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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. Intramolecular ketene-allene cycloadditions.

    PubMed

    McCaleb, K L; Halcomb, R L

    2000-08-24

    [reaction: see text]This report describes intramolecular thermal [2 + 2] cycloadditions between ketenes and allenes. The formation of ketenes and the subsequent cycloadditions occurred under a variety of conditions, affording 7-methylidinebicyclo[3.2.0]heptanones and 7-methylidinebicyclo[3.1.1]heptanones in 45-78% yields. The regioselectivity of the cycloaddition varied with the substitution of the allene, and the yield of cyclized products varied with reaction conditions.

  11. 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

  12. 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

  13. Intramolecular cycloadditions of cyclobutadiene with olefins.

    PubMed

    Limanto, John; Tallarico, John A; Porter, James R; Khuong, Kelli S; Houk, K N; Snapper, Marc L

    2002-12-11

    Intramolecular cycloadditions between cyclobutadiene and olefins can provide highly functionalized cyclobutene-containing products. The outcome of the reaction depends on the nature of the tether connecting the two reactive partners in the cycloaddition. Electronically unactivated olefins attached to cyclobutadiene through a three-atom, heteroatom-containing tether yield successfully the desired cycloadducts, whereas the corresponding substrates without a heteroatom linkage or with a longer tether are less prone to undergo the intramolecular cycloaddition. Calculations were used to help uncover some of the factors that influence the course of the cycloaddition. Successful intramolecular reactions usually require either electronic activation of the dienophile, conformational restriction of the tether, or a slower oxidation protocol. In general, a facile intermolecular dimerization of cyclobutadiene is the major process that competes with the intramolecular cycloaddition.

  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 screening of intermolecular forces

    NASA Astrophysics Data System (ADS)

    Liang, Ying Q.; Hunt, K. L. C.

    1993-03-01

    By use of nonlocal polarizability densities, we analyze the intramolecular screening of intermolecular fields. For two interacting molecules A and B with weak or negligible charge overlap, we show that the reaction field and the field due to the unperturbed charge distribution of the neighboring molecule are screened identically via the Sternheimer shielding tensor and its generalizations to nonuniform fields and nonlinear response. The induction force on nucleus I in molecule A, derived from perturbation theory, results from linear screening of the reaction field due to B and nonlinear screening of the field from the permanent charge distribution of B. In general, at first or second order in the molecular interaction, the screening-tensor expressions for the force on nucleus I involve susceptibilities of one order higher than the expressions derived from perturbation theory. The first-order force from perturbation theory involves permanent charge moments, while the first-order screened force involves linear response tensors; and the second-order screened force depends on hyperpolarizabilities, while second-order induction effects are specified in terms of static, lowest-order susceptibilities. The equivalence of the two formulations for these forces, order by order, is a new illustration of the interrelations we have found among permanent moments, linear-response tensors, and nonlinear response. This work also provides new insight into the dispersion forces on an individual nucleus I in molecule A by separating the forces into two distinct terms—the first term results from changes in the reaction of A to the fluctuating charge distribution of the neighboring molecule B, when nucleus I shifts infinitesimally, and the second term stems from changes in correlations of the fluctuating charge distribution of A itself. Changes in the fluctuation correlations are determined by changes in the classical Coulomb field of nucleus I and by the imaginary part of the

  16. Organocatalyzed Intramolecular Carbonyl-Ene Reactions.

    PubMed

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

    2016-05-31

    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.

  17. 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.

  18. Electrochemical intramolecular aminooxygenation of unactivated alkenes.

    PubMed

    Xu, Fan; Zhu, Lin; Zhu, Shaobin; Yan, Xiaomei; Xu, Hai-Chao

    2014-09-26

    An electrochemical approach to the intramolecular aminooxygenation of unactivated alkenes has been developed. This process is based on the addition of nitrogen-centered radicals, generated through electrochemical oxidation, to alkenes followed by trapping of the cyclized radical intermediate with 2,2,6,6-tetramethylpiperidine-N-oxyl radical (TEMPO). Difunctionalization of a variety of alkenes with easily available carbamates/amides and TEMPO affords aminooxygenation products in high yields and with excellent trans selectivity for cyclic systems (d.r. up to>20:1). The approach provides a much-needed complementary route to existing cis-selective methods.

  19. 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.

  20. Intramolecular interactions in the polar headgroup of sphingosine: serinol.

    PubMed

    Loru, Donatella; Peña, Isabel; Alonso, José L; Sanz, M Eugenia

    2016-03-01

    The intramolecular interactions in the lipid sphingosine have been elucidated through the investigation of the amino alcohol serinol which mimics its polar headgroup. Intricate networks of intramolecular hydrogen bonds involving the hydroxyl groups and the amino group contribute to the stabilisation of five different conformations observed in the broadband rotational spectrum.

  1. Thermal induced intramolecular [2 + 2] cycloaddition of allene-ACPs.

    PubMed

    Chen, Kai; Sun, Run; Xu, Qin; Wei, Yin; Shi, Min

    2013-06-28

    A facile synthetic method for preparation of bicyclo[4.2.0] nitrogen heterocycles has been developed via a thermal induced intramolecular [2 + 2] cycloaddition reaction of allene-ACPs. The DFT calculations indicate that this intramolecular cycloaddition proceeds in a concerted manner and a strained small ring is essential.

  2. Catalytic enantioselective intramolecular aza-diels-alder reactions.

    PubMed

    Min, Chang; Lin, Chih-Tsung; Seidel, Daniel

    2015-05-26

    A readily available chiral Brønsted acid was identified as an efficient catalyst for intramolecular Povarov reactions. Polycyclic amines containing three contiguous stereogenic centers were obtained with excellent stereocontrol in a single step from secondary anilines and aldehydes possessing a pendent dienophile. These transformations constitute the first examples of catalytic enantioselective intramolecular aza-Diels-Alder reactions.

  3. 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.

  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.

  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. 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

  7. Exciton Correlations in Intramolecular Singlet Fission

    DOE PAGESBeta

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

    2016-05-16

    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,more » 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.« less

  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. Extremely slow intramolecular diffusion in unfolded protein L.

    PubMed

    Waldauer, Steven A; Bakajin, Olgica; Lapidus, Lisa J

    2010-08-01

    A crucial parameter in many theories of protein folding is the rate of diffusion over the energy landscape. Using a microfluidic mixer we have observed the rate of intramolecular diffusion within the unfolded B1 domain of protein L before it folds. The diffusion-limited rate of intramolecular contact is about 20 times slower than the rate in 6 M GdnHCl, and because in these conditions the protein is also more compact, the intramolecular diffusion coefficient decreases 100-500 times. The dramatic slowdown in diffusion occurs within the 250 micros mixing time of the mixer, and there appears to be no further evolution of this rate before reaching the transition state of folding. We show that observed folding rates are well predicted by a Kramers model with a denaturant-dependent diffusion coefficient and speculate that this diffusion coefficient is a significant contribution to the observed rate of folding.

  10. Regioselective intramolecular [3+2] annulation of allene-nitrones.

    PubMed

    Inagaki, Fuyuhiko; Kobayashi, Harumi; Mukai, Chisato

    2012-01-01

    The regioselective intramolecular 1,3-dipolar cycloaddition of the phenylsulfonylallene-nitrone derivatives has been developed. This reaction showed that the distal double bond of the allene exclusively reacted with the nitrone group to produce the bicyclic isoxazolidine derivatives regardless of the substitution pattern on the allenyl moiety.

  11. Dendrimer light-harvesting: intramolecular electrodynamics and mechanisms.

    PubMed

    Andrews, David L; Bradshaw, David S; Jenkins, Robert D; Rodríguez, Justo

    2009-12-01

    In the development of highly efficient materials for harvesting solar energy, there is an increasing focus on purpose-built dendrimers and allied multi-chromophore systems. A proliferation of antenna chromophores is not the only factor determining the sought light-harvesting efficiency; the internal geometry and photophysics of these molecules are also crucially important. In particular, the mechanisms by means of which radiant energy is ultimately trapped depends on an intricate interplay of electronic, structural, energetic and symmetry properties. To better understand these processes a sound theoretical representation of the intramolecular electrodynamics is required. A suitable formalism, based on quantum electrodynamics, readily delivers physical insights into the necessary excitation channelling processes, and it affords a rigorous basis for modelling the intramolecular flow of energy.

  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. 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.

  14. Palladium Catalyzed Intramolecular Acylcyanation of Alkenes Using α-Iminonitriles

    PubMed Central

    Rondla, Naveen R.; Ogilvie, Jodi M.; Pan, Zhongda

    2014-01-01

    Reported here is a palladium catalyzed intramolecular acylcyanation of alkenes using α-iminonitriles. Through this method, highly functionalized indanones are synthesized in moderate to high yields using Pd(PPh3)4, without need for any additional ligands, and a common Lewis acid (ZnCl2). Additionally, the reaction tolerates substitution at various positions on the aromatic ring including electron donating, and electron withdrawing groups. PMID:24980625

  15. Synthesis of Normorphans through an Efficient Intramolecular Carbamoylation of Ketones.

    PubMed

    Diaba, Faïza; Montiel, Juan A; Serban, Georgeta; Bonjoch, Josep

    2015-08-01

    An unexpected C-C bond cleavage was observed in trichloroacetamide-tethered ketones under amine treatment and exploited to develop a new synthesis of normophans from 4-amidocyclohexanones. The reaction involves an unprecedented intramolecular haloform-type reaction of trichloroacetamides promoted by enamines (generated in situ from ketones) as counter-reagents. The methodology was applied to the synthesis of compounds embodying the 6-azabicyclo[3.2.1]octane framework.

  16. Influence of receptor flexibility on intramolecular H-bonding interactions.

    PubMed

    Sun, Hongmei; Guo, Kai; Gan, Haifeng; Li, Xin; Hunter, Christopher A

    2015-08-01

    Atropisomers of a series of zinc tetraphenyl porphyrins were synthesized and used as supramolecular receptors. Rotation around the porphyrin-meso phenyl bonds is restricted by installing ortho-chlorine substituents on the phenyl groups. The chlorine substituents allowed chromatographic separation of atropisomers, which did not interconvert at room temperature. The porphyrin meso phenyl groups were also equipped with phenol groups, which led to the formation of intramolecular H-bonds when the zinc porphyrins were bound to pyridine ligands equipped with ester or amide side arms. Binding of the pyridine ligands with the conformationally locked chloroporphyrins was compared with the corresponding unsubstituted porphyrins, which are more flexible. The association constants of 150 zinc porphyrin-pyridine complexes were measured in two different solvents, toluene and 1,1,2,2-tetrachloroethane (TCE). These association constants were then used to construct 120 chemical double mutant cycles to quantify the influence of chlorine substitution on the free energy of intramolecular H-bonds formed between the phenol side arms of the porphyrins and the ester or amide side arms of the pyridine ligands. Conformational restriction leads to increases in the stability of some complexes and decreases in the stability of others with variations in the free energy contribution due to intramolecular H-bonding of -5 to +6 kJ mol(-1).

