs with high coverage of radicals and those of SAM were

  5. Solution-based intramolecular singlet fission in cross-conjugated pentacene dimers

    NASA Astrophysics Data System (ADS)

    Zirzlmeier, Johannes; Casillas, Rubén; Reddy, S. Rajagopala; Coto, Pedro B.; Lehnherr, Dan; Chernick, Erin T.; Papadopoulos, Ilias; Thoss, Michael; Tykwinski, Rik R.; Guldi, Dirk M.

    2016-05-01

    We show unambiguous and compelling evidence by means of pump-probe experiments, which are complemented by calculations using ab initio multireference perturbation theory, for intramolecular singlet fission (SF) within two synthetically tailored pentacene dimers with cross-conjugation, namely XC1 and XC2. The two pentacene dimers differ in terms of electronic interactions as evidenced by perturbation of the ground state absorption spectra stemming from stronger through-bond contributions in XC1 as confirmed by theory. Multiwavelength analysis, on one hand, and global analysis, on the other hand, confirm that the rapid singlet excited state decay and triplet excited state growth relate to SF. SF rate constants and quantum yields increase with solvent polarity. For example, XC2 reveals triplet quantum yields and rate constants as high as 162 +/- 10% and (0.7 +/- 0.1) × 1012 s-1, respectively, in room temperature solutions.We show unambiguous and compelling evidence by means of pump-probe experiments, which are complemented by calculations using ab initio multireference perturbation theory, for intramolecular singlet fission (SF) within two synthetically tailored pentacene dimers with cross-conjugation, namely XC1 and XC2. The two pentacene dimers differ in terms of electronic interactions as evidenced by perturbation of the ground state absorption spectra stemming from stronger through-bond contributions in XC1 as confirmed by theory. Multiwavelength analysis, on one hand, and global analysis, on the other hand, confirm that the rapid singlet excited state decay and triplet excited state growth relate to SF. SF rate constants and quantum yields increase with solvent polarity. For example, XC2 reveals triplet quantum yields and rate constants as high as 162 +/- 10% and (0.7 +/- 0.1) × 1012 s-1, respectively, in room temperature solutions. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr02493a

  6. Excited-state intramolecular proton transfer to carbon atoms: nonadiabatic surface-hopping dynamics simulations.

    PubMed

    Xia, Shu-Hua; Xie, Bin-Bin; Fang, Qiu; Cui, Ganglong; Thiel, Walter

    2015-04-21

    Excited-state intramolecular proton transfer (ESIPT) between two highly electronegative atoms, for example, oxygen and nitrogen, has been intensely studied experimentally and computationally, whereas there has been much less theoretical work on ESIPT to other atoms such as carbon. We have employed CASSCF, MS-CASPT2, RI-ADC(2), OM2/MRCI, DFT, and TDDFT methods to study the mechanistic photochemistry of 2-phenylphenol, for which such an ESIPT has been observed experimentally. According to static electronic structure calculations, irradiation of 2-phenylphenol populates the bright S1 state, which has a rather flat potential in the Franck-Condon region (with a shallow enol minimum at the CASSCF level) and may undergo an essentially barrierless ESIPT to the more stable S1 keto species. There are two S1/S0 conical intersections that mediate relaxation to the ground state, one in the enol region and one in the keto region, with the latter one substantially lower in energy. After S1 → S0 internal conversion, the transient keto species can return back to the S0 enol structure via reverse ground-state hydrogen transfer in a facile tautomerization. This mechanistic scenario is verified by OM2/MRCI-based fewest-switches surface-hopping simulations that provide detailed dynamic information. In these trajectories, ESIPT is complete within 118 fs; the corresponding S1 excited-state lifetime is computed to be 373 fs in vacuum. Most of the trajectories decay to the ground state via the S1/S0 conical intersection in the keto region (67%), and the remaining ones via the enol region (33%). The combination of static electronic structure computations and nonadiabatic dynamics simulations is expected to be generally useful for understanding the mechanistic photophysics and photochemistry of molecules with intramolecular hydrogen bonds. PMID:25711992

  7. Mechanisms of Intramolecular Communication in a Hyperthermophilic Acylaminoacyl Peptidase: A Molecular Dynamics Investigation

    PubMed Central

    Papaleo, Elena; Renzetti, Giulia; Tiberti, Matteo

    2012-01-01

    Protein dynamics and the underlying networks of intramolecular interactions and communicating residues within the three-dimensional (3D) structure are known to influence protein function and stability, as well as to modulate conformational changes and allostery. Acylaminoacyl peptidase (AAP) subfamily of enzymes belongs to a unique class of serine proteases, the prolyl oligopeptidase (POP) family, which has not been thoroughly investigated yet. POPs have a characteristic multidomain three-dimensional architecture with the active site at the interface of the C-terminal catalytic domain and a β-propeller domain, whose N-terminal region acts as a bridge to the hydrolase domain. In the present contribution, protein dynamics signatures of a hyperthermophilic acylaminoacyl peptidase (AAP) of the prolyl oligopeptidase (POP) family, as well as of a deletion variant and alanine mutants (I12A, V13A, V16A, L19A, I20A) are reported. In particular, we aimed at identifying crucial residues for long range communications to the catalytic site or promoting the conformational changes to switch from closed to open ApAAP conformations. Our investigation shows that the N-terminal α1-helix mediates structural intramolecular communication to the catalytic site, concurring to the maintenance of a proper functional architecture of the catalytic triad. Main determinants of the effects induced by α1-helix are a subset of hydrophobic residues (V16, L19 and I20). Moreover, a subset of residues characterized by relevant interaction networks or coupled motions have been identified, which are likely to modulate the conformational properties at the interdomain interface. PMID:22558199

  8. Intramolecular Halogen Transfer via Halonium Ion Intermediates in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Chai, Yunfeng; Xiong, Xingchuang; Yue, Lei; Jiang, You; Pan, Yuanjiang; Fang, Xiang

    2016-01-01

    The fragmentation of halogen-substituted protonated amines and quaternary ammonium ions (R1R2R3N+CH2(CH2)nX, where X = F, Cl, Br, I, n = 1, 2, 3, 4) was studied by electrospray ionization tandem mass spectrometry. A characteristic fragment ion (R1R2R3N+X) resulting from halogen transfer was observed in collision-induced dissociation. A new mechanism for the intramolecular halogen transfer was proposed that involves a reactive intermediate, [amine/halonium ion]. A potential energy surface scan using DFT calculation for CH2-N bond cleavage process of protonated 2-bromo -N,N-dimethylethanamine supports the formation of this intermediate. The bromonium ion intermediate-involved halogen transfer mechanism is supported by an examination of the ion/molecule reaction between isolated ethylenebromonium ion and triethylamine, which generates the N-bromo- N,N,N-triethylammonium cation. For other halogens, Cl and I also can be involved in similar intramolecular halogen transfer, but F cannot be involved. With the elongation of the carbon chain between the halogen (bromine as a representative example) and amine, the migration ability of halogen decreases. When the carbon chain contains two or three CH2 units (n = 1, 2), formal bromine cation transfer can take place, and the transfer is easier when n = 1. When the carbon chain contains four or five CH2 units (n = 3, 4), formal bromine cation transfer does not occur, probably because the five- and six-membered cyclic bromonium ions are very stable and do not donate the bromine to the amine.

  9. Dynamics of the chemical bond: inter- and intra-molecular hydrogen bond.

    PubMed

    Arunan, Elangannan; Mani, Devendra

    2015-01-01

    In this discussion, we show that a static definition of a 'bond' is not viable by looking at a few examples for both inter- and intra-molecular hydrogen bonding. This follows from our earlier work (Goswami and Arunan, Phys. Chem. Chem. Phys. 2009, 11, 8974) which showed a practical way to differentiate 'hydrogen bonding' from 'van der Waals interaction'. We report results from ab initio and atoms in molecules theoretical calculations for a series of Rg∙∙∙HX complexes (Rg=He/Ne/Ar and X=F/Cl/Br) and ethane-1,2-diol. Results for the Rg∙∙∙HX/DX complexes show that Rg∙∙∙DX could have a 'deuterium bond' even when Rg∙∙∙HX is not 'hydrogen bonded', according to the practical criterion given by Goswami and Arunan. Results for ethane-1,2-diol show that an 'intra-molecular hydrogen bond' can appear during a normal mode vibration which is dominated by the OO stretching, though a 'bond' is not found in the equilibrium structure. This dynamical 'bond' formation may nevertheless be important in ensuring the continuity of electron density across a molecule. In the former case, a vibration 'breaks' an existing bond and in the later case, a vibration leads to 'bond' formation. In both cases, the molecule/complex stays bound irrespective of what happens to this 'hydrogen bond'. Both these cases push the borders on the recent IUPAC recommendation on hydrogen bonding (Arunan et al. Pure. Appl. Chem. 2011, 83 1637) and justify the inclusive nature of the definition. PMID:25627627

  10. Dipyrenylphosphatidylcholines as membrane fluidity probes. Pressure and temperature dependence of the intramolecular excimer formation rate.

    PubMed Central

    Sassaroli, M; Vauhkonen, M; Somerharju, P; Scarlata, S

    1993-01-01

    We have measured the pressure dependence of the intramolecular excimer formation rate, K(p), for di-(1'-pyrenedecanoyl)-phosphatidylcholine (dipy10PC) probes in single-component lipid multilamellar vesicles (MLV) as a function of temperature. Apparent volumes of activation (V(a)) for intramolecular excimer formation are obtained from the slopes of plots of log K(p) versus P. For liquid-crystalline saturated lipid MLV (DMPC and DPPC), these plots are linear and yield a unique V(a) at each temperature, whereas for unsaturated lipids (POPC and DOPC) they are curvilinear and V(a) appears to decrease with pressure. The isothermal pressure induced phase transition is marked by an abrupt drop in the values of K(p). The pressure to temperature equivalence values, dPm/dT, estimated from the midpoint of the transitions, are 47.0, 43.5, and 52.5 bar degree C-1 for DMPC, DPPC, and POPC, respectively. In liquid-crystalline DMPC, V(a) decreases linearly as a function of temperature, with a coefficient -dVa/dT = 0.65 +/- 0.11 ml degree C-1 mol-1. Using a modified free volume model of diffusion, we show that this value corresponds to the thermal expansivity of DMPC. Both the apparent energy and entropy of activation, Ea and delta Sa, increase with pressure in DMPC, whereas both decrease in POPC and DOPC. This difference is attributed to the sensitivity of the dynamics and/or packing of the dipy10PC probes to the location of the cis-double bonds in the chains of the unsaturated host phospholipids. Finally, the atmospheric pressure values of Ea and delta Sa for the four host MLV examined are shown to be linearly related. The relevance of this finding with respect to the structure of the excimers formed by the dipy10PC probes is briefly discussed. PMID:8431538

  11. Using equilibrium isotope effects to detect intramolecular OH/OH hydrogen bonds: structural and solvent effects.

    PubMed

    Vasquez, Thomas E; Bergset, Jon M; Fierman, Matthew B; Nelson, Alshakim; Roth, Joshua; Khan, Saeed I; O'Leary, Daniel J

    2002-03-27

    A comparative (1)H NMR study of partially deuterated 1,3- and 1,4-diols has demonstrated that intramolecular hydrogen bonds of different geometry can give rise to equilibrium isotope shifts of opposite sign in hydrogen-bond-accepting solvents such as DMSO-d(6), acetone-d(6), and THF-d(8). The sign inversion is interpreted in terms of the ability of solvent molecules to form competitive intermolecular hydrogen bonds with the diol and in terms of the limiting chemical shifts for the interior and exterior hydroxyl groups. Deuterium is shown to prefer the intermolecular solvent hydrogen bond by 10.9 +/- 0.5 cal/mol for 1,4-diol 3 dissolved in DMSO-d(6) at room temperature. Pyridine-d(5) is shown to be capable of amplifying positive (downfield) isotope shifts measured in DMSO-d(6), in some cases by as much as a factor of 3. Its use is demonstrated for the assignment of the syn or anti relative configuration of 2,4-pentanediol and for the amplification of isotope shifts used to detect intramolecular hydrogen bonds in alpha- and beta-cyclodextrin. Studies in apolar solvents such as CD(2)Cl(2) and benzene-d(6) reveal that the isotope shift is negative (upfield) for all hydrogen bond geometries studied. Larger isotope shifts are measured in benzene-d(6), and a rationale for this amplification is presented. The use of apolar solvents is particularly useful for assigning the syn or anti configuration of 2,4-pentanediol. PMID:11902884

  12. Intramolecular Halogen Transfer via Halonium Ion Intermediates in the Gas Phase.

    PubMed

    Chai, Yunfeng; Xiong, Xingchuang; Yue, Lei; Jiang, You; Pan, Yuanjiang; Fang, Xiang

    2016-01-01

    The fragmentation of halogen-substituted protonated amines and quaternary ammonium ions (R(1)R(2)R(3)N(+)CH2(CH2)nX, where X = F, Cl, Br, I, n = 1, 2, 3, 4) was studied by electrospray ionization tandem mass spectrometry. A characteristic fragment ion (R(1)R(2)R(3)N(+)X) resulting from halogen transfer was observed in collision-induced dissociation. A new mechanism for the intramolecular halogen transfer was proposed that involves a reactive intermediate, [amine/halonium ion]. A potential energy surface scan using DFT calculation for CH2-N bond cleavage process of protonated 2-bromo-N,N-dimethylethanamine supports the formation of this intermediate. The bromonium ion intermediate-involved halogen transfer mechanism is supported by an examination of the ion/molecule reaction between isolated ethylenebromonium ion and triethylamine, which generates the N-bromo-N,N,N-triethylammonium cation. For other halogens, Cl and I also can be involved in similar intramolecular halogen transfer, but F cannot be involved. With the elongation of the carbon chain between the halogen (bromine as a representative example) and amine, the migration ability of halogen decreases. When the carbon chain contains two or three CH2 units (n = 1, 2), formal bromine cation transfer can take place, and the transfer is easier when n = 1. When the carbon chain contains four or five CH2 units (n = 3, 4), formal bromine cation transfer does not occur, probably because the five- and six-membered cyclic bromonium ions are very stable and do not donate the bromine to the amine. PMID:26383734

  13. Exploration of zeroth-order wavefunctions and energies as a first step toward intramolecular symmetry-adapted perturbation theory

    NASA Astrophysics Data System (ADS)

    Gonthier, Jérôme F.; Corminboeuf, Clémence

    2014-04-01

    Non-covalent interactions occur between and within all molecules and have a profound impact on structural and electronic phenomena in chemistry, biology, and material science. Understanding the nature of inter- and intramolecular interactions is essential not only for establishing the relation between structure and properties, but also for facilitating the rational design of molecules with targeted properties. These objectives have motivated the development of theoretical schemes decomposing intermolecular interactions into physically meaningful terms. Among the various existing energy decomposition schemes, Symmetry-Adapted Perturbation Theory (SAPT) is one of the most successful as it naturally decomposes the interaction energy into physical and intuitive terms. Unfortunately, analogous approaches for intramolecular energies are theoretically highly challenging and virtually nonexistent. Here, we introduce a zeroth-order wavefunction and energy, which represent the first step toward the development of an intramolecular variant of the SAPT formalism. The proposed energy expression is based on the Chemical Hamiltonian Approach (CHA), which relies upon an asymmetric interpretation of the electronic integrals. The orbitals are optimized with a non-hermitian Fock matrix based on two variants: one using orbitals strictly localized on individual fragments and the other using canonical (delocalized) orbitals. The zeroth-order wavefunction and energy expression are validated on a series of prototypical systems. The computed intramolecular interaction energies demonstrate that our approach combining the CHA with strictly localized orbitals achieves reasonable interaction energies and basis set dependence in addition to producing intuitive energy trends. Our zeroth-order wavefunction is the primary step fundamental to the derivation of any perturbation theory correction, which has the potential to truly transform our understanding and quantification of non

  14. Exploration of zeroth-order wavefunctions and energies as a first step toward intramolecular symmetry-adapted perturbation theory

    SciTech Connect

    Gonthier, Jérôme F.; Corminboeuf, Clémence

    2014-04-21

    Non-covalent interactions occur between and within all molecules and have a profound impact on structural and electronic phenomena in chemistry, biology, and material science. Understanding the nature of inter- and intramolecular interactions is essential not only for establishing the relation between structure and properties, but also for facilitating the rational design of molecules with targeted properties. These objectives have motivated the development of theoretical schemes decomposing intermolecular interactions into physically meaningful terms. Among the various existing energy decomposition schemes, Symmetry-Adapted Perturbation Theory (SAPT) is one of the most successful as it naturally decomposes the interaction energy into physical and intuitive terms. Unfortunately, analogous approaches for intramolecular energies are theoretically highly challenging and virtually nonexistent. Here, we introduce a zeroth-order wavefunction and energy, which represent the first step toward the development of an intramolecular variant of the SAPT formalism. The proposed energy expression is based on the Chemical Hamiltonian Approach (CHA), which relies upon an asymmetric interpretation of the electronic integrals. The orbitals are optimized with a non-hermitian Fock matrix based on two variants: one using orbitals strictly localized on individual fragments and the other using canonical (delocalized) orbitals. The zeroth-order wavefunction and energy expression are validated on a series of prototypical systems. The computed intramolecular interaction energies demonstrate that our approach combining the CHA with strictly localized orbitals achieves reasonable interaction energies and basis set dependence in addition to producing intuitive energy trends. Our zeroth-order wavefunction is the primary step fundamental to the derivation of any perturbation theory correction, which has the potential to truly transform our understanding and quantification of non

  15. Intramolecular isotope distributions reveal lower than expected increases in photosynthesis over the past 200 years

    NASA Astrophysics Data System (ADS)

    Ehlers, Ina; Augusti, Angela; Köhler, Iris; Zuidema, Pieter; Robertson, Iain; Nilsson, Mats; Schleucher, Jürgen

    2015-04-01

    The ability of the biosphere to act as CO2 sink through photosynthesis strongly influences future atmospheric CO2 concentrations and crop productivity. However, plant responses to increasing atmospheric CO2 are poorly understood, in particular on time scales of decades that are most relevant for the global carbon cycle. Most plants in the global terrestrial vegetation and most crops use the C3 photosynthetic pathway. Photorespiration is a side reaction of C3 photosynthesis that reduces CO2 assimilation in all C3 plants. By studying intramolecular isotope distributions (isotopomer abundances) in century-long archives of plant material, we reconstruct how the atmospheric CO2 increase since industrialization has changed the ratio of photorespiration to photosynthesis. For 12 tree species from five continents, we observe that the CO2 increase has reduced the photorespiration / photosynthesis ratio. However, the observed reduction is on average 50 % smaller than expected from CO2 manipulation experiments. This apparent discrepancy is explained by results from a factorial CO2 / temperature manipulation experiment, which shows that isotopomers reflect the integrated effect of CO2 and temperature on the photorespiration / photosynthesis ratio. Thus, the 50 % smaller suppression of photorespiration in trees is explained by increases in leaf temperature of 2 ° C, due to global warming and a possible contribution of reduced transpirational cooling due to stomatal closure. Previous studies of long-term effects of increasing CO2 on trees have measured 13C fractionation of leaf gas exchange (Δ13C) in tree-ring series. In several studies a discrepancy was observed: strong historic increases in photosynthesis are estimated, but increases in biomass are not observed. The temperature influence revealed by our isotopomer data resolves this discrepancy; the lower estimate of CO2 fertilization has major implications for the future role of forests as CO2 sink and for vegetation

  16. Intra-molecular cross-linking of acidic residues for protein structure studies.

    PubMed

    Novak, Petr; Kruppa, Gary H

    2008-01-01

    Intra-molecular cross-linking has been suggested as a method of obtaining distance constraints that would help to develop structural models of proteins. Recent work published on intra-molecular cross-linking for protein structural studies has employed commercially available primary amine (lysine, the amino terminus) selective reagents. Previous work using these cross-linkers has shown that for several proteins of known structure, the number of cross-links that can be obtained experimentally may be small compared to what would be expected from the known structure, due to the relative reactivity, distribution and solvent accessibility of the lysines in the protein sequence. To overcome these limitations, we have investigated the use of cross-linking reagents that can react with other reactive side chains in proteins. We used 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) to activate the carboxylic acid containing residues, aspartic acid (D), glutamic acid (E) and the carboxy terminus (O), for cross-linking reactions. Once activated, the DEO side chains can react to form "zero-length" cross-links with nearby primary amine containing residues, lysines (K) and the amino terminus (X), via the formation of a new amide bond. We also show that the EDC-activated DEO side chains can be cross-linked to each other using dihydrazides, two hydrazide moieties connected by an alkyl cross-linker arm of variable length. Using these reagents, we have found three new "zero-length" cross-links in ubiquitin consistent with its known structure (M1-E16, M1-E18 and K63-E64). Using the dihydrazide cross-linkers, we have identified two new cross-links (D21-D32 and E24-D32) unambiguously. Using a library of dihydrazide cross-linkers with varying arm length, we have shown that there is a minimum arm length required for the DEO-DEO cross-links of 5.8 A. These results show that additional structural information can be obtained by exploiting new cross-linker chemistry

  17. Intra-molecular cross-linking of acidic residues for protein structure studies.

    SciTech Connect

    Kruppa, Gary Hermann; Young, Malin M.; Novak, Petr; Schoeniger, Joseph S.

    2005-03-01

    Intra-molecular cross-linking has been suggested as a method of obtaining distance constraints that would be useful in developing structural models of proteins. Recent work published on intra-molecular cross-linking for protein structural studies has employed commercially available primary amine selective reagents that can cross-link lysine residues to other lysine residues or the amino terminus. Previous work using these cross-linkers has shown that for several proteins of known structure, the number of cross-links that can be obtained experimentally may be small compared to what would be expected from the known structure, due to the relative reactivity, distribution, and solvent accessibility of the lysines in the protein sequence. To overcome these limitations we have investigated the use of cross-linking reagents that can react with other reactive sidechains in proteins. We used 1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) to activate the carboxylic acid containing residues, aspartic acid (D), glutamic acid (E), and the carboxy terminus (O), for cross-linking reactions. Once activated, the DEO sidechains can react to form 'zero-length' cross-links with nearby primary amine containing resides, lysines (K) and the amino terminus (X), via the formation of a new amide bond. We also show that the EDC-activated DEO sidechains can be cross-linked to each other using dihydrazides, two hydrazide moieties connected by an alkyl cross-linker ann of variable length. Using these reagents, we have found three new 'zero-length' cross-links in ubiquitin consistent with its known structure (M1-E16, M1-E18, and K63-E64). Using the dihydrazide cross-linkers, we have identified 2 new cross-links (D21-D32 and E24-D32) unambiguously. Using a library of dihydrazide cross-linkers with varying arm length, we have shown that there is a minimum arm length required for the DEO-DEO cross-links of 5.8 angstroms. These results show that additional structural information

  18. Towards understanding the unbound state of drug compounds: Implications for the intramolecular reorganization energy upon binding.

    PubMed

    Foloppe, Nicolas; Chen, I-Jen

    2016-05-15

    There has been an explosion of structural information for pharmaceutical compounds bound to biological targets, but the conformations and dynamics of compounds free in solution are poorly characterized, if at all. Yet, knowledge of the unbound state is essential to understand the fundamentals of molecular recognition, including the much debated conformational intramolecular reorganization energy of a compound upon binding (ΔEReorg). Also, dependable observation of the unbound compounds is important for ligand-based drug discovery, e.g. with pharmacophore modelling. Here, these questions are addressed with long (⩾0.5μs) state-of-the-art molecular dynamics (MD) simulations of 26 compounds (including 7 approved drugs) unbound in explicit solvent. These compounds were selected to be chemically diverse, with a range of flexibility, and good quality bioactive X-ray structures. The MD-simulated free compounds are compared to their bioactive structure and conformers generated with ad hoc sampling in vacuo or with implicit generalized Born (GB) aqueous solvation models. The GB conformational models clearly depart from those obtained in explicit solvent, and suffer from conformational collapse almost as severe as in vacuo. Thus, the global energy minima in vacuo or with GB are not suitable representations of the unbound state, which can instead be extensively sampled by MD simulations. Many, but not all, MD-simulated compounds displayed some structural similarity to their bioactive structure, supporting the notion of conformational pre-organization for binding. The ligand-protein complexes were also simulated in explicit solvent, to estimate ΔEReorg as an enthalpic difference ΔHReorg between the intramolecular energies in the bound and unbound states. This fresh approach yielded ΔHReorg values⩽6kcal/mol for 18 out of 26 compounds. For three particularly polar compounds 15⩽ΔHReorg⩽20kcal/mol, supporting the notion that ΔHReorg can be substantial. Those large

  19. A theoretical study on the structure, intramolecular interactions, and detonation performance of hydrazinium dinitramide.

    PubMed

    Zhang, Xueli; Liu, Yan; Wang, Fang; Gong, Xuedong

    2014-01-01

    The structures of hydrazinium dinitramide (HDN) in the gas phase and in aqueous solution have been studied at different levels of theory by using quantum chemistry. The intramolecular hydrogen-bond interactions in HDN were studied by employing the quantum theory of atoms in molecules (QTAIM), as well as those in ammonium dinitramide (ADN), hydrazinium nitroformate (HNF), and ammonium nitroformate (ANF) for comparison. The results showed that HDN possessed the strongest hydrogen bonds, with the largest hydrogen-bond energy (-47.95 kJ mol(-1)) and the largest total hydrogen-bond energy (-60.29 kJ mol(-1)). In addition, the charge transfer between the cation and the anion, the binding energy, the energy difference between the frontier orbitals, and the second-order perturbation energy of HDN were all the largest among the investigated compounds. These strongest intramolecular interactions accounted for the highest decomposition temperature of HDN among all four compounds. The IR spectra in the gas phase and in aqueous solution were very different and showed the significant influence of the solvent. The UV spectrum showed the strongest absorption at about 253 nm. An orbital-interaction diagram demonstrated that the transition of electrons mainly happened inside the anion of HDN. The detonation velocity (D=8.34 km s(-1)) and detonation pressure (P=30.18 GPa) of HDN were both higher than those of ADN (D=7.55 km s(-1) and P=24.83 GPa). The composite explosive HDN/CL-20 with the weight ratio wCL-20 /wHDN =0.388:0.612 showed the best performance (D=9.36 km s(-1) , P=39.82 GPa), which was close to that of CL-20 (D=9.73 km s(-1), P=45.19 GPa) and slightly better than that of the composite explosive ADN/CL-20 (wCL-20 /wADN =0.298:0.702, D=9.34 km s(-1), P=39.63 GPa). PMID:24108480

  20. Excited-state intramolecular proton transfer of 2-acetylindan-1,3-dione studied by ultrafast absorption and fluorescence spectroscopy

    PubMed Central

    Verma, Pramod Kumar; Steinbacher, Andreas; Schmiedel, Alexander; Nuernberger, Patrick; Brixner, Tobias

    2015-01-01

    We employ transient absorption from the deep-UV to the visible region and fluorescence upconversion to investigate the photoinduced excited-state intramolecular proton-transfer dynamics in a biologically relevant drug molecule, 2-acetylindan-1,3-dione. The molecule is a ß-diketone which in the electronic ground state exists as exocyclic enol with an intramolecular H-bond. Upon electronic excitation at 300 nm, the first excited state of the exocyclic enol is initially populated, followed by ultrafast proton transfer (≈160 fs) to form the vibrationally hot endocyclic enol. Subsequently, solvent-induced vibrational relaxation takes place (≈10 ps) followed by decay (≈390 ps) to the corresponding ground state. PMID:26798837

  1. Intramolecular fixation of t-butyl groups in thiolactim ethers influencing molecular conformation and the packing behavior

    NASA Astrophysics Data System (ADS)

    Hübscher, Jörg; Gruber, Thomas; Seichter, Wilhelm; Kortus, Jens; Weber, Edwin

    2015-07-01

    Derived from the result of a previous crystallographic study regarding an ethynylene bridged bispyrimidine, the presence of two intramolecular C-H⋯N hydrogen bonding contacts being responsible for a fixation of the terminal t-butylthio units to the azine nitrogens was noticed. Acting as stimulus, a series of different pyridine and pyridazine derivatives also featuring this unusual functionality has been synthesized and structurally studied. In order to support the investigations concerning this particular bonding pattern performed via X-ray structure analysis, calculations based on the density functional theory were carried out. It was found that the formation of the intramolecular hydrogen bonding motif has not only impact on the molecular stability but in some cases also predictably influences the reactivity and the packing behavior of the different heterocycles.

  2. Photodetachment of Zwitterions: Probing Intramolecular Coulomb Repulsion and Attraction in the Gas Phase Using Pyridinium Dicarboxylate Anions

    SciTech Connect

    Wang, Xue B.; Dacres, J E.; Yang, Xin; Broadus , K M.; Lis, Lev; Wang, Lai S.; Kass, Steven R.

    2003-10-23

    Zwitterions are critically important in many biological transformations and are used in numerous chemical processes. The consequences of electrostatic effects on reactivity and physical properties, however, are largely unknown. In this work, we report the results of negative ion photoelectron spectra of nine isomeric pyridinium dicarboxylate zwitterions and three nonzwitterionic methoxycarbonylpyridine carboxylate isomers (-O(2)CPyrCO(2)CH(3)). Information about the intramolecular electrostatic interactions was directly obtained from the photoelectron spectra. The adiabatic and vertical detachment energies were measured and understood in terms of intramolecular Coulombic forces. Calculations at the B3LYP and CCSD(T) level were performed and compared to the experimental electron binding energies. Structures, relative stabilities, and the electron detachment sites also were obtained from the calculations.

  3. (Z)-1,2-Di(1-pyrenyl)disilene: Synthesis, Structure, and Intramolecular Charge-Transfer Emission.

    PubMed

    Kobayashi, Megumi; Hayakawa, Naoki; Matsuo, Tsukasa; Li, Baolin; Fukunaga, Takeo; Hashizume, Daisuke; Fueno, Hiroyuki; Tanaka, Kazuyoshi; Tamao, Kohei

    2016-01-27

    (Z)-1,2-Di(1-pyrenyl)disilene containing bulky 1,1,3,3,5,5,7,7-octaethyl-s-hydrindacen-4-yl (Eind) groups has been obtained as purple crystals by the reductive coupling reaction of the corresponding dibromosilane with lithium naphthalenide. An X-ray crystallographic analysis revealed an Eind- and pyrenyl-meshed molecular gear around the disilene core adopting the Z configuration, in which the two pyrenyl groups intramolecularly interact through the π-π stacking with a distance of 3.635 Å between the centers of the two pyrene rings. The disilene π-system exhibits a π(Si-Si) → π*(pyrene) intramolecular charge-transfer (ICT) fluorescence at room temperature, whose wavelengths depend on the solvent polarity. The photophysical properties are theoretically supported by computational studies including excited-state calculations. PMID:26727028

  4. Kinetics and intracellular location of intramolecular disulfide bond formation mediated by the cytoplasmic redox system encoded by vaccinia virus

    SciTech Connect

    Bisht, Himani; Brown, Erica; Moss, Bernard

    2010-03-15

    Poxviruses encode a redox system for intramolecular disulfide bond formation in cytoplasmic domains of viral proteins. Our objectives were to determine the kinetics and intracellular location of disulfide bond formation. The vaccinia virus L1 myristoylated membrane protein, used as an example, has three intramolecular disulfide bonds. Reduced and disulfide-bonded forms of L1 were distinguished by electrophoretic mobility and reactivity with monoclonal and polyclonal antibodies. Because disulfide bonds formed during 5 min pulse labeling with radioactive amino acids, a protocol was devised in which dithiothreitol was present at this step. Disulfide bond formation was detected by 2 min after removal of reducing agent and was nearly complete in 10 min. When the penultimate glycine residue was mutated to prevent myristoylation, L1 was mistargeted to the endoplasmic reticulum and disulfide bond formation failed to occur. These data suggested that viral membrane association was required for oxidation of L1, providing specificity for the process.

  5. C-H bond activation with actinides: The first example of intramolecular ring bite of a pentamethylcyclopentadienyl methyl group

    SciTech Connect

    Peters, R.G.; Warner, B.P.; Scott, B.L.; Burns, C.J.

    1999-07-05

    Thermolysis of (C{sub 5}Me{sub 5}){sub 2}U({double_bond}NAd){sub 2}, 1 (Ad = 1-adamantyl), in benzene or hexane results in the intramolecular C-H bond activation of a methyl group on a pentamethylcyclopentadienyl ligand across the two imido functional groups. The product of this reaction has been spectroscopically and structurally characterized. The activation product is a reduced U(IV) metallocene bis(amide) complex with an N-bound methylene unit derived from the methyl group attached to one amide group. The activation parameters for this process have been determined; the results are consistent with a simple unimolecular process. This is the first example of intramolecular activation of a (C{sub 5}Me{sub 5}) methyl C-H bond in an actinide complex.

  6. Simulation of intramolecular hydrogen bond dynamics in manzamine A as a sensitive test for charge distribution quality.

    PubMed

    Shulga, Dmitry A; Osolodkin, Dmitry I; Palyulin, Vladimir A; Zefirov, Nikolay S

    2012-03-01

    Subtle balance of inter- and intramolecular hydrogen bond strength in aqueous solutions often governs the structure and dynamics of molecular species used as potential drugs and in supramolecular applications. In silico molecular dynamics study of water solution of manzamine A has been performed with different atomic charges in order to investigate the influence of charge distribution choice on predicting qualitative and quantitative features of the simulated systems. Various well known charge schemes (MK-ESP, RESP, Mulliken, AMI-BCC, Gasteiger-Hückel, Gasteiger-Marsili, MMFF94, and Dynamic Electronegativity Relaxation - DENR) led to qualitatively different pictures of dynamic behavior of the intramolecular hydrogen bond. The reported calculation framework represents a relatively rare case where differences in charge distributions lead to noticeable differences in simulated properties, thus providing a useful test case for force field and charge distribution development, provided high quality experiments are conducted to use as references. PMID:22545399

  7. Alkali base triggered intramolecular charge transfer metallogels based on symmetrical A-π-D-chiral-D-π-A type ligands.

    PubMed

    Dixit, Manish Kumar; Pandey, Vinay Kumar; Dubey, Mrigendra

    2016-04-13

    Three l-tartaric acid based symmetrical A-π-D-chiral-D-π-A type structural isomeric nitrobenzylidenes () have been synthesized with intent to achieve isomer specific metallogels with intramolecular charge transfer properties. Alkali metal ions in these systems not only trigger charge transfer but also play a vital role in gelation. The presence of intramolecular rather than intermolecular charge transfer as well as aggregation has been well established by various kinds of experiments using UV-vis, CD, (1)H NMR, DFT and crystallography techniques. The role of alkali metal ions in triggering ICT was proved by titration with their respective crown ethers. Notably, Na(+) afforded twisted fiber morphology whilst Li(+) gave merely long range fibers. The true gel phase material was proved by detailed rheological studies. PMID:26974120

  8. Intramolecular photoinduced proton transfer in 2-(2‧-hydroxyphenyl)benzazole family: A TD-DFT quantum chemical study

    NASA Astrophysics Data System (ADS)

    Roohi, Hossein; Mohtamedifar, Nafiseh; Hejazi, Fahemeh

    2014-11-01

    In this work, intramolecular photoinduced proton transfer in 2-(2‧-hydroxyphenyl)benzazole family (HBO, HBI and HBT) was investigated using TD-DFT calculations at PBE1PBE/6-311++G(2d,2p) level of theory. The potential energy surfaces were employed to explore the proton transfer reactions in both states. In contrast to the ground state, photoexcitation from S0 state to S1 one encourages the operation of the excited-state intramolecular proton transfer process. Structural parameters, H-bonding energy, absorption and emission bands, vertical excitation and emission energies, oscillator strength, fluorescence rate constant, dipole moment, atomic charges and electron density at critical points were calculated. Molecular orbital analysis shows that vertical S0 → S1 transition in the studied molecules corresponds essentially to the excitation from HOMO (π) to LUMO (π∗). Our calculated results are in good agreement with the experimental observations.

  9. EVAPORATION: a new vapor pressure estimation method for organic molecules including non-additivity and intramolecular interactions

    NASA Astrophysics Data System (ADS)

    Compernolle, S.; Ceulemans, K.; Müller, J.-F.

    2011-04-01

    We present EVAPORATION (Estimation of VApour Pressure of ORganics, Accounting for Temperature, Intramolecular, and Non-additivity effects), a method to predict vapour pressure p0 of organic molecules needing only molecular structure as input. The method is applicable to zero-, mono- and polyfunctional molecules. A simple formula to describe log10p0(T) is employed, that takes into account both a wide temperature dependence and the non-additivity of functional groups. In order to match the recent data on functionalised diacids an empirical modification to the method was introduced. Contributions due to carbon skeleton, functional groups, and intramolecular interaction between groups are included. Molecules typically originating from oxidation of biogenic molecules are within the scope of this method: carbonyls, alcohols, ethers, esters, nitrates, acids, peroxides, hydroperoxides, peroxy acyl nitrates and peracids. Therefore the method is especially suited to describe compounds forming secondary organic aerosol (SOA).

  10. Intramolecular photo-physical processes and spectral-luminescence properties of a dye merocyanine 540 and its complexes with water

    NASA Astrophysics Data System (ADS)

    Bazyl', O. K.; Svetlichnyi, V. A.

    2015-12-01

    Merocyanine 540 (M540) is famous dye that used in electronics and medicine. An important feature of the dye is a significant intramolecular transfer of the electron density in the excited state. Experimentally was investigated the electronic absorption and fluorescence spectra in different solvents M540. Electronic structure, spectra and rate constants of photo-physical processes of an isolated molecule and its complexes with water molecules were calculated by INDO method with spectroscopic parameterization. Analysis of the results allowed establishing the effect of individual fragments and hydrogen bonds with water on the electronic charge transfer between the terminal units in the state S1. Examination of photo-physical processes of decomposition of the fluorescent state was showed that the intramolecular processes of decay of the S1 state are not the cause of the differences calculated and experimental fluorescence quantum yield. Consideration of trans-cis photoisomerization leads to the elimination of this non-compliance.

  11. Metal-Free Visible Light-Mediated Photocatalysis: Controlling Intramolecular [2 + 2] Photocycloaddition of Enones through Axial Chirality.

    PubMed

    Clay, Anthony; Vallavoju, Nandini; Krishnan, Retheesh; Ugrinov, Angel; Sivaguru, Jayaraman

    2016-08-19

    Atropisomeric enone-imides and enone-amides featuring N-CAryl bond rotation were evaluated for intramolecular [2 + 2] photocycloaddition. Straight addition product was observed over cross-addition product with good control over reactivity. The atropselectivity was found to be dependent on the substituent on the aryl ring. Substitution-dependent atropselectivity was rationalized on the basis of a divergent mechanistic pathway. PMID:27382920

  12. Visible-light photoredox intramolecular difluoroacetamidation: facile synthesis of 3,3-difluoro-2-oxindoles from bromodifluoroacetamides.

    PubMed

    Wei, Xiao-Jing; Wang, Lin; Du, Shao-Fu; Wu, Li-Zhu; Liu, Qiang

    2016-02-21

    We report an operationally simple, visible-light-driven protocol for intramolecular C-H difluoroacetamidation of arenes for the synthesis of biologically relevant 3,3-difluoro-2-oxindoles at room temperature. Using fac-Ir(ppy)3 as a photocatalyst and a 3 W blue LED as a light source, an array of difluoroxindoles was prepared from rapidly available tertiary aryl bromodifluoroacetamides in moderate to excellent yields. PMID:26794806

  13. Atroposelective formation of dibenz[c,e]azepines via intramolecular direct arylation with centre-axis chirality transfer.

    PubMed

    Cheetham, Caroline A; Massey, Richard S; Pira, Silvain L; Pritchard, Robin G; Wallace, Timothy W

    2011-03-21

    5-Substituted 6,7-dihydrodibenz[c,e]azepines, a class of secondary amine incorporating a centre-axis chirality relay, are accessible from 1-substituted N-(2-bromobenzyl)-1-phenylmethanamines via N-acylation and ring-closing intramolecular direct arylation. The ring closure proceeds with high atropodiastereoselectivity due to strain effects that are induced by trigonalisation of the nitrogen atom, as predicted using molecular mechanics calculations. PMID:21267501

  14. Approach to interfacial and intramolecular electron transfer of the diheme protein cytochrome c4 assembled on Au(111) surfaces.

    PubMed

    Chi, Qijin; Zhang, Jingdong; Arslan, Taner; Borg, Lotte; Pedersen, Gert W; Christensen, Hans E M; Nazmudtinov, Renat R; Ulstrup, Jens

    2010-04-29

    Intramolecular electron transfer (ET) between metal centers is a core feature of large protein complexes in photosynthesis, respiration, and redox enzyme catalysis. The number of microscopic redox potentials and ET rate constants is, however, prohibitive for experimental cooperative ET mapping, but two-center proteins are simple enough to offer complete communication networks. At the same time, multicenter redox proteins operate in membrane environments where conformational dynamics may lead to gated ET features different from conditions in homogeneous solution. The bacterial respiratory diheme protein Pseudomonas stutzeri cytochrome c(4) has been a target for intramolecular, interheme ET. We report here voltammetric and in situ scanning tunneling microscopy (STM) data for P. stutzeri cyt c(4) at single-crystal, atomically planar Au(111)-electrode surfaces modified by variable-length omega-mercapto-alkanoic carboxylic acids. As evidenced by in situ STM, the strongly dipolar protein is immobilized in a close to vertical orientation at this surface with the positively charged high-potential heme domain adjacent to the electrode. This orientation gives asymmetric voltammograms with two one-ET peaks in the cathodic direction and a single two-ET peak in the anodic direction. Intramolecular, interheme ET with high, 8,000-30,000 s(-1), rate constants is notably an essential part of this mechanism. The high rate constants are in striking contrast to ET reactions of P. stutzeri cyt c(4) with small reaction partners in homogeneous solution for which kinetic analysis clearly testifies to electrostatic cooperative effects but no intramolecular, interheme ET higher than 0.1-10 s(-1). This difference suggests a strong gating feature of the process. On the basis of the three-dimensional structure of P. stutzeri cyt c(4), gating is understandable due to the through-space, hydrogen-bonded electronic contact between the heme propionates which is highly sensitive to environmental

  15. Palladium-Catalyzed Highly Chemoselective Intramolecular C-H Aminocarbonylation of Phenethylamines to Six-Membered Benzolactams.

    PubMed

    Taneda, Hiroshi; Inamoto, Kiyofumi; Kondo, Yoshinori

    2016-06-01

    A palladium-catalyzed highly selective intramolecular C-H aminocarbonylation of Br-functionalized phenethylamines in the presence of CO was achieved while leaving the C-Br bond unreacted to afford six-membered benzolactams with good to high yields. The remaining C-Br group in the cyclized product was successfully used as a reactive center for further functionalization through various palladium-catalyzed coupling reactions. PMID:27214155

  16. Control of intramolecular π-π stacking interaction in cationic iridium complexes via fluorination of pendant phenyl rings.

    PubMed

    He, Lei; Ma, Dongxin; Duan, Lian; Wei, Yongge; Qiao, Juan; Zhang, Deqiang; Dong, Guifang; Wang, Liduo; Qiu, Yong

    2012-04-16

    Intramolecular π-π stacking interaction in one kind of phosphorescent cationic iridium complexes has been controlled through fluorination of the pendant phenyl rings on the ancillary ligands. Two blue-green-emitting cationic iridium complexes, [Ir(ppy)(2)(F2phpzpy)]PF(6) (2) and [Ir(ppy)(2)(F5phpzpy)]PF(6) (3), with the pendant phenyl rings on the ancillary ligands substituted with two and five fluorine atoms, respectively, have been synthesized and compared to the parent complex, [Ir(ppy)(2)(phpzpy)]PF(6) (1). Here Hppy is 2-phenylpyridine, F2phpzpy is 2-(1-(3,5-difluorophenyl)-1H-pyrazol-3-yl)pyridine, F5phpzpy is 2-(1-pentafluorophenyl-1H-pyrazol-3-yl)-pyridine, and phpzpy is 2-(1-phenyl-1H-pyrazol-3-yl)pyridine. Single crystal structures reveal that the pendant phenyl rings on the ancillary ligands stack to the phenyl rings of the ppy ligands, with dihedral angles of 21°, 18°, and 5.0° between least-squares planes for complexes 1, 2, and 3, respectively, and centroid-centroid distances of 3.75, 3.65, and 3.52 Å for complexes 1, 2, and 3, respectively, indicating progressively reinforced intramolecular π-π stacking interactions from complexes 1 to 2 and 3. Compared to complex 1, complex 3 with a significantly reinforced intramolecular face-to-face π-π stacking interaction exhibits a significantly enhanced (by 1 order of magnitude) photoluminescent efficiency in solution. Theoretical calculations reveal that in complex 3 it is unfavorable in energy for the pentafluorophenyl ring to swing by a large degree and the intramolecular π-π stacking interaction remains on the lowest triplet state. PMID:22462475

  17. Energetic aminated-azole assemblies from intramolecular and intermolecular N-HO and N-HN hydrogen bonds.

    PubMed

    He, Chunlin; Yin, Ping; Mitchell, Lauren A; Parrish, Damon A; Shreeve, Jean'ne M

    2016-06-21

    Compounds with adjacent C-NO2, C-NH2 and N-NH2 groups were designed and synthesized via amination. Their structures were characterized by infrared, and multinuclear NMR spectroscopy, elemental analysis, and X-ray single crystal diffraction. The effect of intramolecular and intermolecular N-HO and N-HN hydrogen bonds is discussed. Detonation properties were calculated by EXPLO 5 software based on calculated HOFs and experimental densities. PMID:27270751

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

    PubMed

    Ito, Hironobu; Tanimura, Yoshitaka

    2016-02-21

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

  19. Synthesis of 4H-chromenes by an unexpected, K3PO4-mediated intramolecular Rauhut-Currier type reaction.

    PubMed

    Bhunia, Anup; Yetra, Santhivardhana Reddy; Gonnade, Rajesh G; Biju, Akkattu T

    2016-06-28

    In an attempt to develop the umpolung of Michael acceptors using chalcones having an enoate moiety under N-heterocyclic carbene (NHC) catalysis, a K3PO4-mediated intramolecular Rauhut-Currier type reaction was observed. This C(sp(2))-C(sp(2)) coupling reaction afforded the biologically important 4H-chromenes in moderate to good yields. It is likely that the enol ether functionality acts as the nucleophilic trigger in this reaction. PMID:27109318

  20. Intramolecular Hgπ interactions of d-character with non-bridging atoms in mercury-aryl complexes.

    PubMed

    Lannes, A; Manceau, A; Rovezzi, M; Glatzel, P; Joly, Y; Gautier-Luneau, I

    2016-09-28

    Mercury 5d-orbitals are involved in intramolecular π-interactions with carbon and sulfur nearest and next-nearest neighbors in mercury-aryl complexes. This unexpected character of the electron cloud of mercury was revealed by high energy-resolution XANES spectroscopy readily interpreted in terms of a final-state local (l,m)-projected density of states (DOS). PMID:27541854

  1. A conformationally persistent pseudo-bicyclic guanidinium for anion coordination as stabilized by dual intramolecular hydrogen bonds

    SciTech Connect

    Seipp, Charles A.; Williams, Neil J.; Bryantsev, Vyacheslav S.; Custelcean, Radu; Moyer, Bruce A.

    2015-11-30

    In this paper, the first example of a pseudo-bicyclic guanidinium ligand is reported. When bound to an anion, the N,N'-bis(2-pyridyl)guanidinium cation persistently adopts the planar α,α conformation featuring intramolecular N···H–N–H···N hydrogen bonds in the solid state, which facilitates crystallization of sulphate from aqueous mixtures of anions.

  2. Probing the critical residues for intramolecular fructosyl transfer reaction of a levan fructotransferase.

    PubMed

    Moon, Keum-Ok; Choi, Kyoung-Hwa; Kang, Ho-Young; Oh, Jeong-Il; Jang, Se Bok; Park, Cheon-Seok; Lee, Jong-Hoon; Cha, Jaeho

    2008-06-01

    Levan fructotransferase (LFTase) preferentially catalyzes the transfructosylation reaction in addition to levan hydrolysis, whereas other levan-degrading enzymes hydrolyze levan into a levan-oligosaccharide and fructose. Based on sequence comparisons and enzymatic properties, the fructosyl transfer activity of LFTase is proposed to have evolved from levanase. In order to probe the residues that are critical to the intramolecular fructosyl transfer reaction of the Microbacterium sp. AL-210 LFTase, an error-prone PCR mutagenesis process was carried out, and the mutants that led to a shift in activity from transfructosylation towards hydrolysis of levan were screened by the DNS method. After two rounds of mutagenesis, TLC and HPLC analyses of the reaction products by the selected mutants revealed two major products; one is a di-D-fructose- 2,6':6,2'-dianhydride (DFAIV) and the other is a levanbiose. The newly detected levanbiose corresponds to the reaction product from LFTase lacking transferring activity. Two mutants (2-F8 and 2-G9) showed a high yield of levanbiose (38-40%) compared with the wild-type enzyme, and thus behaved as levanases. Sequence analysis of the individual mutants responsible for the enhanced hydrolytic activity indicated that Asn-85 was highly involved in the transfructosylation activity of LFTase. PMID:18600048

  3. Transition metal-free intramolecular regioselective couplings of aliphatic and aromatic C-H bonds.

    PubMed

    Tian, Hua; Yang, Haijun; Zhu, Changjin; Fu, Hua

    2016-01-01

    Cross-dehydrogenative couplings of two different C-H bonds have emerged as an attractive goal in organic synthesis. However, achieving regioselective C-H activation is a great challenge because C-H bonds are ubiquitous in organic compounds. Actually, the regioselective couplings promoted by enzymes are a common occurrence in nature. Herein, we have developed simple, efficient and general transition metal-free intramolecular couplings of alphatic and aromatic C-H bonds. The protocol uses readily available aryl triazene as the radical initiator, cheap K2S2O8 as the oxidant, and the couplings were performed well with excellent tolerance of functional groups. Interestingly, α-carbon configuration of some amino acid residues in the substrates was kept after the reactions, and the couplings for substrates with substituted phenylalanine residues exhibited complete β-carbon diastereoselectivity for induction of the chiral α-carbon. Therefore, the present study should provide a novel strategy for regioselective cross-dehydrogenative couplings of two different C-H bonds. PMID:26822836

  4. Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation

    PubMed Central

    Tailford, Louise E.; Owen, C. David; Walshaw, John; Crost, Emmanuelle H.; Hardy-Goddard, Jemma; Le Gall, Gwenaelle; de Vos, Willem M.; Taylor, Garry L.; Juge, Nathalie

    2015-01-01

    The gastrointestinal mucus layer is colonized by a dense community of microbes catabolizing dietary and host carbohydrates during their expansion in the gut. Alterations in mucosal carbohydrate availability impact on the composition of microbial species. Ruminococcus gnavus is a commensal anaerobe present in the gastrointestinal tract of >90% of humans and overrepresented in inflammatory bowel diseases (IBD). Using a combination of genomics, enzymology and crystallography, we show that the mucin-degrader R. gnavus ATCC 29149 strain produces an intramolecular trans-sialidase (IT-sialidase) that cleaves off terminal α2-3-linked sialic acid from glycoproteins, releasing 2,7-anhydro-Neu5Ac instead of sialic acid. Evidence of IT-sialidases in human metagenomes indicates that this enzyme occurs in healthy subjects but is more prevalent in IBD metagenomes. Our results uncover a previously unrecognized enzymatic activity in the gut microbiota, which may contribute to the adaptation of intestinal bacteria to the mucosal environment in health and disease. PMID:26154892

  5. Lipid Regulated Intramolecular Conformational Dynamics of SNARE-Protein Ykt6

    PubMed Central

    Dai, Yawei; Seeger, Markus; Weng, Jingwei; Song, Song; Wang, Wenning; Tan, Yan-Wen

    2016-01-01

    Cellular informational and metabolic processes are propagated with specific membrane fusions governed by soluble N-ethylmaleimide sensitive factor attachment protein receptors (SNARE). SNARE protein Ykt6 is highly expressed in brain neurons and plays a critical role in the membrane-trafficking process. Studies suggested that Ykt6 undergoes a conformational change at the interface between its longin domain and the SNARE core. In this work, we study the conformational state distributions and dynamics of rat Ykt6 by means of single-molecule Förster Resonance Energy Transfer (smFRET) and Fluorescence Cross-Correlation Spectroscopy (FCCS). We observed that intramolecular conformational dynamics between longin domain and SNARE core occurred at the timescale ~200 μs. Furthermore, this dynamics can be regulated and even eliminated by the presence of lipid dodecylphoshpocholine (DPC). Our molecular dynamic (MD) simulations have shown that, the SNARE core exhibits a flexible structure while the longin domain retains relatively stable in apo state. Combining single molecule experiments and theoretical MD simulations, we are the first to provide a quantitative dynamics of Ykt6 and explain the functional conformational change from a qualitative point of view. PMID:27493064

  6. Effect of ionophores on the rate of intramolecular cation exchange in durosemiquinone ion pairs

    NASA Technical Reports Server (NTRS)

    Eastman, M. P.; Bruno, G. V.; Mcguyer, C. A.; Gutierrez, A. R.; Shannon, J. M.

    1979-01-01

    The effects of the ionophores 15-crown-5 (15C5), 18-crown-6 (18C6), dibenzo-18-crown-6 (DBC) and cryptand 222 (C222) on intramolecular cation exchange in ion pairs of the sodium salt of the durosemiquinone anion in benzene solution are investigated. Electron paramagnetic resonance spectra of the 18C6 and 15C5 complexes with durosemiquinone reduced by contact with a sodium mirror show an alternating line width which indicates that the sodium ion is being exchanged between equivalent sites near the oxygens of the semiquinone with activation energies of 8.7 and 6.0 kcal/mole and Arrhenius preexponential factors of 9 x 10 to the 12th/sec and 10 to the 12th/sec, respectively. Spectra obtained for the DBC complexes show no evidence of exchange, while those of C222 indicate rapid exchange. It is also noted that the hyperfine splitting constants measured do not change over the 50-K temperature interval studied.

  7. Femtosecond Heterodyne Transient Grating Spectroscopic Studies of Intramolecular Charge Transfer Character of Peridinin and Peridinin Analogs

    NASA Astrophysics Data System (ADS)

    Bishop, Michael; Khosravi, Soroush; Obaid, Razib; Whitelock, Hope; Carroll, Ann Marie; Lafountain, Amy; Frank, Harry; Beck, Warren; Gibson, George; Berrah, Nora

    2016-05-01

    The peridinin chlorophyll-a protein is a light harvesting complex found in several species of dinoflagellates. Peridinin absorbs strongly in the mid-visible spectral region and, despite the lack of a strong permanent dipole moment in its lowest energy excited state, is able to transfer excitation energy quickly and efficiently to chlorophyll-a. It is believed that the high efficiency arises from the development of intramolecular charge-transfer (ICT) character upon photoexcitation. Recently, heterodyne transient grating spectroscopy has been used to study the ultrafast (<50 fs) dynamics of β carotene and peridinin. The studies show evidence for a structurally displaced intermediate in both cases and strong ICT character in the case of peridinin, but up to now the work has not provided appropriate control experiments. The present experiments examine peridinin and two peridinin analogs, S1-peridinin and S2-peridinin. S1-peridinin is reported to have greatly diminished ICT character, and S2-peridinin is reported to have little-or-no ICT character. Heterodyne transient grating data will be presented and provide a more unambiguous characterization spectral and kinetic properties associated with the peridinin ICT state. Funded by the DoE-BES, Grant No. DE-SC0012376.

  8. Protein docking using an ensemble of spin labels optimized by intra-molecular paramagnetic relaxation enhancement.

    PubMed

    Schilder, Jesika; Liu, Wei-Min; Kumar, Pravin; Overhand, Mark; Huber, Martina; Ubbink, Marcellus

    2016-02-17

    Paramagnetic NMR is a useful technique to study proteins and protein complexes and the use of paramagnetic relaxation enhancement (PRE) for this purpose has become wide-spread. PREs are commonly generated using paramagnetic spin labels (SLs) that contain an unpaired electron in the form of a nitroxide radical, with 1-oxyl-2,2,5,5-tetramethyl-2,5-dihydropyrrol-3-ylmethyl methane thiosulfonate (MTSL) being the most popular tag. The inherent flexibility of the SL causes sampling of several conformations in solution, which can be problematic as over- or underestimation of the spatial distribution of the unpaired electron in structural calculations will lead to errors in the distance restraints. We investigated the effect of this mobility on the accuracy of protein-protein docking calculations using intermolecular PRE data by comparing MTSL and the less mobile 3-methanesulfonilthiomethyl-4-(pyridin-3-yl)-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-1-yloxyl (pyMTSL) on the dynamic complex of cytochrome c and cytochrome c peroxidase. No significant differences were found between the two SLs. Docking was performed using either single or multiple conformers and either fixed or flexible SLs. It was found that mobility of the SLs is the limiting factor for obtaining accurate solutions. Optimization of SL conformer orientations using intra-molecular PRE improves the accuracy of docking. PMID:26356049

  9. Controlling the Conformational Changes in Donor–Acceptor [4]-Dendralenes through Intramolecular Charge-Transfer Processes

    PubMed Central

    Kanibolotsky, Alexander L; Forgie, John C; McEntee, Greg J; Talpur, M Munsif A; Skabara, Peter J; Westgate, Thomas DJ; McDouall, Joseph JW; Auinger, Michael; Coles, Simon J; Hursthouse, Michael B

    2009-01-01

    The synthesis of two [4]-dendralene compounds incorporating thiophene-(p-nitrophenyl) donor–acceptor units is presented. The dendralenes adopt two different conformers in solution and solid state and the transformation between the structures can be controlled by light and heat. The electron-donating components of the dendralenes are represented by bromothienyl (in 13) and ethylenedioxythiophene(EDOT)-thienyl (in 15) end-groups. The most facile transformation involves the isomerisation of donor–acceptor conjugated systems (a conformers) into structures in which only the thiophenes are conjugated (b conformers), and this process is driven by ambient light. The structures of the two conformers of compound 13 are confirmed by single-crystal X-ray diffraction studies and the structural changes in both compounds have been monitored by 1H NMR spectroscopy and absorption studies. The transformations were found to be first-order processes with rate constants of k = 0.0027 s−1 and k = 0.00022 s−1 for 13 and 15, respectively. Density functional theory calculations at the B3LYP/6-31G∗ level give credence to the proposed mechanism for the a→b conversion, which involves photoinduced intramolecular charge transfer (ICT) as the key step. The EDOT derivative (15) can be polymerised by electrochemical oxidation and a combination of cyclic voltammetry and UV/Vis spectroelectrochemical experiments indicate that the a conformer can be trapped and stabilised in the solid state. PMID:19760710

  10. Structures, folding patterns, and functions of intramolecular DNA G-quadruplexes found in eukaryotic promoter regions

    PubMed Central

    Qin, Yong; Hurley, Laurence H.

    2008-01-01

    In its simplest form, a DNA G-quadruplex is a four-stranded DNA structure that is composed of stacked guanine tetrads. G-quadruplex-forming sequences have been identified in eukaryotic telomeres, as well as in non-telomeric genomic regions, such as gene promoters, recombination sites, and DNA tandem repeats. Of particular interest are the G-quadruplex structures that form in gene promoter regions, which have emerged as potential targets for anticancer drug development. Evidence for the formation of G-quadruplex structures in living cells continues to grow. In this review, we examine recent studies on intramolecular G-quadruplex structures that form in the promoter regions of some human genes in living cells and discuss the biological implications of these structures. The identification of G-quadruplex structures in promoter regions provides us with new insights into the fundamental aspects of G-quadruplex topology and DNA sequence–structure relationships. Progress in G-quadruplex structural studies and the validation of the biological role of these structures in cells will further encourage the development of small molecules that target these structures to specifically modulate gene transcription. PMID:18355457

  11. Streptomyces clavuligerus HlmI is an intramolecular disulfide-forming dithiol oxidase in holomycin biosynthesis.

    PubMed

    Li, Bo; Walsh, Christopher T

    2011-05-31

    Holomycin and related dithiolopyrrolone antibiotics display broad-spectrum antimicrobial activities and contain a unique 5,5-bicyclic ring structure with an N-acylated aminopyrrolone fused to a cyclic ene-disulfide. Here we show that the intramolecular disulfide bridge is constructed from the acyclic ene-dithiol at a late stage in the pathway by a thioredoxin oxidoreductase-like enzyme HlmI from the holomycin producer Streptomyces clavuligerus. Recombinant HlmI was purified from E. coli with bound flavin adenine dinucleotide (FAD) and converts reduced holomycin to holomycin utilizing O(2) as cosubstrate. As a dithiol oxidase, HlmI is functionally homologous to GliT and DepH, which perform a similar dithiol to disulfide oxidation in the biosynthesis of fungal natural product gliotoxin and epigenetic regulator compound FK228, respectively. Deletion of the hlmI gene in the wild type S. clavuligerus and in a holomycin-overproducing mutant resulted in decreased level of holomycin production and increased sensitivity toward holomycin, suggesting a self-protection role of HlmI in the holomycin biosynthetic pathway. HlmI belongs to a new clade of uncharacterized thioredoxin oxidoreductase-like enzymes, distinctive from the GliT-like enzymes and the DepH-like enzymes, and represents a third example of oxidoreductases that catalyzes disulfide formation in the biosynthesis of small molecules. PMID:21504228

  12. Transition metal-free intramolecular regioselective couplings of aliphatic and aromatic C-H bonds

    PubMed Central

    Tian, Hua; Yang, Haijun; Zhu, Changjin; Fu, Hua

    2016-01-01

    Cross-dehydrogenative couplings of two different C-H bonds have emerged as an attractive goal in organic synthesis. However, achieving regioselective C-H activation is a great challenge because C-H bonds are ubiquitous in organic compounds. Actually, the regioselective couplings promoted by enzymes are a common occurrence in nature. Herein, we have developed simple, efficient and general transition metal-free intramolecular couplings of alphatic and aromatic C-H bonds. The protocol uses readily available aryl triazene as the radical initiator, cheap K2S2O8 as the oxidant, and the couplings were performed well with excellent tolerance of functional groups. Interestingly, α-carbon configuration of some amino acid residues in the substrates was kept after the reactions, and the couplings for substrates with substituted phenylalanine residues exhibited complete β-carbon diastereoselectivity for induction of the chiral α-carbon. Therefore, the present study should provide a novel strategy for regioselective cross-dehydrogenative couplings of two different C-H bonds. PMID:26822836

  13. On the nature of intramolecular vibrational energy transfer in dense molecular environments

    NASA Astrophysics Data System (ADS)

    von Benten, Rebekka S.; Abel, Bernd

    2010-12-01

    Transient femtosecond-IR-pump-UV-absorption probe-spectroscopy has been employed to shed light on the nature of intramolecular vibrational energy transfer (IVR) in dense molecular environments ranging from the diluted gas phase to the liquid. A general feature in our experiments and those of others is that IVR proceeds via multiple timescales if overtones or combination vibrations of high frequency modes are excited. It has been found that collisions enhance IVR if its (slower) timescales can compete with collisions. This enhancement is, however, much more weaker and rather inefficient as opposed to the effect of collisions on intermolecular energy transfer which is well known. In a series of experiments we found that IVR depends not significantly on the average energy transferred in a collision but rather on the number of collisions. The collisions are much less efficient in affecting IVR than VET. We conclude that collision induced broadening of vibrational energy levels reduces the energy gaps and enhances existing couplings between tiers. The present results are an important step forward to rationalize and understand apparently different and not consistent results from different groups on different molecular systems between gas and liquid phases.

  14. Fluorescence sensing of anions based on inhibition of excited-state intramolecular proton transfer.

    PubMed

    Wu, Yunkou; Peng, Xiaojun; Fan, Jiangli; Gao, Shang; Tian, Maozhong; Zhao, Jianzhang; Sun, Shiguo

    2007-01-01

    Condensation of 2-(2'-aminophenyl)benzoxazole with p-toluenesulfonyl chloride and phenyl isocyanate yields two new anion sensors (TABO and PUBO), which can undergo excited-state intramolecular proton transfer (ESIPT) upon excitation. For the acid receptor TABO, the ESIPT process can be readily disturbed by basic anions such as F-, CH3COO-, and H2PO4- by deprotonating the sulfonamide unit, whereas in the case of PUBO, a good hydrogen-bonding donor, the ESIPT process is inhibited either by the fluoride-induced deprotonation of the urea unit or by the formation of a strong CH3COO--urea intermolecular hydrogen bond complex, and these two types of inhibition mechanisms consequently result in different ratiometric responses. But other anions with less hydrogen-bonding acceptor abilities cannot inhibit the ESIPT. Interestingly, the different inhibition abilities of F-, CH3COO-, and H2PO4- produce different spectral behaviors in PUBO, so this new sensor successfully distinguishes the subtle difference in these three anionic substrates of similar basicity and surface charge density. PMID:17194082

  15. Triggered Excited-State Intramolecular Proton Transfer Fluorescence for Selective Triplex DNA Recognition.

    PubMed

    Wang, Ying; Hu, Yuehua; Wu, Tao; Zhou, Xiaoshun; Shao, Yong

    2015-12-01

    The triplex DNA has received much interest due to its various applications in gene regulation, molecular switch, and sensor development. However, realizing a highly selective recognition using a fluorescence probe specific only for the triplex topology is still a great challenge. Herein, we found that relative to the structural analogues of natural robinetin, myricetin, quercetin, kaempferol, morin, rutin, baicalin, luteolin, naringenin, genistein, chrysin, galangin, isorhamnetin, and several synthetic flavonoids, fisetin (FIS) is the brightest emitter when targeting the triplex DNA in contrast to binding with ss-DNA, ds-DNA (with or without an abasic site), i-motif, and DNA/RNA G-quadruplexes. Only the triplex association triggers the FIS green fluorescence that is relaxed from the tautomer favorable for excited-state intramolecular proton transfer (ESIPT). FIS can stabilize the triplex structure and primarily interact with the two terminals of the triplex via a 2:1 binding mode. This work demonstrates the potential of FIS as a DNA structure-selective switch-on ESIPT probe when evolving the triplex-forming oligonucleotides and developing the novel triplex-based sensors and switches. PMID:26556582

  16. Intramolecular charge transfer of push-pull pyridinium salts in the triplet manifold.

    PubMed

    Carlotti, Benedetta; Consiglio, Giuseppe; Elisei, Fausto; Fortuna, Cosimo G; Mazzucato, Ugo; Spalletti, Anna

    2014-09-11

    The solvent effect on the triplet state properties of the iodides of three trans (E) isomers of 2-D-vinyl-1-methylpyridinium, where D is a donor group (4-(dimethylamino)phenyl, 3,4,5-trimethoxyphenyl, and 1-pyrenyl), was studied by nanosecond transient absorption techniques. The results obtained allowed us to complete a previous study on the negative solvatochromism and the role of the solvent-controlled intramolecular charge transfer (ICT) relaxation pathways in the excited singlet state, carried out by ultrafast absorption techniques and DFT calculations (J. Phys. Chem. A 2014, 118, 3580-3592 ). The solvent effect on the intersystem crossing to the triplet manifold gave information on the competition of the relaxation processes in the singlet and triplet states and the extent and mechanism of the photoreactive deactivation, particularly operative for the pyrenyl derivative. For the latter the results showed that the ICT process also occurs in the triplet manifold. In fact, the formation of two triplet states with different nature and affected differently by oxygen was observed for the pyrenyl derivative in water and assigned to the (3)LE* and (3)ICT* states. The related structure and solvent effects on the trans → cis photoisomerization are briefly discussed. PMID:25146975

  17. Identifying tips for intramolecular NC-AFM imaging via in situ fingerprinting

    NASA Astrophysics Data System (ADS)

    Sang, Hongqian; Jarvis, Samuel P.; Zhou, Zhichao; Sharp, Peter; Moriarty, Philip; Wang, Jianbo; Wang, Yu; Kantorovich, Lev

    2014-10-01

    A practical experimental strategy is proposed that could potentially enable greater control of the tip apex in non-contact atomic force microscopy experiments. It is based on a preparation of a structure of interest alongside a reference surface reconstruction on the same sample. Our proposed strategy is as follows. Spectroscopy measurements are first performed on the reference surface to identify the tip apex structure using a previously collected database of responses of different tips to this surface. Next, immediately following the tip identification protocol, the surface of interest is studied (imaging, manipulation and/or spectroscopy). The prototype system we choose is the mixed Si(111)-7×7 and surface which can be prepared on the same sample with a controlled ratio of reactive and passivated regions. Using an ``in silico'' approach based on ab initio density functional calculations and a set of tips with varying chemical reactivities, we show how one can perform tip fingerprinting using the Si(111)-7×7 reference surface. Then it is found by examining the imaging of a naphthalene tetracarboxylic diimide (NTCDI) molecule adsorbed on surface that negatively charged tips produce the best intramolecular contrast attributed to the enhancement of repulsive interactions.

  18. On prediction of OH stretching frequencies in intramolecularly hydrogen bonded systems

    NASA Astrophysics Data System (ADS)

    Hansen, Poul Erik; Spanget-Larsen, Jens

    2012-06-01

    OH stretching frequencies are investigated for a series of non-tautomerizing systems with intramolecular hydrogen bonds. Effective OH stretching wavenumbers are predicted by the application of empirical correlation procedures based on the results of B3LYP/6-31G(d) theoretical calculations in the harmonic and PT2 anharmonic approximations, as well as on experimental NMR parameters, i.e., proton chemical shifts (δH) and two-bond deuterium isotope effects on 13C chemical shifts (2ΔCOD). The procedures are applied in a discussion of the spectra of 2,6-dihydroxy-4-methylbenzaldehyde and 8-hydroxyquinoline N-oxide. The spectrum of the former displays a broad, composite band between 3500 and 2500 cm-1 which can be assigned to overlapping monomer and dimer contributions. In the latter case, the results support a reassignment of the OH stretching band of 8-hydroxyquinoline N-oxide; the reassignment is supported by correlation with the IR spectra of a series of substituted derivatives.

  19. Molecular Structure and Photoinduced Intramolecular Hydrogen Bonding in 2-Pyrrolylmethylidene Cycloalkanones.

    PubMed

    Sigalov, Mark; Shainyan, Bagrat; Chipanina, Nina; Oznobikhina, Larisa; Strashnikova, Natalia; Sterkhova, Irina

    2015-11-01

    The structures of pyrrolylmethylidene derivatives of 2,3-dihydro-1H-inden-1-one (3), 3,4-dihydro-naphthalen-1(2H)-one (4), and cycloalkanones (5-7) were studied for the first time in the solid state and solution by NMR, IR, and UV spectroscopies supported by DFT quantum mechanical calculations. It was shown that all studied compounds except cycloheptanone derivative 7 both in crystal and in solution exist in the form of dimers where single E or E,E configuration with respect to the exocyclic C═C bond is stabilized by intermolecular hydrogen bonds N-H···O═C. UV irradiation at a wavelength of 365 nm of MeCN or DMSO solutions of 3-6 results, depending on the exposition time and solvent, partial to complete isomerization to the Z or Z,E isomers (in the case of 6, also the Z,Z isomer). The NMR and IR spectroscopy data show the existence of a strong intramolecular hydrogen bond N-H···O═C in the Z moieties of isomerized compounds. The studied compounds are protonated by trifluoroacetic acid at the carbonyl oxygen, in spite of the reverse order of basicity and nucleophilicity of the carbonyl group and the pyrrole ring. Investigation of the behavior of compound 6 with respect to acetate and fluoride anions allows one to consider it as a potential fluoride sensor. PMID:26457975

  20. Carbene-dichlorosilylene stabilized phosphinidenes exhibiting strong intramolecular charge transfer transition.

    PubMed

    Roy, Sudipta; Stollberg, Peter; Herbst-Irmer, Regine; Stalke, Dietmar; Andrada, Diego M; Frenking, Gernot; Roesky, Herbert W

    2015-01-14

    The unstable species dichlorosilylene was previously stabilized by carbene. The lone pair of electrons on the silicon atom of (carbene)SiCl2 can form a coordinate bond with metal-carbonyls. Herein we report that (carbene)SiCl2 can stabilize a phosphinidene (Ar-P, a carbone analogue) with the general formula carbene→SiCl2→P-Ar (carbene = cyclic alkyl(amino) carbene (cAAC; 2) and N-heterocyclic carbene (NHC; 3)). Compounds 2 and 3 are stable, isolable, and storable at 0 °C (2) to room temperature (3) under an inert atmosphere. The crystals of 2 and 3 are dark blue and red, respectively. The intense blue color of 2 arises due to the strong intramolecular charge transfer (ICT) transition from πSi═P→π*cAAC. The electronic structure and bonding of 2, 3 were studied by theoretical calculations. The HOMO of the molecule is located on the πSi═P bond, while the LUMO is located at the carbene moiety (cAAC or NHC). The dramatic change in color of these compounds from red (3, NHC) to blue (2, cAAC) is ascribed to the difference in energy of the LUMO within the carbenes (cAAC/NHC) due to a lower lying LUMO of cAAC. PMID:25539016

  1. Effect of the intramolecular hydrogen bond on the spectral and optical properties in chitosan oligosaccharide

    NASA Astrophysics Data System (ADS)

    Li, Xin; Yang, Mengshi; Shi, Xiao; Chu, Xiuxiang; Chen, Liang; Wu, Qiang; Wang, Yueyue

    2015-05-01

    The geometric structures, hydrogen bond types, IR spectra and nonlinear optical properties of chitosan oligosaccharide (degree of polymerization 2-5) are studied by density-functional theory (DFT) at B3LYP/6-31+G(d) level. We have analyzed the statistics of relationship between IR spectra and bond lengths, and angles of amino, hydroxyl. The results show that: (1) the active groups C3-OH, C6-OH and -NH2 can form intramolecular hydrogen bond in chitosan oligosaccharide; (2) the IR spectra of three active groups have size effect in growth process, however, its IR intensity increases significantly and IR frequencies are red shifted obviously when the active hydroxyl form hydrogen bonds, because the bond length of active hydroxyl becomes longer; (3) the effect of hydrogen bond on intensity and frequency of the three vibration mode of amino is the main factor and complication. The paper also provides the nonlinear optical properties of chitosan oligosaccharide. The reason why hydrogen bond can make an appreciable difference to IR spectra, and the nonlinear optical properties of chitosan oligosaccharide are discussed. This research has important significance in the characterization of chitosan oligosaccharide, the properties of chitosan material and hydrogen bond by infrared spectroscopy.