  17. Stereocontrolled intramolecular iron-mediated diene/olefin cyclocoupling

    NASA Astrophysics Data System (ADS)

    Dorange, Ismet B.

    A methodology for stereocontrol during the intramolecular coupling between cyclohexadiene-Fe(CO)3 complexes and pendant alkenes is presented. Introduction of a methoxy group at the C(3) position of the diene moiety controls pre- and post-cyclization rearrangements of the diene Fe(CO)3 unit, allowing the preparation of spirolactams with defined relative stereochemistry and with a cyclohexenone framework, thus making this reaction a potentially valuable tool for the construction of quaternary carbon centers.* A new methodology for the formation of tricarbonyl(cyclohexadienyl)ketone iron complexes was also developed. This method involves the coupling of a Grignard reagent with an acyl mesylate iron complex, giving rise to ketone derivatives in excellent yields. The possibility of intramolecular coupling between diene-Fe(CO)3 complexes and homoallylic olefin was demonstrated. The stereospecific formation of spiroketones occurred in excellent yields under thermal conditions, but appeared to be limited to the simpler, less substituted pendant alkenes. The control of the stereochemical outcome of these spirocyclization was achieved using the "C(3) substitution method" previously described. The same trends were observed in these series. Also illustrated in these studies is the extension of this spirocoupling to the formation of a spiro[5.5]undecane framework. It is the first time that this framework has been accessed using this intramolecular coupling.* *Please refer to dissertation for diagram.

  18. 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

  19. Application to processing system using intra-molecular BRET

    NASA Astrophysics Data System (ADS)

    Otsuji, Tomomi; Okuda-Ashitaka, Emiko; Kojima, Satoshi; Akiyama, Hidehumi; Ito, Seiji; Ohmiya, Yoshihiro

    2003-07-01

    Luciferases are used as the reporter gene for promoter activity, whereas a green fluorescent protein (GFP) is used as marker for cellular function and localization. Recently, bioluminescence resonance energy transfer (BRET) between luciferase and YFP is used for analysis of inter-molecular reaction such as ligand-receptor in the living cells. The neuropeptides nocistatin (NST) and nociceptin/orphanin FQ (Noc/OFQ) are derived from the same precursor protein, while NST exhibits antagonism against Noc/OFQ-actions. In this study, we attempt an intra-molecular BRET system for monitoring dynamic biological process of the production of NST and Noc/OFQ in the living cells. At first, we constructed a fusion protein (Rluc-GFP) covalently linking luciferase (Renilla luciferase; Rluc) to Aequorea GFP as an intra-molecular BRET partner. Furthermore, we inserted constructs of mouse NST and Noc/OFQ (Rluc-m-GFP) or bovine NST and Noc/OFQ (Rluc-b-GFP) containing a proteolytic cleavage motif (Lys-Arg) within Rluc-GFP. When these constructions were transfected into Cos7 cells, all fusion proteins had luciferase activity and specific fluorescence. Luminescence spectra of Rluc-GFP, Rluc-m-GFP and Rluc-b-GFP fusion proteins with DeepBlueC as a substrate showed two peaks centered at 400 nm and 510 nm, whereas Rluc showed one peak centered at 400 nm. These results indicate that the proteolytic cleavage motif inserted fusion proteins between luciferase and GFP are available for intra-molecular BRET systems at first step.

  20. Intramolecular and dissociation dynamics of the CF2Br radical

    NASA Astrophysics Data System (ADS)

    Bintz, Karen L.; Thompson, Donald L.; Gosnell, T. R.; Hay, P. Jeffrey

    1992-11-01

    Classical trajectory methods were used to investigate the nature of the intramolecular dynamics (quasiperiodic vs chaotic) of the CF2Br radical. The potential energy surface is based on empirical and ab initio results. Power spectra show that the Br-C-F bend exhibits quasiperiodic dynamics while the other modes are chaotic. Despite the presence of quasiperiodic dynamics, the dissociation rates for mode-specific excitations of the normal modes are essentially the same as those for equipartitioning of the excitation energy among all the normal modes.

  1. Recording Intramolecular Mechanics during the Manipulation of a Large Molecule

    NASA Astrophysics Data System (ADS)

    Moresco, Francesca; Meyer, Gerhard; Rieder, Karl-Heinz; Tang, Hao; Gourdon, André; Joachim, Christian

    2001-08-01

    The technique of single atom manipulation by means of the scanning tunneling microscope (STM) applies to the controlled displacement of large molecules. By a combined experimental and theoretical work, we show that in a constant height mode of manipulation the STM current intensity carries detailed information on the internal mechanics of the molecule when guided by the STM tip. Controlling and time following the intramolecular behavior of a large molecule on a surface is the first step towards the design of molecular tunnel-wired nanorobots.

  2. Recording intramolecular mechanics during the manipulation of a large molecule.

    PubMed

    Moresco, F; Meyer, G; Rieder, K H; Tang, H; Gourdon, A; Joachim, C

    2001-08-20

    The technique of single atom manipulation by means of the scanning tunneling microscope (STM) applies to the controlled displacement of large molecules. By a combined experimental and theoretical work, we show that in a constant height mode of manipulation the STM current intensity carries detailed information on the internal mechanics of the molecule when guided by the STM tip. Controlling and time following the intramolecular behavior of a large molecule on a surface is the first step towards the design of molecular tunnel-wired nanorobots.

  3. 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.

  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. Intramolecular carbon isotope distribution of acetic acid in vinegar.

    PubMed

    Hattori, Ryota; Yamada, Keita; Kikuchi, Makiko; Hirano, Satoshi; Yoshida, Naohiro

    2011-09-14

    Compound-specific carbon isotope analysis of acetic acid is useful for origin discrimination and quality control of vinegar. Intramolecular carbon isotope distributions, which are each carbon isotope ratios of the methyl and carboxyl carbons in the acetic acid molecule, may be required to obtain more detailed information to discriminate such origin. In this study, improved gas chromatography-pyrolysis-gas chromatography-combustion-isotope ratio mass spectrometry (GC-Py-GC-C-IRMS) combined with headspace solid-phase microextraction (HS-SPME) was used to measure the intramolecular carbon isotope distributions of acetic acid in 14 Japanese vinegars. The results demonstrated that the methyl carbons of acetic acid molecules in vinegars produced from plants were mostly isotopically depleted in (13)C relative to the carboxyl carbon. Moreover, isotopic differences (δ(13)C(carboxyl) - δ(13)C(methyl)) had a wide range from -0.3 to 18.2‰, and these values differed among botanical origins, C3, C4, and CAM plants.

  6. Intramolecular motion in DIET: Desorption and dissociation of chemisorbed ammonia

    NASA Astrophysics Data System (ADS)

    Burns, A. R.; Stechel, E. B.; Jennison, D. R.

    1995-06-01

    We show that quantum-specific detection of DIET processes of polyatomic adsorbates reveals the multidimensional dynamics of intramolecular motion. Specifically, we present an analysis of the 6-350 eV electron-induced desorption and dissociation of chemisorbed NH 3 and ND 3 on Pt(1 1 1). State-selective detection of the neutral DIET products is accomplished by 2 + 1 resonance-enhanced multiphoton ionization (REMPI). Desorption and dissociation occur as a result of distinct electronic excitations that result in different, uncoupled, modes of intramolecular motion. We find that desorption results from 3a 1-1-induced inversion motion. Trajectories on a two-dimensional potential energy surface reveal that the excited molecule fully inverts; upon deexcitation, the inverted molecule is sufficiently high on the hard wall of the substrate interaction to have enough energy to desorb. Given the short excitation lifetime, the time scale in which the (H) D atoms reach the inversion geometry directly affects the desorption yield and results in an appreciable enhancement of NH 3 desorption over that of ND 3. In general, multidimensional molecule-surface potential energy surfaces should be considered in DIET processes involving molecular adsorbates.

  7. Modulating intramolecular P···N pnictogen interactions.

    PubMed

    Sánchez-Sanz, Goar; Trujillo, Cristina; Alkorta, Ibon; Elguero, José

    2016-04-01

    A computational study of the intramolecular pnictogen bond in 8-phosphinonaphthalen-1-amine derivatives (1-NX2, 8-PX2 with X = H, F, Cl, Br, CH3, CN and NC), proton sponge analogues, has been carried out to determine their structural and geometric parameters, interaction energies and electronic properties such as the electron density of the intramolecular interaction. Our results show that substitution of H atoms in the PH2 group by electron withdrawing groups on the Lewis acid moiety strengthens the P···N pnictogen bond, evidenced by the increasing electron density values at the bond critical point and by shorter distances. However, substitutions on the Lewis base moiety (NX2) show weaker P···N interactions than when the substitution is done on the Lewis acid counterpart (PX2). Nevertheless, in all cases, pnictogen bonds are enhanced upon substitution with respect to the parent 1-NH2, 8-PH2 system. Second-order orbital interaction energies, electron density maps, electron delocalization functions and charge transfer corroborate the evolution of the P···N strength upon substitution. PMID:26972057

  8. Studies on Lewis acid-mediated intramolecular cyclization reactions of allene-ene systems.

    PubMed

    Hiroi, K; Watanabe, T; Tsukui, A

    2000-03-01

    The Lewis acid-mediated reactions of allene-ene compounds, derived from 3-methylcitronellal or dimethyl malonate, were carried out using various Lewis acids such as ethylaluminum dichloride, diethylaluminum chloride, titanium chloride, zinc chloride etherate, or boron trifluoride etherate, affording unexpectedly intramolecular [2+2]cycloaddition products under some particular reaction conditions without any formation of intramolecular ene reaction products.

  9. 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

  10. Intramolecular charge transfer effects on 4-hydroxy-3-methoxybenzaldehyde

    NASA Astrophysics Data System (ADS)

    Rajendiran, N.; Balasubramanian, T.

    2008-03-01

    The absorption and fluorescence spectral characteristics of 4-hydroxy-3-methoxybenzaldehyde (HMB) have been studied in different solvents, pH and β-cyclodextrin (β-CD) and compared with 4-hydroxy-3,5-dimethoxybenzaldehyde (HDMB). The inclusion complex of HMB with β-CD is analysed by UV-vis, fluorimetry, FT-IR, 1H NMR, SEM and AM1 methods. In HMB, the normal emission (B band) is originates from a locally excited state and the longer emission (A band) is due to intramolecular charge transfer state (ICT). The OH group of HMB is present in the interior part of the β-CD cavity and aldehyde group present in the upper part of the β-CD cavity.