  2. Polymer globule with fractal properties caused by intramolecular nanostructuring and spatial constrains.

    PubMed

    Glagoleva, Anna A; Vasilevskaya, Valentina V; Khokhlov, Alexei R

    2016-06-21

    By means of computer simulation, we studied macromolecules composed of N dumbbell amphiphilic monomer units with attractive pendant groups. In poor solvents, these macromolecules form spherical globules that are dense in the case of short chains (the gyration radius RG∼N(1/3)), or hollow inside and obey the RG∼N(1/2) law when the macromolecules are sufficiently long. Due to the specific intramolecular nanostructuring, the vesicle-like globules of long amphiphilic macromolecules posses some properties of fractal globules, by which they (i) could demonstrate the same scaling statistics for the entire macromolecule and for short subchains with m monomer units and (ii) possess a specific territorial structure. Within a narrow slit, the globule loses its inner cavity, takes a disk-like shape and scales as N(1/2) for much shorter macromolecules. However, the field of end-to-end distance r(m) ∼m(1/2) dependence for subchains becomes visibly smaller. The results obtained were compared with the homopolymer case. PMID:27198966

  3. A manganese catalyst for highly reactive yet chemoselective intramolecular C(sp3)-H amination

    NASA Astrophysics Data System (ADS)

    Paradine, Shauna M.; Griffin, Jennifer R.; Zhao, Jinpeng; Petronico, Aaron L.; Miller, Shannon M.; Christina White, M.

    2015-12-01

    C-H bond oxidation reactions underscore the existing paradigm wherein high reactivity and high selectivity are inversely correlated. The development of catalysts capable of oxidizing strong aliphatic C(sp3)-H bonds while displaying chemoselectivity (that is, tolerance of more oxidizable functionality) remains an unsolved problem. Here, we describe a catalyst, manganese tert-butylphthalocyanine [Mn(tBuPc)], that is an outlier to the reactivity-selectivity paradigm. It is unique in its capacity to functionalize all types of C(sp3)-H bond intramolecularly, while displaying excellent chemoselectivity in the presence of π functionality. Mechanistic studies indicate that [Mn(tBuPc)] transfers bound nitrenes to C(sp3)-H bonds via a pathway that lies between concerted C-H insertion, observed with reactive noble metals such as rhodium, and stepwise radical C-H abstraction/rebound, as observed with chemoselective base metals such as iron. Rather than achieving a blending of effects, [Mn(tBuPc)] aminates even 1° aliphatic and propargylic C-H bonds, demonstrating reactivity and selectivity unusual for previously known catalysts.

  4. Towards in vivo imaging of intramolecular fluorescence resonance energy transfer parameters.

    PubMed

    Gaind, Vaibhav; Webb, Kevin J; Kularatne, Sumith; Bouman, Charles A

    2009-08-01

    Fluorescence resonance energy transfer (FRET) is a nonradiative energy transfer process based on dipole-dipole interaction between donor and acceptor fluorophores that are spatially separated by a distance of a few nanometers. FRET has proved to be of immense value in the study of cellular function and the underlying cause of disease due to, for example, protein misfolding (of consequence in Alzheimer's disease). The standard parameterization in intramolecular FRET is the lifetime and yield, which can be related to the donor-acceptor (DA) distance. FRET imaging has thus far been limited to in vitro or near-surface microscopy because of the deleterious effects of substantial scatter. We show that it is possible to extract the microscopic FRET parameters in a highly scattering environment by incorporating the FRET kinetics of an ensemble of DA molecules connected by a flexible or rigid linker into an optical diffusion tomography (ODT) framework. We demonstrate the efficacy of our approach for extracting the microscopic DA distance through simulations and an experiment using a phantom with scattering properties similar to tissue. Our method will allow the in vivo imaging of FRET parameters in deep tissue, and hence provide a new vehicle for the fundamental study of disease. PMID:19649115

  5. Lipid Regulated Intramolecular Conformational Dynamics of SNARE-Protein Ykt6

    NASA Astrophysics Data System (ADS)

    Dai, Yawei; Seeger, Markus; Weng, Jingwei; Song, Song; Wang, Wenning; Tan, Yan-Wen

    2016-08-01

    Cellular informational and metabolic processes are propagated with specific membrane fusions governed by soluble N-ethylmaleimide sensitive factor attachment protein receptors (SNARE). SNARE protein Ykt6 is highly expressed in brain neurons and plays a critical role in the membrane-trafficking process. Studies suggested that Ykt6 undergoes a conformational change at the interface between its longin domain and the SNARE core. In this work, we study the conformational state distributions and dynamics of rat Ykt6 by means of single-molecule Förster Resonance Energy Transfer (smFRET) and Fluorescence Cross-Correlation Spectroscopy (FCCS). We observed that intramolecular conformational dynamics between longin domain and SNARE core occurred at the timescale ~200 μs. Furthermore, this dynamics can be regulated and even eliminated by the presence of lipid dodecylphoshpocholine (DPC). Our molecular dynamic (MD) simulations have shown that, the SNARE core exhibits a flexible structure while the longin domain retains relatively stable in apo state. Combining single molecule experiments and theoretical MD simulations, we are the first to provide a quantitative dynamics of Ykt6 and explain the functional conformational change from a qualitative point of view.

  6. Intramolecular co-action of two independent photosensory modules in the fern phytochrome 3

    PubMed Central

    Kanegae, Takeshi

    2015-01-01

    Fern phytochrome3/neochrome1 (phy3/neo1) is a chimeric photoreceptor composed of a phytochrome-chromophore binding domain and an almost full-length phototropin. phy3 thus contains two different light-sensing modules; a red/far-red light receptor phytochrome and a blue light receptor phototropin. phy3 induces both red light- and blue light-dependent phototropism in phototropin-deficient Arabidopsis thaliana (phot1 phot2) seedlings. The red-light response is dependent on the phytochrome module of phy3, and the blue-light response is dependent on the phototropin module. We recently showed that both the phototropin-sensing module and the phytochrome-sensing module mediate the blue light-dependent phototropic response. Particularly under low-light conditions, these two light-sensing modules cooperate to induce the blue light-dependent phototropic response. This intramolecular co-action of two independent light-sensing modules in phy3 enhances light sensitivity, and perhaps allowed ferns to adapt to the low-light canopy conditions present in angiosperm forests. PMID:26340326

  7. Optimized measurements of separations and angles between intra-molecular fluorescent markers

    PubMed Central

    Mortensen, Kim I.; Sung, Jongmin; Flyvbjerg, Henrik; Spudich, James A.

    2015-01-01

    We demonstrate a novel, yet simple tool for the study of structure and function of biomolecules by extending two-colour co-localization microscopy to fluorescent molecules with fixed orientations and in intra-molecular proximity. From each colour-separated microscope image in a time-lapse movie and using only simple means, we simultaneously determine both the relative (x,y)-separation of the fluorophores and their individual orientations in space with accuracy and precision. The positions and orientations of two domains of the same molecule are thus time-resolved. Using short double-stranded DNA molecules internally labelled with two fixed fluorophores, we demonstrate the accuracy and precision of our method using the known structure of double-stranded DNA as a benchmark, resolve 10-base-pair differences in fluorophore separations, and determine the unique 3D orientation of each DNA molecule, thereby establishing short, double-labelled DNA molecules as probes of 3D orientation of anything to which one can attach them firmly. PMID:26509412

  8. Modeling vibrational dephasing and energy relaxation of intramolecular anharmonic modes for multidimensional infrared spectroscopies.

    PubMed

    Ishizaki, Akihito; Tanimura, Yoshitaka

    2006-08-28

    Starting from a system-bath Hamiltonian in a molecular coordinate representation, we examine an applicability of a stochastic multilevel model for vibrational dephasing and energy relaxation in multidimensional infrared spectroscopy. We consider an intramolecular anharmonic mode nonlinearly coupled to a colored noise bath at finite temperature. The system-bath interaction is assumed linear plus square in the system coordinate, but linear in the bath coordinates. The square-linear system-bath interaction leads to dephasing due to the frequency fluctuation of system vibration, while the linear-linear interaction contributes to energy relaxation and a part of dephasing arises from anharmonicity. To clarify the role and origin of vibrational dephasing and energy relaxation in the stochastic model, the system part is then transformed into an energy eigenstate representation without using the rotating wave approximation. Two-dimensional (2D) infrared spectra are then calculated by solving a low-temperature corrected quantum Fokker-Planck (LTC-QFP) equation for a colored noise bath and by the stochastic theory. In motional narrowing regime, the spectra from the stochastic model are quite different from those from the LTC-QFP. In spectral diffusion regime, however, the 2D line shapes from the stochastic model resemble those from the LTC-QFP besides the blueshifts caused by the dissipation from the colored noise bath. The preconditions for validity of the stochastic theory for molecular vibrational motion are also discussed. PMID:16965023

  9. Dynamics of intramolecular spin exchange interaction of a nitronyl nitroxide diradical in solution and on surfaces

    NASA Astrophysics Data System (ADS)

    Lloveras, V.; Badetti, E.; Veciana, J.; Vidal-Gancedo, J.

    2016-02-01

    In this paper we report the study of the dynamics of a thermally modulated intramolecular spin exchange interaction of a novel diradical nitronyl nitroxide-substituted disulfide in solution and when it is grafted on a gold surface. The structure of this diradical was designed to have flexible chains leading to intramolecular collisions and hence spin exchange interaction, and with an appropriate binding group to be grafted on the gold surface to study its behavior on the surface. In solution, this diradical shows a strong spin exchange interaction between both radicals which is modulated by temperature, but also gold nanoparticles (AuNPs) functionalized with this diradical permit investigation of such a phenomenon in surface-grafted radicals. The spin-labelled AuNP synthesis was optimized to obtain high coverage of spin labels to lead to high spin exchange interaction. The obtained AuNPs were studied by Electron Paramagnetic Resonance (EPR), UV-Vis, and IR spectroscopies, HR-TEM microscopy, Cyclic Voltammetry (CV), Energy Dispersive X-ray analysis (EDX) and Thermogravimetric Analysis (TGA). This inorganic-organic hybrid material also showed dipolar interactions between its radicals which were confirmed by the appearance in the EPR spectra of an |Δms| = 2 transition at half-field. This signal gives direct evidence of the presence of a high-spin state and permitted us to study the nature of the magnetic coupling between the spins which was found to be antiferromagnetic. Self-Assembled Monolayers (SAMs) of these radicals on the Au (111) substrate were also prepared and studied by contact angle, X-Ray Photoelectron Spectroscopy (XPS), Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS), Cyclic Voltammetry and EPR. The magnetic as well as the electrochemical properties of the hybrid surfaces were studied and compared with the properties of this diradical in solution. Analogies between the properties of AuNPs with high coverage of radicals and those of SAM were

  10. Intramolecular Cyclization of Thiophene-Based [7]Helicenes to Quasi-[8]Circulenes

    SciTech Connect

    Rajca, Andrzej; Miyasaka, Makoto; Xiao, Shuzhang; Boratynski, Przemystaw J.; Pink, Maren; Rajca, Suchada

    2009-12-08

    Intramolecular cyclization in a series of thiophene-based dibromo[7]helicenes (4-6) with different helix structures is investigated by vacuum pyrolysis, tin- and palladium-mediated C-C bond forming reactions. The product with the cyclic structure of the annelated aromatic rings, which resembles [8]circulene devoid of an atom linkage, is referred to as quasi-[8]circulene. Vacuum pyrolysis of 4 gives insoluble, unidentified products, while 5 and 6 yield the corresponding quasi-[8]circulenes under similar conditions. Thermogravimetry (TG) and differential scanning calorimetry (DSC) analyses for 4 indicate complex reaction pathways, while those for 5 and 6 show a single process corresponding to a loss of 1 equiv of Br2 at about 330 C. Pd-mediated reductive cyclization provides quasi-[8]circulenes for all three [7]helicenes, though only 4 gives a good isolated yield. Tributyltin hydride-mediated radical cyclization of 4-6 provides quasi-[8]circulenes in excellent yields, and it is practically insensitive to the helix structure. Experimental and calculated UV-vis absorption spectra for quasi-[8]circulenes and [8]circulenes are reported. The results suggest that the lack of atom linkage in quasi-[8]circulene does not significantly affect properties and conformation, compared to those for the corresponding [8]circulenes.

  11. Sensitive detection of acetylcholine based on a novel boronate intramolecular charge transfer fluorescence probe.

    PubMed

    Liu, Chang; Shen, Youming; Yin, Peng; Li, Lidong; Liu, Meiling; Zhang, Youyu; Li, Haitao; Yao, Shouzhuo

    2014-11-15

    A highly sensitive and selective fluorescence method for the detection of acetylcholine (ACh) based on enzyme-generated hydrogen peroxide (H2O2) and a new boronate intramolecular charge transfer (ICT) fluorescence probe, 4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-N-butyl-1,8-naphthalimide (BN), was developed. This strategy involves the reaction of ACh with acetylcholinesterase (AChE) to produce choline, which is further oxidized by choline oxidase (ChOx) to obtain betaine and H2O2. The enzyme-generated H2O2 reacts with BN and results in hydrolytic deprotection of BN to generate fluorescent product (4-hydroxyl-N-butyl-1,8-naphthalimide, ON). Two consecutive linear response ranges allow determining ACh in a wide concentration range with a low detection limit of 2.7 nM (signal/noise=3). Compared with other fluorescent probes based on the mechanism of nonspecific oxidation, this reported boronate probe has the advantage of no interference from other biologically relevant reactive oxygen species (ROS) on the detection of ACh. This study provides a new method for the detection of ACh with high selectivity and sensitivity. PMID:25132563

  12. Theoretical investigation of intramolecular vibrational energy redistribution in highly excited HFCO

    NASA Astrophysics Data System (ADS)

    Pasin, Gauthier; Gatti, Fabien; Iung, Christophe; Meyer, Hans-Dieter

    2006-05-01

    The present paper is devoted to the simulations of the intramolecular vibrational energy redistribution (IVR) in HFCO initiated by an excitation of the out-of-plane bending vibration [nν6=2,4,6,…,18,20]. Using a full six-dimensional ab initio potential energy, the multiconfiguration time-dependent Hartree (MCTDH) method was exploited to propagate the corresponding six-dimensional wave packets. This study emphasizes the stability of highly excited states of the out-of-plane bending mode which exist even above the dissociation threshold. More strikingly, the structure of the IVR during the first step of the dynamics is very stable for initial excitations ranging from 2ν6 to 20ν6. This latter result is consistent with the analysis of the eigenstates obtained, up to 10ν6, with the aid of the Davidson algorithm in a foregoing paper [Iung and Ribeiro, J. Chem. Phys. 121, 174105 (2005)]. The present study can be considered as complementary to this previous investigation. This paper also shows how MCTDH can be used to predict the dynamical behavior of a strongly excited system and to determine the energies of the corresponding highly excited states.

  13. Asymmetric intramolecular α-cyclopropanation of aldehydes using a donor/acceptor carbene mimetic

    PubMed Central

    Luo, Chaosheng; Wang, Zhen; Huang, Yong

    2015-01-01

    Enantioselective α-alkylation of carbonyl is considered as one of the most important processes for asymmetric synthesis. Common alkylation agents, that is, alkyl halides, are notorious substrates for both Lewis acids and organocatalysts. Recently, olefins emerged as a benign alkylating species via photo/radical mechanisms. However, examples of enantioselective alkylation of aldehydes/ketones are scarce and direct asymmetric dialkylation remains elusive. Here we report an intramolecular α-cyclopropanation reaction of olefinic aldehydes to form chiral cyclopropane aldehydes. We demonstrate that an α-iodo aldehyde can function as a donor/acceptor carbene equivalent, which engages in a formal [2+1] annulation with a tethered double bond. Privileged bicyclo[3.1.0]hexane-type scaffolds are prepared in good optical purity using a chiral amine. The synthetic utility of the products is demonstrated by versatile transformations of the bridgehead formyl functionality. We expect the concept of using α-iodo iminium as a donor/acceptor carbene surrogate will find wide applications in chemical reaction development. PMID:26644194

  14. Mechanistic Analysis and Optimization of the Copper-Catalyzed Enantioselective Intramolecular Alkene Aminooxygenation

    PubMed Central

    Paderes, Monissa C.; Keister, Jerome B.; Chemler, Sherry R.

    2013-01-01

    The catalytic asymmetric aminooxygenation of alkenes provides an efficient and straightforward approach to prepare chiral vicinal amino alcohols. We have reported a copper(II)-catalyzed enantioselective intramolecular alkene aminooxygenation, using (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO) as the oxygen source, which results in the synthesis of chiral indolines and pyrrolidines. Herein we disclose that kinetics studies indicate the reaction is first order both in substrate and the [Cu(R,R)-Ph-bis(oxazoline)]OTf2 catalyst, and zero order in TEMPO. Furthermore, kinetic isotope effect studies support that the cis aminocupration step, the addition of N-Cu across the alkene, is the rate-limiting step. Subsequent formation of a carbon radical intermediate, and direct carbon radical trapping with TEMPO is the indicated mechanism for the C-O bond formation as suggested by a deuterium labeling experiment. A ligand screen revealed that C(4)-phenyl substitution on the bis(oxazoline) is optimal for high asymmetric induction. The size of the substrate’s N-sulfonyl group also influences the enantioselectivity of the reaction. The preparative scale catalytic aminooxygenation reaction (gram scale) was demonstrated and an unexpected dependence on reaction temperature was uncovered on the larger scale reaction. PMID:23244027

  15. Mechanistic analysis and optimization of the copper-catalyzed enantioselective intramolecular alkene aminooxygenation.

    PubMed

    Paderes, Monissa C; Keister, Jerome B; Chemler, Sherry R

    2013-01-18

    The catalytic asymmetric aminooxygenation of alkenes provides an efficient and straightforward approach to prepare chiral vicinal amino alcohols. We have reported a copper(II)-catalyzed enantioselective intramolecular alkene aminooxygenation, using (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO) as the oxygen source, which results in the synthesis of chiral indolines and pyrrolidines. Herein we disclose that kinetics studies indicate the reaction is first order both in substrate and the [Cu(R,R)-Ph-bis(oxazoline)]OTf(2) catalyst and zero order in TEMPO. Furthermore, kinetic isotope effect studies support that the cis-aminocupration step, the addition of N-Cu across the alkene, is the rate-limiting step. Subsequent formation of a carbon radical intermediate and direct carbon radical trapping with TEMPO is the indicated mechanism for the C-O bond formation as suggested by a deuterium labeling experiment. A ligand screen revealed that C(4)-phenyl substitution on the bis(oxazoline) is optimal for high asymmetric induction. The size of the substrate's N-sulfonyl group also influences the enantioselectivity of the reaction. The preparative-scale catalytic aminooxygenation reaction (gram scale) was demonstrated, and an unexpected dependence on reaction temperature was uncovered on the larger scale reaction. PMID:23244027

  16. Intramolecular hydrogen bonding in 5-nitrosalicylaldehyde: IR spectrum and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Moosavi-Tekyeh, Zainab; Taherian, Fatemeh; Tayyari, Sayyed Faramarz

    2016-05-01

    The structural parameters, and vibrational frequencies of 5-nitrosalicylaldehyde (5NSA) were studied by the FT-IR and Raman spectra and the quantum chemical calculations carried out at the B3LYP/6-311++G(d,p) level of theory in order to investigate the intramolecular hydrogen bonding (IHB) present in its structure. The strength and nature of IHB in the optimized structure of 5NSA were studied in detail by means of the atoms in molecules (AIM) and the natural bond orbital (NBO) approaches. The results obtained were then compared with the corresponding data for its parent molecule, salicylaldehyde (SA). Comparisons made between the geometrical structures for 5NSA and SA, their OH/OD stretching and out-of-plane bending modes, their enthalpies for the hydrogen bond, and their AIM parameters demonstrated a stronger H-bonding in 5NSA compared with that in SA. The calculated binding enthalpy (ΔHbind) for 5NSA was -10.92 kcal mol-1. The observed νOH and γOH appeared at about 3120 cm-1 and 786 cm-1 respectively. The stretching frequency shift of H-bond formation was 426 cm-1 which is consistent with ΔHbind and the strength of H-bond in 5NSA. The delocalization energies and electron delocalization indices derived by the NBO and AIM approaches indicate that the resonance effects were responsible for the stronger IHB in 5NSA than in SA.

  17. Very strong intramolecular hydrogen bonding of 1,2-dithenoylcyclopentadiene; DFT and spectroscopic studies

    NASA Astrophysics Data System (ADS)

    Nekoei, A.-R.; Tayyari, S. F.; Vakili, M.

    2014-10-01

    Structure and intramolecular hydrogen bond (IHB) of 1,2-dithenoylcyclopentadiene (DTCP) have been investigated with quantum mechanical calculations using density functional theory at B3LYP level using some Pople-style basis sets augmented with polarized and diffuse functions. The full isomeric and conformational analyses have been done, and the relative stabilities for different chelated and non-chelated enol and different keto forms have been reported. The estimated IHB energy and the barrier height for proton transfer (19.34 and 0.31 kcal/mol, respectively), together with the value of 0.082 Å for the Q Gilli’s symmetry coordinate and the σ-skeleton of the molecule (O⋯O distance of 1.463 Å), confirm a very strong, nearly symmetric, linear and short distance resonance assisted IHB (RAHB) in DTCP. The values of 18.29 ppm for the enolated proton chemical shift and 1128 cm-1 for out-of-plain bending of the OH bond, besides investigations on other IR and Raman bands associated with the IHB strength and electron delocalization in different segments of the molecule, confirm the results of the theoretical studies and a very strong RAHB in DTCP.

  18. Intramolecular interactions, isomerization and vibrational frequencies of two paracetamol analogues: A spectroscopic and a computational approach

    NASA Astrophysics Data System (ADS)

    Viana, Rommel B.; Ribeiro, Gabriela L. O.; Santos, Sinara F. F.; Quintero, David E.; Viana, Anderson B.; da Silva, Albérico B. F.; Moreno-Fuquen, Rodolfo

    2016-06-01

    The aim of this investigation was to determine the molecular properties and provide an interpretation of the vibrational mode couplings of these two paracetamol analogues: 2-bromo-2-methyl-N-(4-nitrophenyl)-propanamide and 2-bromo-2-methyl-N-p-tolyl-propanamide. E/Z isomers, keto/enol unimolecular rearrangement and prediction of the transition state structures in each mechanism were also assessed using the Density Functional Theory (DFT). The DFT estimates a high energy gap between E and Z isomers (9-11 kcal·mol- 1), with barrier heights ranging from 16 to 19 kcal·mol- 1. In contrast, the barrier energies on the keto/enol isomerization are almost 10 kcal·mol- 1 higher than those estimated for the E/Z rearrangement. The kinetic rate constant was also determined for each reaction mechanism. Natural bond orbital analysis and the quantum theory of atoms in molecules were used to interpret the intramolecular hydrogen bonds and to understand the most important interactions that govern the stabilization of each isomer. Furthermore, an analysis of the atomic charge distribution using different population methodologies was also performed.

  19. Intramolecular interactions, isomerization and vibrational frequencies of two paracetamol analogues: A spectroscopic and a computational approach.

    PubMed

    Viana, Rommel B; Ribeiro, Gabriela L O; Santos, Sinara F F; Quintero, David E; Viana, Anderson B; da Silva, Albérico B F; Moreno-Fuquen, Rodolfo

    2016-06-01

    The aim of this investigation was to determine the molecular properties and provide an interpretation of the vibrational mode couplings of these two paracetamol analogues: 2-bromo-2-methyl-N-(4-nitrophenyl)-propanamide and 2-bromo-2-methyl-N-p-tolyl-propanamide. E/Z isomers, keto/enol unimolecular rearrangement and prediction of the transition state structures in each mechanism were also assessed using the Density Functional Theory (DFT). The DFT estimates a high energy gap between E and Z isomers (9-11 kcal·mol(-1)), with barrier heights ranging from 16 to 19 kcal·mol(-1). In contrast, the barrier energies on the keto/enol isomerization are almost 10 kcal·mol(-1) higher than those estimated for the E/Z rearrangement. The kinetic rate constant was also determined for each reaction mechanism. Natural bond orbital analysis and the quantum theory of atoms in molecules were used to interpret the intramolecular hydrogen bonds and to understand the most important interactions that govern the stabilization of each isomer. Furthermore, an analysis of the atomic charge distribution using different population methodologies was also performed. PMID:26974474

  20. Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation

    NASA Astrophysics Data System (ADS)

    Tailford, Louise E.; Owen, C. David; Walshaw, John; Crost, Emmanuelle H.; Hardy-Goddard, Jemma; Le Gall, Gwenaelle; de Vos, Willem M.; Taylor, Garry L.; Juge, Nathalie

    2015-07-01

    The gastrointestinal mucus layer is colonized by a dense community of microbes catabolizing dietary and host carbohydrates during their expansion in the gut. Alterations in mucosal carbohydrate availability impact on the composition of microbial species. Ruminococcus gnavus is a commensal anaerobe present in the gastrointestinal tract of >90% of humans and overrepresented in inflammatory bowel diseases (IBD). Using a combination of genomics, enzymology and crystallography, we show that the mucin-degrader R. gnavus ATCC 29149 strain produces an intramolecular trans-sialidase (IT-sialidase) that cleaves off terminal α2-3-linked sialic acid from glycoproteins, releasing 2,7-anhydro-Neu5Ac instead of sialic acid. Evidence of IT-sialidases in human metagenomes indicates that this enzyme occurs in healthy subjects but is more prevalent in IBD metagenomes. Our results uncover a previously unrecognized enzymatic activity in the gut microbiota, which may contribute to the adaptation of intestinal bacteria to the mucosal environment in health and disease.

  1. Lipid Regulated Intramolecular Conformational Dynamics of SNARE-Protein Ykt6.

    PubMed

    Dai, Yawei; Seeger, Markus; Weng, Jingwei; Song, Song; Wang, Wenning; Tan, Yan-Wen

    2016-01-01

    Cellular informational and metabolic processes are propagated with specific membrane fusions governed by soluble N-ethylmaleimide sensitive factor attachment protein receptors (SNARE). SNARE protein Ykt6 is highly expressed in brain neurons and plays a critical role in the membrane-trafficking process. Studies suggested that Ykt6 undergoes a conformational change at the interface between its longin domain and the SNARE core. In this work, we study the conformational state distributions and dynamics of rat Ykt6 by means of single-molecule Förster Resonance Energy Transfer (smFRET) and Fluorescence Cross-Correlation Spectroscopy (FCCS). We observed that intramolecular conformational dynamics between longin domain and SNARE core occurred at the timescale ~200 μs. Furthermore, this dynamics can be regulated and even eliminated by the presence of lipid dodecylphoshpocholine (DPC). Our molecular dynamic (MD) simulations have shown that, the SNARE core exhibits a flexible structure while the longin domain retains relatively stable in apo state. Combining single molecule experiments and theoretical MD simulations, we are the first to provide a quantitative dynamics of Ykt6 and explain the functional conformational change from a qualitative point of view. PMID:27493064

  2. Preferential sites for intramolecular glucosepane cross-link formation in type I collagen: A thermodynamic study.

    PubMed

    Collier, Thomas A; Nash, Anthony; Birch, Helen L; de Leeuw, Nora H

    2015-10-01

    The extracellular matrix (ECM) undergoes progressive age-related stiffening and loss of proteolytic digestibility due to an increase in concentration of advanced glycation end products (AGEs). The most abundant AGE, glucosepane, accumulates in collagen with concentrations over 100 times greater than all other AGEs. Detrimental collagen stiffening properties are believed to play a significant role in several age-related diseases such as osteoporosis and cardiovascular disease. Currently little is known of the potential location of covalently cross-linked glucosepane formation within collagen molecules; neither are there reports on how the respective cross-link sites affect the physical and biochemical properties of collagen. Using fully atomistic molecular dynamics simulations (MD) we have identified six sites where the formation of a covalent intra-molecular glucosepane cross-link within a single collagen molecule in a fibrillar environment is energetically favourable. Identification of these favourable sites enables us to align collagen cross-linking with experimentally observed changes to the ECM. For example, formation of glucosepane was found to be energetically favourable within close proximity of the Matrix Metalloproteinase-1 (MMP1) binding site, which could potentially disrupt collagen degradation. PMID:26049074

  3. Analysis of longitudinal vibration band gaps in periodic carbon nanotube intramolecular junctions using finite element method

    NASA Astrophysics Data System (ADS)

    Li, Jiaqian; Shen, Haijun

    2015-12-01

    The longitudinal vibration band gaps in periodic (n, 0)-(2n, 0) single-walled carbon nanotube(SWCNT) intramolecular junctions(IMJs) are investigated based on the finite element calculation. The frequency ranges of band gaps in frequency response functions(FRF) simulated by finite element method (FEM) show good agreement with those in band structure obtained by simple spring-mass model. Moreover, a comprehensive parametric study is also conducted to highlight the influences of the geometrical parameters such as the size of unit cell, component ratios of the IMJs and diameters of the CNT segments as well as geometric imperfections on the first band gap. The results show that the frequency ranges and the bandwidth of the gap strongly depend on the geometrical parameters. Furthermore, the influences of geometrical parameters on gaps are nuanced in IMJs with different topological defects. The existence of vibration band gaps in periodic IMJs lends a new insight into the development of CNT-based nano-devices in application of vibration isolation.

  4. Preferential sites for intramolecular glucosepane cross-link formation in type I collagen: A thermodynamic study

    PubMed Central

    Collier, Thomas A.; Nash, Anthony; Birch, Helen L.; de Leeuw, Nora H.

    2015-01-01

    The extracellular matrix (ECM) undergoes progressive age-related stiffening and loss of proteolytic digestibility due to an increase in concentration of advanced glycation end products (AGEs). The most abundant AGE, glucosepane, accumulates in collagen with concentrations over 100 times greater than all other AGEs. Detrimental collagen stiffening properties are believed to play a significant role in several age-related diseases such as osteoporosis and cardiovascular disease. Currently little is known of the potential location of covalently cross-linked glucosepane formation within collagen molecules; neither are there reports on how the respective cross-link sites affect the physical and biochemical properties of collagen. Using fully atomistic molecular dynamics simulations (MD) we have identified six sites where the formation of a covalent intra-molecular glucosepane cross-link within a single collagen molecule in a fibrillar environment is energetically favourable. Identification of these favourable sites enables us to align collagen cross-linking with experimentally observed changes to the ECM. For example, formation of glucosepane was found to be energetically favourable within close proximity of the Matrix Metalloproteinase-1 (MMP1) binding site, which could potentially disrupt collagen degradation. PMID:26049074

  5. Slow Intramolecular Vibrational Relaxation Leads to Long-Lived Excited-State Wavepackets.

    PubMed

    Rafiq, Shahnawaz; Scholes, Gregory D

    2016-09-01

    Broadband optical pump and compressed white light continuum probe were used to measure the transient excited-state absorption, ground-state bleach, and stimulated emission signals of cresyl violet solution in methanol. Amplitude oscillations caused by wavepacket motion in the ground and excited electronic states were analyzed. It was found that vibrational coherences in the excited state persist for more than the experimental waiting time window of 6 ps, and the strongest mode had a dephasing time constant of 2.4 ps. We hypothesize the dephasing of the wavepacket in the excited state is predominantly caused by intramolecular vibrational relaxation (IVR). Slow IVR indicates weak mode-mode coupling and therefore weak anharmonicity of the potential of this vibration. Thus, the initially prepared vibrational wavepacket in the excited state is not significantly perturbed by nonadiabatic coupling to other electronic states, and hence the diabatic and adiabatic representations of the system are essentially identical within the Born-Oppenheimer approximation. The wavepacket therefore evolves with time in an almost harmonic potential, slowly dephased by IVR and the pure vibrational decoherence. The consistency in the position of node (phase change in the wavepacket) in the excited-state absorption and stimulated emission signals without undergoing any frequency shift until the wavepacket is completely dephased conforms to the absence of any reactive internal conversion. PMID:27510098

  6. Simple and efficient generation in vitro of nested deletions and inversions: Tn5 intramolecular transposition.

    PubMed Central

    York, D; Welch, K; Goryshin, I Y; Reznikoff, W S

    1998-01-01

    We have exploited the intramolecular transposition preference of the Tn 5 in vitro transposition system to test its effectiveness as a tool for generation of nested families of deletions and inversions. A synthetic transposon was constructed containing an ori, an ampicillin resistance (Ampr) gene, a multi-cloning site (MCS) and two hyperactive end sequences. The donor DNA that adjoins the transposon contains a kanamycin resistance (Kanr) gene. Any Amprreplicating plasmid that has undergone a transposition event (Kans) will be targeted primarily to any insert in the MCS. Two different size targets were tested in the in vitro system. Synthetic transposon plasmids containing either target were incubated in the presence of purified transposase (Tnp) protein and transformed. Transposition frequencies (Ampr/Kans) for both targets were found to be 30-50%, of which >95% occur within the target sequence, in an apparently random manner. By a conservative estimate 10(5) or more deletions/inversions within a given segment of DNA can be expected from a single one-step 20 microl transposition reaction. These nested deletions can be used for structure-function analysis of proteins and for sequence analysis. The inversions provide nested sequencing templates of the opposite strand from the deletions. PMID:9518484

  7. Asymmetric intramolecular α-cyclopropanation of aldehydes using a donor/acceptor carbene mimetic.

    PubMed

    Luo, Chaosheng; Wang, Zhen; Huang, Yong

    2015-01-01

    Enantioselective α-alkylation of carbonyl is considered as one of the most important processes for asymmetric synthesis. Common alkylation agents, that is, alkyl halides, are notorious substrates for both Lewis acids and organocatalysts. Recently, olefins emerged as a benign alkylating species via photo/radical mechanisms. However, examples of enantioselective alkylation of aldehydes/ketones are scarce and direct asymmetric dialkylation remains elusive. Here we report an intramolecular α-cyclopropanation reaction of olefinic aldehydes to form chiral cyclopropane aldehydes. We demonstrate that an α-iodo aldehyde can function as a donor/acceptor carbene equivalent, which engages in a formal [2+1] annulation with a tethered double bond. Privileged bicyclo[3.1.0]hexane-type scaffolds are prepared in good optical purity using a chiral amine. The synthetic utility of the products is demonstrated by versatile transformations of the bridgehead formyl functionality. We expect the concept of using α-iodo iminium as a donor/acceptor carbene surrogate will find wide applications in chemical reaction development. PMID:26644194

  8. Fluorescent sensors for selective detection of thiols: expanding the intramolecular displacement based mechanism to new chromophores.

    PubMed

    Niu, Li-Ya; Zheng, Hai-Rong; Chen, Yu-Zhe; Wu, Li-Zhu; Tung, Chen-Ho; Yang, Qing-Zheng

    2014-03-21

    Biological thiols, including cysteine (Cys), homocystein (Hcy) and glutathione (GSH), play crucial roles in maintaining the appropriate redox status of biological systems. An abnormal level of biothiols is associated with different diseases, therefore, the discrimination between them is of great importance. Herein, we present two fluorescent sensors for selective detection of biothiols based on our recently reported intramolecular displacement mechanism. We expanded this mechanism to commercially available chromophores, 4-chloro-7-nitro-2,1,3-benzoxadiazole (NBD-Cl) and heptamethine cyanine dye IR-780. The sensors operate by undergoing displacement of chloride by thiolate. The amino groups of Cys/Hcy further replace the thiolate to form amino-substituted products, which exhibit dramatically different photophysical properties compared to sulfur-substituted products from the reaction with GSH. NBD-Cl is highly selective towards Cys/Hcy and exhibits significant fluorescence enhancement. IR-780 showed a variation in its fluorescence ratio towards Cys over other thiols. Both of the sensors can be used for live-cell imaging of Cys. The wide applicability of the mechanism may provide a powerful tool for developing novel fluorescent sensors for selective detection of biothiols. PMID:24466567

  9. Intramolecular condensation reactions of {alpha},{omega}-bis(triethoxysilyl)alkanes. Formation of cyclic disilsesquioxanes

    SciTech Connect

    Loy, D.A.; Carpenter, J.P.; Myers, S.A.; Assink, R.A.; Small, J.H.; Greaves, J.; Shea, K.J.

    1996-09-04

    In this paper, we used mass spectrometry and {sup 29}Si NMR spectroscopy to discover that the length of the alkylene-bridging groups had a pronounced effect on the competition between cyclization and polymerization of {alpha},{omega}-bis(triethoxysilyl)alkanes and on the formation of polymeric gels. While the intramolecular reaction clearly slows gelation, the cyclic disilsesquioxanes are still tetrafunctional monomers theoretically capable of forming polymeric gels. If the ring structures, which bear a striking resemblence to carbohydrates, are preserved through the polymerization, the resulting poly(cyclic disilsesquioxane) gels may have structural similarities to branched or cross-linked carbohydrates, such as cellulose or chitosan. Under base-catalyzed sol-gel polymerization conditions, 3 and 4 (six- and seven-membered cyclic disilsesquioxanes, respectively) quickly reacted to give gels with significant ring opening as determined from the {sup 29}Si chemical shifts in solid-state (CP MAS) NMR spectra. However, gels prepared under acidic conditions reveal some or all of the cyclic disilsesquioxane functionality was preserved in the polymers. 13 refs., 1 fig.

  10. Optimized measurements of separations and angles between intra-molecular fluorescent markers

    NASA Astrophysics Data System (ADS)

    Mortensen, Kim I.; Sung, Jongmin; Flyvbjerg, Henrik; Spudich, James A.

    2015-10-01

    We demonstrate a novel, yet simple tool for the study of structure and function of biomolecules by extending two-colour co-localization microscopy to fluorescent molecules with fixed orientations and in intra-molecular proximity. From each colour-separated microscope image in a time-lapse movie and using only simple means, we simultaneously determine both the relative (x,y)-separation of the fluorophores and their individual orientations in space with accuracy and precision. The positions and orientations of two domains of the same molecule are thus time-resolved. Using short double-stranded DNA molecules internally labelled with two fixed fluorophores, we demonstrate the accuracy and precision of our method using the known structure of double-stranded DNA as a benchmark, resolve 10-base-pair differences in fluorophore separations, and determine the unique 3D orientation of each DNA molecule, thereby establishing short, double-labelled DNA molecules as probes of 3D orientation of anything to which one can attach them firmly.

  11. Photophysical Properties of Intramolecular Charge Transfer in a Tribranched Donor-π-Acceptor Chromophore.

    PubMed

    Hu, Jiangpu; Li, Yang; Zhu, Huaning; Qiu, Shuhai; He, Guiying; Zhu, Xiaozhang; Xia, Andong

    2015-08-01

    The photophysical properties of intramolecular charge transfer (ICT) in a novel tribranched donor-π-acceptor chromophore, triphenoxazine-2,4,6-triphenyl-1,3,5-triazine (tri-PXZ-TRZ), with thermally activated delayed fluorescence character was investigated in different aprotic solvents by steady-state spectroscopy and femtosecond and nanosecond transient absorption spectroscopy measurements. Increasing the solvent polarity led to a significant increase in the Stokes shift. The large Stokes shift in highly polar solvents was attributed to ICT properties upon excitation; this resulted in a strong interaction between the tri-PXZ-TRZ molecule and the surrounding solvent, which led to a strong solvation process. Quantum-chemical calculations and changes in the dipole moment showed that this compound has a large degree of ICT. Furthermore, an apolar environment helped to preserve the symmetry of tri-PXZ-TRZ and to enhance its emission efficiency. The femtosecond and nanosecond transient absorption spectroscopy results indicated that the excited-state dynamics of this push-pull molecule were strongly influenced by solvent polarity through the formation of a solvent-stabilized ICT state. The excited-state relaxation mechanism of tri-PXZ-TRZ was proposed by performing target model analysis on the femtosecond transient absorption spectra. In addition, the delayed fluorescence of tri-PXZ-TRZ was significantly modulated by a potential competition between solvation and intersystem crossing processes. PMID:26018143

  12. Dynamics and intramolecular ligand binding of DtxR studied by MD simulations and NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Yi, Myunggi; Bhattacharya, Nilakshee; Zhou, Huan-Xiang

    2005-11-01

    Diphtheria toxin repressor (DtxR) regulates the expression of the diphtheria toxin gene through intramolecular ligand binding (Wylie et al., Biochemistry 2005, 44:40-51). Protein dynamics is essential to the binding process of the Pro-rich (Pr) ligand to the C-terminal SH3 domain. We present MD and NMR results on the dynamics and ligand interactions of a Pr-SH3 construct of DtxR. NMR relaxation data (T1, T2, and NOE) showed that the Pr ligand is very flexible, suggesting that it undergoes binding/unbinding transitions. A 50-ns MD trajectory of the protein was used to calculate T1, T2, and NOE, reproducing the NMR results for the SH3 domain but not for the Pr segment. During the MD simulation, the ligand stayed bound to the SH3 domain; thus the simulation represented the bound state. The NMR data for the Pr-segment could be explained by assuming that they represented the average behavior of a fast binding/unbinding exchange. Though unbinding was not observed in the MD simulation, the simulation did show large fluctuations of a loop which forms part of the wall of the binding pocket. The fluctuations led to opening up of the binding pocket, thus weakening the interaction with the Pr segment and perhaps ultimately leading to ligand unbinding.

  13. Intramolecular condensation reactions of {alpha}, {omega}- bis(triethoxy-silyl)alkanes. Formation of cyclic disilsesquioxanes

    SciTech Connect

    Loy, D.A.; Carpenter, J.P.; Myers, S.A.; Assink, R.A.; Small, J.H.; Greaves, J.; Shea, K.J.

    1996-08-01

    Under acidic sol-gel polymerization conditions, 1,3-bis(triethoxysilyl)-propane (1) and 1,4-bis(triethoxysilyl)butane (2) were shown to preferentially form cyclic disilsesquioxanes 3 and 4 rather than the expected 1,3-propylene- and 1,4-butylene-bridged polysilsesquioxane gels. Formation of 3 and 4 is driven by a combination of an intramolecular cyclization to six and seven membered rings, and a pronounced reduction in reactivity under acidic conditions as a function of increasing degree of condensation. The ease with which these relatively unreactive cyclic monomers and dimers are formed (under acidic conditions) helps to explain the difficulties in forming gels from 1 and 2. The stability of cyclic disilsesquioxanes was confirmed withe the synthesis of 3 and 4 in gram quantities; the cyclic disilsesquioxanes react slowly to give tricyclic dimers containing a thermodynamically stable eight membered siloxane ring. Continued reactions were shown to perserve the cyclic structure, opening up the possibility of utilizing cyclic disilsesquioxanes as sol-gel monomers. Preliminary polymerization studies with these new, carbohydrate-like monomers revealed the formation of network poly(cyclic disilsesquioxanes) under acidic conditions and polymerization with ring-opening under basic conditions.

  14. Suppression of human immunodeficiency virus type 1 activity in vitro by oligonucleotides which form intramolecular tetrads.

    PubMed

    Rando, R F; Ojwang, J; Elbaggari, A; Reyes, G R; Tinder, R; McGrath, M S; Hogan, M E

    1995-01-27

    An oligonucleotide (I100-15) composed of only deoxyguanosine and thymidine was able to inhibit human immunodeficiency virus type-1 (HIV-1) in culture assay systems. I100-15 did not block virus entry into cells but did reduce viral-specific transcripts. As assessed by NMR and polyacrylamide gel methods, I100-15 appears to form a structure in which two stacked guanosine tetrads are connected by three two-base long loops. Structure/activity experiments indicated that formation of intramolecular guanosine tetrads was necessary to achieve maximum antiviral activity. The single deoxyguanosine nucleotide present in each loop was found to be extremely important for the overall antiviral activity. The toxicity of I100-15 was determined to be well above the 50% effective dose (ED50) in culture which yielded a high therapeutic index (> 100). The addition of a cholesterol moiety to the 3' terminus of I100-15 (I100-23) reduced the ED50 value to less than 50 nM (from 0.12 microM for I100-15) and increased the duration of viral suppression to greater than 21 days (versus 7-10 days for I100-15) after removal of the drug from infected cell cultures. The favorable therapeutic index of such molecules coupled with the prolonged suppression of HIV-1, suggest that such compounds further warrant investigation as potential therapeutic agents. PMID:7829511

  15. Intramolecular interactions contributing for the conformational preference of bioactive diphenhydramine: Manifestation of the gauche effect

    NASA Astrophysics Data System (ADS)

    de Rezende, Fátima M. P.; Andrade, Laize A. F.; Freitas, Matheus P.

    2015-08-01

    Diphenhydramine is an antihistamine used to treat some symptoms of allergies and the common cold. It is usually marketed as the hydrochloride salt, and both the neutral and cation forms have the O-C-C-N fragment. The gauche effect is well known in fluorine-containing chains, because its main origin is hyperconjugative and the σ∗C-F is a low-lying acceptor orbital, allowing electron delocalization in the conformation where F and an adjacent electronegative substituent in an ethane fragment are in the gauche orientation. Our experimental (NMR) and theoretical findings indicate that diphenhydramine exhibits the gauche effect, since the preferential conformations have the O-C-C-N moiety in this orientation due especially to antiperiplanar σC-H → σ∗C-O and σC-H → σ∗C-N interactions. This conformational preference is strengthened in the protonated form due to an incremental electrostatic gauche effect. Because the gauche conformation matches the bioactive structure of diphenhydramine complexed with histamine methyltransferase, it is suggested that intramolecular interactions, and not only induced fit, rule its bioactive form.

  16. Enantioselective approach to polycyclic polyprenylated acylphloroglucinols via catalytic asymmetric intramolecular cyclopropanation.

    PubMed

    Uetake, Yuta; Uwamori, Masahiro; Nakada, Masahisa

    2015-02-01

    The formal enantioselective total synthesis of nemorosone, garsubellin A, clusianone, and hyperforin is described. The catalytic asymmetric intramolecular cyclopropanation (CAIMCP) of an α-diazo ketone, a common synthetic intermediate for the above four polycyclic polyprenylated acylphloroglucinols previously reported by us, exhibited low enantioselectivity. However, CAIMCP of the corresponding α-diazo β-keto sulfone afforded the desired product in 79% yield with 84% ee. Investigation of the CAIMCP of the α-diazo β-keto sulfone demonstrated the formation of a rearrangement product in the presence of molecular sieves 4 Å, whereas, in the presence of H2O, the byproduct derived from ring-opening of the desired cyclopropane was observed. X-ray crystallographic analysis suggested that the above two products are derived from the same chiral intermediate. The product derived from ring-opening of the cyclopropane was successfully transformed to the respective synthetic intermediates for the total syntheses of nemorosone, garsubellin A, clusianone, and hyperforin, which had previously been reported by us. PMID:25581002

  17. Factors affecting the intramolecular decomposition of hexamethylene triperoxide diamine and implications for detection.

    PubMed

    Steinkamp, Frank Lucus; DeGreeff, Lauryn E; Collins, Greg E; Rose-Pehrsson, Susan L

    2016-06-17

    Hexamethylene triperoxide diamine (HMTD) is an easily synthesized and highly sensitive organic peroxide frequently used as a primary explosive. The vapor pressure of HMTD is very low, impeding vapor detection, especially when compared to other peroxide explosives, such as triacetone triperoxide (TATP) or diacetone diperoxide (DADP). Despite this fact, HMTD has a perceptible odor that could be utilized in the indirect detection of HMTD vapor. Headspace measurements above solid HMTD samples confirm that HMTD readily decomposes under ambient conditions to form highly volatile products that include formic acid, ammonia, trimethylamine and formamides. The presence and quantity of these compounds are affected by storage condition, time, and synthetic method, with synthetic method having the most significant effect on the content of the headspace. A kinetic study of HMTD decomposition in solution indicated a correlation between degradation rate and the presence of decomposition species identified in the headspace, and provided further insight into the mechanism of decomposition. The study provided evidence for a proton assisted decomposition reaction with water, as well as an intramolecular decomposition process facilitated by the presence of water. PMID:27207576

  18. An intramolecular interaction between the FHA domain and a coiled coil negatively regulates the kinesin motor KIF1A

    PubMed Central

    Lee, Jae-Ran; Shin, Hyewon; Choi, Jeonghoon; Ko, Jaewon; Kim, Seho; Lee, Hyun Woo; Kim, Karam; Rho, Seong-Hwan; Lee, Jun Hyuck; Song, Hye-Eun; Eom, Soo Hyun; Kim, Eunjoon

    2004-01-01

    Motor proteins not actively involved in transporting cargoes should remain inactive at sites of cargo loading to save energy and remain available for loading. KIF1A/Unc104 is a monomeric kinesin known to dimerize into a processive motor at high protein concentrations. However, the molecular mechanisms underlying monomer stabilization and monomer-to-dimer transition are not well understood. Here, we report an intramolecular interaction in KIF1A between the forkhead-associated (FHA) domain and a coiled-coil domain (CC2) immediately following the FHA domain. Disrupting this interaction by point mutations in the FHA or CC2 domains leads to a dramatic accumulation of KIF1A in the periphery of living cultured neurons and an enhancement of the microtubule (MT) binding and self-multimerization of KIF1A. In addition, point mutations causing rigidity in the predicted flexible hinge disrupt the intramolecular FHA–CC2 interaction and increase MT binding and peripheral accumulation of KIF1A. These results suggest that the intramolecular FHA–CC2 interaction negatively regulates KIF1A activity by inhibiting MT binding and dimerization of KIF1A, and point to a novel role of the FHA domain in the regulation of kinesin motors. PMID:15014437

  19. Spectroelectrochemical investigation of intramolecular and interfacial electron-transfer rates reveals differences between nitrite reductase at rest and during turnover.

    PubMed

    Krzemiński, Łukasz; Ndamba, Lionel; Canters, Gerard W; Aartsma, Thijs J; Evans, Stephen D; Jeuken, Lars J C

    2011-09-28

    A combined fluorescence and electrochemical method is described that is used to simultaneously monitor the type-1 copper oxidation state and the nitrite turnover rate of a nitrite reductase (NiR) from Alcaligenes faecalis S-6. The catalytic activity of NiR is measured electrochemically by exploiting a direct electron transfer to fluorescently labeled enzyme molecules immobilized on modified gold electrodes, whereas the redox state of the type-1 copper site is determined from fluorescence intensity changes caused by Förster resonance energy transfer (FRET) between a fluorophore attached to NiR and its type-1 copper site. The homotrimeric structure of the enzyme is reflected in heterogeneous interfacial electron-transfer kinetics with two monomers having a 25-fold slower kinetics than the third monomer. The intramolecular electron-transfer rate between the type-1 and type-2 copper site changes at high nitrite concentration (≥520 μM), resulting in an inhibition effect at low pH and a catalytic gain in enzyme activity at high pH. We propose that the intramolecular rate is significantly reduced in turnover conditions compared to the enzyme at rest, with an exception at low pH/nitrite conditions. This effect is attributed to slower reduction rate of type-2 copper center due to a rate-limiting protonation step of residues in the enzyme's active site, gating the intramolecular electron transfer. PMID:21863850

  20. Self-consistent field/density functional study of conformational properties of polymers at interfaces: role of intramolecular interactions.

    PubMed

    Bryk, Paweł; Macdowell, Luis G

    2008-09-14

    We study the properties of athermal polymers at hard walls using two different versions of self-consistent field theory (SCFT). We calculate the segment density profiles, center of mass profiles, bond orientation vector profiles, and end-to-end vector distributions and compare with grand canonical Monte Carlo simulations. Using the same excess free energy prescription for both theories, we investigate the role of the excluded volume intramolecular interactions on these properties, show the relation between SCFT and density functional theory, and discuss several numerical implementations of the SCFT method. The phantom chain model gives Gaussian chain statistics independent of the conditions. Including the full intramolecular potential leads to an improved description of the low density regime but it does not produce any significant improvement in the semidiluted and concentrated regimes. We show that a viable compromise is achieved by using the effective field resulting from the phantom chain model and by calculating single chain properties using the full intramolecular potential. PMID:19044937

  1. Pyrrolidine and Piperidine Formation Via Copper(II) Carboxylate Promoted Intramolecular Carboamination of Unactivated Olefins: Diastereoselectivity and Mechanism

    PubMed Central

    Sherman, Eric S.; Fuller, Peter H.; Kasi, Dhanalakshmi; Chemler, Sherry R.

    2008-01-01

    An expanded substrate scope and in depth analysis of the reaction mechanism of the copper(II) carboxylate promoted intramolecular carboamination of unactivated alkenes is described. This method provides access to N-functionalized pyrrolidines and piperidines. Both aromatic and aliphatic γ- and δ-alkenyl N-arylsulfonamides undergo the oxidative cyclization reaction efficiently. N-Benzoyl-2-allylaniline also underwent the oxidative cyclization. The terminal olefin substrates examined were more reactive than those with internal olefins, and the latter terminated in elimination rather than carbon-carbon bond formation. The efficiency of the reaction was enhanced by the use of more organic soluble copper(II) carboxylate salts, copper(II) neodecanoate in particular. The reaction times were reduced by the use of microwave heating. High levels of diastereoselectivity were observed in the synthesis of 2,5-disubstituted pyrrolidines, wherein the cis substitution pattern predominates. The mechanism of the reaction is discussed in the context of the observed reactivity and in comparison to analogous reactions promoted by other reagents and conditions. Our evidence supports a mechanism wherein the N-C bond is formed via intramolecular syn aminocupration and the C-C bond is formed via intramolecular addition of a primary carbon radical to an aromatic ring. PMID:17428100

  2. Molecular dynamics and principal components of potassium binding with human telomeric intra-molecular G-quadruplex.

    PubMed

    Wang, Zhiguo; Chen, Ruping; Hou, Ling; Li, Jianfeng; Liu, Jun-Ping

    2015-06-01

    Telomere assumes intra-molecular G-quadruplex that is a significant drug target for inhibiting telomerase maintenance of telomeres in cancer. Metal cations have been recognized as playing important roles in stabilizing G-quadruplex, but their binding processes to human telomeric G-quadruplex remain uncharacterized. To investigate the detailed binding procedures, molecular dynamics simulations were conducted on the hybrid [3 + 1] form-one human telomeric intra-molecular G-quadruplex. We show here that the binding of a potassium ion to a G-tetrad core is mediated by two alternative pathways. Principal component analysis illustrated the dominant concerted motions of G-quadruplex occurred at the loop domains. MM-PBSA calculations revealed that binding was energetically favorable and driven by the electrostatic interactions. The lower binding site was found more constructive favorable for binding. Our data provide useful information on a potassium-mediated stable structure of human telomeric intra-molecular G-quadruplex, implicating in ion disorder associated conformational changes and targeted drug design. PMID:25894091

  3. Role of Intramolecular Vibrations in Long-Range Electron Transfer between Pheophytin and Ubiquinone in Bacterial Photosynthetic Reaction Centers

    PubMed Central

    Borrelli, Raffaele; Di Donato, Mariangela; Peluso, Andrea

    2005-01-01

    The dynamics of the elementary electron transfer step between pheophytin and primary ubiquinone in bacterial photosynthetic reaction centers is investigated by using a discrete state approach, including only the intramolecular normal modes of vibration of the two redox partners. The whole set of normal coordinates of the acceptor and donor groups have been employed in the computations of the Hamiltonian matrix, to reliably account both for shifts and mixing of the normal coordinates, and for changes in vibrational frequencies upon ET. It is shown that intramolecular modes provide not only a discrete set of states more strongly coupled to the initial state but also a quasicontinuum of weakly coupled states, which account for the spreading of the wave packet after ET. The computed transition probabilities are sufficiently high for asserting that electron transfer from bacteriopheophytin to the primary quinone can occur via tunneling solely promoted by intramolecular modes; the transition times, computed for different values of the electronic energy difference and coupling term, are of the same order of magnitude (102 ps) of the observed one. PMID:15894646

  4. Density functional investigation of photo induced Intramolecular Proton Transfer (IPT) in Indole-7-carboxaldehyde and its experimental verification

    NASA Astrophysics Data System (ADS)

    Singla, Nidhi; Chowdhury, Papia

    2013-08-01

    A detail theoretical study has been performed using Density functional theory (DFT) and Time dependent DFT (TDDFT) to investigate the Intramolecular Proton Transfer (IPT) mechanism in Indole-7-carboxaldehyde (I7C) from its normal (I*) to zwitterion (II*) form. B3LYP/6-311++G (d, p) basis set has been used to obtain structural parameters and relative energies in the ground state (S0) and excited state (S1). Atoms in Molecules (AIMs), Mulliken and Natural bond orbitals (NBOs) analysis proves the existence of intramolecular hydrogen bonding (IHB). The electron density (ρ) at Bond critical points (BCPs) on a hydrogen bridge (N15sbnd H12⋯O18) certify IHB and possibility of IPT from acidic (N15sbnd H12) to basic (lbond2 C16dbnd O18) group and creation of II*. Transition state (TS) with dual minima in the Potential energy surface (PES) confirms the I* → TS → II* transition due to excited state Intramolecular Proton Transfer (ESIPT). Photo-physical pathway from I* → II* agrees well with computed/experimental emission peaks.

  5. The intramolecular cyclization of bis-2,5-dimethylene-2,5-dihydrofurans and bis-2,5-dimethylene-2,5-dihydrothiophenes: An approach to macrocycles

    SciTech Connect

    Klumpp, D.A.

    1994-01-11

    The first two papers of this dissertation present our work with the intramolecular cyclizations of a pair of p-quinodimethanes. The p-quinodimethanes were generated by flash vacuum pyrolysis (FVP) and were linked by a bridging chain. The third paper of this dissertation presents our work in the synthetic manipulation of the products formed from the intramolecular reactions of the p-quinodimethanes.

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

    PubMed

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

    2010-05-01

    An intramolecular exciplex is formed upon excitation of the cyclohexane solution of the 1,4-dicyano-2-methylnaphthalene-N,N-dimethyl-p-toluidine dyad, but little if any intramolecular CT complex exists in the ground state of this substance in solution. In contrast, in the crystalline state, the dyad forms an intermolecular mixed-stack CT complex in the ground state and an intermolecular exciplex when it is photoexcited. PMID:20353197

  7. Intramolecular allosteric communication in dopamine D2 receptor revealed by evolutionary amino acid covariation

    PubMed Central

    Sung, Yun-Min; Wilkins, Angela D.; Rodriguez, Gustavo J.; Wensel, Theodore G.; Lichtarge, Olivier

    2016-01-01

    The structural basis of allosteric signaling in G protein-coupled receptors (GPCRs) is important in guiding design of therapeutics and understanding phenotypic consequences of genetic variation. The Evolutionary Trace (ET) algorithm previously proved effective in redesigning receptors to mimic the ligand specificities of functionally distinct homologs. We now expand ET to consider mutual information, with validation in GPCR structure and dopamine D2 receptor (D2R) function. The new algorithm, called ET-MIp, identifies evolutionarily relevant patterns of amino acid covariations. The improved predictions of structural proximity and D2R mutagenesis demonstrate that ET-MIp predicts functional interactions between residue pairs, particularly potency and efficacy of activation by dopamine. Remarkably, although most of the residue pairs chosen for mutagenesis are neither in the binding pocket nor in contact with each other, many exhibited functional interactions, implying at-a-distance coupling. The functional interaction between the coupled pairs correlated best with the evolutionary coupling potential derived from dopamine receptor sequences rather than with broader sets of GPCR sequences. These data suggest that the allosteric communication responsible for dopamine responses is resolved by ET-MIp and best discerned within a short evolutionary distance. Most double mutants restored dopamine response to wild-type levels, also suggesting that tight regulation of the response to dopamine drove the coevolution and intramolecular communications between coupled residues. Our approach provides a general tool to identify evolutionary covariation patterns in small sets of close sequence homologs and to translate them into functional linkages between residues. PMID:26979958

  8. Non-equivalent Role of Inter- and Intramolecular Hydrogen Bonds in the Insulin Dimer Interface*

    PubMed Central

    Antolíková, Emília; Žáková, Lenka; Turkenburg, Johan P.; Watson, Christopher J.; Hančlová, Ivona; Šanda, Miloslav; Cooper, Alan; Kraus, Tomáš; Brzozowski, A. Marek; Jiráček, Jiří

    2011-01-01

    Apart from its role in insulin receptor (IR) activation, the C terminus of the B-chain of insulin is also responsible for the formation of insulin dimers. The dimerization of insulin plays an important role in the endogenous delivery of the hormone and in the administration of insulin to patients. Here, we investigated insulin analogues with selective N-methylations of peptide bond amides at positions B24, B25, or B26 to delineate their structural and functional contribution to the dimer interface. All N-methylated analogues showed impaired binding affinities to IR, which suggests a direct IR-interacting role for the respective amide hydrogens. The dimerization capabilities of analogues were investigated by isothermal microcalorimetry. Selective N-methylations of B24, B25, or B26 amides resulted in reduced dimerization abilities compared with native insulin (Kd = 8.8 μm). Interestingly, although the N-methylation in [NMeTyrB26]-insulin or [NMePheB24]-insulin resulted in Kd values of 142 and 587 μm, respectively, the [NMePheB25]-insulin did not form dimers even at high concentrations. This effect may be attributed to the loss of intramolecular hydrogen bonding between NHB25 and COA19, which connects the B-chain β-strand to the core of the molecule. The release of the B-chain β-strand from this hydrogen bond lock may result in its higher mobility, thereby shifting solution equilibrium toward the monomeric state of the hormone. The study was complemented by analyses of two novel analogue crystal structures. All examined analogues crystallized only in the most stable R6 form of insulin oligomers (even if the dimer interface was totally disrupted), confirming the role of R6-specific intra/intermolecular interactions for hexamer stability. PMID:21880708

  9. Excited state intramolecular charge transfer reaction in nonaqueous electrolyte solutions: Temperature dependence

    SciTech Connect

    Pradhan, Tuhin; Gazi, Harun Al Rasid; Biswas, Ranjit

    2009-08-07

    Temperature dependence of the excited state intramolecular charge transfer reaction of 4-(1-azetidinyl)benzonitrile (P4C) in ethyl acetate (EA), acetonitrile (ACN), and ethanol at several concentrations of lithium perchlorate (LiClO{sub 4}) has been investigated by using the steady state and time resolved fluorescence spectroscopic techniques. The temperature range considered is 267-343 K. The temperature dependent spectral peak shifts and reaction driving force (-{Delta}G{sub r}) in electrolyte solutions of these solvents can be explained qualitatively in terms of interaction between the reactant molecule and ion-atmosphere. Time resolved studies indicate that the decay kinetics of P4C is biexponential, regardless of solvents, LiClO{sub 4} concentrations, and temperatures considered. Except at higher electrolyte concentrations in EA, reaction rates in solutions follow the Arrhenius-type temperature dependence where the estimated activation energy exhibits substantial electrolyte concentration dependence. The average of the experimentally measured activation energies in these three neat solvents is found to be in very good agreement with the predicted value based on data in room temperature solvents. While the rate constant in EA shows a electrolyte concentration induced parabolic dependence on reaction driving force (-{Delta}G{sub r}), the former in ethanol and ACN increases only linearly with the increase in driving force (-{Delta}G{sub r}). The data presented here also indicate that the step-wise increase in solvent reorganization energy via sequential addition of electrolyte induces the ICT reaction in weakly polar solvents to crossover from the Marcus inverted region to the normal region.

  10. ``PROTON Sponges": a Rigid Organic Scaffold to Reveal the Quantum Structure of the Intramolecular Proton Bond

    NASA Astrophysics Data System (ADS)

    Deblase, Andrew F.; Johnson, Mark A.; Scerba, Michael T.; Bloom, Steven; Lectka, Thomas; Dudding, Travis

    2012-06-01

    Spectroscopic analysis of systems containing charged hydrogen bonds (e.g. the Zundel ion, {H}5{O}2+) in a vibrationally cold regime is useful in decongesting numerous anharmonic features common to room temperature measurements.[Roscioli, J. R.; et. al. Science 2007] This approach has been extended to conjugate acids of the ``Proton Sponge" family of organic compounds, which contain strong intramolecular hydrogen bonds between proton donor (D) and acceptor (A) groups at the 1- and 8-positions. By performing {H}_2/{D}_2 vibrational predissociation spectroscopy on cryogenically cooled ions, we explore how the proximity and spatial orientation of D and A moieties relates to the spectroscopic signature of the shared proton. In the cases studied ({D = Me2N-H+; A = OH, O(C=O)Ph}), we observe strong anharmonic couplings between the shared proton and dark states that persist at these cryogenic temperatures. This leads to intense NH stretching features throughout the nominal CH stretching region (2800-3000 {cm}-1). Isotopic substitution has verified that the oscillator strength of these broad features is driven by NH stretching. Furthermore, the study of A = O(C=O)Ph has provided a spectroscopic snapshot of the shared proton at work as an active catalytic moiety fostering ester hydrolysis by first order acylium fission ({AAC1}). This is apparent by the high frequency carbonyl stretch at 1792 {cm}-1, which is a consequence of the strong hydrogen bond to the ether-ester oxygen atom. Thus, these ``Proton Sponges" are useful model systems that unearth the quantum structure and reactivity of shared proton interactions in organic compounds.

  11. Close intramolecular sulfur-oxygen contacts: modified force field parameters for improved conformation generation.

    PubMed

    Lupyan, Dmitry; Abramov, Yuriy A; Sherman, Woody

    2012-11-01

    The Cambridge Structural Database (CSD) offers an excellent data source to study small molecule conformations and molecular interactions. We have analyzed 130 small molecules from the CSD containing an intramolecular sulfur-oxygen distance less than the sum of their van der Waals (vdW) radii. Close S···O distances are observed in several important medicinal chemistry motifs (e.g. a carbonyl oxygen connected by a carbon or nitrogen linker to a sulfur) and are not treated well with existing parameters in the MMFFs or OPLS_2005 force fields, resulting in suboptimal geometries and energetics. In this work, we develop modified parameters for the OPLS_2005 force field to better treat this specific interaction in order to generate conformations close to those found in the CSD structures. We use a combination of refitting a force field torsional parameter, adding a specific atom pair vdW term, and attenuating the electrostatic interactions to obtain an improvement in the accuracy of geometry minimizations and conformational searches for these molecules. Specifically, in a conformational search 58 % of the cases produced a conformation less than 0.25 Å from the CSD crystal conformation with the modified OPLS force field parameters developed in this work. In contrast, 25 and 37 % produced a conformation less than 0.25 Å with the MMFFs and OPLS_2005 force fields, respectively. As an application of the new parameters, we generated conformations for the tyrosine kinase inhibitor axitinib (trade name Inlyta) that could be correctly repacked into three observed polymorphic structures, which was not possible with conformations generated using MMFFs or OPLS_2005. The improved parameters can be mapped directly onto physical characteristics of the systems that are treated inadequately with the molecular mechanics force fields used in this study and potentially other force fields as well. PMID:23053737

  12. Excited-State Intramolecular Proton Transfer in a Blue Fluorescence Chromophore Induces Dual Emission.

    PubMed

    Wu, Dan; Guo, Wei-Wei; Liu, Xiang-Yang; Cui, Ganglong

    2016-08-01

    Compared with green fluorescence protein (GFP) chromophores, the recently synthesized blue fluorescence protein (BFP) chromophore variant presents intriguing photochemical properties, for example, dual fluorescence emission, enhanced fluorescence quantum yield, and ultra-slow excited-state intramolecular proton transfer (ESIPT; J. Phys. Chem. Lett., 2014, 5, 92); however, its photochemical mechanism is still elusive. Herein we have employed the CASSCF and CASPT2 methods to study the mechanistic photochemistry of a truncated BFP chromophore variant in the S0 and S1 states. Based on the optimized minima, conical intersections, and minimum-energy paths (ESIPT, photoisomerization, and deactivation), we have found that the system has two competitive S1 relaxation pathways from the Franck-Condon point of the BFP chromophore variant. One is the ESIPT path to generate an S1 tautomer that exhibits a large Stokes shift in experiments. The generated S1 tautomer can further evolve toward the nearby S1 /S0 conical intersection and then jumps down to the S0 state. The other is the photoisomerization path along the rotation of the central double bond. Along this path, the S1 system runs into an S1 /S0 conical intersection region and eventually hops to the S0 state. The two energetically allowed S1 excited-state deactivation pathways are responsible for the in-part loss of fluorescence quantum yield. The considerable S1 ESIPT barrier and the sizable barriers that separate the S1 tautomers from the S1 /S0 conical intersections make these two tautomers establish a kinetic equilibrium in the S1 state, which thus results in dual fluorescence emission. PMID:27128380

  13. Kinetics of Intramolecular Electron Transfer in Cytochrome bo3 from Escherichia coli

    PubMed Central

    Ching, Erin; Gennis, Robert B.; Larsen, Randy W.

    2003-01-01

    We have examined the temperature dependence of the intramolecular electron transfer (ET) between heme b and heme o3 in CO-mixed valence cytochrome bo3 (Cbo) from Escherichia coli. Upon photolysis of CO-mixed valence Cbo rapid ET occurs between heme o3 and heme b with a rate constant of 2.2 × 105 s−1 at room temperature. The corresponding rate of CO recombination is found to be 86 s−1. From Eyring plots the activation energies for these two processes are found to be 3.4 kcal/mol and 6.7 kcal/mol for the ligand binding and ET reactions, respectively. Using variants of the Marcus equation the reorganization energy (λ), electronic coupling factor (HAB), and the ET distance were found to be 1.4 ± 0.2 eV, (2 ± 1) × 10−3 eV, and 9 ± 1 Å, respectively. These values are quite distinct from the analogous values previously obtained for bovine heart cytochrome c oxidase (CcO) (0.76 eV, 9.9 × 10−5 eV, 13.2 Å). The differences in mechanisms/pathways for heme b/heme o3 and heme a/heme a3 ET suggested by the Marcus parameters can be attributed to structural changes at the CuB site upon change in oxidation state as well as differences in electronic coupling pathways between Heme b and heme o3. PMID:12668481

  14. Spectral engineering in π-conjugated polymers with intramolecular donor-acceptor interactions.

    PubMed

    Beaujuge, Pierre M; Amb, Chad M; Reynolds, John R

    2010-11-16

    complex interactions taking place in π-conjugated polymers with intramolecular "donor-acceptor" characteristics. PMID:20726543

  15. Weak intramolecular interaction effects on the torsional spectra of ethylene glycol, an astrophysical species

    NASA Astrophysics Data System (ADS)

    Boussessi, R.; Senent, M. L.; Jaïdane, N.

    2016-04-01

    An elaborate variational procedure of reduced dimensionality based on explicitly correlated coupled clusters calculations is applied to understand the far infrared spectrum of ethylene-glycol, an astrophysical species. This molecule can be classified in the double molecular symmetry group G8 and displays nine stable conformers, gauche and trans. In the gauche region, the effect of the potential energy surface anisotropy due to the formation of intramolecular hydrogen bonds is relevant. For the primary conformer, stabilized by a hydrogen bond, the ground vibrational state rotational constants are computed to be A0 = 15 369.57 MHz, B0 = 5579.87 MHz, and C0 = 4610.02 MHz corresponding to differences of 6.3 MHz, 7.2 MHz, and 3.5 MHz from the experimental parameters. Ethylene glycol displays very low torsional energy levels whose classification is not straightforward and requires a detailed analysis of the torsional wavefunctions. Tunneling splittings are significant and unpredictable due to the anisotropy of the potential energy surface PES. The ground vibrational state splits into 16 sublevels separated ˜142 cm-1. The splitting of the "G1 sublevels" was calculated to be ˜0.26 cm-1 in very good agreement with the experimental data (0.2 cm-1 = 6.95 MHz). Transitions corresponding to the three internal rotation modes allow assignment of previously observed Q branches. Band patterns, calculated between 362.3 cm-1 and 375.2 cm-1, 504 cm-1 and 517 cm-1, and 223.3 cm-1 and 224.1 cm-1, that correspond to the tunnelling components of the v21 fundamental (v21 = OH-torsional mode), are assigned to the prominent experimental Q branches.

  16. Intramolecular interactions in aminoacyl nucleotides: Implications regarding the origin of genetic coding and protein synthesis

    NASA Technical Reports Server (NTRS)

    Lacey, J. C., Jr.; Mullins, D. W., Jr.; Watkins, C. L.; Hall, L. M.

    1986-01-01

    Cellular organisms store information as sequences of nucleotides in double stranded DNA. This information is useless unless it can be converted into the active molecular species, protein. This is done in contemporary creatures first by transcription of one strand to give a complementary strand of mRNA. The sequence of nucleotides is then translated into a specific sequence of amino acids in a protein. Translation is made possible by a genetic coding system in which a sequence of three nucleotides codes for a specific amino acid. The origin and evolution of any chemical system can be understood through elucidation of the properties of the chemical entities which make up the system. There is an underlying logic to the coding system revealed by a correlation of the hydrophobicities of amino acids and their anticodonic nucleotides (i.e., the complement of the codon). Its importance lies in the fact that every amino acid going into protein synthesis must first be activated. This is universally accomplished with ATP. Past studies have concentrated on the chemistry of the adenylates, but more recently we have found, through the use of NMR, that we can observe intramolecular interactions even at low concentrations, between amino acid side chains and nucleotide base rings in these adenylates. The use of this type of compound thus affords a novel way of elucidating the manner in which amino acids and nucleotides interact with each other. In aqueous solution, when a hydrophobic amino acid is attached to the most hydrophobic nucleotide, AMP, a hydrophobic interaction takes place between the amino acid side chain and the adenine ring. The studies to be reported concern these hydrophobic interactions.