  11. 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.

  12. Intramolecular hydrophobic interactions are critical mediators of STAT5 dimerization

    PubMed Central

    Fahrenkamp, Dirk; Li, Jinyu; Ernst, Sabrina; Schmitz-Van de Leur, Hildegard; Chatain, Nicolas; Küster, Andrea; Koschmieder, Steffen; Lüscher, Bernhard; Rossetti, Giulia; Müller-Newen, Gerhard

    2016-01-01

    STAT5 is an essential transcription factor in hematopoiesis, which is activated through tyrosine phosphorylation in response to cytokine stimulation. Constitutive activation of STAT5 is a hallmark of myeloid and lymphoblastic leukemia. Using homology modeling and molecular dynamics simulations, a model of the STAT5 phosphotyrosine-SH2 domain interface was generated providing first structural information on the activated STAT5 dimer including a sequence, for which no structural information is available for any of the STAT proteins. We identified a novel intramolecular interaction mediated through F706, adjacent to the phosphotyrosine motif, and a unique hydrophobic interface on the surface of the SH2 domain. Analysis of corresponding STAT5 mutants revealed that this interaction is dispensable for Epo receptor-mediated phosphorylation of STAT5 but essential for dimer formation and subsequent nuclear accumulation. Moreover, the herein presented model clarifies molecular mechanisms of recently discovered leukemic STAT5 mutants and will help to guide future drug development. PMID:27752093

  13. Easy access to modified cyclodextrins by an intramolecular radical approach.

    PubMed

    Alvarez-Dorta, Dimitri; León, Elisa I; Kennedy, Alan R; Martín, Angeles; Pérez-Martín, Inés; Suárez, Ernesto

    2015-03-16

    A simple method to modify the primary face of cyclodextrins (CDs) is described. The 6(I)-O-yl radical of α-, β-, and γ-CDs regioselectively abstracts the H5(II), located in the adjacent D-glucose unit, by an intramolecular 1,8-hydrogen-atom-transfer reaction through a geometrically restricted nine-membered transition state to give a stable 1,3,5-trioxocane ring. The reaction has been extended to the 1,4-diols of α- and β-CD to give the corresponding bis(trioxocane)s. The C2-symmetric bis(trioxocane) corresponding to the α-CD is a stable crystalline solid whose structure was confirmed by X-ray diffraction analysis. The calculated geometric parameters confirm that the primary face is severely distorted toward a narrower elliptical shape for this rim.

  14. Intramolecular transposition by a synthetic IS50 (Tn5) derivative

    SciTech Connect

    Tomcsanyi, T.; Phadnis, S.H.; Berg, D.E. ); Berg, C.M. )

    1990-11-01

    We report the formation of deletions and inversions by intramolecular transposition of Tn5-derived mobile elements. The synthetic transposons used contained the IS50 O and I end segments and the transposase gene, a contraselectable gene encoding sucrose sensitivity (sacB), antibiotic resistance genes, and a plasmid replication origin. Both deletions and inversions were associated with loss of a 300-bp segment that is designated the vector because it is outside of the transposon. Deletions were severalfold more frequent than inversions, perhaps reflecting constraints on DNA twisting or abortive transposition. Restriction and DNA sequence analyses showed that both types of rearrangements extended from one transposon end to many different sites in target DNA. In the case of inversions, transposition generated 9-bp direct repeats of target sequences.

  15. 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.

  16. 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

  17. 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

  18. Deep evolutionary conservation of an intramolecular protein kinase activation mechanism.

    PubMed

    Han, Jingfen; Miranda-Saavedra, Diego; Luebbering, Nathan; Singh, Aman; Sibbet, Gary; Ferguson, Michael A J; Cleghon, Vaughn

    2012-01-01

    DYRK-family kinases employ an intramolecular mechanism to autophosphorylate a critical tyrosine residue in the activation loop. Once phosphorylated, DYRKs lose tyrosine kinase activity and function as serine/threonine kinases. DYRKs have been characterized in organisms from yeast to human; however, all entities belong to the Unikont supergroup, only one of five eukaryotic supergroups. To assess the evolutionary age and conservation of the DYRK intramolecular kinase-activation mechanism, we surveyed 21 genomes representing four of the five eukaryotic supergroups for the presence of DYRKs. We also analyzed the activation mechanism of the sole DYRK (class 2 DYRK) present in Trypanosoma brucei (TbDYRK2), a member of the excavate supergroup and separated from Drosophila by ∼850 million years. Bioinformatics showed the DYRKs clustering into five known subfamilies, class 1, class 2, Yaks, HIPKs and Prp4s. Only class 2 DYRKs were present in all four supergroups. These diverse class 2 DYRKs also exhibited conservation of N-terminal NAPA regions located outside of the kinase domain, and were shown to have an essential role in activation loop autophosphorylation of Drosophila DmDYRK2. Class 2 TbDYRK2 required the activation loop tyrosine conserved in other DYRKs, the NAPA regions were critical for this autophosphorylation event, and the NAPA-regions of Trypanosoma and human DYRK2 complemented autophosphorylation by the kinase domain of DmDYRK2 in trans. Finally, sequential deletion analysis was used to further define the minimal region required for trans-complementation. Our analysis provides strong evidence that class 2 DYRKs were present in the primordial or root eukaryote, and suggest this subgroup may be the oldest, founding member of the DYRK family. The conservation of activation loop autophosphorylation demonstrates that kinase self-activation mechanisms are also primitive.

  19. 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

  20. Solvent-controlled intramolecular [2 + 2] photocycloadditions of alpha-substituted enones.

    PubMed

    Ng, Stephanie M; Bader, Scott J; Snapper, Marc L

    2006-06-01

    The regio- and stereoselectivity of intramolecular [2 + 2] photocycloadditions of 2'-hydroxyenones are shown to be solvent-dependent. In the presence of aprotic solvents, 2'-hydroxyenones undergo photocycloadditions in a manner consistent with the presence of an intramolecular hydrogen bond between the carbonyl group and the tether's hydroxy functionality. In protic solvents, intermolecular interactions appear to disrupt the intramolecular hydrogen bond, providing products with complementary diastereoselectivity. If the facial accessibility of the alpha-tethered olefin is limited, the cycloadditions proceed to give head-to-tail or head-to-head regioisomers, depending on the nature of the solvent employed.

  1. Revising Intramolecular Photoinduced Electron Transfer (PET) from First-Principles.

    PubMed

    Escudero, Daniel

    2016-09-20

    Photoinduced electron transfer (PET) plays relevant roles in many areas of chemistry, including charge separation processes in photovoltaics, natural and artificial photosynthesis, and photoluminescence sensors and switches. As in many other photochemical scenarios, the structural and energetic factors play relevant roles in determining the rates and efficiencies of PET and its competitive photodeactivation processes. Particularly, in the field of fluorescent sensors and switches, intramolecular PET is believed (in many cases without compelling experimental proof) to be responsible of the quench of fluorescence. There is an increasing experimental interest in fluorophore's molecular design and on achieving optimal excitation/emission spectra, excitation coefficients, and fluorescence quantum yields (importantly for bioimaging purposes), but less efforts are devoted to fundamental mechanistic studies. In this Account, I revise the origins of the fluorescence quenching in some of these systems with state-of-the-art quantum chemical tools. These studies go beyond the common strategy of analyzing frontier orbital energy diagrams and performing PET thermodynamics calculations. Instead, the potential energy surfaces (PESs) of the lowest-lying excited states are explored with time-dependent density functional theory (TD-DFT) and complete active space self-consistent field (CASSCF) calculations and the radiative and nonradiative decay rates from the involved excited states are computed from first-principles using a thermal vibration correlation function formalism. With such a strategy, this work reveals the real origins of the fluorescence quenching, herein entitled as dark-state quenching. Dark states (those that do not absorb or emit light) are often elusive to experiments and thus, computational investigations can provide novel insights into the actual photodeactivation mechanisms. The success of the dark-state quenching mechanism is demonstrated for a wide variety of

  2. 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.}

  3. Revising Intramolecular Photoinduced Electron Transfer (PET) from First-Principles.

    PubMed

    Escudero, Daniel

    2016-09-20

    Photoinduced electron transfer (PET) plays relevant roles in many areas of chemistry, including charge separation processes in photovoltaics, natural and artificial photosynthesis, and photoluminescence sensors and switches. As in many other photochemical scenarios, the structural and energetic factors play relevant roles in determining the rates and efficiencies of PET and its competitive photodeactivation processes. Particularly, in the field of fluorescent sensors and switches, intramolecular PET is believed (in many cases without compelling experimental proof) to be responsible of the quench of fluorescence. There is an increasing experimental interest in fluorophore's molecular design and on achieving optimal excitation/emission spectra, excitation coefficients, and fluorescence quantum yields (importantly for bioimaging purposes), but less efforts are devoted to fundamental mechanistic studies. In this Account, I revise the origins of the fluorescence quenching in some of these systems with state-of-the-art quantum chemical tools. These studies go beyond the common strategy of analyzing frontier orbital energy diagrams and performing PET thermodynamics calculations. Instead, the potential energy surfaces (PESs) of the lowest-lying excited states are explored with time-dependent density functional theory (TD-DFT) and complete active space self-consistent field (CASSCF) calculations and the radiative and nonradiative decay rates from the involved excited states are computed from first-principles using a thermal vibration correlation function formalism. With such a strategy, this work reveals the real origins of the fluorescence quenching, herein entitled as dark-state quenching. Dark states (those that do not absorb or emit light) are often elusive to experiments and thus, computational investigations can provide novel insights into the actual photodeactivation mechanisms. The success of the dark-state quenching mechanism is demonstrated for a wide variety of

  4. Detection of a transient intramolecular hydrogen bond using (1)JNH scalar couplings.

    PubMed

    Xiang, ShengQi; Zweckstetter, Markus

    2014-06-01

    Hydrogen bonds are essential for the structure, stability and folding of proteins. The identification of intramolecular hydrogen bonds, however, is challenging, in particular in transiently folded states. Here we studied the presence of intramolecular hydrogen bonds in the folding nucleus of the coiled-coil structure of the GCN4 leucine zipper. Using one-bond (1)JNH spin-spin coupling constants and hydrogen/deuterium exchange, we demonstrate that a transient intramolecular hydrogen bond is present in the partially helical folding nucleus of GCN(16-31). The data demonstrate that (1)JNH couplings are a sensitive tool for the detection of transient intramolecular hydrogen bonds in challenging systems where the effective/useable protein concentration is low. This includes peptides at natural abundance but also uniformly labeled biomolecules that are limited to low concentrations because of precipitation or aggregation.

  5. Intramolecular charge transfer effects on 3-aminobenzoic acid

    NASA Astrophysics Data System (ADS)

    Stalin, T.; Rajendiran, N.

    2006-03-01

    Effect of solvents, buffer solutions of different pH and β-cyclodextrin on the absorption and fluorescence spectra of 3-aminobenzoic acid (3ABA) have been investigated. The solid inclusion complex of 3ABA with β-CD is discussed by UV-Vis, fluorimetry, semiempirical quantum calculations (AM1), FT-IR, 1H NMR and Scanning Electron Microscope (SEM). The thermodynamic parameters (Δ H, Δ G and Δ S) of the inclusion process are also determined. The experimental results indicated that the inclusion processes is an exothermic and spontaneous. The large Stokes shift emission in solvents with 3ABA are correlated with different solvent polarity scales suggest that, 3ABA molecule is more polar in the S 1 state. Solvent, β-CD studies and excited state dipole moment values confirms that the presence of intramolecular charge transfer (ICT) in 3ABA. Acidity constants for different prototropic equilibria of 3ABA in the S 0 and S 1 states are calculated. β-Cyclodextrin studies shows that 3ABA forms a 1:1 inclusion complex with β-CD. β-CD studies suggest COOH group present in non-polar part and amino group present in hydrophilic part of the β-CD cavity. A mechanism is proposed to explain the inclusion process.

  6. Tryptophan synthase: a multienzyme complex with an intramolecular tunnel.

    PubMed

    Miles, E W

    2001-01-01

    Tryptophan synthase is a classic enzyme that channels a metabolic intermediate, indole. The crystal structure of the tryptophan synthase alpha2beta2 complex from Salmonella typhimurium revealed for the first time the architecture of a multienzyme complex and the presence of an intramolecular tunnel. This remarkable hydrophobic tunnel provides a likely passageway for indole from the active site of the alpha subunit, where it is produced, to the active site of the beta subunit, where it reacts with L-serine to form L-tryptophan in a pyridoxal phosphate-dependent reaction. Rapid kinetic studies of the wild type enzyme and of channel-impaired mutant enzymes provide strong evidence for the proposed channeling mechanism. Structures of a series of enzyme-substrate intermediates at the alpha and beta active sites are elucidating enzyme mechanisms and dynamics. These structural results are providing a fascinating picture of loops opening and closing, of domain movements, and of conformational changes in the indole tunnel. Solution studies provide further evidence for ligand-induced conformational changes that send signals between the alpha and beta subunits. The combined results show that the switching of the enzyme between open and closed conformations couples the catalytic reactions at the alpha and beta active sites and prevents the escape of indole.

  7. 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.

  8. Thiol dependent intramolecular locking of Orai1 channels

    PubMed Central

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

    2016-01-01

    Store-operated Ca2+ 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 Ca2+ 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

  9. 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

  10. Intramolecular vibrational energy relaxation in nitrous acid (HONO)

    NASA Astrophysics Data System (ADS)

    Botan, Virgiliu; Hamm, Peter

    2008-10-01

    Intramolecular vibrational energy relaxation (IVR) in nitrous acid (HONO) is studied with the help of ultrafast two-color pump-probe spectroscopy. In a previous paper [V. Botan et al., J. Chem. Phys. 124, 234511 (2006)], it has been observed that trans-HONO cools through a cascade of overtones of one specific mode after pumping the OH stretch vibration. We had suggested that this cooling mode is the ONO bend vibration. Furthermore, molecules that have initially been excited by the OH stretch vibration of cis-HONO and then underwent isomerization follow the same relaxation pathway. In the present study, we extend the investigation of IVR of cis- and trans-HONO to the N=O stretch and HON bend spectral regions, finding further evidence that the bottleneck of trans cooling is indeed the ONO bend vibration. In combination with information on the anharmonic coupling constants of different modes, the energy relaxation dynamics preceding this cooling cascade can also be followed in unprecedented detail.

  11. Synthesis of fluorescent naphthoquinolizines via intramolecular Houben-Hoesch reaction.

    PubMed

    Stasyuk, Anton J; Smoleń, Sabina; Glodkowska-Mrowka, Eliza; Brutkowski, Wojciech; Cyrański, Michał K; Tkachenko, Nikolai; Gryko, Daniel T

    2015-03-01

    The repertoire of synthetic methods leading to aza-analogues of polycyclic aromatic heterocycles has been enlarged by the discovery of the rearrangement of 10-substituted benzo[h]quinolines into compounds bearing an azonia-pyrene moiety. Acid-mediated intramolecular cyclization of derivatives bearing -CH2 CN and -CH2 CO2 Et groups led to compounds bearing a 5-substituted benzo[de]pyrido[3,2,1-ij]quinolinium core. Advanced photophysical studies including time-correlated single photon counting (TCSPC) and transient absorption spectroscopy of 5-aminobenzo[de]pyrido[3,2,1-ij]quinolin-4-ium salt and 5H-benzo[de]pyrido[3,2,1-ij]quinolin-5-one showed their promising optical properties such as high fluorescence quantum yields (37-59%), which was almost independent of the solvent, and high tenability of the absorption band position upon changing the solvent. The benzo[de]pyrido[3,2,1-ij]quinolinium salt selectively stains nucleic acids (in the nucleus and mitochondria) in eukaryotic cells. PMID:25580599

  12. Metal complexes with varying intramolecular hydrogen bonding networks

    PubMed Central

    Lacy, David C.; Mukherjee, Jhumpa; Lucas, Robie L.; Day, Victor W.; Borovik, A.S.

    2013-01-01

    Alfred Werner described the attributes of the primary and secondary coordination spheres in his development of coordination chemistry. To examine the effects of the secondary coordination sphere on coordination chemistry, a series of tripodal ligands containing differing numbers of hydrogen bond (H-bond) donors were used to examine the effects of H-bonds on Fe(II), Mn(II)–acetato, and Mn(III)–OH complexes. The ligands containing varying numbers of urea and amidate donors allowed for systematic changes in the secondary coordination spheres of the complexes. Two of the Fe(II) complexes that were isolated as their Bu4N+ salts formed dimers in the solid-state as determined by X-ray diffraction methods, which correlates with the number of H-bonds present in the complexes (i.e., dimerization is favored as the number of H-bond donors increases). Electron paramagnetic resonance (EPR) studies suggested that the dimeric structures persist in acetonitrile. The Mn(II) complexes were all isolated as their acetato adducts. Furthermore, the synthesis of a rare Mn(III)–OH complex via dioxygen activation was achieved that contains a single intramolecular H-bond; its physical properties are discussed within the context of other Mn(III)–OH complexes. PMID:24904193

  13. 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

  14. 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.

  15. 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

  16. 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

  17. Intramolecular indicator displacement assay for anions: supramolecular sensor for glyphosate.

    PubMed

    Minami, Tsuyoshi; Liu, Yuanli; Akdeniz, Ali; Koutnik, Petr; Esipenko, Nina A; Nishiyabu, Ryuhei; Kubo, Yuji; Anzenbacher, Pavel

    2014-08-13

    One of the well-known strategies for anion sensing is an indicator (dye) displacement assay. However, the disadvantage of the dye displacement assays is the low sensitivity due to the excess of the dye used. To overcome this setback, we have developed an "Intramolecular Indicator Displacement Assay (IIDA)". The IIDAs comprise a receptor and a spacer with an attached anionic chromophore in a single-molecule assembly. In the resting state, the environment-sensitive anionic chromophore is bound by the receptor, while the anionic substrate competes for binding into the receptor. The photophysical properties of the dye exhibit change in fluorescence when displaced by anions, which results in cross-reactive response. To illustrate the concept, we have prepared IID sensors 1 and 2. Here, the characterization of sensors and microtiter arrays comprising the IIDA are reported. The microtiter array including IID sensors 1 and 2 is capable of recognizing biological phosphates in water. The utility of the IIDA approach is demonstrated on sensing of a phosphonate herbicide glyphosate and other biologically important anions such as pyrophosphate in the presence of interferent sodium chloride.

  18. 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

  19. Normal coordinate analysis of bilirubin vibrational spectra: Effects of intramolecular hydrogen bonding

    NASA Astrophysics Data System (ADS)

    Yang, Bijun; Taylor, Robert C.; Morris, Michael D.; Wang, Xiu-Zhen; Wu, Jin-guang; Yu, Bao-Zhu; Xu, Guang-xian; Soloway, Roger D.

    1993-11-01

    Normal coordinate analyses are presented for half-bilirubin molecules. Calculations for the AB pyrromethenone include intramolecular hydrogen bonds, while those for the CD chromophore exclude intramolecular hydrogen bonds. Valence force-field parameters have been optimized to correlate closely with the IR and Raman spectra of the target molecules. The results of the calculations are compared with the spectra of bilirubin IXa and various model compounds in the solid state and solution.

  20. 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.

  1. Accounting for intra-molecular vibrational modes in open quantum system description of molecular systems.

    PubMed

    Roden, Jan; Strunz, Walter T; Whaley, K Birgitta; Eisfeld, Alexander

    2012-11-28

    Electronic-vibrational dynamics in molecular systems that interact with an environment involve a large number of degrees of freedom and are therefore often described by means of open quantum system approaches. A popular approach is to include only the electronic degrees of freedom into the system part and to couple these to a non-Markovian bath of harmonic vibrational modes that is characterized by a spectral density. Since this bath represents both intra-molecular and external vibrations, it is important to understand how to construct a spectral density that accounts for intra-molecular vibrational modes that couple further to other modes. Here, we address this problem by explicitly incorporating an intra-molecular vibrational mode together with the electronic degrees of freedom into the system part and using the Fano theory for a resonance coupled to a continuum to derive an "effective" bath spectral density, which describes the contribution of intra-molecular modes. We compare this effective model for the intra-molecular mode with the method of pseudomodes, a widely used approach in simulation of non-Markovian dynamics. We clarify the difference between these two approaches and demonstrate that the respective resulting dynamics and optical spectra can be very different.

  2. Intramolecular aggregation and optical limiting properties of triazine-linked mono-, bis- and tris-phthalocyanines.

    PubMed

    Chen, Jun; Zhang, Tao; Wang, Shuangqing; Hu, Rui; Li, Shayu; Ma, Jin Shi; Yang, Guoqiang

    2015-10-01

    A series of triazine-linked mono-, bis- and tris-phthalocyanines are synthesized, intramolecular aggregation is found in bis- and tris-phthalocyanines via π-π stacking interaction. Theoretical and experimental studies reveal the formation of the intramolecular aggregation. The spectrographic, photophysical and nonlinear optical properties of these compounds are adjusted for the formation of the intramolecular aggregation. The bis-phthalocyanine dimer presents smaller fluorescence quantum yield, lower triplet formation yield and the triplet-minus-ground state extinction coefficient, which causes poorer optical limiting performance. It is interesting that the tris-phthalocyanine is composed of a mono-phthalocyanine part and a bis-phthalocyanine part, the optical limiting property of the tris-phthalocyanine is similar to that of mono-phthalocyanine.