  17. Photoinduced intramolecular charge transfer in an electronically modified flavin derivative: roseoflavin.

    PubMed

    Karasulu, Bora; Thiel, Walter

    2015-01-22

    The photophysical properties of a push-pull flavin derivative, roseoflavin (RoF), are investigated in different surroundings at the molecular level, with focus on intramolecular charge transfer (ICT). Time-dependent density functional theory (TD-DFT, CAM-B3LYP functional) and DFT-based multireference configuration interaction (DFT/MRCI) are used to compute excited-state energies and one-electron properties of a truncated RoF model, roseolumiflavin (RoLF). Solvent effects are taken into account implicitly by the conductor-like polarizable continuum model and explicitly through a microsolvation scheme. In the gas phase, the calculations predict no crossing between the lowest locally excited (LE) and charge-transfer (CT) states upon twisting the dimethylamine donor group relative to the plane of the isoalloxazine acceptor moiety, whereas this crossing is found to be facile in solution (i.e., in water or benzene). Crossing of the LE and CT states facilitates ICT, which is the main cause of the fluorescence quenching and dual fluorescence character experimentally observed for roseoflavin in solution. The barrier for the ICT process is computed to be lower in water than in benzene, consistent with the enhanced ICT rates observed in more polar solvents. We present a detailed study of the molecular mechanism of the photoinduced ICT process in RoLF. For a typical donor-acceptor chromophore, three such mechanisms are discussed in the literature, which differ in the alignment of the donor and acceptor planes, namely, planar ICT (PICT), perpendicular-twisted ICT (TICT), and wagging ICT (WICT). Our theoretical results suggest that the TICT mechanism is favored in RoLF. PMID:25214319

  18. 2,2'-Disilylazobenzenes featuring double intramolecular nitrogen∙∙∙silicon coordination: a photoisomerizable fluorophore.

    PubMed

    Kano, Naokazu; Yamamura, Masaki; Kawashima, Takayuki

    2015-10-01

    (E)-4,4'-Dimethyl-2,2'-disilylazobenzenes were synthesized. Double intramolecular N∙∙∙Si coordination in the bis(fluorodimethylsilyl) and bis(trifluorosilyl) derivatives was confirmed using X-ray crystallographic analysis and (29)Si NMR spectroscopy. In the absorption bands, due to the π,π* transitions, introduction of silyl groups was found to cause a bathochromic shift. In contrast to most azobenzenes, which do not fluoresce at all, the (E)-2,2'-bis(trifluorosilyl)azobenzene derivative with the N∙∙∙Si coordination fluoresced a yellow-green colour at room temperature. Methyl and trifluorosilyl groups lowered the n and π* orbitals, as revealed by DFT calculations. As a result, the lowest singlet excitation energy state is found to be the allowed π,π* transition, different from the forbidden n,π* transition in general azobenzenes, as revealed by TD-DFT calculations. The allowed transition character of the lowest singlet excited state and moderately rigid conformation of the azo moiety, provided by the double N∙∙∙Si coordination, account for the fluorescence emission. Nevertheless, the N∙∙∙Si coordination is weak enough to be cleaved upon photoexcitation, and thus the (E)-2,2'-disilylazobenzenes undergo photoisomerization to the (Z)-isomers. Both the photoisomerization and fluorescence emission properties of the azobenzene moiety have been achieved for the first time. After photoisomerization of the (E)-2,2'-disilylazobenzenes to the corresponding (Z)-isomer, they do not fluoresce. This change in the fluorescence intensity upon photoisomerization is useful for the regulation of fluorescence properties. Therefore, this compound can be recognized as a unique photoisomerizable fluorophore to regulate the fluorescence intensity using a single light source. PMID:26205678

  19. A supersandwich electrochemiluminescence immunosensor based on mimic-intramolecular interaction for sensitive detection of proteins.

    PubMed

    He, Ying; Chai, Yaqin; Yuan, Ruo; Wang, Haijun; Bai, Lijuan; Liao, Ni

    2014-10-21

    An electrochemiluminescence (ECL) immunoassay protocol was developed based on mimic-intramolecular interaction for sensitive detection of prostate specific antigen (PSA). It was constructed by integrating the ECL luminophore (tris(4,4'-dicarboxylicacid-2,2'-bipyridyl)-ruthenium(ii)dichloride (Ru(dcbpy)3(2+))) and coreactant (histidine) into the supersandwich DNA structure. This strategy was more effective in amplifying the ECL signal by shortening the electronic transmission distance, improving the ECL luminous stability and enhancing the ECL luminous efficiency. The ECL matrices denoted as MWCNTs@PDA-AuNPs were fabricated through spontaneous oxidative polymerization of dopamine (DA) on multiwalled carbon nanotubes (MWCNTs) and reducing HAuCl4 to produce gold nanoparticles (AuNPs) by DA simultaneously. Then, the prepared matrices were applied to bind capture antibodies. Moreover, supersandwich Ab2 bioconjugate was designed using a PAMAM dendrimer to immobilize the detection antibody and supersandwich DNA structure. The PAMAM dendrimer, with a plurality of secondary and tertiary amine groups, not only facilitated high-density immobilization of the detection antibody and supersandwich DNA structure, but also greatly amplified the ECL signal of Ru(dcbpy)3(2+). The supersandwich DNA structure contained multiple Ru(dcbpy)3(2+) and histidine, further amplifying the ECL signal. The proposed supersandwich immunosensor showed high sensitivity with a detection limit of 4.2 fg mL(-1) and a wide linear range of 0.01 pg mL(-1)-40.00 ng mL(-1). With the excellent stability, satisfying precision and reproducibility, the proposed immunosensor indicates promising practicability for clinical diagnosis. PMID:25122008

  20. Intramolecular allosteric communication in dopamine D2 receptor revealed by evolutionary amino acid covariation.

    PubMed

    Sung, Yun-Min; Wilkins, Angela D; Rodriguez, Gustavo J; Wensel, Theodore G; Lichtarge, Olivier

    2016-03-29

    The structural basis of allosteric signaling in G protein-coupled receptors (GPCRs) is important in guiding design of therapeutics and understanding phenotypic consequences of genetic variation. The Evolutionary Trace (ET) algorithm previously proved effective in redesigning receptors to mimic the ligand specificities of functionally distinct homologs. We now expand ET to consider mutual information, with validation in GPCR structure and dopamine D2 receptor (D2R) function. The new algorithm, called ET-MIp, identifies evolutionarily relevant patterns of amino acid covariations. The improved predictions of structural proximity and D2R mutagenesis demonstrate that ET-MIp predicts functional interactions between residue pairs, particularly potency and efficacy of activation by dopamine. Remarkably, although most of the residue pairs chosen for mutagenesis are neither in the binding pocket nor in contact with each other, many exhibited functional interactions, implying at-a-distance coupling. The functional interaction between the coupled pairs correlated best with the evolutionary coupling potential derived from dopamine receptor sequences rather than with broader sets of GPCR sequences. These data suggest that the allosteric communication responsible for dopamine responses is resolved by ET-MIp and best discerned within a short evolutionary distance. Most double mutants restored dopamine response to wild-type levels, also suggesting that tight regulation of the response to dopamine drove the coevolution and intramolecular communications between coupled residues. Our approach provides a general tool to identify evolutionary covariation patterns in small sets of close sequence homologs and to translate them into functional linkages between residues. PMID:26979958

  1. High-resolution electronic spectroscopy of the doorway states to intramolecular charge transfer.

    PubMed

    Fleisher, Adam J; Bird, Ryan G; Zaleski, Daniel P; Pate, Brooks H; Pratt, David W

    2013-04-25

    Reported here are several of the ground, first, and second excited state structures and dipole moments of three benchmark intramolecular charge transfer (ICT) systems; 4-(1H-pyrrol-1-yl)benzonitrile (PBN), 4,4'-dimethylaminobenzonitrile (DMABN), and 4-(1-pyrrolidinyl)benzonitrile (PYRBN), isolated in the gas phase and probed by rotationally resolved spectroscopy in a molecular beam. The related molecules 1-phenylpyrrole (PP) and 4-aminobenzonitrile (ABN) also are discussed. We find that the S1 electronic state is of B symmetry in all five molecules. In PBN, a second excited state (S2) of A symmetry is found only ~400 cm(-1) above the presumed origin of the S1 state. The change in dipole moment upon excitation to the A state is measured to be Δμ ≈ 3.0 D, significantly smaller than the value predicted by theory and also smaller than that observed for the "anomalous" ICT band of PBN in solution. The B state dipole moments of DMABN and PYRBN are large, ~10.6 D, slightly larger than those attributed to "normal" LE fluorescence in solution. In addition, we find the unsaturated donor molecules (PP, PBN) to be twisted in their ground states and to become more planar upon excitation, even in the A state, whereas the saturated donor molecules (ABN, DMABN, PYRBN), initially planar, either remain planar or become more twisted in their excited states. It thus appears that the model that is appropriate for describing ICT in these systems depends on the geometry of the ground state. PMID:22913563

  2. Conserved Intramolecular Interactions Maintain Myosin Interacting-Heads Motifs Explaining Tarantula Muscle Super-Relaxed State Structural Basis.

    PubMed

    Alamo, Lorenzo; Qi, Dan; Wriggers, Willy; Pinto, Antonio; Zhu, Jingui; Bilbao, Aivett; Gillilan, Richard E; Hu, Songnian; Padrón, Raúl

    2016-03-27

    Tarantula striated muscle is an outstanding system for understanding the molecular organization of myosin filaments. Three-dimensional reconstruction based on cryo-electron microscopy images and single-particle image processing revealed that, in a relaxed state, myosin molecules undergo intramolecular head-head interactions, explaining why head activity switches off. The filament model obtained by rigidly docking a chicken smooth muscle myosin structure to the reconstruction was improved by flexibly fitting an atomic model built by mixing structures from different species to a tilt-corrected 2-nm three-dimensional map of frozen-hydrated tarantula thick filament. We used heavy and light chain sequences from tarantula myosin to build a single-species homology model of two heavy meromyosin interacting-heads motifs (IHMs). The flexibly fitted model includes previously missing loops and shows five intramolecular and five intermolecular interactions that keep the IHM in a compact off structure, forming four helical tracks of IHMs around the backbone. The residues involved in these interactions are oppositely charged, and their sequence conservation suggests that IHM is present across animal species. The new model, PDB 3JBH, explains the structural origin of the ATP turnover rates detected in relaxed tarantula muscle by ascribing the very slow rate to docked unphosphorylated heads, the slow rate to phosphorylated docked heads, and the fast rate to phosphorylated undocked heads. The conservation of intramolecular interactions across animal species and the presence of IHM in bilaterians suggest that a super-relaxed state should be maintained, as it plays a role in saving ATP in skeletal, cardiac, and smooth muscles. PMID:26851071

  3. Vibrational lifetimes of cyanide ion in aqueous solution from molecular dynamics simulations: intermolecular vs intramolecular accepting modes.

    PubMed

    Talapatra, Surma; Geva, Eitan

    2014-07-01

    The lifetimes of the first vibrational state of (12)C(14)N(-) and (13)C(15)N(-) dissolved in H2O or D2O were calculated. The calculations were based on the Landau-Teller formula that puts the vibrational lifetimes in terms of the autocorrelation function of the force exerted on the C-N stretch by the remaining degrees of freedom. The force autocorrelation functions were calculated from classical molecular dynamics simulations of the four cyanide/water isotopomer combinations ((12)C(14)N(-)/H2O, (12)C(14)N(-)/D2O, (13)C(15)N(-)/H2O, (13)C(15)N(-)/D2O). The cyanide ion was described by a polarizable force field, and the water was described by either the rigid SPC/E model or the flexible SPC/Fw model, in order to compare two different types of accepting modes, namely, (1) intermolecular (translational and rotational) solvent accepting modes (rigid SPC/E water) and (2) intramolecular (vibrational) solvent accepting modes (flexible SPC/Fw water). Since quantum effects are expected to increase in size with increasing frequency mismatch between relaxing and accepting modes, different quantum correction factors were employed depending on the identity of the accepting modes, more specifically, the harmonic/Schofield quantum correction factor in the case of intermolecular accepting modes and the standard quantum correction factor in the case of intramolecular accepting modes. The lifetimes with either the rigid SPC/E or flexible SPC/Fw water models were found to be in good quantitative agreement with the experimentally measured values for all isotopomer combinations. Our results suggest that taking into account quantum effects on the vibrational energy relaxation of cyanide in aqueous solution can make the intermolecular pathway at least as likely as the intramolecular pathway. PMID:24927159

  4. Activation of a Ca(2+)-dependent protein kinase involves intramolecular binding of a calmodulin-like regulatory domain

    NASA Technical Reports Server (NTRS)

    Huang, J. F.; Teyton, L.; Harper, J. F.; Evans, M. L. (Principal Investigator)

    1996-01-01

    Ca(2+)-dependent protein kinases (CDPKs) are regulated by a C-terminal calmodulin-like domain (CaM-LD). The CaM-LD is connected to the kinase by a short junction sequence which contains a pseudosubstrate autoinhibitor. To understand how the CaM-LD regulates a CDPK, a recombinant CDPK (isoform CPK-1 from Arabidopsis, accession no. L14771) was made as a fusion protein in Escherichia coli. We show here that a truncated CDPK lacking a CaM-LD (e.g. mutant delta NC-26H) can be activated by exogenous calmodulin or an isolated CaM-LD (Kact approximately 2 microM). We propose that Ca2+ activation of a CDPK normally occurs through intramolecular binding of the CaM-LD to the junction. When the junction and CaM-LD are made as two separate polypeptides, the CaM-LD can bind the junction in a Ca(2+)-dependent fashion with a dissociation constant (KD) of 6 x 10(-6) M, as determined by kinetic binding analyses. When the junction and CaM-LD are tethered in a single polypeptide (e.g. in protein JC-1), their ability to engage in bimolecular binding is suppressed (e.g. the tethered CaM-LD cannot bind a separate junction). A mutation which disrupts the putative CaM-LD binding sequence (e.g. substitution LRV-1444 to DLPG) appears to block intramolecular binding, as indicated by the restored ability of a tethered CaM-LD to engage in bimolecular binding. This mutation, in the context of a full-length enzyme (mutant KJM46H), appears to block Ca2+ activation. Thus, a disruption of intramolecular binding correlates with a disruption of the Ca2+ activation mechanism. CDPKs provide the first example of a member of the calmodulin superfamily where a target binding sequence is located within the same polypeptide.

  5. Selective determination of cysteines through precolumn double-labeling and liquid chromatography followed by detection of intramolecular FRET.

    PubMed

    Yoshitake, Makoto; Nohta, Hitoshi; Sejima, Naoko; Todoroki, Kenichiro; Yoshida, Hideyuki; Yamaguchi, Masatoshi

    2011-02-01

    In this paper we introduce a novel approach for highly selective and sensitive analysis of cysteines (glutathione, cysteine, and homocysteine). This method is based on the detection of intramolecular fluorescence resonance energy transfer (FRET) in a liquid chromatography (LC) system after double-labeling of the amino and sulfhydryl groups of the cysteines. In this detection process, we monitored the FRET between the amine-derivatized and thiol-derivatized fluorophores. We screened 16 combinations of fluorescent reagents. As a result, FRET occurred most effectively when the sulfhydryl and amino groups of the cysteines were derivatized with 7-diethylamino-3-[{4'-(iodoacetyl)amino}phenyl]-4-methylcoumarin (DCIA, Ex/Em 390/480 nm) and 4-fluoro-7-nitrobenz-2-oxo-1,3-diazole (NBD-F, Ex/Em 480/540 nm), respectively, in this order. The double-labeled cysteines emitted NBD-F fluorescence (540 nm) through an intramolecular FRET process when they were excited at the wavelength of maximum excitation of DCIA (390 nm). The generation of FRET was confirmed by comparison with analysis of n-amylamine or tryptophan (amines without a sulfhydryl group) and 6-mercaptohexanol (thiol without an amino group) performed using LC and a three-dimensional fluorescence detection system. We were able to separate the double-labeled cysteines (DCIA and NBD-F) when performing LC on an ODS column with isocratic elution. The limits of quantification (signal-to-noise ratio = 10) and detection (signal-to-noise ratio = 3) for the cysteines, for a 20-μL injection volume, were in the range 150-670 fmol and 46-200 fmol, respectively. The sensitivity of the intramolecular FRET-forming derivatization method is higher than that of a system which takes advantage of conventional detection of the derivatives. Furthermore, this method provides sufficient selectivity and sensitivity to determine the total cysteines present in the plasma of healthy humans. PMID:21153590

  6. Microwave and Quantum Chemical Study of Intramolecular Hydrogen Bonding in 2-Propenylhydrazine (H2C═CHCH2NHNH2).

    PubMed

    Møllendal, Harald; Samdal, Svein; Guillemin, Jean-Claude

    2016-01-28

    The microwave spectrum of 2-propenylhydrazine (H2C═CHCH2NHNH2) was studied in the 12-61 and 72-123 GHz spectral regions. A variety of intramolecular hydrogen bonds between one or more of the hydrogen atoms of the hydrazino group and the π-electrons are possible for this compound. Assignments of the spectra of four conformers, all of which are stabilized with intramolecular hydrogen bonds are reported. One hydrogen bond exists in two of these conformers, whereas the π-electrons are shared by two hydrogen atoms in the two other rotamers. Vibrationally excited-state spectra were assigned for three of the four conformers. The internal hydrogen bonds are weak, probably in the 3-6 kJ/mol range. A total of about 4400 transitions were assigned for these four forms. The microwave work was guided by quantum chemical calculations at the B3LYP/cc-pVTZ and CCSD/cc-pVTZ levels of theory. These calculations indicated that as many as 18 conformers may exist for 2-propenylhydrazine and 11 of these have either one or two intramolecular hydrogen bonds. The four conformers detected in this work are among the rotamers with the lowest CCSD electronic energies. The CCSD method predicts rotational constants that are very close to the experimental rotational constants. The B3LYP calculations yielded quartic centrifugal distortion constants that deviated considerably from their experimental counterparts in most cases. The calculation of vibration-rotation constants and sextic centrifugal distortion constants by the B3LYP method were generally found to be in poor agreement with the corresponding experimental constants. PMID:26696467

  7. Use of fluorescent probes that form intramolecular excimers to monitor structural changes in model and biological membranes.

    PubMed Central

    Melnick, R L; Haspel, H C; Goldenberg, M; Greenbaum, L M; Weinstein, S

    1981-01-01

    1,3-dipyrenylpropane (PC3P) and bis(4-biphenylmethyl)ether, two molecules that form intramolecular excimers, were embedded in phospholipid vesicles and biological membranes to monitor dynamic properties of membrane lipids. Excimer formation was evaluated from determinations of excimer to monomer emission intensity ratios (ID/IM). ID/IM values of PC3P and bis(4-biphenylmethyl)ether were reduced when cholesterol was added to egg lecithin vesicles. PC3P was sensitive to the temperature-induced crystalline to liquid-crystalline phase transition in dimyristoyl phosphatidylcholine vesicles. For studies of cellular membranes, membranes, PC3P was used exclusively, because of the fluorescence of tryptophan residues of membrane proteins interferes with the responses bis(4-biphenylmethyl)ether. Microviscosities of membrane interiors were calculated from standard curves of IM/ID plotted against solvent viscosity. Microviscosity values of egg lecithin vesicles and biological membranes, especially those obtained with PC3P, were more than an order of magnitude lower than values obtained by other techniques. We concluded that the intramolecular process leading to the formation of the excimer is influenced differently in isotropic solvents than in anisotropic environments, such as lipid bilayers. Although distinguishable ID/IM ratios can be obtained for different biological membranes (mitochondrial, microsomal, and plasma membranes were studied), this parameter may be phenomenological and not simply related to membrane microviscosity. As such, fluorescent probes that form intramolecular excimers are of value in making qualitative comparisons of different membranes and in studying the relative effects of physical changes and chemical agents on membrane structure. These probes may also be valuable for studying structural anisotropy of biological membranes. PMID:7248471

  8. Mass Spectrometry Profiles Superoxide-Induced Intra-molecular Disulfide in the FMN-binding Subunit of Mitochondrial Complex I

    PubMed Central

    Zhang, Liwen; Xu, Hua; Chen, Chwen-Lih; Green-Church, Kari B.; Freitas, Michael A.; Chen, Yeong-Renn

    2008-01-01

    Protein thiols with regulatory functions play a critical role in maintaining the homeostasis of the redox state in mitochondria. One major host of regulatory cysteines in mitochondria is complex I, with the thiols primarily located on its 51 kDa FMN-binding subunit. In response to oxidative stress, these thiols are expected to form intra-molecular disulfide bridges as one of their oxidative post-translational modifications. Here, to test this hypothesis and gain insights into the molecular pattern of disulfide in complex I, the isolated bovine complex I was prepared. Superoxide (O2•−) is generated by complex I under the conditions of enzyme turnover. O2•−-induced intra-molecular disulfide formation at the 51 kDa subunit was determined by tandem mass spectrometry and database searching, with the latter accomplished by adaptation of the in-house developed database search engine, MassMatrix [Xu H., et. al J. Proteome Res. (2008) 7, 138–44]. LC/MS/MS analysis of tryptic/chymotryptic digests of the 51 kDa subunit from alkylated complex I revealed that four specific cysteines (C125, C142, C187, and C206) of the 51 kDa subunit were involved in the formation of mixed intra-molecular disulfide linkages. In all, three cysteine pairs were observed: C125/C142, C187/C206, and C142/C206. The formation of disulfide bond was subsequently inhibited by superoxide dismutase, indicating the involvement of O2•−. These results elucidated by mass spectrometry indicates that the residues of C125, C142, C187, and C206 are the specific regulatory cysteines of complex I, and they participate in the oxidative modification with disulfide formation under the physiological or pathophysiological conditions of oxidative stress. PMID:18789718

  9. Exploiting the Bis-Nucleophilicity of α-Aminoboronates: Copper-Catalyzed, Intramolecular Aminoalkylations of Bromobenzoyl Chlorides.

    PubMed

    Dumas, Aaron M; Sieradzki, Adrian J; Donnelly, Liam J

    2016-04-15

    α-Aminoboronate salts are interesting examples of heteroatomic species containing adjacent nucleophilic centers. We have developed an acylation/arylation reaction using 2-bromobenzoyl chlorides as bis-electrophiles that harnesses the nucleophilicity of both positions, leading to isoindolinones. The reactions proceed under mild conditions via an intramolecular, Cu-catalyzed sp(3)-sp(2) coupling, giving products in up to 95% yield. These conditions enable arylation of α,α-disubstituted aminoboronates, which are difficult to accomplish using methods based on less abundant and more expensive transition metals. PMID:27017848

  10. Synthesis of a Tight Intramolecular OH···Olefin Interaction, Probed by IR, (1)H NMR, and Quantum Chemistry.

    PubMed

    Struble, Mark D; Holl, Maxwell Gargiulo; Coombs, Gavin; Siegler, Maxime A; Lectka, Thomas

    2015-05-01

    We have synthesized a molecule containing a tight hydrogen-bonding interaction between an alcohol and a nonconjugated π-system. The strength of this hydrogen bond results in a large red shift, nearly 189 cm(-1), on the alcohol stretching frequency in the IR spectrum in comparison to a free alcohol control. The interaction is notable in that it possesses a better defined intramolecular hydrogen bond compared to the usual molecules for which it is noted, such as syn-7-norbornenol. This interaction was studied through the use of IR and NMR spectroscopy, X-ray crystallography, and molecular modeling calculations. PMID:25822846

  11. Expansion of neonatal tolerance to self in adult life: II. Tolerance preferentially spreads in an intramolecular manner.

    PubMed

    Grabie, N; Karin, N

    1999-06-01

    Newborn rats exposed to a myelin basic protein determinant acquired long-lasting resistance to experimental autoimmune encephalomyelitis induced by another determinant only if both determinants are co-administered in adult life. We demonstrate here that during the course of disease both the anti-self response and the tolerant state spread in an intramolecular and not an intermolecular manner. Mechanisms involved in tolerance elicitation and expansion are then explored using an in vitro system in which indirect suppression could be measured. PMID:10360964

  12. Studies of intramolecular hydrogen bonds (IMHB): crystal and molecular structure of 2-(2'-hydroxy-phenyl)imidazoles

    NASA Astrophysics Data System (ADS)

    Foces-Foces, Concepción; Llamas-Saiz, Antonio L.; Claramunt, Rosa María; Cabildo, Pilar; Elguero, José

    1998-01-01

    The molecular and crystal structure of 2-(2'-hydroxyphenyl)imidazole (2) and 1-methyl-2-(2'-hydroxyphenyl)imidazole (5) have been determined by X-ray analysis. Compound (2) presents a strong intramolecular hydrogen bond (IMHB) responsible for the planarity of the molecule. In both compounds the molecules form chains through NH…O (compound 2) and OH…N hydrogen bonds (compound 5) but giving rise to the same packing mode. Ab initio calculations (6-31G∗∗) have been carried out on both compounds in order to study the effect of the IMHB on the structure.

  13. Effects of organized media on the excited-state intramolecular proton transfer of 10-hydroxybenzo[h]quinoline

    SciTech Connect

    Roberts, E.L.; Alexander, T.A.; Agbaria, R.A.; Warner, I.M.; Chou, P.T.

    1995-04-13

    Absorbance and fluorescence characteristics of 10-hydroxybenzo[h]quinoline (HBQ) are studied in the presence of {alpha}-, {beta}-, and {gamma}-cyclodextrins, and the surfactants, hexadecyltrimethylammonium bromide (CTAB), sodium dodecyl sulfate (SDS), and polyoxyethylene(23) lauryl ether (Brij 35). Fluorescence measurements are used to investigate the effect of organized media on the excited-state intramolecular proton transfer (ESIPT) reaction of HBQ by monitoring the large Stokes-shifted tautomer emission. Absorbance measurements are used to further characterize the interactions of HBQ with the various media. 38 refs., 9 figs., 1 tab.

  14. Divergent Synthesis of Multisubstituted Tetrahydrofurans and Pyrrolidines via Intramolecular Aldol-type Trapping of Onium Ylide Intermediates.

    PubMed

    Jing, Changcheng; Xing, Dong; Gao, Lixin; Li, Jia; Hu, Wenhao

    2015-12-21

    This paper reports a divergent strategy for the synthesis of multisubstituted tetrahydrofurans and pyrrolidines, starting from easily accessible β-hydroxyketones or β-aminoketones to react with diazo compounds. Under Rh(II) catalysis, this transformation is proposed to proceed through a metal-carbene-induced oxonium ylide or ammonium ylide formation followed by an intramolecular aldol-type trapping of these active intermediates. A series of highly substituted tetrahydrofurans and pyrrolidines are synthesized in high yields with good to excellent diastereoselectivities. Preliminary biological evaluations revealed that both types of heterocycles show good PTP1B inhibitory activities. PMID:26592374

  15. Enaminones in a multicomponent synthesis of 4-aryldihydropyridines for potential applications in photoinduced intramolecular electron-transfer systems

    PubMed Central

    Ibrahim, Maher R; Elnagdi, Mohamed H; John, Elizabeth; Ibrahim, Yehia A

    2012-01-01

    Summary An efficient three component reaction with enaminones, primary amines and aldehydes resulted in easy access to 1,4-dihydropyridines with different substituents at the 1-, 3-, 4- and 5-positions. Microwaves improved the reaction yield, reducing also considerably the reaction time and the amount of solvent used. Chiral primary amines gave chiral 1-substituted-1,4-dihydropyridines. The 4-(1-naphthyl) and 4-(phenanthren-9-yl)dihydropyridine derivatives exhibited an interesting photoluminescence behavior, which suggests their potential application as suitable photoinduced intramolecular electron-transfer systems. PMID:22509215

  16. Synthesis of Dibenzosultams by "Transition-Metal-Free" Photoinduced Intramolecular Arylation of N-Aryl-2-halobenzenesulfonamides.

    PubMed

    Guerra, Walter D; Rossi, Roberto A; Pierini, Adriana B; Barolo, Silvia M

    2016-06-17

    A new and general synthetic route to prepare dibenzosultams is here reported. This approach involves the synthesis of N-aryl-2-halobenzenesulfonamides (3), followed by intramolecular C-C photoinduced arylation under soft conditions without the use of "Transition Metal". The photostimulated reactions exhibit very good tolerance to different substituent groups with good to excellent isolated yields (42-98%) of products. Moreover, it is shown that LED (λ = 395 nm) is an efficient light energy source to initiate efficiently the reactions. Theoretical inspection of the mechanism was made to probe the involvement of the radical-anion SRN1 process. PMID:27166973

  17. Two-photon-induced excited state intramolecular proton transfer process and nonlinear optical properties of HBT in cyclohexane solution

    NASA Astrophysics Data System (ADS)

    Zheng, Jiajin; Guo, Yangxue; Li, Xiangpin; Zhang, Guilan; Chen, Wenju

    2006-10-01

    The two-photon-induced excited state intramolecular proton transfer (ESIPT) process of 2-(2'-hydroxyphenyl) benzothiazole (HBT) in cyclohexane solution has been investigated. We focus on the calculation of the two-photon absorption (TPA) coefficient and nonlinear refraction index of HBT, and the theoretical computational results are in good agreement with the experimental ones. By establishing the ESIPT kinetic model for HBT based on TPA, the TPA cross section is obtained. The numerical results show that HBT exhibits a rather large TPA cross section compared with that of 2-(2'-hydroxyphenyl)benzoxazole (HBO) reported previously. Therefore, HBT is a promising TPA material and is worthy of further research.

  18. Blue organic light-emitting devices with an oxadiazole-containing emitting layer exhibiting excited state intramolecular proton transfer

    NASA Astrophysics Data System (ADS)

    Ma, Dongge; Liang, Fushun; Wang, Lixiang; Lee, S. T.; Hung, L. S.

    2002-05-01

    We report a blue organic light-emitting device having an emissive layer of 2-(2-hydroxyphenyl)-5-phenyl-1,3,4-oxadiazole (HOXD), that exhibits excited state intramolecular proton transfer (ESIPT). The device had a luminance efficiency of 0.8 cd/A and a maximum brightness of 870 cd/ m2. Electroluminescence spectra revealed a dominating peak at 450 nm and two additional peaks at 480 and 515 nm with a full width at half maximum of 50 nm. Our studies indicate that some EL may originate from the triplet excitation state of the enol form of HOXD.

  19. Cu-Catalyzed Intramolecular Amidation of Unactivated C(sp(3) )-H Bonds To Synthesize N-Substituted Indolines.

    PubMed

    Pan, Fei; Wu, Bin; Shi, Zhang-Jie

    2016-05-01

    A copper-catalyzed intramolecular amidation of unactivated C(sp(3) )-H bonds to construct indoline derivatives has been developed. Such an amidation proceeded well at primary C-H bonds preferred to secondary C-H bonds. The transformation owned a broad substrate scope. The corresponding indolines were obtained in good to excellent yields. N-Formal and other carbonyl groups were suitable and were easily deprotected and transformed into methyl or long-chained alkyl groups. Preliminary mechanistic studies suggested a radical pathway. PMID:26945702

  20. Theoretical study on the intramolecular hydrogen bond in chloro-substituted N,N-dimethylaminomethylphenols. I. Structural effects*1

    NASA Astrophysics Data System (ADS)

    Koll, A.; Parasuk, V.; Parasuk, W.; Karpfen, A.; Wolschann, P.

    2004-08-01

    Ab initio and density functional calculations are applied to study the influence of an increasing number of chlorine substituents on the properties of the intramolecular hydrogen bond in substituted Mannich bases. It is shown, that not only the acidity of the proton donor, which depends on the number of chlorine atoms at the aromatic ring, but also steric interactions modify the geometry of the hydrogen bond. Specific interactions of O-Cl⋯H-O hydrogen-bonding in some derivatives are estimated by calculations on related chlorophenols.

  1. Theoretical study on the intramolecular hydrogen bond in chloro-substituted N, N-dimethylaminomethylphenols. I. Structural effects

    NASA Astrophysics Data System (ADS)

    Koll, A.; Parasuk, V.; Parasuk, W.; Karpfen, A.; Wolschann, P.

    2004-03-01

    Ab initio and density functional calculations are applied to study the influence of an increasing number of chlorine substituents on the properties of the intramolecular hydrogen bond in substituted Mannich bases. It is shown, that not only the acidity of the proton donor, which depends on the number of chlorine atoms at the aromatic ring, but also steric interactions modify the geometry of the hydrogen bond. Specific interactions of O-Cl⋯H-O hydrogen-bonding in some derivatives are estimated by calculations on related chlorophenols.

  2. Influence of end-to-end diffusion on intramolecular energy transfer as observed by frequency-domain fluorometry

    NASA Astrophysics Data System (ADS)

    Lakowicz, Joseph R.; Wiczk, Wieslaw M.; Gryczynski, Ignacy; Szmacinski, Henryk; Johnson, Michael L.

    1990-05-01

    We investigated the influence of end-to-end diffusion on intramolecular energy transfer between a naphthalene donor and dansyl acceptor linked by polymethylene chain. A range of viscosities of 0.6 - 200cP were obtained using propylene glycol at different temperatures (0-80°C) and methanol at 20°C. The intensity decays of naphthalene were measured in frequency-domain. Several theoretical models, including distance distributions were used to fit the data. The results indicate that end-to-end diffusion of flexible donor - acceptor pairs can be readily detected and quantified using frequency-domain fluorometry.

  3. Rhodium-catalyzed silylation and intramolecular arylation of nitriles via the silicon-assisted cleavage of carbon-cyano bonds.