  3. 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.

  4. Intermolecular and intramolecular contributions to the relaxation process in sorbitol and maltitol

    NASA Astrophysics Data System (ADS)

    Sixou, B.; Faivre, A.; David, L.; Vigier, G.

    Molecular mobility in sorbitol and maltitol is studied with spectroscopic techniques and molecular dynamics simulations in order to evaluate the relative contributions of the intermolecular and intramolecular interactions involved in the relaxation processes. The results of the molecular dynamics simulations performed on the polyols in the bulk or in vacuum compares well with the results of the analysis of the relaxation diagrams in the framework of the Perez et al . model. They both imply that the difference in the relative contributions of the intermolecular and intramolecular interactions associated with the different chemical architectures of the two polyols must be taken into account. The intermolecular interactions cannot be neglected and they are stronger in sorbitol than in maltitol in relation with the linear structure of this polyol. The intramolecular barrier, higher in the maltitol molecule with a more complex structure, could be at the origin of the higher junction temperature between the αand βrelaxation processes.

  5. Ratiometric fluorescent/colorimetric cyanide-selective sensor based on excited-state intramolecular charge transfer-excited-state intramolecular proton transfer switching.

    PubMed

    Lin, Wei-Chi; Fang, Sin-Kai; Hu, Jiun-Wei; Tsai, Hsing-Yang; Chen, Kew-Yu

    2014-05-20

    A novel salicylideneaniline-based fluorescent sensor, SB1, with a unique excited-state intramolecular charge transfer-excited-state intramolecular proton transfer (ESICT-ESIPT) coupled system was synthesized and demonstrated to fluorescently sense CN(-) with specific selectivity and high sensitivity in aqueous media based on ESICT-ESIPT switching. A large blue shift (96 nm) was also observed in the absorption spectra in response to CN(-). The bleaching of the color could be clearly observed by the naked eye. Moreover, SB1-based test strips were easily fabricated and low-cost, and could be used in practical and efficient CN(-) test kits. Density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations further support the cyanide-induced ESICT-ESIPT switching mechanism. The results provide the proof of concept that the colorimetric and ratiometric fluorescent cyanide-selective chemodosimeter can be created based on an ESICT-ESIPT coupled system. PMID:24809868

  6. 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

  7. 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

  8. 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.

  9. 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

  10. Enantioselective desymmetrization of cyclohexadienones via an intramolecular Rauhut-Currier reaction of allenoates

    NASA Astrophysics Data System (ADS)

    Yao, Weijun; Dou, Xiaowei; Wen, Shan; Wu, Ji'en; Vittal, Jagadese J.; Lu, Yixin

    2016-10-01

    The Rauhut-Currier (RC) reaction represents an efficient method for the construction of carbon-carbon bond in organic synthesis. However, the RC reactions involving allenoate substrates are very rare, and in particular, asymmetric intramolecular RC reaction of allenoates is yet to be discovered. Here, we show that the intramolecular RC reaction proceeds smoothly in the presence of 1 mol% β-ICD, and bicyclic lactones are obtained in high yields and with excellent enantiomeric excesses. With the employment of γ-substituted allenoates as racemic precursors, a novel dynamic kinetic resolution of allenes via RC reaction is observed, which allows for facile synthesis of highly enantiomerically enriched allenes.

  11. 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.

  12. 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

  13. An insight into the Lewis acid-catalyzed intramolecular aminocyanation and oxycyanation of alkenes: a concerted or stepwise mechanism.

    PubMed

    Zhao, Jiyang; Wang, Guoqiang; Li, Shuhua

    2015-10-28

    Density functional theory investigations reveal that the intramolecular additions of N-CN bonds to alkenes proceed in a novel asynchronous and concerted mechanism, while the intramolecular addition of O-CN bonds to alkenes may occur by both concerted and stepwise pathways.

  14. Organocatalytic Michael addition/intramolecular Julia-Kocienski olefination for the preparation of nitrocyclohexenes.

    PubMed

    Rodrigo, Eduardo; García Ruano, José Luis; Cid, M Belén

    2013-11-01

    An asymmetric organocatalytic [3 + 3] annulation strategy based on a Michael addition/intramolecular Julia-Kocienski olefination sequence has been developed for the synthesis of 4-substituted-5-nitrocyclohex-1-ene compounds. The strategy is an alternative to the direct reluctant enantioselective Diels-Alder approach. The potential of the methodology has been demonstrated with a concise enantioselective formal synthesis of trandolapril.

  15. Intramolecular benzyl protection delivery: a practical synthesis of DMDP and DGDP from D-fructose.

    PubMed

    García-Moreno, M Isabel; Aguilar, Matilde; Ortiz Mellet, Carmen; García Fernández, José M

    2006-01-19

    [reaction: see text] A two-step protection of 1,2-diols as the corresponding o-xylylene cyclic ethers, involving an intramolecular ring-closing O-benzylation reaction, has been developed to overcome the problems associated to regioselective benzylation reactions. The strategy has been applied to the high-yielding synthesis of the pyrrolidine glycosidase inhibitors DMDP and DGDP.

  16. 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

  17. Remarkable stereoselectivity in intramolecular Borono-Mannich reactions: synthesis of conduramines.

    PubMed

    Norsikian, Stéphanie; Soulé, Jean-François; Cannillo, Alexandre; Guillot, Régis; Dau, Marie-Elise Tran Huu; Beau, Jean-Marie

    2012-01-20

    An unprecedented intramolecular Petasis condensation provides a novel approach to biologically important conduramines. The compounds are produced with an exclusive anti stereoselectivity for the newly created β-amino alcohol motif. The stereochemical outcome of the reaction is opposite to the one usually observed in the intermolecular reaction.

  18. Distance dependence in photoinduced intramolecular electron transfer. Additional remarks and calculations

    NASA Astrophysics Data System (ADS)

    Larsson, Sven; Volosov, Andrey

    1987-12-01

    Rate constants for photoinduced intramolecular electron transfer are calculated for four of the molecules studied by Hush et al. The electronic factor is obtained in quantum chemical calculations using the CNDO/S method. The results agree reasonably well with experiments for the forward reaction. Possible reasons for the disagreement for the charge recombination process are offered.

  19. 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

  20. Copper(II) Carboxylate Promoted Intramolecular Carboamination of Alkenes for the Synthesis of Polycyclic Lactams

    PubMed Central

    Fuller, Peter H.; Chemler, Sherry R.

    2008-01-01

    The copper(II) carboxylate promoted intramolecular carboamination reactions of variously substituted γ-alkenyl amides have been investigated. These oxidative cyclization reactions efficiently provide polycyclic lactams, useful intermediates in nitrogen heterocycle synthesis, in good to excellent yields. The efficiency of the carboamination process is dependent upon the structure of the amide backbone as well as the nitrogen substituent. PMID:18044907

  1. A novel chiral yttrium complex with a tridentate linked amido-indenyl ligand for intramolecular hydroamination.

    PubMed

    Chai, Zhuo; Hua, Dezhi; Li, Kui; Chu, Jiang; Yang, Gaosheng

    2014-01-01

    A new chiral silicon-linked tridentate amido-indenyl ligand was developed from indene and enantiopure 1,2-cyclohexanediamine. Its yttrium complex was synthesized, characterized and applied to efficiently catalyze the intramolecular hydroamination of non-activated olefins with up to 97% ee.

  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. Intramolecular Schmidt reaction involving primary azidoalcohols under nonacidic conditions: synthesis of indolizidine (-)-167B.

    PubMed

    Kapat, Ajoy; Nyfeler, Erich; Giuffredi, Guy T; Renaud, Philippe

    2009-12-16

    A powerful intramolecular Schmidt reaction starting from primary azidoalcohols is reported. This approach involves a nonacidic activation of the alcohol via triflation. The synthetic potential offered by the mild reaction conditions is demonstrated by a highly selective synthesis of (-)-indolizidine 167B. PMID:19928759

  4. 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…

  5. 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…

  6. The first porphyrin-subphthalocyaninatoboron(iii)-fused hybrid with unique conformation and intramolecular charge transfer behavior.

    PubMed

    Zhang, Yuehong; Oh, Juwon; Wang, Kang; Shin, Dongju; Zhan, Xiaopeng; Zheng, Yingting; Kim, Dongho; Jiang, Jianzhuang

    2016-08-18

    Porphyrin and subphthalocyaninatoboron(iii) chromophores have been fused through a quinoxaline moiety, resulting in the first porphyrin-subphthalocyaninatoboron(iii)-fused hybrid with intramolecular charge transfer from tetrapyrrole/tripyrrole chromophores to the quinoxaline moiety. The unique plane-bowl molecular structure of this hybrid was revealed based on single crystal X-ray diffraction analysis for the first time. PMID:27492136

  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. Direct inter- and intramolecular addition of amides to arylalkenes promoted by KOt-Bu/DMF.

    PubMed

    Wang, Wei-juan; Zhao, Xu; Tong, Lang; Chen, Jia-hua; Zhang, Xue-jing; Yan, Ming

    2014-09-19

    Direct addition of tetrahydroisoquinoline derived amides to arylalkenes has been achieved in the presence of KOt-Bu/DMF. Both intermolecular and intramolecular reactions could occur in good yields. α-Amido alkyl radicals are proposed to be generated under the reaction conditions. The reaction is efficient for the synthesis of seven-membered nitrogen heterocycles. A homoprotoberberine was prepared conveniently via this method.

  9. 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

  10. 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

  11. 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.

  12. Using intramolecular disulfide bonds in tau protein to deduce structural features of aggregation-resistant conformations.

    PubMed

    Walker, Sophie; Ullman, Orly; Stultz, Collin M

    2012-03-16

    Because tau aggregation likely plays a role in a number of neurodegenerative diseases, understanding the processes that affect tau aggregation is of considerable importance. One factor that has been shown to influence the aggregation propensity is the oxidation state of the protein itself. Tau protein, which contains two naturally occurring cysteine residues, can form both intermolecular disulfide bonds and intramolecular disulfide bonds. Several studies suggest that intermolecular disulfide bonds can promote tau aggregation in vitro. By contrast, although there are data to suggest that intramolecular disulfide bond formation retards tau aggregation in vitro, the precise mechanism underlying this observation remains unclear. While it has been hypothesized that a single intramolecular disulfide bond in tau leads to compact conformations that cannot form extended structure consistent with tau fibrils, there are few data to support this conjecture. In the present study we generate oxidized forms of the truncation mutant, K18, which contains all four microtubule binding repeats, and isolate the monomeric fraction, which corresponds to K18 monomers that have a single intramolecular disulfide bond. We study the aggregation propensity of the oxidized monomeric fraction and relate these data to an atomistic model of the K18 unfolded ensemble. Our results argue that the main effect of intramolecular disulfide bond formation is to preferentially stabilize conformers within the unfolded ensemble that place the aggregation-prone tau subsequences, PHF6* and PHF6, in conformations that are inconsistent with the formation of cross-β-structure. These data further our understanding of the precise structural features that retard tau aggregation.