    PubMed

    Tobisu, Mamoru; Kita, Yusuke; Ano, Yusuke; Chatani, Naoto

    2008-11-26

    A rhodium-catalyzed silylation reaction of carbon-cyano bonds using disilane has been developed. Under these catalytic conditions, carbon-cyano bonds in aryl, alkenyl, allyl, and benzyl cyanides bearing a variety of functional groups can be silylated. The observation of an enamine side product in the silylation of benzyl cyanides and related stoichiometric studies indicate that the carbon-cyano bond cleavage proceeds through the deinsertion of silyl isocyanide from eta(2)-iminoacyl complex B. Knowledge gained from these studies has led to the development of a new intramolecular biaryl coupling reaction in which aryl cyanides and aryl chlorides are cross-coupled. PMID:18975946

  4. Tandem cross enyne metathesis (CEYM)–intramolecular Diels–Alder reaction (IMDAR). An easy entry to linear bicyclic scaffolds

    PubMed Central

    Miró, Javier; Sánchez-Roselló, María; Sanz, Álvaro; Rabasa, Fernando

    2015-01-01

    Summary A new tandem cross enyne metathesis (CEYM)–intramolecular Diels–Alder reaction (IMDAR) has been carried out. It involves conjugated ketones, esters or amides bearing a remote olefin and aromatic alkynes as the starting materials. The overall process enables the preparation of a small family of linear bicyclic scaffolds in a very simple manner with moderate to good levels of diastereoselectivity. This methodology constitutes one of the few examples that employ olefins differently than ethylene in tandem CEYM–IMDAR protocols. PMID:26425205

  5. Intramolecular resonance-assisted hydrogen bonds: A theoretical description by means of atomic charges and charge fluxes

    NASA Astrophysics Data System (ADS)

    Baranović, Goran

    2014-01-01

    The characterization of intramolecular H-bonds in terms of atomic charges and charge fluxes (at the B3LYP/cc-pVTZ level of theory) has been extended to the case of the so called resonance-assisted (RA) H-bonds. A quadratic correlation between the charge fluxes ϕH and the molecular IR absorption coefficients E that includes the entire family of the studied systems (31 of them) containing both intra- and intermolecular hydrogen bonds (O-H⋯O/N) confirmed the critical importance of the charge fluxes on the IR intensity enhancements. Since they reflect changing of the atomic charge distribution during the normal modes of vibrations, the dynamic nature of hydrogen bonding properties has been re-emphasized. The changes of the charge flux of the hydroxyl hydrogen in an RA intramolecular H-bond are between those for “free” OH bonds and the values calculated for intermolecular H-bonds. The transition “free” → intramolecular → intermolecular is gradual and therefore the hydrogen charge flux can be considered as practically sufficient to give quantitative measure to the intuitively obvious statement that “intramolecular H-bonding is somehow in between no H-bonding situation and intermolecular H-bonding” and thus provide a quantitative and yet simple parameterization of H-bond strength. In strictly planar molecules, the difference of the sums of charges of atoms participating in the 6-membered H-bond ring ΔΣ can serve as a measure of the charge delocalization after the H-bond is formed. The electronic charge is withdrawn from the group of six atoms when the H-bond is formed in nitrophenol (ΔΣ = -0.07), while the opposite is true (ΔΣ = +0.03) for 2-hydroxy benzylidene amine. The corresponding values of the geometrical resonance parameter Δ are 0.39 and 0.37, respectively, similar to those found for 2-hydroxy acetophenone and 2-hydroxy benzaldehyde. The extent of the π-electron delocalization as measured by the resonance parameter Δ does not follow

  6. Self-assembly of intramolecular charge-transfer compounds into functional molecular systems.

    PubMed

    Li, Yongjun; Liu, Taifeng; Liu, Huibiao; Tian, Mao-Zhong; Li, Yuliang

    2014-04-15

    Highly polarized compounds exhibiting intramolecular charge transfer (ICT) are used widely as nonlinear optical (NLO) materials and red emitters and in organic light emitting diodes. Low-molecular-weight donor/acceptor (D/A)-substituted ICT compounds are ideal candidates for use as the building blocks of hierarchically structured, multifunctional self-assembled supramolecular systems. This Account describes our recent studies into the development of functional molecular systems with well-defined self-assembled structures based on charge-transfer (CT) interactions. From solution (sensors) to the solid state (assembled structures), we have fully utilized intrinsic and stimulus-induced CT interactions to construct these functional molecular systems. We have designed some organic molecules capable of ICT, with diversity and tailorability, that can be used to develop novel self-assembled materials. These ICT organic molecules are based on a variety of simple structures such as perylene bisimide, benzothiadiazole, tetracyanobutadiene, fluorenone, isoxazolone, BODIPY, and their derivatives. The degree of ICT is influenced by the nature of both the bridge and the substituents. We have developed new methods to synthesize ICT compounds through the introduction of heterocycles or heteroatoms to the π-conjugated systems or through extending the conjugation of diverse aromatic systems via another aromatic ring. Combining these ICT compounds featuring different D/A units and different degrees of conjugation with phase transfer methodologies and solvent-vapor techniques, we have self-assembled various organic nanostructures, including hollow nanospheres, wires, tubes, and ribbonlike architectures, with controllable morphologies and sizes. For example, we obtained a noncentrosymmetric microfiber structure that possessed a permanent dipole along its fibers' long axis and a transition dipole perpendicular to it; the independent NLO responses of this material can be separated and

  7. Long-Lived Triplet Excited States of Bent-Shaped Pentacene Dimers by Intramolecular Singlet Fission.

    PubMed

    Sakuma, Takao; Sakai, Hayato; Araki, Yasuyuki; Mori, Tadashi; Wada, Takehiko; Tkachenko, Nikolai V; Hasobe, Taku

    2016-03-24

    Intramolecular singlet fission (ISF) is a promising photophysical process to construct more efficient light energy conversion systems as one excited singlet state converts into two excited triplet states. Herein we synthesized and evaluated bent-shaped pentacene dimers as a prototype of ISF to reveal intrinsic characters of triplet states (e.g., lifetimes of triplet excited states). In this study, meta-phenylene-bridged TIPS-pentacene dimer (PcD-3Ph) and 2,2'-bipheynyl bridged TIPS-pentacene dimer (PcD-Biph) were newly synthesized as bent-shaped dimers. In the steady-state spectroscopy, absorption and emission bands of these dimers were fully characterized, suggesting the appropriate degree of electronic coupling between pentacene moieties in these dimers. In addition, the electrochemical measurements were also performed to check the electronic interaction between two pentacene moieties. Whereas the successive two oxidation peaks owing to the delocalization were observed in a directly linked-pentacene dimer (PcD) by a single bond, the cyclic voltammograms in PcD-Biph and PcD-3Ph implied the weaker interaction compared to that of p-phenylene-bridged TIPS-pentacene dimer (PcD-4Ph) and PcD. The femtosecond and nanosecond transient absorption spectra clearly revealed the slower ISF process in bent-shaped pentacene dimers (PcD-Biph and PcD-3Ph), more notably, the slower relaxation of the excited triplet states in PcD-Biph and PcD-3Ph. Namely, the quantum yields of triplet states (ΦT) by ISF approximately remain constant (ca. 180-200%) in all dimer systems, whereas the lifetimes of the triplet excited states became much longer (up to 360 ns) in PcD-Biph as compared to PcD-4Ph (15 ns). Additionally, the lifetimes of the corresponding triplet states in PcD-Biph and PcD-3Ph were sufficiently affected by solvent viscosity. In particular, the lifetimes of PcD-Biph triplet state in THF/paraffin (1.0 μs) increased up to approximately three times as compared to that in THF

  8. Relaxation dynamics in quantum dissipative systems: The microscopic effect of intramolecular vibrational energy redistribution

    SciTech Connect

    Uranga-Piña, L.; Tremblay, J. C.

    2014-08-21

    We investigate the effect of inter-mode coupling on the vibrational relaxation dynamics of molecules in weak dissipative environments. The simulations are performed within the reduced density matrix formalism in the Markovian regime, assuming a Lindblad form for the system-bath interaction. The prototypical two-dimensional model system representing two CO molecules approaching a Cu(100) surface is adapted from an ab initio potential, while the diatom-diatom vibrational coupling strength is systematically varied. In the weak system-bath coupling limit and at low temperatures, only first order non-adiabatic uni-modal coupling terms contribute to surface-mediated vibrational relaxation. Since dissipative dynamics is non-unitary, the choice of representation will affect the evolution of the reduced density matrix. Two alternative representations for computing the relaxation rates and the associated operators are thus compared: the fully coupled spectral basis, and a factorizable ansatz. The former is well-established and serves as a benchmark for the solution of Liouville-von Neumann equation. In the latter, a contracted grid basis of potential-optimized discrete variable representation is tailored to incorporate most of the inter-mode coupling, while the Lindblad operators are represented as tensor products of one-dimensional operators, for consistency. This procedure results in a marked reduction of the grid size and in a much more advantageous scaling of the computational cost with respect to the increase of the dimensionality of the system. The factorizable method is found to provide an accurate description of the dissipative quantum dynamics of the model system, specifically of the time evolution of the state populations and of the probability density distribution of the molecular wave packet. The influence of intra-molecular vibrational energy redistribution appears to be properly taken into account by the new model on the whole range of coupling strengths. It

  9. A classical trajectory study of the intramolecular dynamics, isomerization, and unimolecular dissociation of HO2

    NASA Astrophysics Data System (ADS)

    Perry, Jamin W.; Dawes, Richard; Wagner, Albert F.; Thompson, Donald L.

    2013-08-01

    The classical dynamics and rates of isomerization and dissociation of HO2 have been studied using two potential energy surfaces (PESs) based on interpolative fittings of ab initio data: An interpolative moving least-squares (IMLS) surface [A. Li, D. Xie, R. Dawes, A. W. Jasper, J. Ma, and H. Guo, J. Chem. Phys. 133, 144306 (2010)] and the cubic-spline-fitted PES reported by Xu, Xie, Zhang, Lin, and Guo (XXZLG) [J. Chem. Phys. 127, 024304 (2007)]. Both PESs are based on similar, though not identical, internally contracted multi-reference configuration interaction with Davidson correction (icMRCI+Q) electronic structure calculations; the IMLS PES includes complete basis set (CBS) extrapolation. The coordinate range of the IMLS PES is limited to non-reactive processes. Surfaces-of-section show similar generally regular phase space structures for the IMLS and XXZLG PESs with increasing energy. The intramolecular vibrational energy redistribution (IVR) at energies above and below the threshold of isomerization is slow, especially for O-O stretch excitations, consistent with the regularity in the surfaces-of-section. The slow IVR rates lead to mode-specific effects that are prominent for isomerization (on both the IMLS and XXZLG) and modest for unimolecular dissociation to H + O2 (accessible only on the XXZLG PES). Even with statistical distributions of initial energy, slow IVR rates result in double exponential decay for isomerization, with the slower rate correlated with slow IVR rates for O-O vibrational excitation. The IVR and isomerization rates computed for the IMLS and XXZLG PESs are quantitatively, but not qualitatively, different from one another with the largest differences ascribed to the ˜2 kcal/mol difference in the isomerization barrier heights. The IMLS and XXZLG results are compared with those obtained using the global, semi-empirical double-many-body expansion DMBE-IV PES [M. R. Pastrana, L. A. M. Quintales, J. Brandão, and A. J. C. Varandas, J. Chem

  10. Covalent Conjugation of a Peptide Triazole to HIV-1 gp120 Enables Intramolecular Binding Site Occupancy

    PubMed Central

    2015-01-01

    The HIV-1 gp120 glycoprotein is the main viral surface protein responsible for initiation of the entry process and, as such, can be targeted for the development of entry inhibitors. We previously identified a class of broadly active peptide triazole (PT) dual antagonists that inhibit gp120 interactions at both its target receptor and coreceptor binding sites, induce shedding of gp120 from virus particles prior to host–cell encounter, and consequently can prevent viral entry and infection. However, our understanding of the conformational alterations in gp120 by which PT elicits its dual receptor antagonism and virus inactivation functions is limited. Here, we used a recently developed computational model of the PT–gp120 complex as a blueprint to design a covalently conjugated PT–gp120 recombinant protein. Initially, a single-cysteine gp120 mutant, E275CYU-2, was expressed and characterized. This variant retains excellent binding affinity for peptide triazoles, for sCD4 and other CD4 binding site (CD4bs) ligands, and for a CD4-induced (CD4i) ligand that binds the coreceptor recognition site. In parallel, we synthesized a PEGylated and biotinylated peptide triazole variant that retained gp120 binding activity. An N-terminally maleimido variant of this PEGylated PT, denoted AE21, was conjugated to E275C gp120 to produce the AE21–E275C covalent conjugate. Surface plasmon resonance interaction analysis revealed that the PT–gp120 conjugate exhibited suppressed binding of sCD4 and 17b to gp120, signatures of a PT-bound state of envelope protein. Similar to the noncovalent PT–gp120 complex, the covalent conjugate was able to bind the conformationally dependent mAb 2G12. The results argue that the PT–gp120 conjugate is structurally organized, with an intramolecular interaction between the PT and gp120 domains, and that this structured state embodies a conformationally entrapped gp120 with an altered bridging sheet but intact 2G12 epitope. The similarities of

  11. Failures of TDDFT in describing the lowest intramolecular charge-transfer excitation in para-nitroaniline

    NASA Astrophysics Data System (ADS)

    Eriksen, Janus J.; Sauer, Stephan P. A.; Mikkelsen, Kurt V.; Christiansen, Ove; Jensen, Hans Jørgen Aa.; Kongsted, Jacob

    2013-07-01

    We investigate the failure of time-dependent density functional theory (TDDFT) with the CAM-B3LYP exchange-correlation (xc) functional coupled to the polarisable embedding (PE) scheme (PE-CAM-B3LYP) in reproducing the solvatochromic shift of the lowest intense charge-transfer excitation in para-nitroaniline (pNA) in water by comparing with results obtained with the coupled cluster singles and doubles (CCSD) model also coupled to the polarisable embedding scheme (PE-CCSD). We determine the amount of charge separation in the ground and excited charge-transfer state with both methods by calculating the electric dipole moments in the gas phase and for 100 solvent configurations. We find that CAM-B3LYP overestimates the amount of charge separation inherent in the ground state and TDDFT/CAM-B3LYP drastically underestimates this amount in the excited charge-transfer state. As the errors in the solvatochromatic shift are found to be inverse proportional to the change in dipole moment upon excitation, we conclude that the flaws in the description of the solvatochromic shift of this excitation are related to TDDFT itself and how it responds to the solvent effects modelled by the PE scheme. We recommend therefore to benchmark results of TDDFT calculations with CAM-B3LYP for intramolecular charge-transfer excitations in molecular systems similar to pNA against higher level ab initio wave function methods, like, e.g. CCSD, prior to their use. Using the calculated change in dipole moment upon excitation as a measure for charge-transfer character, we furthermore confirm that the difference between excitation energies calculated with TDDFT and with the Tamm-Dancoff approximation (TDA) to TDDFT is indeed correlated with the charge-transfer character of a given electronic transition both in vacuo and in solution. This is supported by a corresponding correlation between the change in dipole moment and the size of the Λ index diagnostic for the investigated CT excitation.

  12. Further studies on cation clock reactions in glycosylation: observation of a configuration specific intramolecular sulfenyl transfer and isolation and characterization of a tricyclic acetal.

    PubMed

    Huang, Min; Furukawa, Takayuki; Retailleau, Pascal; Crich, David; Bohé, Luis

    2016-06-01

    The use of the 2-O-(2-trimethylsilylmethallyl) group as intramolecular nucleophile and cation clock reaction in the glucopyranose series depends on the nature of the glycosyl donor. As previously reported, with trichloroacetimidates the anticipated intramolecular Sakurai reaction proceeds efficiently and is an effective clock, whereas with sulfoxides complications arise. The source of these complications is now shown to be an intramolecular sulfenyl transfer reaction between the tethered allylsilane and the activated sulfoxide. These results illustrate how a different unimolecular clock reaction may be required for a given cation when it is generated from different donors in order to avoid side reactions. The synthesis and cyclization of a 2-O-(3-hydroxypropyl) glucopyranosyl sulfoxide leading on activation to the formation of a trans-fused acetal is also described. The formation of this crystallographically-established trans-fused acetal is discussed in terms of the high effective concentration of the intramolecular nucleophile which leads to a high degree of a SN2 character in the displacement of the α-glucosyl triflate or at the level of the corresponding α-CIP. The possible use of such intramolecular alcohols as clock reactions and their limitations is discussed. PMID:27085740

  13. TDDFT study of twisted intramolecular charge transfer and intermolecular double proton transfer in the excited state of 4'-dimethylaminoflavonol in ethanol solvent.

    PubMed

    Wang, Ye; Shi, Ying; Cong, Lin; Li, Hui

    2015-02-25

    Time-dependent density functional theory method at the def-TZVP/B3LYP level was employed to investigate the intramolecular and intermolecular hydrogen bonding dynamics in the first excited (S1) state of 4'-dimethylaminoflavonol (DMAF) monomer and in ethanol solution. In the DMAF monomer, we demonstrated that the intramolecular charge transfer (ICT) takes place in the S1 state. This excited state ICT process was followed by intramolecular proton transfer. Our calculated results are in good agreement with the mechanism proposed in experimental work. For the hydrogen-bonded DMAF-EtOH complex, it was demonstrated that the intermolecular hydrogen bonds can induce the formation of the twisted intramolecular charge transfer (TICT) state and the conformational twisting is along the C3-C4 bond. Moreover, the intermolecular hydrogen bonds can also facilitate the intermolecular double proton transfer in the TICT state. A stepwise intermolecular double proton transfer process was revealed. Therefore, the intermolecular hydrogen bonds can alter the mechanism of intramolecular charge transfer and proton transfer in the excited state for the DMAF molecule. PMID:25282020

  14. Imaging and energetics of single SSB-ssDNA molecules reveal intramolecular condensation and insight into RecOR function

    PubMed Central

    Bell, Jason C; Liu, Bian; Kowalczykowski, Stephen C

    2015-01-01

    Escherichia coli single-stranded DNA (ssDNA) binding protein (SSB) is the defining bacterial member of ssDNA binding proteins essential for DNA maintenance. SSB binds ssDNA with a variable footprint of ∼30–70 nucleotides, reflecting partial or full wrapping of ssDNA around a tetramer of SSB. We directly imaged single molecules of SSB-coated ssDNA using total internal reflection fluorescence (TIRF) microscopy and observed intramolecular condensation of nucleoprotein complexes exceeding expectations based on simple wrapping transitions. We further examined this unexpected property by single-molecule force spectroscopy using magnetic tweezers. In conditions favoring complete wrapping, SSB engages in long-range reversible intramolecular interactions resulting in condensation of the SSB-ssDNA complex. RecO and RecOR, which interact with SSB, further condensed the complex. Our data support the idea that RecOR--and possibly other SSB-interacting proteins—function(s) in part to alter long-range, macroscopic interactions between or throughout nucleoprotein complexes by microscopically altering wrapping and bridging distant sites. DOI: http://dx.doi.org/10.7554/eLife.08646.001 PMID:26381353

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

    PubMed

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

    2016-03-14

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

  16. A design strategy for intramolecular singlet fission mediated by charge-transfer states in donor-acceptor organic materials

    NASA Astrophysics Data System (ADS)

    Busby, Erik; Xia, Jianlong; Wu, Qin; Low, Jonathan Z.; Song, Rui; Miller, John R.; Zhu, X.-Y.; Campos, Luis M.; Sfeir, Matthew Y.

    2015-04-01

    The ability to advance our understanding of multiple exciton generation (MEG) in organic materials has been restricted by the limited number of materials capable of singlet fission. A particular challenge is the development of materials that undergo efficient intramolecular fission, such that local order and strong nearest-neighbour coupling is no longer a design constraint. Here we address these challenges by demonstrating that strong intrachain donor-acceptor interactions are a key design feature for organic materials capable of intramolecular singlet fission. By conjugating strong-acceptor and strong-donor building blocks, small molecules and polymers with charge-transfer states that mediate population transfer between singlet excitons and triplet excitons are synthesized. Using transient optical techniques, we show that triplet populations can be generated with yields up to 170%. These guidelines are widely applicable to similar families of polymers and small molecules, and can lead to the development of new fission-capable materials with tunable electronic structure, as well as a deeper fundamental understanding of MEG.

  17. Control of intramolecular electron transfer by protonation: Dimers and polymers containing ruthenium II/III and 44' azopyridine

    NASA Astrophysics Data System (ADS)

    Launay, Jean-Pierre; Marvaud, Valérie

    1992-07-01

    The association of pentammine ruthenium(II) with the reducible ligand 44' azopyridine leads to a pH induced redox reaction in which ruthenium is oxidized to the III state, while 44' azopyridine is reduced to hydrazopyridine. In this process, the conjugated ligand is transformed in a nonconjugated one, with loss of its intramolecular electron transfer properties. In order to exploit this control of an intramolecular electron transfer by a protonation process, we have prepared ``shish-kebab'' polymers by first inserting ruthenium in tetrakis (3,5-diterbutyl 4-hydroxyphenyl) porphyrin under a CO atmosphere. The resulting Ru(CO)porphyrin complex is photochemically decarbonylated in the presence of bridging ligands (44×azopyridine or pyrazine). Polymers are thus obtained, which can be oxidized by iodine, giving rise to intervalence transitions between ruthenium(II) and (III) in the near-infrared. This provides a convenient way to monitor electron transfer along the polymer chain. In the case of 44' azopyridine, the pH induced redox reaction is again observed. Starting from a homovalent ruthenium(II) chain, this gives the possibility to switch ``ON'' or ``OFF'' the intervalence transition by a protonation/deprotonation reaction.

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

    PubMed Central

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

    2008-01-01

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

  19. Comparative study of E⋯N (E=Se/Te) intramolecular interactions in organochalcogen compounds using density functional theory.

    PubMed

    Panda, Arunashree; Behera, Raghu Nath

    2014-03-30

    The intramolecular E⋯N (E=Se, Te) interactions between the selenium (and tellurium) and the nitrogen atom in four series of o-substituted organochalcogen compounds have been analyzed using density functional theory. The nature and the strength of this interactions and their dependence on substituents and the rigidity are predicted using B3LYP/6-31G(d)/LanL2DZ method. The strength of these E⋯N interactions are found to be dependent on the nature of EX (X=Cl, Br, I, SPh, CH2Ph; Ph: Phenyl) acceptor orbitals and follows the order I>Br>Cl>SPh>CH2Ph. The Natural Bond Orbital (NBO) analysis using DFT methods points to nN→σE-X electron delocalization as the key contributing factor toward E⋯N nonbonding interactions. Both NBO and AIM methods suggest that the intramolecular interaction in these compounds is dominantly covalent in nature. Studies on the effect of solvent on the E⋯N interactions show that polar solvent stabilizes these interactions by shortening the E⋯N distances. PMID:24412286

  20. A design strategy for intramolecular singlet fission mediated by charge-transfer states in donor-acceptor organic materials.

    PubMed

    Busby, Erik; Xia, Jianlong; Wu, Qin; Low, Jonathan Z; Song, Rui; Miller, John R; Zhu, X-Y; Campos, Luis M; Sfeir, Matthew Y

    2015-04-01

    The ability to advance our understanding of multiple exciton generation (MEG) in organic materials has been restricted by the limited number of materials capable of singlet fission. A particular challenge is the development of materials that undergo efficient intramolecular fission, such that local order and strong nearest-neighbour coupling is no longer a design constraint. Here we address these challenges by demonstrating that strong intrachain donor-acceptor interactions are a key design feature for organic materials capable of intramolecular singlet fission. By conjugating strong-acceptor and strong-donor building blocks, small molecules and polymers with charge-transfer states that mediate population transfer between singlet excitons and triplet excitons are synthesized. Using transient optical techniques, we show that triplet populations can be generated with yields up to 170%. These guidelines are widely applicable to similar families of polymers and small molecules, and can lead to the development of new fission-capable materials with tunable electronic structure, as well as a deeper fundamental understanding of MEG. PMID:25581625

  1. A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states.

    PubMed

    Nguyen, Trong-Nghia; Putikam, Raghunath; Lin, M C

    2015-03-28

    We have discovered a new and highly competitive product channel in the unimolecular decay process for small Criegee intermediates, CH2OO and anti/syn-CH3C(H)OO, occurring by intramolecular insertion reactions via a roaming-like transition state (TS) based on quantum-chemical calculations. Our results show that in the decomposition of CH2OO and anti-CH3C(H)OO, the predominant paths directly produce cis-HC(O)OH and syn-CH3C(O)OH acids with >110 kcal/mol exothermicities via loose roaming-like insertion TSs involving the terminal O atom and the neighboring C-H bonds. For syn-CH3C(H)OO, the major decomposition channel occurs by abstraction of a H atom from the CH3 group by the terminal O atom producing CH2C(H)O-OH. At 298 K, the intramolecular insertion process in CH2OO was found to be 600 times faster than the commonly assumed ring-closing reaction. PMID:25833584

  2. A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states

    NASA Astrophysics Data System (ADS)

    Nguyen, Trong-Nghia; Putikam, Raghunath; Lin, M. C.

    2015-03-01

    We have discovered a new and highly competitive product channel in the unimolecular decay process for small Criegee intermediates, CH2OO and anti/syn-CH3C(H)OO, occurring by intramolecular insertion reactions via a roaming-like transition state (TS) based on quantum-chemical calculations. Our results show that in the decomposition of CH2OO and anti-CH3C(H)OO, the predominant paths directly produce cis-HC(O)OH and syn-CH3C(O)OH acids with >110 kcal/mol exothermicities via loose roaming-like insertion TSs involving the terminal O atom and the neighboring C-H bonds. For syn-CH3C(H)OO, the major decomposition channel occurs by abstraction of a H atom from the CH3 group by the terminal O atom producing CH2C(H)O-OH. At 298 K, the intramolecular insertion process in CH2OO was found to be 600 times faster than the commonly assumed ring-closing reaction.

  3. 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.

  4. Cooperative intramolecular hydrogen bonds in the structure of 5,5'-dibromo-3-diethylaminomethyl-2,2'-biphenol

    NASA Astrophysics Data System (ADS)

    Bartoszak-Adamska, E.; Wojciechowski, G.; Jaskólski, M.; Brzezinski, B.

    2000-07-01

    Crystals of 5,5'-dibromo-3-diethylaminomethyl-2,2'-biphenol were examined using X-ray diffraction and FT-IR spectroscopy. The space group is P2 1/ n with a=8.617(2), b=16.356(3), c=12.854(3) Å, β=108.03(3)° and Z=4. The molecule exists in the crystal in zwitterionic state as a result of proton transfer from a hydroxyl group to the adjacent amino group. These two groups, together with the hydroxyl group of the second phenol moiety are involved in a system of cooperative intramolecular hydrogen bonds, O(2)H⋯O(1) -H +N(1). The O⋯O and O⋯N distances are 2.476(5) and 2.584(5) Å, the O-H and H-N distances 0.89 and 1.04 Å, and the O-H⋯O and O⋯H-N + angles 163 and 141°, respectively. The IR spectra of the crystals are consistent with the results of the X-ray analysis. Instead of a continuous absorption, only broad bands are found indicating very low proton polarizability in the two types of intramolecular hydrogen bonds.

  5. Intramolecular interactions of L-phenylalanine: Valence ionization spectra and orbital momentum distributions of its fragment molecules.

    PubMed

    Ganesan, Aravindhan; Wang, Feng; Falzon, Chantal

    2011-02-01

    Intramolecular interactions between fragments of L-phenylalanine, i.e., phenyl and alaninyl, have been investigated using dual space analysis (DSA) quantum mechanically. Valence space photoelectron spectra (PES), orbital energy topology and correlation diagram, as well as orbital momentum distributions (MDs) of L-phenylalanine, benzene and L-alanine are studied using density functional theory methods. While fully resolved experimental PES of L-phenylalanine is not yet available, our simulated PES reproduces major features of the experimental measurement. For benzene, the simulated orbital MDs for 1e(1g) and 1a(2u) orbitals also agree well with those measured using electron momentum spectra. Our theoretical models are then applied to reveal intramolecular interactions of the species on an orbital base, using DSA. Valence orbitals of L-phenylalanine can be essentially deduced into contributions from its fragments such as phenyl and alaninyl as well as their interactions. The fragment orbitals inherit properties of their parent species in energy and shape (ie., MDs). Phenylalanine orbitals show strong bonding in the energy range of 14-20 eV, rather than outside of this region. This study presents a competent orbital based fragments-in-molecules picture in the valence space, which supports the fragment molecular orbital picture and building block principle in valence space. The optimized structures of the molecules are represented using the recently developed interactive 3D-PDF technique. PMID:20806261

  6. A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states

    SciTech Connect

    Nguyen, Trong-Nghia; Putikam, Raghunath; Lin, M. C.

    2015-03-28

    We have discovered a new and highly competitive product channel in the unimolecular decay process for small Criegee intermediates, CH{sub 2}OO and anti/syn-CH{sub 3}C(H)OO, occurring by intramolecular insertion reactions via a roaming-like transition state (TS) based on quantum-chemical calculations. Our results show that in the decomposition of CH{sub 2}OO and anti-CH{sub 3}C(H)OO, the predominant paths directly produce cis-HC(O)OH and syn-CH{sub 3}C(O)OH acids with >110 kcal/mol exothermicities via loose roaming-like insertion TSs involving the terminal O atom and the neighboring C–H bonds. For syn-CH{sub 3}C(H)OO, the major decomposition channel occurs by abstraction of a H atom from the CH{sub 3} group by the terminal O atom producing CH{sub 2}C(H)O–OH. At 298 K, the intramolecular insertion process in CH{sub 2}OO was found to be 600 times faster than the commonly assumed ring-closing reaction.

  7. Enthalpy difference between conformations of normal alkanes: effects of basis set and chain length on intramolecular basis set superposition error

    NASA Astrophysics Data System (ADS)

    Balabin, Roman M.

    2011-03-01

    The quantum chemistry of conformation equilibrium is a field where great accuracy (better than 100 cal mol-1) is needed because the energy difference between molecular conformers rarely exceeds 1000-3000 cal mol-1. The conformation equilibrium of straight-chain (normal) alkanes is of particular interest and importance for modern chemistry. In this paper, an extra error source for high-quality ab initio (first principles) and DFT calculations of the conformation equilibrium of normal alkanes, namely the intramolecular basis set superposition error (BSSE), is discussed. In contrast to out-of-plane vibrations in benzene molecules, diffuse functions on carbon and hydrogen atoms were found to greatly reduce the relative BSSE of n-alkanes. The corrections due to the intramolecular BSSE were found to be almost identical for the MP2, MP4, and CCSD(T) levels of theory. Their cancelation is expected when CCSD(T)/CBS (CBS, complete basis set) energies are evaluated by addition schemes. For larger normal alkanes (N > 12), the magnitude of the BSSE correction was found to be up to three times larger than the relative stability of the conformer; in this case, the basis set superposition error led to a two orders of magnitude difference in conformer abundance. No error cancelation due to the basis set superposition was found. A comparison with amino acid, peptide, and protein data was provided.

  8. Intramolecular Cohesion of Coils Mediated by Phenylalanine–Glycine Motifs in the Natively Unfolded Domain of a Nucleoporin

    PubMed Central

    Krishnan, V. V.; Lau, Edmond Y.; Yamada, Justin; Denning, Daniel P.; Patel, Samir S.; Colvin, Michael E.; Rexach, Michael F.

    2008-01-01

    The nuclear pore complex (NPC) provides the sole aqueous conduit for macromolecular exchange between the nucleus and the cytoplasm of cells. Its diffusion conduit contains a size-selective gate formed by a family of NPC proteins that feature large, natively unfolded domains with phenylalanine–glycine repeats (FG domains). These domains of nucleoporins play key roles in establishing the NPC permeability barrier, but little is known about their dynamic structure. Here we used molecular modeling and biophysical techniques to characterize the dynamic ensemble of structures of a representative FG domain from the yeast nucleoporin Nup116. The results showed that its FG motifs function as intramolecular cohesion elements that impart order to the FG domain and compact its ensemble of structures into native premolten globular configurations. At the NPC, the FG motifs of nucleoporins may exert this cohesive effect intermolecularly as well as intramolecularly to form a malleable yet cohesive quaternary structure composed of highly flexible polypeptide chains. Dynamic shifts in the equilibrium or competition between intra- and intermolecular FG motif interactions could facilitate the rapid and reversible structural transitions at the NPC conduit needed to accommodate passing karyopherin–cargo complexes of various shapes and sizes while simultaneously maintaining a size-selective gate against protein diffusion. PMID:18688269

  9. Cytoglobin ligand binding regulated by changing haem-co-ordination in response to intramolecular disulfide bond formation and lipid interaction.

    PubMed

    Beckerson, Penny; Wilson, Michael T; Svistunenko, Dimitri A; Reeder, Brandon J

    2015-01-01

    Cytoglobin (Cygb) is a hexa-co-ordinate haem protein from the globin superfamily with a physiological function that is unclear. We have previously reported that the haem co-ordination is changed in the presence of lipids, potentially transforming the redox properties of the protein and hence the function of Cygb in vivo. Recent research suggests that the protein can exist in a number of states depending on the integrity and position of disulfide bonds. In the present study, we show that the monomeric protein with an internal disulfide bond between the two cysteine residues Cys38 and Cys83, interacts with lipids to induce a change in haem co-ordination. The dimeric protein with intermolecular disulfide bonds and monomeric protein without an intramolecular disulfide bond does not exhibit these changes in haem co-ordination. Furthermore, monomeric Cygb with an intramolecular disulfide bond has significantly different properties, oxidizing lipid membranes and binding ligands more rapidly as compared with the other forms of the protein. The redox state of these cysteine residues in vivo is therefore highly significant and may be a mechanism to modulate the biochemical properties of the haem under conditions of stress. PMID:25327890

  10. The role of intramolecular barriers on the glass transition of polymers: Computer simulations versus mode coupling theory.

    PubMed

    Bernabei, Marco; Moreno, Angel J; Colmenero, Juan

    2009-11-28

    We present computer simulations of a simple bead-spring model for polymer melts with intramolecular barriers. By systematically tuning the strength of the barriers, we investigate their role on the glass transition. Dynamic observables are analyzed within the framework of the mode coupling theory (MCT). Critical nonergodicity parameters, critical temperatures, and dynamic exponents are obtained from consistent fits of simulation data to MCT asymptotic laws. The so-obtained MCT lambda-exponent increases from standard values for fully flexible chains to values close to the upper limit for stiff chains. In analogy with systems exhibiting higher-order MCT transitions, we suggest that the observed large lambda-values arise form the interplay between two distinct mechanisms for dynamic arrest: general packing effects and polymer-specific intramolecular barriers. We compare simulation results with numerical solutions of the MCT equations for polymer systems, within the polymer reference interaction site model (PRISM) for static correlations. We verify that the approximations introduced by the PRISM are fulfilled by simulations, with the same quality for all the range of investigated barrier strength. The numerical solutions reproduce the qualitative trends of simulations for the dependence of the nonergodicity parameters and critical temperatures on the barrier strength. In particular, the increase in the barrier strength at fixed density increases the localization length and the critical temperature. However the qualitative agreement between theory and simulation breaks in the limit of stiff chains. We discuss the possible origin of this feature. PMID:19947689

  11. Intramolecular effects on the kinetics of unimolecular reactions of β-HOROO˙ and HOQ˙OOH radicals.

    PubMed

    Lizardo-Huerta, J C; Sirjean, B; Bounaceur, R; Fournet, R

    2016-04-28

    A theoretical study describing the influence of intramolecular effects on the energy barriers and rate constants of unimolecular reactions involving β-HOROO˙ and HOQ˙OOH radicals is proposed. The reactions considered are HO2˙ elimination, the Waddington mechanism, H-shift, cyclic ether formation and β-scission. All the calculations are performed at the CBS-QB3 level of theory along with canonical transition state theory and statistical thermodynamics, including a specific treatment of hindered rotors. Several structural parameters are investigated, such as the location of the hydroxyl function in the cyclic transition states or the substitution of H atoms by alkyl groups on carbon atoms involved in the reaction coordinate. It is shown that these molecular systems involve numerous transition states, especially for reactions such as 1,5 or 1,6 H-shift, and that, a priori simplification is not possible. It is also shown that the position of the -OH group in the transition state can largely modify both the barrier heights and the rate constants. However, opposite trends can be observed depending on the competition between energetic and entropic effects. Similar observations are made when H atoms are replaced by methyl or alkyl groups. These results can largely be explained by intramolecular effects such as hydrogen bonds, stabilization effects (from -OH or -CH3 groups), steric influences and by the coupling between them. The last point renders the classic establishment of the structure-reactivity relationship challenging. PMID:27080359

  12. Preferential domain orientation of HMGB2 determined by the weak intramolecular interactions mediated by the interdomain linker

    NASA Astrophysics Data System (ADS)

    Uewaki, Jun-ichi; Kamikubo, Hironari; Kurita, Jun-ichi; Hiroguchi, Noriteru; Moriuchi, Hiroshi; Yoshida, Michiteru; Kataoka, Mikio; Utsunomiya-Tate, Naoko; Tate, Shin-ichi

    2013-06-01

    High mobility group box protein 2 (HMGB2) contains homologous tandem HMG box DNA-binding domains, boxes A and B. These two boxes are linked by a short basic linker having a sequence characteristic of an intrinsically disordered element. The combined use of NMR and small angle X-ray scattering (SAXS) showed that the two boxes assume a preferred orientation to make their DNA binding surface in opposite directions, although the linker does not keep any specific conformation. A series of site directed mutations to the residues in the linker showed that a network of CH-π interactions connects the N-terminal part of the linker to box A. The mutants having impaired intramolecular CH-π interactions changed the interdomain dynamics and their dynamic averaged orientation relative to the wild-type. This work demonstrates that the apparently unstructured linker plays a role in defining the preferential domain orientation through the intramolecular CH-π interactions, even though the interactions are weak and transient.

  13. Fingerprints of Intramolecular Hydrogen Bonds: Synchrotron-Based Far IR Study of the CIS and Trans Conformers of 2-FLUOROPHENOL

    NASA Astrophysics Data System (ADS)

    Bell, Aimee; Singer, James; van Wijngaarden, Jennifer

    2015-06-01

    Rotationally-resolved vibrational spectra of two planar conformers of 2-fluorophenol have been collected from 100-1000 cm-1 using the Bruker IFS125HR FTIR spectrometer at the Canadian Light Source with a resolution of 0.000959 cm-1. The cis conformer is lower in energy by ~2.9 kcal/mol (MP2/aug-cc-pvDZ) and is thought to be stabilized by an intramolecular hydrogen bond between the hydroxyl group and neighbouring fluorine atom on the ring. The OH out-of-plane torsion bands below 400 cm-1 provide the best fingerprint to distinguish between the two conformers in the gas phase spectrum as the c-type band origin of the cis conformer is blue-shifted by ~36 cm-1 from that of the trans conformer as result of the intramolecular interaction. In this talk, we will discuss the progress of the analysis of this complex far infrared spectrum of 2-fluorophenol.

  14. Development of a General, Sequential, Ring Closing Metathesis/Intramolecular Cross-Coupling Reaction for the Synthesis of Polyunsaturated Macrolactones

    PubMed Central

    Denmark, Scott E.; Muhuhi, Joseck M.

    2010-01-01

    A general strategy for the construction of macrocyclic lactones containing conjugated Z,Z-1,3-diene subunits has been is described. The centerpiece of the strategy is a sequential ring-closing metathesis that forms an unsaturated siloxane ring followed by an intramolecular cross-coupling reaction with a pendant alkenyl iodide. A highly modular assembly of the various precursors allowed the preparation of unsaturated macrolactones containing 11-, 12-, 13- and 14-membered rings. Although the ring closing metathesis process proceeded uneventfully, the intramolecular cross-coupling required extensive optimization of palladium source, solvent, fluoride source and particularly fluoride hydration level. Under the optimal conditions (including syringe pump high dilution), the macrolactones were produced in 53-78% yield as single stereoisomers. A benzo fused 12-membered ring macrolactone containing an E,Z-1,3-diene unit was also prepared by the same general strategy. The E-2-styryl iodide was prepared by a novel Heck reaction of an aryl nonaflate with vinyltrimethylsilane followed by iododesilylation with ICl. PMID:20666473

  15. A new class of N-H excited-state intramolecular proton transfer (ESIPT) molecules bearing localized zwitterionic tautomers.

    PubMed

    Stasyuk, Anton J; Chen, Yi-Ting; Chen, Chi-Lin; Wu, Pei-Jhen; Chou, Pi-Tai

    2016-09-21

    A series of new amino (NH)-type intramolecular hydrogen-bonding (H-bonding) compounds have been strategically designed and synthesized. These molecules comprise a 2-(imidazo[1,2-a]pyridin-2-yl)aniline moiety, in which one of the amino hydrogens was replaced with substituents of different electronic properties. This, together with the versatile capability for modifying the parent moiety, makes feasible comprehensive spectroscopy and dynamics studies of excited-state intramolecular proton transfer (ESIPT) as a function of N-H acidity. Different from other (NH)-type ESIPT systems where the ESIPT rate and exergonicity increase with an increase in the N-H acidity and hence the H-bonding strength, the results reveal an irregular relationship among ESIPT dynamics, thermodynamics and H-bond strength. This discrepancy may be rationalized by the localized zwitterionic nature of 2-(imidazo[1,2-a]pyridin-2-yl)aniline in the proton-transfer tautomer form, which is different from the π-delocalized tautomer form in other (NH)-type ESIPT systems. PMID:27537476

  16. Gas-Phase Intramolecular Protein Crosslinking via Ion/Ion Reactions: Ubiquitin and a Homobifunctional sulfo-NHS Ester

    PubMed Central

    Webb, Ian K.; Mentinova, Marija; McGee, William M.; McLuckey, Scott A.

    2013-01-01

    Gas-phase intra-molecular crosslinking of protein ubiquitin cations has been demonstrated via ion/ion reactions with anions of a homobifunctional N-hydroxysulfosuccinimide (sulfo-NHS) ester reagent. The ion/ion reaction between multiply-protonated ubiquitin and crosslinker monoanions produces a stable, charge reduced complex. Covalent crosslinking is indicated by the consecutive loss of two molecules of sulfo-NHS under ion trap collisional activation conditions. Covalent modification is verified by the presence of covalently crosslinked sequence ions produced by ion-trap collision-induced dissociation of the ion generated from the losses of sulfo-NHS. Analysis of the crosslinked sequence fragments allows for the localization of crosslinked primary amines, enabling proximity mapping of the gas-phase 3-D structures. The presence of two unprotonated reactive sites within the distance constraint of the crosslinker is required for successful crosslinking. The ability to covalently crosslink is therefore sensitive to protein charge state. As the charge state increases, fewer reactive sites are available and protein structure is more likely to become extended due to intramolecular electrostatic repulsion. At high charge states, the reagent shows little evidence for covalent crosslinking but does show evidence for ‘electrostatic crosslinking’ in that the binding of the sulfonate groups to the protein is sufficiently strong that backbone cleavages are favored over reagent detachment under ion trap collisional activation conditions. PMID:23463545

  17. Diffracted X-ray tracking for monitoring intramolecular motion in individual protein molecules using broad band X-ray

    SciTech Connect

    Ichiyanagi, Kouhei; Sasaki, Yuji C.; Sekiguchi, Hiroshi; Hoshino, Masato; Kajiwara, Kentaro; Senba, Yasunori; Ohashi, Haruhiko; Ohta, Noboru; Hoshisashi, Kentaro; Jae-won, Chang; Tokue, Maki; Matsushita, Yufuku; Nishijima, Masaki; Inoue, Yoshihisa; Yagi, Naoto

    2013-10-15

    Diffracted X-ray tracking (DXT) enables the tilting and twisting motions of single protein molecules to be monitored with micro- to milliradian resolution using a highly brilliant X-ray source with a wide energy bandwidth. We have developed a technique to monitor single molecules using gold nanocrystals attached to individual protein molecules using the BL28B2 beamline at SPring-8. In this paper we present the installation of a single toroidal X-ray mirror at BL28B2 to focus X-rays in an energy range of 10–20 keV (△E/E = 82% for an X-ray with a wide energy bandwidth). With this beamline we tracked diffraction spots from gold nanocrystals over a wide angle range than that using quasi-monochromatic X-rays. Application of the wide angle DXT technique to biological systems enabled us to observe the on-site motions of single protein molecules that have been functionalized in vivo. We further extend the capability of DXT by observing the fractional tilting and twisting motions of inner proteins under various conditions. As a proof of this methodology and to determine instrumental performance the intramolecular motions of a human serum albumin complex with 2-anthracenecarboxylic acid was investigated using the BL28B2 beamline. The random tilting and twisting intramolecular motions are shown to be directly linked to the movement of individual protein molecules in the buffer solution.

  18. Gas-phase intramolecular protein crosslinking via ion/ion reactions: ubiquitin and a homobifunctional sulfo-NHS ester.

    PubMed

    Webb, Ian K; Mentinova, Marija; McGee, William M; McLuckey, Scott A

    2013-05-01

    Gas-phase intra-molecular crosslinking of protein ubiquitin cations has been demonstrated via ion/ion reactions with anions of a homobifunctional N-hydroxysulfosuccinimide (sulfo-NHS) ester reagent. The ion/ion reaction between multiply-protonated ubiquitin and crosslinker monoanions produces a stable, charge-reduced complex. Covalent crosslinking is indicated by the consecutive loss of 2 molecules of sulfo-NHS under ion trap collisional activation conditions. Covalent modification is verified by the presence of covalently crosslinked sequence ions produced by ion-trap collision-induced dissociation of the ion generated from the losses of sulfo-NHS. Analysis of the crosslinked sequence fragments allows for the localization of crosslinked primary amines, enabling proximity mapping of the gas-phase 3-D structures. The presence of two unprotonated reactive sites within the distance constraint of the crosslinker is required for successful crosslinking. The ability to covalently crosslink is, therefore, sensitive to protein charge state. As the charge state increases, fewer reactive sites are available and protein structure is more likely to become extended because of intramolecular electrostatic repulsion. At high charge states, the reagent shows little evidence for covalent crosslinking but does show evidence for 'electrostatic crosslinking' in that the binding of the sulfonate groups to the protein is sufficiently strong that backbone cleavages are favored over reagent detachment under ion trap collisional activation conditions. PMID:23463545

  19. Synthesis of Substituted Benzenes via Bi(OTf)3-Mediated Intramolecular Carbonyl Allylation of α-Prenyl or α-Geranyl β-Arylketosulfones.

    PubMed

    Chang, Meng-Yang; Cheng, Yu-Chieh; Lu, Yi-Ju

    2015-06-19

    Intramolecular carbonyl allylation of α-prenyl or α-geranyl β-arylketosulfones 5 in the presence of molecule sieves (MS) affords substituted benzenes 6-7 in moderate to good yields. The facile transformation proceeds by a synthetic sequence starting with the α-prenylation or α-geranylation of 1 and the Bi(OTf)3-mediated annulation of 5 followed by a sequential desulfonative aromatization or then an intramolecular Friedel-Crafts alkylation. A plausible mechanism has been studied and proposed. PMID:26068123

  20. Photoinduced intramolecular electron transfer in a bridged C{sub 60}. (Acceptor)-Aniline (donor) system. Photophysical properties of the first `active` fullerene diad

    SciTech Connect

    Williams, R.M.; Zwier, J.M.; Verhoeven, J.W.

    1995-04-12

    A covalently functionalized fullerene comprising an electron donating aniline group coupled to the fullerene unit by a saturated heterocyclic bridge is shown to undergo a photoinduced intramolecular electron transfer process that causes quenching of the fluorescence of the adduct and strong decrease triplet population in polar solvents. VIS-absorption, fluorescence and phosphorescence at 77 K, triplet-triplet absorption, time resolved fluorescence and redox potentials of the fullerene adduct are presented. Analysis of the solvent dependence of the energetics of the intramolecular electron transfer is given and is in good agreement with the experimental results. 17 refs., 6 figs., 3 tabs.

  1. Mammalian DNA δ15N exhibits 40‰ intramolecular variation and is unresponsive to dietary protein level

    PubMed Central

    Strable, Maggie S.; Tschanz, Carolyn L.; Varamini, Behzad; Chikaraishi, Yoshito; Ohkouchi, Naohiko; Brenna, J. Thomas

    2014-01-01

    We report the first high precision characterization of molecular and intramolecular δ15N of nucleosides derived from mammalian DNA. The influence of dietary protein level on brain amino acids and deoxyribonucleosides was determined to investigate whether high protein turnover would alter amino acid 15N or 13C. Pregnant guinea pig dams were fed control diets, or high or low levels of dietary protein throughout gestation, and all pups were fed control diets. Cerebellar DNA of offspring was extracted at 2 and 120 days of life, nucleosides isolated and δ15N and δ13C characterized. Mean diet δ15N = 0.45±0.33‰, compared to cerebellar whole tissue and DNA δ15N = +4.1±0.7‰ and −4.5±0.4‰, respectively. Cerebellar deoxythymidine (dT), deoxycytidine (dC), deoxyadenosine (dA), and deoxyguanosine (dG) δ15N were +1.4±0.4, −2.1±0.9, −7.2±0.3, and −10.4±0.5‰, respectively. There were no changes in amino acid or deoxyribonucleoside δ15N due to dietary protein level. Using known metabolic relationships, we developed equations to calculate the intramolecular δ15N originating from aspartate (asp) in purines (pur) or pyrimidines (pyr), glutamine (glu), and glycine (gly) to be δ15NASP-PUR, δ15NASP-PYR, δ15NGLN, and δ15NGLY +11.9±2.3‰, +7.0±2.0‰, −9.1±2.4‰, and −31.8±8.9‰, respectively. A subset of twelve amino acids from food and brain had mean δ15N of 4.3±3.2‰ and 13.8±3.1‰, respectively, and δ15N for gly and asp were 12.6±2.2‰ and 15.2±0.8‰, respectively. A separate isotope tracer study detected no significant turnover of cerebellar DNA in the first six months of life. The large negative δ15N difference between gly and cerebellar purine N at the gly (7) position implies either that there is a major isotope effect during DNA synthesis, or that in utero gly has a different isotope ratio during rapid growth and metabolism than in adult life. Our data show that cerebellar nucleoside intramolecular δ15N vary over more than

  2. Dynamic NMR of Intramolecular Exchange Processes in EDTA Complexes of Sc[superscript 3+], Y[superscript 3+], and La[superscript 3+

    ERIC Educational Resources Information Center

    Ba, Yong; Han, Steven; Ni, Lily; Su, Tony; Garcia, Andres

    2006-01-01

    Dynamic NMR makes use of the effect of chemical exchanges on NMR spectra to study kinetics and thermodynamics. An advanced physical chemistry lab experiment was developed to study the intramolecular exchange processes of EDTA (the disodium salt of ethylenediaminetetraacetic acid) metal complexes. EDTA is an important chelating agent, used in…

  3. Asymmetric Intramolecular Desymmetrization of meso-α,α'-Diazido Alcohols with Aryldiazoacetates: Assembly of Chiral C3 Fragments with Three Continuous Stereocenters.

    PubMed

    Qiao, Jin-Bao; Zhao, Yu-Ming; Gu, Peiming

    2016-05-01

    The chiral Cu-complex-catalyzed intramolecular interception of meso-α,α'-diazido alcohols with aryldiazoacetates is explored. Most of the enantioenriched α-imino esters with three continuous stereocenters are produced with good to excellent yield and enantioselectivity, and a chiral pocket model is proposed for rationalization of the asymmetric desymmetrization. PMID:27109428

  4. Intramolecular 1,5-H transfer reaction of aryl iodides through visible-light photoredox catalysis: a concise method for the synthesis of natural product scaffolds.

    PubMed

    Chen, Jian-Qiang; Wei, Yun-Long; Xu, Guo-Qiang; Liang, Yong-Min; Xu, Peng-Fei

    2016-05-11

    The intramolecular 1,5-H transfer reaction of the aryl radicals generated from unactivated aryl iodides by photocatalysis is described. The features of this transformation are operational simplicity, excellent yields, mild reaction conditions, and good functional group tolerance. With this approach, a more concise formal synthesis of (±)-coerulescine and (±)-physovenine is accomplished. PMID:27100267

  5. Bicyclic Guanidine Catalyzed Asymmetric Tandem Isomerization Intramolecular-Diels-Alder Reaction: The First Catalytic Enantioselective Total Synthesis of (+)-alpha-Yohimbine.

    PubMed

    Feng, Wei; Jiang, Danfeng; Kee, Choon-Wee; Liu, Hongjun; Tan, Choon-Hong

    2016-02-01

    Hydroisoquinoline derivatives were prepared in moderate to good enantioselectivities via a bicyclic guanidine-catalyzed tandem isomerization intramolecular-Diels-Alder (IMDA) reaction of alkynes. With this synthetic method, the first enantioselective synthesis of (+)-alpha-yohimbine was completed in 9 steps from the IMDA products. PMID:25932622

  6. Influence of chlorine substitution on intramolecular hydrogen bond energy and ESIPT barrier: Experimental and theoretical measurements on the photophysics of 3,5-dichlorosalicylic acid

    NASA Astrophysics Data System (ADS)

    Paul, Bijan Kumar; Samanta, Anuva; Guchhait, Nikhil

    2010-08-01

    The effect of chlorine atom on the intramolecular hydrogen bond strength and excited state proton transfer barrier in pharmaceutically important chloro-substituted derivative of salicylic acid viz., 3,5-dichlorosalicylic acid (3,5DCSA) has been explored through steady-state absorption, emission and time-resolved fluorescence spectroscopy. Stokes shifted emission band with negligible solvent polarity dependency corresponds to the spectroscopic signature of excited state intramolecular proton transfer (ESIPT) reaction. The spectral signature was compared with its parent molecule salicylic acid (SA) and 5-chlorosalicylic acid (5ClSA). Quantum chemical calculations by ab initio Hartree-Fock (HF) and Density Functional Theory (DFT) methods have been fruitfully employed to correlate experimental findings. Calculated S0 and S1 states potential energy surfaces across the proton transfer co-ordinate substantiates the experimental evidence for the occurrence of ESIPT process and negates the ground state intramolecular proton transfer (GSIPT) reaction. Weakening of intramolecular hydrogen bond (IMHB) energy and subsequent enhancement of barrier to ESIPT reaction in 3,5DCSA as compared to SA and 5ClSA appears to be a reflection of conjugate impact of electron withdrawing inductive and electron donating resonance effects of chlorine substitutions depending on its location on the aromatic benzene nucleus.

  7. Application of Thio-Ugi Adducts for the Preparation of Benzo[b]thiophene and S-Heterocycle Library via Copper Catalyzed Intramolecular C-S Bond Formation.

    PubMed

    Kim, Yong-Sang; Kwak, Se Hun; Gong, Young-Dae

    2015-06-01

    Fused heterocycles, such as benzo[b]thiophene, thiochroman, benzo[b][1,4]thiazine, and 1,4-benzothiazepine were generated from thio-Ugi adducts containing a thioamide group through copper-catalyzed intramolecular C-S bond formation under microwave irradiation. PMID:25961783

  8. A novel intramolecular through-space interaction between F and CN: a strategy for the conformational control of an acyclic system.

    PubMed

    Nishide, K; Hagimoto, Y; Hasegawa, H; Shiro, M; Node, M

    2001-11-21

    X-Ray crystallographic analyses of fluorocyanides anti-1 and 2 revealed a novel intramolecular through-space interaction between F and CN in an acyclic system, which was applied to a stereoselective protonation of acyclic fluorocyanides 2 having flexible conformation. PMID:12240092

  9. Gallium(III)- and calcium(II)-catalyzed Meyer-Schuster rearrangements followed by intramolecular aldol condensation or endo-Michael addition.

    PubMed

    Presset, M; Michelet, B; Guillot, R; Bour, C; Bezzenine-Lafollée, S; Gandon, V

    2015-03-28

    The first gallium- and calcium-catalyzed Meyer-Schuster rearrangements are described. Under substrate control, the incipient conjugated ketones can be trapped intramolecularly by β-keto esters or amides to yield cyclic products after aldol condensation or endo-Michael addition. An interesting additive effect that promotes the latter tandem process with calcium has been found. PMID:25503868

  10. Picosecond infrared study of intramolecular energy transfer in [(phen)(CO){sub 3}Re{sup I}(NC)Ru{sup II}(CN)(bpy){sub 2}]{sup +}

    SciTech Connect

    Dyer, R.B.; Peterson, K.A.; Gordon, K.C.; Woodruff, W.H.; Schoonover, J.R.; Meyer, T.J.; Bignozzi, C.A.

    1992-03-01

    The dynamics and mechanism of intramolecular energy transfer in [(phen)(CO){sub 3}Re{sup I}(NC)Ru{sup II}(CN)(bpy){sub 2}]+ following metal-to-ligand charge transfer excitation have been studied using picosecond infrared spectroscopy.

  11. Picosecond infrared study of intramolecular energy transfer in ((phen)(CO) sub 3 Re sup I (NC)Ru sup II (CN)(bpy) sub 2 ) sup +

    SciTech Connect

    Dyer, R.B.; Peterson, K.A.; Gordon, K.C.; Woodruff, W.H. ); Schoonover, J.R.; Meyer, T.J. . Dept. of Chemistry); Bignozzi, C.A. )

    1992-01-01

    The dynamics and mechanism of intramolecular energy transfer in ((phen)(CO){sub 3}Re{sup I}(NC)Ru{sup II}(CN)(bpy){sub 2})+ following metal-to-ligand charge transfer excitation have been studied using picosecond infrared spectroscopy.

  12. Visible light-induced intramolecular dearomative cyclization of α-bromo-N-benzyl-alkylamides: efficient construction of 2-azaspiro[4.5]decanes.

    PubMed

    Hu, Bei; Li, Yuyuan; Dong, Wuheng; Ren, Kai; Xie, Xiaomin; Wan, Jun; Zhang, Zhaoguo

    2016-03-01

    An efficient intramolecular dearomative cyclization via visible light-induced photoredox catalysis allows for a highly regioselective dearomative cyclization of α-bromo-N-benzyl-alkylamides to construct 2-azaspiro[4.5]decanes in the presence of an iridium catalyst. PMID:26865333

  13. Discovery of molluscicidal and cercaricidal activities of 3-substituted quinazolinone derivatives by a scaffold hopping approach using a pseudo-ring based on the intramolecular hydrogen bond formation.

    PubMed

    Guo, Wei; Zheng, Lv-Yin; Li, Yong-Dong; Wu, Ren-Miao; Chen, Qiang; Yang, Ding-Qiao; Fan, Xiao-Lin

    2016-06-10

    Discovery of novel topological agents against Oncomelania hupensis snails and cercariae remains a significant challenge in current Schistosomiasis control. A pseudo-ring formed from salicylanilide by an intramolecular hydrogen bond led to the discovery of 3-substituted quinazolinone derivatives which showed a potent molluscicidal and cercaricidal activities. PMID:27017555

  14. The whole of intramolecular H-bonding in the isolated DNA nucleoside thymidine. AIM electron density topological study

    NASA Astrophysics Data System (ADS)

    Yurenko, Yevgen P.; Zhurakivsky, Roman O.; Samijlenko, Svitlana P.; Ghomi, Mahmoud; Hovorun, Dmytro M.

    2007-10-01

    Based on comprehensive conformational analysis at the DFT B3LYP/6-31G(d,p) level of theory [Ye.P. Yurenko et al., J. Phys. Chem. B, 111 (2007) 9655] 13 types of intramolecular hydrogen bonds (171 in total number, from 1 to 3 H-bonds per conformer) were identified in the 92 allowed conformers of isolated thymidine, a DNA canonical nucleoside. Weak interactions CH⋯ O, OH⋯ HC and CH⋯ HC were analyzed by all the Koch and Popelier criteria of H-bonding. Quite satisfactory linear correlation was found between Grabowski complex measure of H-bond strength Δcom and Iogansen H-bond energy -Δ H for 17 OH⋯O hydrogen bonds.

  15. Copper-Catalyzed Cascade Reaction via Intramolecular Hydroamination Cyclization of Homopropargylic Amines and Intermolecular Povarov Reaction with Imines.

    PubMed

    Wang, Hongkai; Wang, Chan; Huang, Kaimeng; Liu, Lingyan; Chang, Weixing; Li, Jing

    2016-05-20

    A new one-pot cascade reaction of homopropargylic amines with simple imines is developed in the presence of Cu(OTf)2 and affords a series of hexahydro-1H-pyrrolo[3,2-c]quinoline derivatives in good to high yields. This reaction proceeds through an intramolecular hydroamination cyclization of homopropargylic amine to generate a highly reactive dihydropyrrole intermediate in situ. It subsequently reacts with imine via an intermolecular inverse-electron-demand aza-Diels-Alder reaction and a 1,3-H shift to give the fused pyrroloquinoline structures, forming two new C-C bonds and one C-N bond and one N-H bond. PMID:27128977

  16. Elucidation and Control of an Intramolecular Charge Transfer Property of Fucoxanthin by a Modification of Its Polyene Chain Length.

    PubMed

    Kosumi, Daisuke; Kajikawa, Takayuki; Okumura, Satoshi; Sugisaki, Mitsuru; Sakaguchi, Kazuhiko; Katsumura, Shigeo; Hashimoto, Hideki

    2014-03-01

    Fucoxanthin is an essential pigment for the highly efficient light-harvesting function of marine algal photosynthesis. It exhibits excited state properties attributed to intramolecular charge transfer (ICT) in polar environments due to the presence of the carbonyl group in its polyene backbone. This report describes the excited state properties of fucoxanthin homologues with four to eight conjugated double bonds in various solvents using the femtosecond pump-probe technique. The results clarified that fucoxanthin homologues with longer polyene chains did not possess pronounced ICT spectroscopic signatures, while the shorter fucoxanthin homologues had a strong ICT character, even in a nonpolar solvent. On the basis of the observations, we quantitatively correlated the ICT character in the excited state to the conjugated polyene chain lengths of fucoxanthin molecules. PMID:26274069

  17. Ruthenium-catalyzed intramolecular metathesis of dienes and its application in the synthesis of bridged and spiro azabicycles

    NASA Astrophysics Data System (ADS)

    Kuznetsov, N. Yu; Bubnov, Yu N.

    2015-07-01

    The review presents a historical excursion into catalytic alkene metathesis, covering the problems of history of the discovery of this process, as well as investigations on the properties, structure and reactivity of the most popular ruthenium catalysts for metathesis, mechanism of their action and decomposition. The main part covers studies devoted to the syntheses of bridged azabicyclic and 1-azaspirocyclic compounds comprising the intramolecular metathesis of dienes as the key step. The formation of a bicyclic skeleton of a series of natural bridged (cocaine, ferruginine, calystegines, and anatoxin-a) and spiro (pinnaic acids, halichlorine, hystrionicotoxin, and cephalotaxine) azabicycles, as well as their analogues and compounds with larger rings is demonstrated. The methods for the synthesis of diene precursors and the conditions for final assembling of the bicyclic compounds are considered in detail. The generalization of the literature data allows one to efficiently carry out the mentioned process taking into account the most important features. The bibliography includes 129 references.

  18. Large three-photon absorption and intramolecular charge transfer of the bis-donor fluorene-based molecules

    NASA Astrophysics Data System (ADS)

    Ma, Wenbo; Wu, Yiqun; Han, Junhe; Gu, Donghong; Gan, Fuxi

    2005-10-01

    Three-photon absorption (3PA) of two fluorene-based molecules with D-π-D structural motifs (abbreviated as BPAF and BCZF) has been determined by using a Q-switched Nd: YAG laser pumped with 38 ps pulses at 1064 nm in DMF. The measured 3PA cross-sections are 222 and 140×10 -78 cm 6 s 2 for BPAF and BCZF, respectively. AM1 calculations show that attaching different donors changes the charge density distribution of the fluorene skeleton, and it is observed that the 3PA cross-section can be enhanced with increasing intramolecular charge transfer character, measured by the parameter Δ ρ1/Δ ρ2/Δ ρ1'.

  19. Approximate constants of motion for classically chaotic vibrational dynamics - Vague tori, semiclassical quantization, and classical intramolecular energy flow

    NASA Technical Reports Server (NTRS)

    Shirts, R. B.; Reinhardt, W. P.

    1982-01-01

    Substantial short time regularity, even in the chaotic regions of phase space, is found for what is seen as a large class of systems. This regularity manifests itself through the behavior of approximate constants of motion calculated by Pade summation of the Birkhoff-Gustavson normal form expansion; it is attributed to remnants of destroyed invariant tori in phase space. The remnant torus-like manifold structures are used to justify Einstein-Brillouin-Keller semiclassical quantization procedures for obtaining quantum energy levels, even in the absence of complete tori. They also provide a theoretical basis for the calculation of rate constants for intramolecular mode-mode energy transfer. These results are illustrated by means of a thorough analysis of the Henon-Heiles oscillator problem. Possible generality of the analysis is demonstrated by brief consideration of classical dynamics for the Barbanis Hamiltonian, Zeeman effect in hydrogen and recent results of Wolf and Hase (1980) for the H-C-C fragment.

  20. A Spectroscopic and Theoretical Study of Weak Intramolecular OH\\cdots π Interactions in Allyl Carbinol and Methallyl Carbinol

    NASA Astrophysics Data System (ADS)

    Schroeder, Sidsel D.; Mackeprang, Kasper; Kjaergaard, Henrik G.

    2013-06-01

    The weak intramolecular OH\\cdots π interactions in allyl carbinol and methallyl carbinol have been studied using a combination of NIR spectroscopy and theory. The third OH-stretching overtone region of vapor phase allyl carbinol and methallyl carbinol have been recorded with intracavity laser photoacoustic spectroscopy to study the effect of an enhanced OH\\cdots π interaction in methallyl carbinol arising from the electron donating methyl group. Local mode calculations were employed to assign the observed bands. The OH-stretching transition frequency of methallyl carbinol was observed to be red shifted relative to the OH-stretching transition frequency of allyl carbinol. A red shift of the transition frequency is in this context normally interpreted as a signature of hydrogen bonding. Whether the OH\\cdots π interaction can be categorized as a hydrogen bond will be discussed in this talk.

  1. Oxygen activation and intramolecular C-H bond activation by an amidate-bridged diiron(II) complex.

    PubMed

    Jones, Matthew B; Hardcastle, Kenneth I; Hagen, Karl S; MacBeth, Cora E

    2011-07-18

    A diiron(II) complex containing two μ-1,3-(κN:κO)-amidate linkages has been synthesized using the 2,2',2''-tris(isobutyrylamido)triphenylamine (H(3)L(iPr)) ligand. The resulting diiron complex, 1, reacts with dioxygen (or iodosylbenzene) to effect intramolecular C-H bond activation at the methine position of the ligand isopropyl group. The ligand-activated product, 2, has been isolated and characterized by a variety of methods including X-ray crystallography. Electrospray ionization mass spectroscopy of 2 prepared from(18)O(2) was used to confirm that the oxygen atom incorporated into the ligand framework is derived from molecular oxygen. PMID:21667986

  2. Vertex function for the coupling of an electron with intramolecular phonons: Exact results in the antiadiabatic limit

    NASA Astrophysics Data System (ADS)

    Takada, Yasutami; Higuchi, Takatoshi

    1995-11-01

    The Green's-function techniques, especially the one developed in the preceding paper [Takada, Phys. Rev. B 52, 12 708 (1995)], are employed to calculate the electron-phonon vertex part as well as the electronic self-energy exactly on both real- and imaginary-frequency axes in the electron-phonon Holstein model with the on-site Coulomb repulsion in the limit in which the intramolecular phonon energy ω0 is much larger than the electronic bandwidth. The rigorous vertex part is found to diverge at the frequencies at which an electron is locked by such local phonons with an infinitely strong effective coupling. Characteristic frequencies of this divergence, which are not equal to multiples of ω0, are calculated as a function of the electron-phonon bare coupling constant. Our results for the self-energy are checked successfully with the exact ones obtained by the Lang-Firsov canonical transformation.

  3. Signatures of field-induced intramolecular quantum interference in high-order harmonic generation by laser-irradiated homonuclear diatomics

    NASA Astrophysics Data System (ADS)

    Usachenko, Vladimir; Kim, Vyacheslav; Pyak, Pavel

    2015-05-01

    We report about the results of our theoretical study of the strong-field phenomenon of high-order harmonic generation (HHG) in homonuclear diatomics H2+ andH2 irradiated by a high-intensity laser field of mid-infrared wavelengths corresponding to intermediate values of the so-called Keldysh parameter (γ <= 1). The problem is addressed within the length-gauge (LG) formulation of strong-field approximation (SFA) additionally exploiting the density-functional-theory (DFT) method for numerical composition of initial (laser-free) molecular state using the routines of GAUSSIAN-03 code. The results of our present LG-VGA calculation well reproduce a pronounced interference-related minimum arising in high-frequency region of respective molecular HHG spectra and suggesting clear signatures of the field-induced intramolecular interference corresponding to photoelectron emission to intermediate continuum states from different atomic centers.

  4. Steric effects on intramolecular reactivity in cyclic dipeptides: Conformational analysis validated by a combined MD/DFT approach

    NASA Astrophysics Data System (ADS)

    Lewandowska, A.; Carmichael, I.; Hörner, G.; Hug, G. L.; Marciniak, B.

    2011-08-01

    The present Molecular Dynamics (MD) simulation study addresses the geometric requirements of close-contact formation in short peptides. This process, that is probed herein by intramolecular H-atom transfer, initiated by triplet-excited ketones, demands close contact between the H-donating and H-accepting moieties. Thus, any deduction about the compound's reactivity based just on MD simulations, requires independent verification of the computed conformational preferences. In this study, a procedure was developed using diketopiperazine-linked benzophenone/tyrosine dyads. Specifically, it involves a comparison of the dyads' experimental 3J(H α-H β(a/b)) spin-spin coupling constants with the theoretical values obtained by weighting DFT-computed spin-spin coupling constants with the MD-computed probability distributions for the dyads' configurations.

  5. Intramolecular hydrogen bonding and vibrational assignment of 1,1,1-trifluoro-5,5-dimethyl-2,4-hexanedione

    NASA Astrophysics Data System (ADS)

    Afzali, R.; Vakili, M.; Nekoei, A.-R.; Tayyari, S. F.

    2014-11-01

    Intramolecular hydrogen bonding (IHB) and vibrational frequencies of 1,1,1-trifluoro-5,5-dimethyl-2,4-hexanedione (TFDMHD) have been investigated by means of density functional theory (DFT) calculations, Atoms in Molecules (AIM) analysis, natural bond orbital (NBO) theory, and IR and Raman spectroscopies. The results are compared with those of 1,1,1-trifluoro-2,4-pentanedione (TFAA) and 5,5-dimethyl hexane-2,4-dione (DMHD). The hydrogen bonding energies (EHB) of the most stable chelated enol forms, obtained by AIM theory are in the range of 17.1-20.0 kcal/mol. The IR and Raman spectra of TFDMHD and its deuterated analog were clearly assigned. Comparing the calculated and experimental band frequencies and intensities suggests coexisting of three stable cis-enol forms in comparable proportions in the sample. The theoretical calculations and spectroscopic results indicate that the IHB strength of TFDMHD is between those of TFAA and DMHD.

  6. Calculation of high-pressure phase transitions in solid N2 and the pressure dependence of intramolecular mode frequencies

    NASA Technical Reports Server (NTRS)

    Chandrasekharan, V.; Etters, R. D.; Kobashi, K.

    1983-01-01

    A calculation that minimizes the energy of solid N2 with respect to a rhombohedral distortion of the Pm 3n structure shows that a low-temperature phase transition occurs into the R 3c calcite structure at P = 19.2 kbar with a volume change of 0.125 cu cm/mole. This transition agrees with recent Raman scattering measurements. Another transition from R 3c into R3(bar)m is predicted at P = 67.5 kbar, with a volume change of 0.1 cu cm/mole. The pressure dependence of the intramolecular mode frequencies for the R 3c structure are in reasonably good agreement with the two main branches observed experimentally.

  7. Twisted intramolecular charge transfer and its contribution to the NLO activity of Diglycine Picrate: A vibrational spectroscopic study

    NASA Astrophysics Data System (ADS)

    Alen, S.; Sajan, D.; Umadevi, T.; Němec, Ivan; Baburaj, M. S.; Bena Jothy, V.; Selin Joy, B. H.

    2015-01-01

    Single crystals of Diglycine Picrate (DGLP) were grown by slow evaporation technique and the vibrational spectral analysis is carried out using FT Raman and FT-IR spectroscopy, supported by Density Functional Theoretical (DFT) computations to derive equilibrium geometry, vibrational wavenumbers and first hyperpolarizability. The vibrational spectra confirm the existence of NH3+ in DGLP. The influence of Twisted Intramolecular Charge Transfer (TICT) caused by the strong ionic ground state hydrogen bonding between charged species making DGLP crystal to have the non-centrosymmetric structure has been discussed. The Natural Bond Orbital (NBO) analysis confirms the occurrence of strong intermolecular Nsbnd H⋯O hydrogen bond. The HOMO-LUMO energy gap and the first order hyperpolarizability were calculated and it supports the nonlinear optical activity of the Diglycine Picrate crystal.

  8. Intramolecular [4 + 2] cycloaddition reaction of six- and seven-membered cyclic N-allyl-C-arylethynyl iminium salts.

    PubMed

    Herz, H G; Schatz, J; Maas, G

    2001-05-01

    N-Allyl-2-(het)arylethynyl-3,4,5,6-tetrahydropyridinium triflates 1c,d,e and N-allyl-2-(het)aryl-4,5,6,7-tetrahydro-3H-azepinium triflates 1g,h undergo a thermal isomerization reaction leading to derivatives of [a,f]-annulated isoindolium salts 2 in good yields. Similarly, N-allyl-2-phenylethynyl-pyridinium triflate 4 is transformed into the condensed pyridinium salt 5. An intramolecular [4 + 2] cycloaddition reaction, in which the (het)arylethynyl moiety acts as the 4pi component, is considered as the key step of this transformation. In contrast, the related N-allyl-4,5-dihydro-3H-pyrrolium salts 1a,b and N-homoallyl-3,4,5,6-tetrahydropyridinium salt 1f undergo unspecific decomposition under thermal impact. PMID:11325285

  9. Photochemically induced intramolecular six-electron reductive elimination and oxidative addition of nitric oxide by the nitridoosmate(VIII) anion.

    PubMed

    Thornley, Wyatt A; Bitterwolf, Thomas E

    2015-02-01

    UV photolysis of the nitridoosmate(VIII) anion, OsO3 N(-) , in low-temperature frozen matrices results in nitrogen-oxygen bond formation to give the Os(II) nitrosyl complex OsO2 (NO)(-) . Photolysis of the Os(II) nitrosyl product with visible wavelengths results in reversion to the parent Os(VIII) complex. Formally a six-electron reductive elimination and oxidative addition, respectively, this represents the first reported example of such an intramolecular transformation. DFT modelling of this reaction proceeds through a step-wise mechanism taking place through a side-on nitroxyl Os(VI) intermediate, OsO2 (η(2) -NO)(-) . PMID:25537499

  10. Nuclear magnetic resonance study of the intramolecular rearrangement of 2-(5-cyanotetrazolato)pentaammine cobalt (III) perchlorate. [Perdeuterodimethylsulfoxide

    SciTech Connect

    Attalla, A.; Pitre, E.M.

    1985-03-11

    The intramolecular rearrangement of 2-(5-cyanotetrazolato)pentaammine cobalt (III) perchlorate (CP) to form the amidine chelate perchlorate coordination complex has been investigated by variable-temperature high-resolution proton nuclear magnetic resonance (NMR) spectroscopy. Using a concentration of 30 wt % CP in perdeuterodimethylsulfoxide ((CD/sub 3/)/sub 2/SO), the rate of formation of the amidine chelate was determined at five different temperatures (60, 70, 80, 90, and 100/sup 0/C). The logarithm of the specific rate constant at each temperature was plotted as a function of the reciprocal absolute temperature to arrive at the activation energy, E/sub a/ (19.5 kcal/mole), for the rearrangement process. 4 refs., 4 figs., 1 tab.

  11. Twisted intramolecular charge transfer and its contribution to the NLO activity of Diglycine Picrate: a vibrational spectroscopic study.