  13. 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.

  14. [Analyses of biogenic related compounds based on intramolecular excimer-forming fluorescence derivatization].

    PubMed

    Yoshida, Hideyuki

    2003-08-01

    A highly selective and sensitive method based on a novel concept is introduced for the assay of biological substances. This method is based on an intramolecular excimer-forming fluorescence derivatization with a pyrene reagent, followed by reverse-phase HPLC. Polyamines, polyphenols, and dicarboxylic acids, which have two or more reactive functional groups in a molecule, were converted to the corresponding polypyrene-labeled derivatives by reaction with the appropriate pyrene reagent. The derivatives exhibited intramolecular excimer fluorescence (440-520 nm), which can clearly be discriminated from the monomer (normal) fluorescence (360-420 nm) emitted by pyrene reagents and monopyrene-labeled derivatives of monofunctional compounds. With excimer fluorescence detection, highly selective and sensitive determination of polyamines, polyphenols, and dicarboxylic acids can be achieved. Furthermore, the methods were successfully applied to the determination of various biological and environmental substances in real samples, which require only a small amount of sample and simple pretreatment.

  15. 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.

  16. Enantioselective desymmetrization of cyclohexadienones via an intramolecular Rauhut–Currier reaction of allenoates

    PubMed Central

    Yao, Weijun; Dou, Xiaowei; Wen, Shan; Wu, Ji'en; Vittal, Jagadese J.; Lu, Yixin

    2016-01-01

    The Rauhut–Currier (RC) reaction represents an efficient method for the construction of carbon–carbon bond in organic synthesis. However, the RC reactions involving allenoate substrates are very rare, and in particular, asymmetric intramolecular RC reaction of allenoates is yet to be discovered. Here, we show that the intramolecular RC reaction proceeds smoothly in the presence of 1 mol% β-ICD, and bicyclic lactones are obtained in high yields and with excellent enantiomeric excesses. With the employment of γ-substituted allenoates as racemic precursors, a novel dynamic kinetic resolution of allenes via RC reaction is observed, which allows for facile synthesis of highly enantiomerically enriched allenes. PMID:27698487

  17. Acidic C-H Bond as a Proton Donor in Excited State Intramolecular Proton Transfer Reactions.

    PubMed

    Stasyuk, Anton J; Cyrański, Michał K; Gryko, Daniel T; Solà, Miquel

    2015-03-10

    An unprecedented type of excited state intramolecular proton transfer in a series of benzo[h]quinoline (BHQ) derivatives substituted at position 10 with strong CH acid character is described using density functional theory/time-dependent density functional theory computational approaches with a hybrid functional and the 6-311++G(d,p) triple-ξ quality basis set. Our results show that for 10-malononitrile-substituted BHQ (2CNBHQ) the excited state intramolecular proton transfer C-H···N reaction is a barrierless process. Calculations also reveal that the reaction profiles of the 4-amino-substituted 2CNBHQ show a large dependence on the polarity of the environment. PMID:26579756

  18. 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

  19. Isotope effects on chemical shifts in the study of intramolecular hydrogen bonds.

    PubMed

    Hansen, Poul Erik

    2015-01-30

    The paper deals with the use of isotope effects on chemical shifts in characterizing intramolecular hydrogen bonds. Both so-called resonance-assisted (RAHB) and non-RAHB systems are treated. The importance of RAHB will be discussed. Another very important issue is the borderline between "static" and tautomeric systems. Isotope effects on chemical shifts are particularly useful in such studies. All kinds of intramolecular hydrogen bonded systems will be treated, typical hydrogen bond donors: OH, NH, SH and NH+, typical acceptors C=O, C=N, C=S C=N-. The paper will be deal with both secondary and primary isotope effects on chemical shifts. These two types of isotope effects monitor the same hydrogen bond, but from different angles.

  20. 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.

  1. Vibrational assignment, structure and intramolecular hydrogen bond of 4-methylamino-3-penten-2-one.

    PubMed

    Raissi, Heidar; Moshfeghi, Effat; Farzad, Farzaneh

    2005-12-01

    The molecular structure, intramolecular hydrogen and vibrational frequencies of 4-methylamino-3-penten-2-one were investigated by a series of density functional theoretical (DFT) calculations and ab initio calculation at the post-Hartree-Fock (MP2) level. Fourier transform infrared and Fourier transform Raman spectra of this compound and its deuterated analogue were clearly assigned. The calculated geometrical parameters show a strong intramolecular hydrogen bond with a N...O distance of 2.622-2.670 A. This bond length is about 0.02 A shorter than that in its parent, 4-amino-3- penten-2-one which is in agreement with spectroscopic results. Furthermore, the conformations of methyl groups with respect to the plane of the molecule and with respect to each other were investigated.

  2. 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

  3. 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.

  4. 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.

  5. Intramolecular Charge-Transfer Interaction of Donor-Acceptor-Donor Arrays Based on Anthracene Bisimide.

    PubMed

    Iwanaga, Tetsuo; Ogawa, Marina; Yamauchi, Tomokazu; Toyota, Shinji

    2016-05-20

    We designed anthracene bisimide (ABI) derivatives having two triphenylamine (TPA) groups as donor units at the 9,10-positions to form a novel π-conjugated donor-acceptor system. These compounds and their analogues with ethynylene linkers were synthesized by Suzuki-Miyaura and Sonogashira coupling reactions, respectively. In UV-vis spectra, the linker-free derivatives showed broad absorption bands arising from intramolecular charge-transfer interactions. Introducing ethynylene linkers resulted in a considerable red shift of the absorption bands. In fluorescence spectra, the ethynylene derivatives showed intense emission bands at 600-650 nm. Their photophysical and electrochemical properties were compared with those of the corresponding mono TPA derivatives on the basis of theoretical calculations and cyclic voltammetry to evaluate the intramolecular electronic interactions between the donor and acceptor units.

  6. New domino transposition/intramolecular Diels-Alder reaction in monocyclic allenols: a general strategy for tricyclic compounds.

    PubMed

    Alcaide, Benito; Almendros, Pedro; Aragoncillo, Cristina; Redondo, María C

    2002-07-21

    A novel and direct synthetic strategy to prepare fused tricycles has been developed from monocyclic allenols, masked functionalized dienes, which underwent a domino allenol transposition/intramolecular Diels-Alder reaction.

  7. 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.

  8. Synthesis of Fused Polycyclic Indoles by Brønsted Acid-Catalyzed Intramolecular Alkylation of Indoles with Alcohols.

    PubMed

    Suárez, Anisley; Gohain, Mukut; Fernández-Rodríguez, Manuel A; Sanz, Roberto

    2015-10-16

    An efficient methodology for the synthesis of a series of new fused polyclyclic indoles has been developed by Brønsted acid-catalyzed intramolecular Friedel-Crafts reactions of properly designed indolyl alcohols. PMID:26418556

  9. Rh(I)-catalyzed intramolecular [3 + 2] cycloaddition reactions of 1-ene-, 1-yne- and 1-allene-vinylcyclopropanes.

    PubMed

    Jiao, Lei; Lin, Mu; Yu, Zhi-Xiang

    2010-02-21

    New Rh(I)-catalyzed intramolecular [3 + 2] cycloaddition reactions of 1-ene-, 1-yne and 1-allene-vinylcyclopropanes have been developed, affording an efficient and versatile synthesis of cyclopentane- and cyclopentene-embedded bicyclic structures.

  10. Intramolecular addition of diarylmethanols to imines promoted by KOt-Bu/DMF: a new synthetic approach to indole derivatives.

    PubMed

    Chen, Jia-Hua; Chen, Zi-Cong; Zhao, Hong; Zhang, Ting; Wang, Wei-Juan; Zou, Yong; Zhang, Xue-Jing; Yan, Ming

    2016-04-26

    KOt-Bu/DMF promoted intramolecular addition of diarylmethanols to imines was developed. A series of 2,3-disubstituted indoles was obtained in good yields. A reaction mechanism of radical cyclization and subsequent dehydration is proposed. PMID:27055383

  11. 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

  12. Highly efficient route to functionalized tetrahydrocarbazoles using a tandem cross-metathesis/intramolecular-hydroarylation sequence.

    PubMed

    An, Xiao-Lei; Chen, Jia-Rong; Li, Chang-Feng; Zhang, Fu-Gen; Zou, You-Quan; Guo, Ying-Cen; Xiao, Wen-Jing

    2010-10-01

    The scope of the novel ruthenium-catalyzed tandem cross-metathesis/intramolecular-hydroarylation sequence is described. This methodology offers a practical and efficient synthesis of structurally diverse and complex tetrahydrocarbazoles in good to excellent yields (up to 98%). Moreover, preliminary efforts towards the development of an enantioselective version of the current process by sequential catalysis with ruthenium complex and chiral amine are presented, with high yields and enantioselectivities (up to 88% yield and 91% ee).

  13. 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

  14. Thermally-Induced Substrate Release Via Intramolecular Cyclizations of Amino Esters and Amino Carbonates

    PubMed Central

    Knipp, Ralph J.; Estrada, Rosendo; Sethu, Palaniappan; Nantz, Michael H.

    2014-01-01

    The relative cleavage of an alcohol from a panel of amino esters and amino carbonates via intramolecular cyclization was examined as a mechanism for substrate release. Thermal stability at 37 °C was observed only for the 7-membered ring progenitors. Applicability of the approach was illustrated by δ-lactam formation within a poly(dimethylsiloxane) microchannel for release of a captured fluorescent probe. PMID:25061237

  15. 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.

  16. Intramolecular vibrational relaxation in a triatomic van der Waals molecule: ArCl2

    NASA Astrophysics Data System (ADS)

    Halberstadt, Nadine; Beswick, Alberto; Roncero, Octavio; Janda, Kenneth C.

    1992-02-01

    Exact quantum mechanical calculations of the vibrational predissociation of ArCl2 are reported. The results confirm the hypothesis that Δv=-2 dissociation of the B state, v'=10 level occurs by preliminary coupling to the Δv=-1 manifold followed by coupling to the Δv=-2 continuum. The intensity borrowing due to the coupling is consistent with intramolecular vibrational relaxation (IVR) in the sparse limit, ρV≤1.