    PubMed

    Alen, S; Sajan, D; Umadevi, T; Němec, Ivan; Baburaj, M S; Bena Jothy, V; Selin Joy, B H

    2015-01-25

    Single crystals of Diglycine Picrate (DGLP) were grown by slow evaporation technique and the vibrational spectral analysis is carried out using FT Raman and FT-IR spectroscopy, supported by Density Functional Theoretical (DFT) computations to derive equilibrium geometry, vibrational wavenumbers and first hyperpolarizability. The vibrational spectra confirm the existence of NH3(+) in DGLP. The influence of Twisted Intramolecular Charge Transfer (TICT) caused by the strong ionic ground state hydrogen bonding between charged species making DGLP crystal to have the non-centrosymmetric structure has been discussed. The Natural Bond Orbital (NBO) analysis confirms the occurrence of strong intermolecular N-H⋯O hydrogen bond. The HOMO-LUMO energy gap and the first order hyperpolarizability were calculated and it supports the nonlinear optical activity of the Diglycine Picrate crystal. PMID:25137250

  12. In vivo distribution and elimination of hemoglobin modified by intramolecular cross-linking with 2-nor-2-formylpyridoxal 5'-phosphate

    SciTech Connect

    Bleeker, W.K.; van der Plas, J.; Feitsma, R.I.; Agterberg, J.; Rigter, G.; de Vries-van Rossen, A.; Pauwels, E.K.; Bakker, J.C.

    1989-02-01

    Modified hemoglobin solutions have potential application as plasma expanders with oxygen-transporting capacity. In a previous study it was found that modification of hemoglobin by intramolecular cross-linking with 2-nor-2-formylpyridoxal 5'-phosphate (NFPLP) improves the vascular retention time by a factor of three, and it also improves the oxygen-transporting properties. In the present study we investigated in rats how, after exchange transfusion of a clinically relevant dose, the modified hemoglobin (HbNFPLP) was distributed in the body compared with how the unmodified hemoglobin was distributed. By using a new technetium 99m labeling technique, we found in a scintigraphic study that accumulation of hemoglobin in the kidneys was greatly diminished by the intramolecular cross-linking with NFPLP. These findings were confirmed by light-microscopic observations after diaminobenzidine staining. It was concluded that the impairment of kidney function caused by blockade of the tubuli is not to be expected from HbNFPLP. In the liver and spleen, where the free HbNFPLP is possibly eliminated, some accumulation of 99mTc label was observed, but the major part of the extravascular label was diffusely spread throughout the body. This led to the conclusion that important accumulation of undegraded HbNFPLP does not occur in the liver and spleen. Rapid appearance of both hemoglobin and HbNFPLP in the lymph showed that cross-linking with NFPLP does not prevent the distribution of hemoglobin over the interstitial space in the first hours after administration. However, pharmacokinetic analysis demonstrated that transcapillary transfer contributes only to a limited extent to the disappearance from the circulation. During 24-hour infusions of HbNFPLP, a steady state with a constant plasma concentration was easily reached.

  13. Mechanism of the reduction of the native intermediate in the multicopper oxidases: insights into rapid intramolecular electron transfer in turnover.

    PubMed

    Heppner, David E; Kjaergaard, Christian H; Solomon, Edward I

    2014-12-24

    The multicopper oxidases (MCOs) are the family of enzymes that catalyze the 4-electron reduction of O2 to H2O coupled to the four 1-electron oxidations of substrate. In the catalytic cycle electrons are transferred intramolecularly over ∼13 Å from a Type 1 (T1) Cu site that accepts electrons from substrate to a trinuclear Cu cluster (TNC) where O2 is reduced to H2O at rapid rates consistent with turnover (560 s(-1)). The oxygen reduction mechanism for the MCOs is well-characterized, whereas the rereduction is less understood. Our initial study of Rhus vernicifera Laccase (Heppner et al. J. Am. Chem. Soc. 2013, 135, 12212) experimentally established that the native intermediate (NI), the species formed upon O-O bond cleavage, is reduced with an IET rate >700 s(-1) and is the catalytically relevant fully oxidized form of the enzyme, rather than the resting state. In this report, we present kinetic and spectroscopic results coupled to DFT calculations that evaluate the mechanism of the 3 e(-)/3 H(+) reduction of NI, where all three catalytically relevant intramolecular electron transfer (IET) steps are rapid and involve three different structural changes. These three rapid IET processes reflect the sophisticated mechanistic control of the TNC to enable rapid turnover. All three IET processes are fast due to the associated protonation of the bridging oxo and hydroxo ligands, generated by O-O cleavage, to form water products that are extruded from the TNC upon full reduction, thereby defining a unifying mechanism for oxygen reduction and rapid IET by the TNC in the catalytic cycle of the MCOs. PMID:25490729

  14. Do resonance-assisted intramolecular halogen bonds exist without a charge transfer and a σ-hole?

    PubMed

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

    2015-11-01

    To analyze the properties and mechanisms of six types of intramolecular resonance-assisted halogen bonds (Br···O, Cl···O, F···O, Br···O, Cl···S and F···S), we have chosen the five-membered closed ring system X-C1R1=C3R2-C2R3=Y (X = Br, Cl & F; Y = O & S) of unsaturated compounds with the substituents NO2, CH3 and H. A total of 78 structures were investigated by quantum chemical calculations at the MP2/aug-cc-pVTZ level of theory. A molecular electrostatic potential (MESP) map reveals that the cusp point of the σ-hole was not utilized but the belt point was used for all these intramolecular halogen-bonding interactions, indicating that all are electrostatic interactions. The halogen-bonding angle is below 100° with the strongest interactions. The value of the nucleus-independent chemical shift (NICS (1)) reflects the changes and efficiency of resonance in all structures with a long bond. The presence of all interactions was proved by the bond critical point (BCP) and analyzed through its electron density, Laplacian of electron density and ellipticity parameter. The linear-probability correlation between the difference of the sum of the van der Waals radius and the non-covalent bond length (∑vdW-L) and the electron density of the BCP was reported. 2D and 3D-NCI (non covalent interactions) plots show that halogen-bonding interactions are a mixed type of interactions with an attractive term. Natural bond orbital (NBO) analysis clearly indicates that the halogen bond lacks charge transfer and orbital overlapping through non-interacting lobes. PMID:26426450

  15. Cooperativity and Site-Selectivity of Intramolecular Hydrogen Bonds on the Fluorescence Quenching of Modified GFP Chromophores.

    PubMed

    Chang, Deng-Hsiang; Ou, Chun-Lin; Hsu, Hung-Yu; Huang, Guan-Jhih; Kao, Chen-Yi; Liu, Yi-Hung; Peng, Shie-Ming; Diau, Eric Wei-Guang; Yang, Jye-Shane

    2015-12-18

    This paper provides the first example of experimentally characterized hydrogen-bond cooperativity on fluorescence quenching with a modified green fluorescence protein (GFP) chromophore that contains a 6-membered C═N···H-O and a 7-membered C═O···H-O intramolecular H-bonds. Variable-temperature (1)H NMR and electronic absorption and emission spectroscopies were used to elucidate the preference of intra- vs intermolecular H-bonding at different concentrations (1 mM and 10 μM), and X-ray crystal structures provide clues of possible intermolecular H-bonding modes. In the ground state, the 6-membered H-bond is significant but the 7-membered one is rather weak. However, fluorescence quenching is dominated by the 7-membered H-bond, indicating a strengthening of the H-bond in the excited state. The H-bonding effect is more pronounced in more polar solvents, and no intermediates were observed from femtosecond fluorescence decays. The fluorescence quenching is attributed to the occurrence of diabatic excited-state proton transfer. Cooperativity of the two intramolecular H-bonds on spectral shifts and fluorescence quenching is evidenced by comparing with both the single H-bonded and the non-H-bonded counterparts. The H-bond cooperativity does not belong to the conventional patterns of σ- and π-cooperativity but a new type of polarization interactions, which demonstrates the significant interplay of H-bonds for multiple H-bonding systems in the electronically excited states. PMID:26583964

  16. Analytical model for rates of electron attachment and intramolecular electron transfer in electron transfer dissociation mass spectrometry.

    PubMed

    Simons, Jack

    2010-05-26

    A new physical model is put forth to allow the prediction of electron transfer rates and distances for (i) intramolecular transfer from an n > or = 3 Rydberg orbital on a positive site to a disulfide or amide bond site and (ii) intermolecular transfer from an anion donor to an n > or = 3 Rydberg orbital of a positively charged polypeptide. Although ab initio methods have proven capable of handling such electron transfer events when the Rydberg orbital has principal quantum number n = 3, they have proven to be incapable of handling Rydberg states having quantum number n > 3, so having a new tool capable of handling n > 3 Rydberg states is important. The model (i) focuses on each Rydberg orbital's large peak of high amplitude, (ii) approximates the electron density within this peak as constant within a radial shell characterized by a radius and thickness T both of which depend on the quantum number n, and (iii) assumes that strong coupling (either with an orbital of an anion donor or to a disulfide sigma* or a backbone amide pi* orbital) occurs when the valence orbital penetrates fully within the radial shell of the Rydberg orbital. These assumptions permit a derivation of the ratios of rates of electron transfer for n > 3 to those for n = 3. Combining these ratios with ab initio rates for n = 3 allows one to make rate predictions for inter- and intramolecular electron transfer involving Rydberg orbitals appropriate to the electron transfer dissociation process. One important prediction of this model is that the combination of large-penetration and Landau-Zener surface-crossing conditions places very severe limitations on which Rydberg levels can initially be populated in electron transfer dissociation. Another prediction is that a Rydberg orbital of a given principal quantum number n has a limited range of distances over which it can transfer an electron; sigma* or pi* orbitals either too far from or too close to a given Rydberg orbital cannot accept an electron

  17. The formation of a luminescent Mn(III,IV) intermediate of bis(2-pyridylmethyl)amine and acetone assistant its intramolecular C-H oxidation.

    PubMed

    Zhou, Dong-Fang; Chen, Qiu-Yun; Fu, Hai-Jian; Yan, Qi-

    2011-10-15

    The dinuclear Mn(II) complexes of bis(2-pyridylmethyl)amine (dpa) reacted with H(2)O(2) producing a fluorescent dioxodimanganese(III,IV) intermediate [(dpa)Mn(2)Cl(2)(μ-O(2))(OHdpa)](3+), which was characterized by IR, UV, ESR, ES-MS and fluorescence spectra. ES-MS data show that this intermediate could bind an acetone molecule forming dioxodimanganese(III,IV)-acetone adduct [(dpa)Mn(2)Cl(2)(μ-O)(CH(3)COCH(3))(OHdpa)](3+). The emission of dioxodimanganese(III,IV)-acetone at 378 nm was stronger than that of dioxodimanganese(III,IV) complex. Excess acetone molecules promoted the intramolecular C-H oxidation and the formation of one dimensional chain Mn(II) complex [(2-picolinic-acid)Mn(H(2)O)(2)Cl(O)](n) through possible intramolecular oxygen transfer reaction. PMID:21782502

  18. Gelation-induced enhanced fluorescence emission from organogels of salicylanilide-containing compounds exhibiting excited-state intramolecular proton transfer: synthesis and self-assembly.

    PubMed

    Nayak, Manoj Kumar; Kim, Byung-Hwa; Kwon, Ji Eon; Park, Sanghyuk; Seo, Jangwon; Chung, Jong Won; Park, Soo Young

    2010-07-01

    Self-assembly structure, stability, hydrogen-bonding interaction, and optical properties of a new class of low molecular weight organogelators (LMOGs) formed by salicylanilides 3 and 4 have been investigated by field-emission scanning electron microscopy (FESEM), X-ray diffraction (XRD), UV/Vis absorption and photoluminescence, as well as theoretical studies by DFT and semiempirical calculations with CI (AM1/PECI=8) methods. It was found that salicylanilides form gels in nonpolar solvents due to pi-stacking interaction complemented by the presence of both inter- and intramolecular hydrogen bonding. The supramolecular arrangement in these organogels predicted by XRD shows lamellar and hexagonal columnar structures for gelators 3 and 4, respectively. Of particular interest is the observation of significant fluorescence enhancement accompanying gelation, which was ascribed to the formation of J-aggregates and inhibition of intramolecular rotation in the gel state. PMID:20491121

  19. Substrate Controlled Synthesis of Benzisoxazole and Benzisothiazole Derivatives via PhI(OAc)2-Mediated Oxidation Followed by Intramolecular Oxidative O-N/S-N Bond Formation.

    PubMed

    Anand, Devireddy; Patel, Om P S; Maurya, Rahul K; Kant, Ruchir; Yadav, Prem P

    2015-12-18

    A phenyliodine(III) diacetate (PIDA)-mediated, highly efficient and tandem approach for the synthesis of aryldiazenylisoxazolo(isothiazolo)arenes from simple 2-amino-N'-arylbenzohydrazides has been developed. The reaction proceeds via formation of (E)-(2-aminoaryl)(aryldiazenyl)methanone as the key intermediate, followed by intramolecular oxidative O-N/S-N bond formation in one pot at room temperature. The quiet different reactivity of the substrate is due to the formation of a diazo intermediate which encounters a nucleophilic attack by carbonyl oxygen on the electrophilic amine to produce isoxazole products, as compared to the previous reportsa,b,4 in which an N-acylnitrenium ion intermediate is intramolecularly trapped by an amine group. PMID:26565748

  20. Intramolecular C–H and C–F Bond Oxygenation Mediated by a Putative Terminal Oxo Species in Tetranuclear Iron Complexes

    PubMed Central

    de Ruiter, Graham; Thompson, Niklas B.; Takase, Michael K.; Agapie, Theodor

    2016-01-01

    Herein we report the intramolecular arene C–H and C–F bond oxygenation by tetranuclear iron complexes. Treatment of [LFe3(PhPz)3OFe][OTf]2 (1) or its fluorinated analog [LFe3(F2ArPz)3OFe][OTf]2 (5) with iodosobenzene results in the regioselective hydroxylation of a bridging pyrazolate ligand, converting a C–H or C–F bond into a C–O bond. The observed reactivity suggests the formation of terminal and reactive Fe-oxo intermediates. With the possibility of intramolecular electron transfer within clusters in 1 and 5, different reaction pathways (FeIV-oxo vs FeIII-oxo) might be responsible for the observed arene hydroxylation. PMID:26760217

  1. Regioselective synthesis of dihydrothiophene and thiopyran frameworks via catalyst-controlled intramolecular Cγ/Cδ-S fusion of α-allyl-β'-oxodithioesters.

    PubMed

    Chowdhury, Sushobhan; Chanda, Tanmoy; Koley, Suvajit; Anand, Namrata; Singh, Maya Shankar

    2014-11-01

    A highly efficient and atom-economic dual reaction manifold has been developed to synthesize 4H-thiopyran and 4,5-dihydrothiophene frameworks via regioselective intramolecular C-S fusion of α-allyl-β'-oxodithioesters. The ring size of the sulfur-heterocycles has been efficiently tuned by the use of two different catalytic systems. Palladium activates the Cδ-H of the allyl termini and facilitates the intramolecular Cδ-S coupling to furnish six-membered thiopyran skeletons exclusively. Conversely, the allylic double bond of the same substrate has been activated by BF3·Et2O to promote the Cγ-S cyclization leading to the formation of a five-membered dihydrothiophene nucleus. PMID:25343754

  2. Intramolecular Photoreactions of (5S)-5-Oxymethyl-2(5H)-furanones as a Tool for the Stereoselective Generation of Diverse Polycyclic Scaffolds.

    PubMed

    Lejeune, Guillaume; Font, Josep; Parella, Teodor; Alibés, Ramon; Figueredo, Marta

    2015-10-01

    The photoactivated evolution of a series of enantiomerically pure 5-oxymethyl-2(5H)-furanones has been investigated. The observed intramolecular photoreactions have proven to be a straightforward entry to diverse and stereochemically rich fragment-molecules, most of which contain the privileged tetrahydropyran (THP) scaffold. The formation of the THP involves a 1,5-hydrogen atom transfer process, leading to a diradical intermediate that recombines to form a new σ C-C bond. These reactions take place under both sensitized and nonsensitized conditions, and they are highly stereoselective. When the substrate contains an allyl residue, the intramolecular [2 + 2] cycloaddition leading to cyclobutanes competes advantageously. When the substrate contains a THP residue, the cyclization involves the concomitant formation of [6,6]-spiroketals with nonanomeric relationships. PMID:26352803

  3. Synthesis, characterization and intramolecular proton transfer of 3,3";-dihydroxy-4,4";-[5-methyl-1,3-phenylenebis(nitrilomethylidyne)]-bis-phenol

    NASA Astrophysics Data System (ADS)

    Eshtiagh-Hosseini, Hossein; Beyramabadi, S. Ali; Morsali, Ali; Mirzaei, Masoud; Chegini, Hamed; Elahi, Morteza; Naseri, Mohammad Ali

    2014-08-01

    A newly synthesized Schiff base, 3,3";-dihydroxy-4,4";-[5-methyl-1,3-phenylenebis(nitrilomethylidyne)]-bis-phenol, was characterized experimentally. Its geometries optimization, tautomerization, assignment of the IR bands and NMR chemical shifts were calculated by using density functional theory (DFT) method. In addition, the atoms in molecules (AIM) analysis was employed for investigation of its tautomerization. Four possible tautomers of the investigated Schiff base were optimized in both of the gas and solution phases. The Schiff base has no planar structure, but each of the benzene rings is in a separate plane. In the most stable tautomer, the phenolic protons of the two sbnd OH groups are engaged in the intramolecular-hydrogen bond with the azomethine nitrogens. Good consistency between the theoretical and experimental results confirms validity of the optimized geometry. Also, kinetics and mechanism of the intramolecular-proton transfer of the studied Schiff base was demonstrated theoretically.

  4. Effect of intramolecular Paternò-Büchi reaction on the thermodynamics and kinetics of nearly degenerate [3,3]-sigmatropic shift in fluxional polycycles.

    PubMed

    Valiulin, Roman A; Dressen, Donald G; Riggs, Jennifer R; Habte, Faven M; Kutateladze, Andrei G

    2009-05-01

    In reactions with weak dienophiles, cyclooctatetraene (COT) often yields 2:1 adducts possessing the fluxional bicyclo[5.1.0]octadiene moiety. They undergo fast, nearly degenerate Cope rearrangement with an activation barrier similar to that of the parent dihydrobullvalene. Irradiation to excite the carbonyl moiety induces an intramolecular Paterno-Buchi cyclization yielding endo-oxetanes and significantly changing the Cope-averaged NMR spectra. In this paper we examine the effect of skeletal distortion caused by intramolecular [2 + 2]-photoaddition on thermodynamics and the activation barrier of the [3,3]-sigmatropic tautomerism. Our finding is that such a distortion lifts the energetic degeneracy of the two valence tautomers, while not affecting the activation barrier. PMID:19344135

  5. Construction of Azabicyclo[6.4.0]dodecatrienes Based on Rhodium(I)-Catalyzed Intramolecular [6+2] Cycloaddition between Azetidine, Allene, and Alkynes.

    PubMed

    Yasuda, Shigeo; Yokosawa, Haruna; Mukai, Chisato

    2016-01-01

    Treatment of the allenylazetidine-alkynes with a catalytic amount of [RhCl(CO)dppp]2 (dppp: 1,3-bis(diphenylphosphino)propane) effected the intramolecular hetero-[6+2]-type ring-closing reaction via the C-C bond cleavage of the azetidine ring to produce azabicyclo[6.4.0]dodecatriene derivatives in good to excellent yields. The formation of the oxa analogue could also be achieved. PMID:27373635

  6. Synthesis of 2-Indolyltetrahydroquinolines by Zinc(II)-Catalyzed Intramolecular Hydroarylation-Redox Cross-Dehydrogenative Coupling of N-Propargylanilines with Indoles.

    PubMed

    Li, Guangzhe; Nakamura, Hiroyuki

    2016-06-01

    An intramolecular hydroarylation-redox cross-dehydrogenative coupling (CDC) of propargylic anilines with indoles proceeded in the presence of zinc(II) catalysts to give 2-indolyltetrahydroquinolines in good to high yields. Three C-H bonds (two sp(2) and one sp(3) ) are activated in one shot and these hydrogen atoms are trapped by a propargylic triple bond in the molecule. PMID:27097846

  7. Iodine-Mediated Intramolecular Dehydrogenative Coupling: Synthesis of N-Alkylindolo[3,2-c]- and -[2,3-c]quinoline Iodides.

    PubMed

    Volvoikar, Prajesh S; Tilve, Santosh G

    2016-03-01

    An I2/TBHP-mediated intramolecular dehydrogenative coupling reaction is developed for the synthesis of a library of medicinally important 5,11-dialkylindolo[3,2-c]quinoline salts and 5,7-dimethylindolo[2,3-c]quinoline salts. The annulation reaction is followed by aromatization to yield tetracycles in good yield. This protocol is also demonstrated for the synthesis of the naturally occurring isocryptolepine in salt form. PMID:26866309

  8. Intramolecular activation of a Ca(2+)-dependent protein kinase is disrupted by insertions in the tether that connects the calmodulin-like domain to the kinase

    NASA Technical Reports Server (NTRS)

    Vitart, V.; Christodoulou, J.; Huang, J. F.; Chazin, W. J.; Harper, J. F.; Evans, M. L. (Principal Investigator)

    2000-01-01

    Ca(2+)-dependent protein kinases (CDPK) have a calmodulin-like domain (CaM-LD) tethered to the C-terminal end of the kinase. Activation is proposed to involve intramolecular binding of the CaM-LD to a junction sequence that connects the CaM-LD to the kinase domain. Consistent with this model, a truncated CDPK (DeltaNC) in which the CaM-LD has been deleted can be activated in a bimolecular interaction with an isolated CaM-LD or calmodulin, similar to the activation of a calmodulin-dependent protein kinase (CaMK) by calmodulin. Here we provide genetic evidence that this bimolecular activation requires a nine-residue binding segment from F436 to I444 (numbers correspond to CPK-1 accession number L14771). Two mutations at either end of this core segment (F436/A and VI444/AA) severely disrupted bimolecular activation, whereas flanking mutations had only minor effects. Intramolecular activation of a full-length kinase was also disrupted by a VI444/AA mutation, but surprisingly not by a F436/A mutation (at the N-terminal end of the binding site). Interestingly, intramolecular but not bimolecular activation was disrupted by insertion mutations placed immediately downstream of I444. To show that mutant enzymes were not misfolded, latent kinase activity was stimulated through binding of an antijunction antibody. Results here support a model of intramolecular activation in which the tether (A445 to G455) that connects the CaM-LD to the kinase provides an important structural constraint and is not just a simple flexible connection.

  9. Stereoselective Synthesis of Diazabicyclic β-Lactams through Intramolecular Amination of Unactivated C(sp(3))-H Bonds of Carboxamides by Palladium Catalysis.

    PubMed

    Zhang, Shi-Jin; Sun, Wen-Wu; Cao, Pei; Dong, Xiao-Ping; Liu, Ji-Kai; Wu, Bin

    2016-02-01

    An efficient C(sp(3))-H bond activation and intramolecular amination reaction via palladium catalysis at the β-position of carboxyamides to make β-lactams was described. The investigation of the substrate scope showed that the current reaction conditions favored activation of the β-methylene group. Short sequences were developed for preparation of various diazabicyclic β-lactam compounds with this method as the key step from chiral proline and piperidine derivatives. PMID:26745308

  10. Barriers to intramolecular rotation determined from the temperature dependence of the Henry constant in the region of adsorbed molecule rigidity failure

    NASA Astrophysics Data System (ADS)

    Dolgonosov, A. M.; Prudkovskii, A. G.

    2008-05-01

    A distribution for the rigid and nonrigid adsorbed molecule forms was found. Adsorbed molecule rigidity failure was shown to be accompanied by a weak nonlinear effect, which manifested itself as a temperature dependence of the Henry constant. A method for the determination of the barrier to intramolecular rotation from the temperature dependence of the molecule adsorption constant was suggested. Barriers to rotation about the C-C and C-O bonds were determined for several molecules.

  11. Synthesis of silicon-functionalized dibenzosilaborins by intramolecular B-H/C-H dehydrogenative cyclization and their tunable photophysical and chemical properties by silyl groups.

    PubMed

    Kawachi, Atsushi; Morisaki, Hiroshi; Hirofuji, Tatsuya; Yamamoto, Yohsuke

    2013-09-27

    A bit borane: Silicon-functionalized dibenzosilaborins were prepared by intramolecular B-H/C-H dehydrogenative cyclization of o-(silyl)(hydroboryl)benzenes. The hydrosilyl derivative (X=H) can be converted into the fluorosilane (X=F) and chlorosilane (X=Cl). UV/Vis and fluorescence spectra are influenced by the functional groups X on the silicon atom through σ*-π* conjugation. PMID:24027003

  12. New and Concise Syntheses of the Bicyclic Oxamazin Core Using an Intramolecular Nitroso Diels-Alder Reaction and Ring-Closing Olefin Metathesis

    PubMed Central

    Watson, Kyle D.; Carosso, Serena

    2013-01-01

    Herein two new and concise synthetic approaches for making an unsaturated bicyclic oxamazin core are reported. The first involves the use of an intramolecular Diels-Alder reaction to form both of the fused rings in one step. The second approach incorporates ring-closing olefin metathesis in the final step to form the second fused ring of the core. The scope of the second approach was also expanded further to afford larger ringed bicyclic systems. PMID:23276301

  13. Transition Metal Donor-Peptide-Acceptor Complexes: From Intramolecular Electron Transfer Reactions to the Study of Reactive Intermediates

    SciTech Connect

    Isied, Stephan S.

    2003-03-11

    The trans-polyproline (PII) oligomers (Figure 1) are unusually rigid peptide structures which have been extensively studied by our group for peptide mediated intramolecular electron transfer (ET) at long distances. We have previously studied ET across a series of metal ion donor (D) acceptor (A) oligoproline peptides with different distances, driving forces and reorganizational energies. The majority of these experiments involve generating the ET intermediate using pulse radiolysis methods, although more recently photochemical methods are also used. Results of these studies showed that ET across peptides can vary by more than twelve orders of magnitude. Using ruthenium bipyridine donors, ET reaction rate constants across several proline residues (n = 4 - 9) occurred in the millisecond (ms) to {micro}s timescale, thus limiting the proline peptide conformational motions to only minor changes (far smaller than the large changes that occur on the ms to sec timescale, such as trans to cis proline isomerization). The present report describes our large data base of experimental results for D-peptide-A complexes in terms of a model where the involvement of both superexchange and hopping (hole and electron) mechanisms account for the long range ET rate constants observed. Our data shows that the change from superexchange to hopping mechanisms occurs at different distances depending on the type of D and A and their interactions with the peptides. Our model is also consistent with generalized models for superexchange and hopping which have been put forward by a number of theoretical groups to account for long range ET phenomena.

  14. Visualizing the non-equilibrium dynamics of photoinduced intramolecular electron transfer with femtosecond X-ray pulses

    SciTech Connect

    Canton, Sophie E.; Kjær, Kasper S.; Vankó, György; van Driel, Tim B.; Adachi, Shin -ichi; Bordage, Amélie; Bressler, Christian; Chabera, Pavel; Christensen, Morten; Dohn, Asmus O.; Galler, Andreas; Gawelda, Wojciech; Gosztola, David; Haldrup, Kristoffer; Harlang, Tobias; Liu, Yizhu; Møller, Klaus B.; Németh, Zoltán; Nozawa, Shunsuke; Pápai, Mátyás; Sato, Tokushi; Sato, Takahiro; Suarez-Alcantara, Karina; Togashi, Tadashi; Tono, Kensuke; Uhlig, Jens; Vithanage, Dimali A.; Wärnmark, Kenneth; Yabashi, Makina; Zhang, Jianxin; Sundström, Villy; Nielsen, Martin M.

    2015-03-02

    Ultrafast photoinduced electron transfer preceding energy equilibration still poses many experimental and conceptual challenges to the optimization of photoconversion since an atomic-scale description has so far been beyond reach. Here we combine femtosecond transient optical absorption spectroscopy with ultrafast X-ray emission spectroscopy and diffuse X-ray scattering at the SACLA facility to track the non-equilibrated electronic and structural dynamics within a bimetallic donor–acceptor complex that contains an optically dark centre. Exploiting the 100-fold increase in temporal resolution as compared with storage ring facilities, these measurements constitute the first X-ray-based visualization of a non-equilibrated intramolecular electron transfer process over large interatomic distances. Thus experimental and theoretical results establish that mediation through electronically excited molecular states is a key mechanistic feature. The present study demonstrates the extensive potential of femtosecond X-ray techniques as diagnostics of non-adiabatic electron transfer processes in synthetic and biological systems, and some directions for future studies, are outlined.

  15. Visualizing the non-equilibrium dynamics of photoinduced intramolecular electron transfer with femtosecond X-ray pulses

    DOE PAGESBeta

    Canton, Sophie E.; Kjær, Kasper S.; Vankó, György; van Driel, Tim B.; Adachi, Shin -ichi; Bordage, Amélie; Bressler, Christian; Chabera, Pavel; Christensen, Morten; Dohn, Asmus O.; et al

    2015-03-02

    Ultrafast photoinduced electron transfer preceding energy equilibration still poses many experimental and conceptual challenges to the optimization of photoconversion since an atomic-scale description has so far been beyond reach. Here we combine femtosecond transient optical absorption spectroscopy with ultrafast X-ray emission spectroscopy and diffuse X-ray scattering at the SACLA facility to track the non-equilibrated electronic and structural dynamics within a bimetallic donor–acceptor complex that contains an optically dark centre. Exploiting the 100-fold increase in temporal resolution as compared with storage ring facilities, these measurements constitute the first X-ray-based visualization of a non-equilibrated intramolecular electron transfer process over large interatomic distances.more » Thus experimental and theoretical results establish that mediation through electronically excited molecular states is a key mechanistic feature. The present study demonstrates the extensive potential of femtosecond X-ray techniques as diagnostics of non-adiabatic electron transfer processes in synthetic and biological systems, and some directions for future studies, are outlined.« less

  16. Visualizing the non-equilibrium dynamics of photoinduced intramolecular electron transfer with femtosecond X-ray pulses

    PubMed Central

    Canton, Sophie E.; Kjær, Kasper S.; Vankó, György; van Driel, Tim B.; Adachi, Shin-ichi; Bordage, Amélie; Bressler, Christian; Chabera, Pavel; Christensen, Morten; Dohn, Asmus O.; Galler, Andreas; Gawelda, Wojciech; Gosztola, David; Haldrup, Kristoffer; Harlang, Tobias; Liu, Yizhu; Møller, Klaus B.; Németh, Zoltán; Nozawa, Shunsuke; Pápai, Mátyás; Sato, Tokushi; Sato, Takahiro; Suarez-Alcantara, Karina; Togashi, Tadashi; Tono, Kensuke; Uhlig, Jens; Vithanage, Dimali A.; Wärnmark, Kenneth; Yabashi, Makina; Zhang, Jianxin; Sundström, Villy; Nielsen, Martin M.

    2015-01-01

    Ultrafast photoinduced electron transfer preceding energy equilibration still poses many experimental and conceptual challenges to the optimization of photoconversion since an atomic-scale description has so far been beyond reach. Here we combine femtosecond transient optical absorption spectroscopy with ultrafast X-ray emission spectroscopy and diffuse X-ray scattering at the SACLA facility to track the non-equilibrated electronic and structural dynamics within a bimetallic donor–acceptor complex that contains an optically dark centre. Exploiting the 100-fold increase in temporal resolution as compared with storage ring facilities, these measurements constitute the first X-ray-based visualization of a non-equilibrated intramolecular electron transfer process over large interatomic distances. Experimental and theoretical results establish that mediation through electronically excited molecular states is a key mechanistic feature. The present study demonstrates the extensive potential of femtosecond X-ray techniques as diagnostics of non-adiabatic electron transfer processes in synthetic and biological systems, and some directions for future studies, are outlined. PMID:25727920

  17. A Manganese Catalyst for Highly Reactive Yet Chemoselective Intramolecular C(sp3)—H Amination

    PubMed Central

    Paradine, Shauna M.; Griffin, Jennifer R.; Zhao, Jinpeng; Petronico, Aaron L.; Miller, Shannon M.; White, M. Christina

    2016-01-01

    C—H bond oxidation reactions underscore the existing paradigm wherein high reactivity and high selectivity are inversely correlated. The development of catalysts capable of oxidizing strong aliphatic C(sp3)—H bonds while displaying chemoselectivity (i.e. tolerance of more oxidizable functionality) remains an unsolved problem. Herein, we describe a catalyst, manganese tert-butylphthalocyanine [Mn(tBuPc)], that is an outlier to the reactivity-selectivity paradigm. It is unique in its capacity to functionalize all types of C(sp3)—H bonds intramolecularly, while displaying excellent chemoselectivity in the presence of π-functionality. Mechanistic studies indicate that [Mn(tBuPc)] transfers bound nitrenes to C(sp3)—H bonds via a pathway that lies between concerted C—H insertion, observed with reactive noble metals (e.g. rhodium), and stepwise radical C—H abstraction/rebound, observed with chemoselective base metals (e.g. iron). Rather than achieving a blending of effects, [Mn(tBuPc)] aminates even 1° aliphatic and propargylic C—H bonds, reactivity and selectivity unusual for previously known catalysts. PMID:26587714

  18. The low-lying {pi}{sigma}* state and its role in the intramolecular charge transfer of aminobenzonitriles and aminobenzethyne

    SciTech Connect

    Lee, Jae-Kwang; Fujiwara, Takashige; Kofron, William G.; Zgierski, Marek Z.; Lim, Edward C.

    2008-04-28

    Electronic absorption spectra of the low-lying {pi}{pi}* and {pi}{sigma}* states of several aminobenzonitriles and 4-dimethylaminobenzethyne have been studied by time-resolved transient absorption and time-dependent density functional theory calculation. In acetonitrile, the lifetime of the {pi}{sigma}*-state absorption is very short (picoseconds or subpicosecond) for molecules that exhibit intramolecular charge transfer (ICT), and very long (nanoseconds) for those that do not. Where direct comparison of the temporal characteristics of the {pi}{sigma}*-state and the ICT-state transients could be made, the formation rate of the ICT state is identical to the decay rate of the {pi}{sigma}* state within the experimental uncertainty. These results are consistent with the {pi}{sigma}*-mediated ICT mechanism, L{sub a} ({pi}{pi}*){yields}{pi}{sigma}*{yields}ICT, in which the decay rate of the {pi}{sigma}* state is determined by the rate of the solvent-controlled {pi}{sigma}*{yields}ICT charge-shift reaction. The {pi}{pi}*{yields}{pi}{sigma}* state crossing does not occur in 3-dimethylaminobenzonitrile or 2-dimethylaminobenzonitrile, as predicted by the calculation, and 4-aminobenzonitrile and 4-dimethylaminobenzethyne does not exhibit the ICT reaction, consistent with the higher energy of the ICT state relative to the {pi}{sigma}* state.

  19. Fast intramolecular electron transfer and dual fluorescence. Configurational change of the amino nitrogen (pyramidal{yields}planar)

    SciTech Connect

    Haar, Th. von der; Hebecker, A.; Il'Ichev, Yu.; Kuehnle, W.; Zachariasse, K. A.

    1996-04-01

    The fast excited state intramolecular charge transfer (ICT) and dual fluorescence observed with several 4-aminobenzonitriles is discussed. It is shown that the magnitude of the energy gap between the two lowest excited states determines the occurrence or absence of ICT. The photophysical behavior of a series of four 4-aminobenzonitriles in which the amino nitrogen atom is part of a four- to seven-membered heterocyclic ring, P4C to P7C, is studied by using time-resolved fluorescence measurements. The ICT rate constant strongly decreases with decreasing ring size. With P4C in diethyl ether ICT does not occur. This is attributed to the increase of the amino nitrogen inversion barrier with decreasing ring size. The change of the amino nitrogen from pyramidal to planar is considered to be an important reaction coordinate. The photophysics of the 4-aminobenzonitriles is different from that of other ICT systems such as donor/acceptor-substituted stilbenes and 9,9'-bianthryl, which are governed by the charge distribution and macroscopic Coulombic interaction in their CT states.

  20. Ultrafast Investigation of Intramolecular Charge Transfer and Solvation Dynamics of Tetrahydro[5]-helicene-Based Imide Derivatives

    NASA Astrophysics Data System (ADS)

    Zhu, Huaning; Li, Meng; Hu, Jiangpu; Wang, Xian; Jie, Jialong; Guo, Qianjin; Chen, Chuanfeng; Xia, Andong

    2016-04-01

    We report the excited-state intramolecular charge transfer (ICT) characteristics of four tetrahydro[5] helicene-based imide (THHBI) derivatives with various electron-donating substitutes in different polarity of solvents using steady-state, time-resolved transient absorption (TA) spectroscopy. It is found that, the small bathochromic-shift of the absorption spectra but large red shift of the emission spectra for all dyes with increasing solvent polarity indicates the larger dipole moment of the excited state compared to ground state. The results of theoretical calculations exhibit the charge transfer from the terminal donors to helical backbone, which accounts for the degrees of red shift of the emission spectra from different extent of ICT nature. Time-resolved TA spectra recorded as a function of electron-donating substitutes and solvent polarity show the dye with stronger donors (THHBI-PhNPh2) in more polar solvent behaves faster excited-state ICT relaxation, leading to the formation of solvent-stabilized ICT state (ICT’ state) from the excited ICT state; The dyes (THHBI-Ph, THHBI-PhCF3 and THHBI-PhOMe) with relative weaker donors show weaker dependence on solvent polarity, and instead of that intersystem crossing (ISC) becomes possible from ICT state to triplet state.