  17. 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

  18. Coupling of electrons and intramolecular vibrations in TTF-TCNQ (tetrathiafulvalene-tetracyanoquinodimethane)

    NASA Astrophysics Data System (ADS)

    Etemad, Shahab

    1981-11-01

    We report experimental evidence for electron-intramolecular vibration coupling in TTF-TCNQ (tetrathiafulvalene-tetracyanoquinodimethane). Linear coupling of totally symmetric vibrations of ag modes to the oscillation in the phase of the charge-density waves gives rise to a set of IR-(infrared-) active modes which grow in intensity with the onset of the Peierls transition. Our experimental estimates of electron-intramolecular coupling constants of the TCNQ molecule are in good agreement with previous values. Moreover, the experimentally determined total electron-intramolecular coupling constant is λ≃0.35 for TCNQ stacks in TTF-TCNQ. These results indicate that the Peierls distorted state is predominantly stabilized by coupling of the unpaired electrons to the intramolecular vibrations. With the onset of Peierls transition, the two IR-active modes of CN-stretching vibration show a splitting due to a shift in frequency of the mode with the dipole component parallel to the crystallographic b and c axes. The splitting is also seen in the selenium analog TSeF-TCNQ and is consistent with the x-ray diffuse scattering result that the Peierls distortion is due to a rigid molecular translation in the bc plane. The temperature dependence of both effects show the presence of the sizable amplitude of the fluctuating charge-density waves in the temperature range 53[Bull. Am. Phys. Soc. 23, 381 (1978)].

  19. Intramolecular [4 + 2] trapping of a hexadehydro-Diels-Alder (HDDA) benzyne by tethered arenes.

    PubMed

    Pogula, Vedamayee D; Wang, Tao; Hoye, Thomas R

    2015-02-20

    We report here the efficient, intramolecular trapping in a Diels-Alder (DA) sense of thermally generated benzynes by one of two pendant arene rings. A more electron-rich ring (p-methoxyphenyl) reacted substantially faster than a simple phenyl ring, which was, in turn, slightly more reactive vs a 4-carbomethoxyphenyl ring. Photoinduced di-π-methane rearrangement of the initial DA adducts gave rise to unusual isomeric polycyclic adducts.

  20. Copper-catalysed intramolecular O-arylation: a simple and efficient method for benzoxazole synthesis.

    PubMed

    Wu, Fengtian; Zhang, Jie; Wei, Qianbing; Liu, Ping; Xie, Jianwei; Jiang, Haojie; Dai, Bin

    2014-12-21

    A wide range of 2-substituted benzoxazoles can be efficiently synthesized from N-(2-iodo-/bromo-phenyl)benzamides, and even the less reactive N-(2-chlorophenyl)benzamides, via Cu-catalysed intramolecular coupling cyclization reactions using methyl 2-methoxybenzoate as the ligand under mild reaction conditions. In addition, the benzoxazoles can be easily prepared from the primary amides coupling with o-dihalobenzenes in a single step.

  1. 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

  2. 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.

  3. 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.

  4. On the Intramolecular Hydrogen Bond in Solution: Car-Parrinello and Path Integral Molecular Dynamics Perspective.

    PubMed

    Dopieralski, Przemyslaw; Perrin, Charles L; Latajka, Zdzislaw

    2011-11-01

    The issue of the symmetry of short, low-barrier hydrogen bonds in solution is addressed here with advanced ab initio simulations of a hydrogen maleate anion in different environments, starting with the isolated anion, going through two crystal structures (sodium and potassium salts), then to an aqueous solution, and finally in the presence of counterions. By Car-Parrinello and path integral molecular dynamics simulations, it is demonstrated that the position of the proton in the intramolecular hydrogen bond of an aqueous hydrogen maleate anion is entirely related to the solvation pattern around the oxygen atoms of the intramolecular hydrogen bond. In particular, this anion has an asymmetric hydrogen bond, with the proton always located on the oxygen atom that is less solvated, owing to the instantaneous solvation environment. Simulations of water solutions of hydrogen maleate ion with two different counterions, K(+) and Na(+), surprisingly show that the intramolecular hydrogen-bond potential in the case of the Na(+) salt is always asymmetric, regardless of the hydrogen bonds to water, whereas for the K(+) salt, the potential for H motion depends on the location of the K(+). It is proposed that repulsion by the larger and more hydrated K(+) is weaker than that by Na(+) and competitive with solvation by water. PMID:26598249

  5. Theoretical study on the reactive sites and intramolecular interactions in taxol and its four analogues

    NASA Astrophysics Data System (ADS)

    Zhou, Hongwei; Zhang, Zhiqiang; Cheung, Hon-Yeung

    A density-functional study of the paclitaxel (Taxol) molecule and its four analogues has been performed. The theory of Bader's atoms in molecules (AIM) was applied to examine the electronic structure of these molecules at their ground state. Topological analysis reveals that the esterification of hydroxyl group attached to the oxetane ring results in great change of conformation of the taxane ring, and thus is responsible for bioactivity of the oxetane oxygen atom. It was found that there exists some intramolecular interactions in the molecule, including normal hydrogen bonds (HBs) and double HBs. Visualization of the molecule shows that the central bodies (the four fused rings) of the molecules are wrapped by the intramolecular interactions. It is supposed that these intramolecular interactions lower the aqueous solubility and protect the flexible oxetane ring, which is regarded as the dominating bioactivity site of the drug, from being opened. Our results provide an extended and consistent set of data to gauge classical force fields in view of the atomistic investigations of the interaction of the bioactive molecules.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. Intramolecular RNA replicase: Possibly the first self-replicating molecule in the RNA world

    NASA Astrophysics Data System (ADS)

    Ma, Wentao; Yu, Chunwu

    2006-08-01

    Although there is more and more evidence suggested the existence of an RNA World during the origin of life, the scenario concerning the origin of the RNA World remains blurry. Usually it is speculated that it originated from a prebiotic nucleotide pool, during which a self-replicating RNA synthesis ribozyme may have emerged as the first ribozyme the RNA replicase. However, there is yet no ersuasive supposition for the mechanism for the self-favouring feature of the replicase, thus the speculation remains unconvincing. Here we suggest that intramolecular catalysis is a possible solution. Two RNA synthesis ribozymes may be integrated into one RNA molecule, as two functional domains which could catalyze the copy of each other. Thus the RNA molecule could self-replicate and be referred to as “intramolecular replicase“ here. Computational simulation to get insight into the dynamic mechanism of emergence of the intramolecular replicase from a nucleotide pool is valuable and would be included in a following work of our group.

  11. 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.

  12. 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.

  13. Ladderlike oligomers; intramolecular hydrogen bonding, push-pull character, and electron affinity.

    PubMed

    Pieterse, K; Vekemans, J A; Kooijman, H; Spek, A L; Meijer, E W

    2000-12-15

    Symmetrical 2,5-bis(2-aminophenyl)pyrazines have been synthesized by application of the Stille coupling strategy. These cotrimers feature three important properties, namely strong intramolecular hydrogen bonding, push-pull character, and high electron affinity. The presence of intramolecular hydrogen bonds has been confirmed by 1H NMR, IR spectroscopy, and single-crystal X-ray diffraction. The hydrogen bond strength can be increased by substituting the amino groups with stronger electron-withdrawing functionalities. Despite the anticipated enhanced pi-conjugation through planarization, a hypsochromic shift was observed in the UV/Vis spectra, explained by a decrease in push-pull character. The electron affinity of the cotrimers was deduced from the first reduction potentials measured by cyclic voltammetry and is related to the electron-withdrawing character of the amino substituents. The results obtained have been compared with those of the corresponding 4-aminophenyl analogues and show that intramolecular hydrogen bonds can be used to design polymers with enhanced pi conjugation as well as a high electron affinity.

  14. 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

  15. Intramolecular vibrational energy redistribution in bridged azulene-anthracene compounds: ballistic energy transport through molecular chains.

    PubMed

    Schwarzer, D; Kutne, P; Schröder, C; Troe, J

    2004-07-22

    Intramolecular vibrational energy flow in excited bridged azulene-anthracene compounds is investigated by time-resolved pump-probe laser spectroscopy. The bridges consist of molecular chains and are of the type (CH(2))(m) with m up to 6 as well as (CH(2)OCH(2))(n) (n=1,2) and CH(2)SCH(2). After light absorption into the azulene S(1) band and subsequent fast internal conversion, excited molecules are formed where the vibrational energy is localized at the azulene side. The vibrational energy transfer through the molecular bridge to the anthracene side and, finally, to the surrounding medium is followed by probing the red edge of the azulene S(3) absorption band at 300 nm and/or the anthracene S(1) absorption band at 400 nm. In order to separate the time scales for intramolecular and intermolecular energy transfer, most of the experiments were performed in supercritical xenon where vibrational energy transfer to the bath is comparably slow. The intramolecular equilibration proceeds in two steps. About 15%-20% of the excitation energy leaves the azulene side within a short period of 300 fs. This component accompanies the intramolecular vibrational energy redistribution (IVR) within the azulene chromophore and it is caused by dephasing of normal modes contributing to the initial local excitation of the azulene side and extending over large parts of the molecule. Later, IVR in the whole molecule takes place transferring vibrational energy from the azulene through the bridge to the anthracene side and thereby leading to microcanonical equilibrium. The corresponding time constants tau(IVR) for short bridges increase with the chain length. For longer bridges consisting of more than three elements, however, tau(IVR) is constant at around 4-5 ps. Comparison with molecular dynamics simulations suggests that the coupling of these chains to the two chromophores limits the rate of intramolecular vibrational energy transfer. Inside the bridges the energy transport is essentially

  16. 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

  17. Effect of α- and β-cyclodextrins on the intramolecular charge transfer and intramolecular proton transfer fluorescence of methyl o-hydroxy p-dimethylaminobenzoate

    NASA Astrophysics Data System (ADS)

    Józefowicz, Marek

    The influence of α- and β-cyclodextrins on the spectral characteristics of methyl o-hydroxy p-dimethylaminobenzoate has been studied using steady-state and time-resolved spectroscopic technique. The stoichiometries and equilibrium constants of the solute molecule-cyclodextrin inclusion complexes have been determined by the steady-state fluorescence measurements. Nonlinear least-squares regression analysis indicates that both 1:1 and 1:2 inclusion complexes were formed between studied compound and α- and β-cyclodextrins. The contribution of the fluorophore in free, 1:1, and 1:2 complexes was calculated for a particular concentration of α- and β-CD. Additionally, the location of the fluorophore inside the cavity was reported, with regard to the intra- and intermolecular proton transfer and intramolecular charge transfer processes.

  18. Temporary silicon connection strategies in intramolecular allylation of aldehydes with allylsilanes.

    PubMed

    Beignet, Julien; Jervis, Peter J; Cox, Liam R

    2008-07-18

    Three gamma-(amino)silyl-substituted allylsilanes 14a-c have been prepared in three steps from the corresponding dialkyldichlorosilane. The aminosilyl group has been used to link this allylsilane nucleophile to a series of beta-hydroxy aldehydes through a silyl ether temporary connection. The size of the alkyl substituents at the silyl ether tether governs the outcome of the reaction on exposure to acid. Thus, treatment of aldehyde (E)-9aa, which contains a dimethylsilyl ether connection between the aldehyde and allylsilane, with a range of Lewis and Brønsted acid activators provides an (E)-diene product. The mechanism of formation of this undesired product is discussed. Systems containing a sterically more bulky diethylsilyl ether connection react differently: thus in the presence of TMSOTf and a Brønsted acid scavenger, intramolecular allylation proceeds smoothly to provide two out of the possible four diastereoisomeric oxasilacycles, 23 (major) and 21 (minor). A diene product again accounts for the remaining mass balance in the reaction. This side product can be completely suppressed by using a sterically even more bulky diisopropylsilyl ether connection in the cyclization precursor, although this is now at the expense of a slight erosion in the 1,3-stereoinduction in the allylation products. The sense of 1,3-stereoinduction observed in these intramolecular allylations has been rationalized by using an electrostatic argument, which can also explain the stereochemical outcome of a number of related reactions. Levels of 1,4-stereoinduction in the intramolecular allylation are more modest but can be significantly improved in some cases by using a tethered (Z)-allylsilane in place of its (E)-stereoisomer. Oxidation of the major diastereoisomeric allylation product 23 under Tamao-Kumada conditions provides an entry into stereodefined 1,2-anti-2,4-syn triols 28.

  19. 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.

  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. 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.

  2. 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

  3. Ruthenium-Catalyzed Intramolecular Hydroarylation of Arenes and Mechanistic Study: Synthesis of Dihydrobenzofurans, Indolines, and Chromans.

    PubMed

    Rit, Raja K; Ghosh, Koushik; Mandal, Rajib; Sahoo, Akhila K

    2016-09-16

    A ruthenium-catalyzed, amide-directed intramolecular hydroarylation of alkene-tethered benzamide derivatives is discussed. This method proficiently constructs dihydrobenzofuran, indoline, and chroman skeletons of biological significance in good to excellent yields; the overall process is atom-economical and step-efficient. The reaction exhibits broad scope, tolerating common functional groups, labile protecting units, and heteroaryl motifs. The use of a catalytic amount of base suffices the need. Deuterium scrambling and kinetic studies offer valuable facts for understanding the reaction mechanism.

  4. Intramolecular recombination between partially homologous sequences in Escherichia coli and Xenopus laevis oocytes.

    PubMed Central

    Abastado, J P; Darche, S; Godeau, F; Cami, B; Kourilsky, P

    1987-01-01

    We describe a system to analyze the individual contribution of a single physical DNA end on intramolecular recombination between partially homologous sequences. We took advantage of this partial sequence divergence to measure the distance separating the DNA end from the final recombination event. We show that a single physical DNA end stimulates recombination when located in a region of homology. Recombination frequency decreases gradually with the distance from the DNA end. A recombinational hot spot is found at the end of the region of homology. A large insertion of unrelated DNA interferes asymmetrically with this process, suggesting that a recombinogenic signal propagates along the region of homology. Images PMID:3306681

  5. Ruthenium-Catalyzed Intramolecular Hydroarylation of Arenes and Mechanistic Study: Synthesis of Dihydrobenzofurans, Indolines, and Chromans.

    PubMed

    Rit, Raja K; Ghosh, Koushik; Mandal, Rajib; Sahoo, Akhila K

    2016-09-16

    A ruthenium-catalyzed, amide-directed intramolecular hydroarylation of alkene-tethered benzamide derivatives is discussed. This method proficiently constructs dihydrobenzofuran, indoline, and chroman skeletons of biological significance in good to excellent yields; the overall process is atom-economical and step-efficient. The reaction exhibits broad scope, tolerating common functional groups, labile protecting units, and heteroaryl motifs. The use of a catalytic amount of base suffices the need. Deuterium scrambling and kinetic studies offer valuable facts for understanding the reaction mechanism. PMID:27548436

  6. 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

  7. 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.

  8. Intramolecular Dehydro-Diels–Alder Reaction Affords Selective Entry to Arylnaphthalene or Aryldihydronaphthalene Lignans

    PubMed Central

    2015-01-01

    Intramolecular dehydro-Diels–Alder (DDA) reactions are performed affording arylnaphthalene or aryldihydronaphthalene lactones selectively as determined by choice of reaction solvent. This constitutes the first report of an entirely selective formation of arylnaphthalene lactones utilizing DDA reactions of styrene-ynes. The synthetic utility of the DDA reaction is demonstrated by the synthesis of taiwanin C, retrohelioxanthin, justicidin B, isojusticidin B, and their dihydronaphthalene derivatives. Computational methods for chemical shift assignment are presented that allow for regioisomeric lignans to be distinguished. PMID:25061845

  9. 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

  10. 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.

  11. Molecular orbital assistance in the design of intramolecular and photoinduced electron transfer systems

    NASA Astrophysics Data System (ADS)

    Petsalakis, Ioannis D.; Theodorakopoulos, Giannoula

    2012-02-01

    A theoretical approach is described for the design of donor-acceptor intramolecular charge transfer (ICT) systems and for photoinduced electron transfer (PET) hybrids of fullerene, based on orbital level diagrams of the separate donor and acceptor moieties. Minimization of the HOMO-LUMO (highest occupied-lowest unoccupied orbital) gap in ICT systems, translates to a requirement for near degeneracy of the HOMO of the donor and LUMO of the acceptor, determined separately for the two moieties by density functional theory calculations. Similarly, near degeneracy of the LUMO of the donor and LUMO of the acceptor moieties would indicate the possibility of PET in the combined hybrid.

  12. Enantioselective Organocatalytic Construction of Spiroindane Derivatives by Intramolecular Friedel-Crafts-Type 1,4-Addition.

    PubMed

    Yoshida, Keisuke; Itatsu, Yukihiro; Fujino, Yuta; Inoue, Hiroki; Takao, Ken-Ichi

    2016-06-01

    The highly enantioselective organocatalytic construction of spiroindanes containing an all-carbon quaternary stereocenter by intramolecular Friedel-Crafts-type 1,4-addition is described. The reaction was catalyzed by a cinchonidine-based primary amine and accelerated by water and p-bromophenol. A variety of spiro compounds containing quaternary stereocenters were obtained with excellent enantioselectivity (up to 95 % ee). The reaction was applied to the asymmetric formal synthesis of the spirocyclic natural products (-)-cannabispirenones A and B. PMID:27111396

  13. 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

  14. Intramolecular interactions in ortho-methoxyalkylphenylboronic acids and their catechol esters

    NASA Astrophysics Data System (ADS)

    Adamczyk-Woźniak, Agnieszka; Borys, Krzysztof M.; Czerwińska, Karolina; Gierczyk, Błażej; Jakubczyk, Michał; Madura, Izabela D.; Sporzyński, Andrzej; Tomecka, Ewelina

    2013-12-01

    Catechol esters of ortho-methoxyalkylphenylboronic acids have been synthesized and characterized by 17O NMR spectroscopy. The results were compared with the data for the parent acids. The influence of intramolecular and intermolecular hydrogen bonds on the properties of the boronic acids has been discussed. The 17O NMR data for the boronic esters proved that there are no O → B interactions in the investigated compounds. This fact is connected with weak Lewis acidity of the parent acids and their low sugars' receptors activity. Crystal structure of ortho-methoxyphenylboronic acid catechol ester was determined.

  15. Palladium-catalyzed intramolecular cyclization of ynamides: synthesis of 4-halo-oxazolones.

    PubMed

    Huang, Hai; He, Guangke; Zhu, Guohao; Zhu, Xiaolin; Qiu, Shineng; Zhu, Hongjun

    2015-04-01

    A mild and efficient methodology involving Pd(PPh3)4-catalyzed intramolecular cyclization of N-alkynyl alkyloxycarbamates with CuCl2 or CuBr2 for the synthesis of 4-halo-oxazolones was developed. This reaction exhibiting good functional tolerance provided a new, efficient, and rapid synthetic process to 4-halo-oxazolones. The resulting 4-halo-oxazolones can serve as great potential precursors for the 3,4,5-trisubstituted oxazolones via a Pd-catalyzed cross-coupling reaction.

  16. Indolizino[5,6-b]quinoxaline Derivatives: Intramolecular Charge Transfer Characters and NIR Fluorescence.

    PubMed

    Kojima, Mitsuru; Hayashi, Hironobu; Aotake, Tatsuya; Ikeda, Shinya; Suzuki, Mitsuharu; Aratani, Naoki; Kuzuhara, Daiki; Yamada, Hiroko

    2015-11-01

    Indolizino[5,6-b]quinoxaline derivatives (1 a and 1 b) with a push-pull structure were prepared to show intramolecular charge-transfer properties. Compounds 1 a and 1 b are strongly fluorescent in aprotic solvents while symmetrical derivatives (2 a and 2 b) were non-fluorescent. The π-expanded α-α linked dimer (10) of indolizino[5,6-b]quinoxaline 1 b was serendipitously obtained to show NIR absorption over 800 nm and the fluorescence edge reached to 1400 nm.

  17. Intramolecular bond length dependence of the anisotropic dispersion coefficients for H2-rare gas interactions

    NASA Astrophysics Data System (ADS)

    Wormer, Paul E. S.; Hettema, Hinne; Thakkar, Ajit J.

    1993-05-01

    Effective states arising from variational perturbation calculations in a full configuration interaction basis are used to calculate dynamic multipole polarizabilities for H2 at seven different bond lengths. These are combined with previously calculated dynamic polarizabilities for rare gas atoms to obtain the intramolecular bond length dependence of the anisotropic C6, C8, and C10 dispersion coefficients for H2-X (X=He, Ne, Ar, Kr, Xe) interactions. The results are generally in good agreement with previous semiempirical estimates where available.

  18. Photoinduced intramolecular charge transfer process of betaine pyridinium: A theoretical spectroscopic study

    NASA Astrophysics Data System (ADS)

    Perrier, Aurélie; Aloïse, Stéphane; Pawlowska, Zuzanna; Sliwa, Michel; Maurel, François; Abe, Jiro

    2011-10-01

    Using Time-Dependent Density Functional Theory and taking into account bulk solvent effects, we investigate the absorption and emission spectra of a betaine pyridinium molecule, the 2-(1-pyridinio) benzimidazolate (SBPa). This molecule exhibits strong photoinduced intramolecular charge transfer (ICT). We have identified two different electronic states involved, respectively, in the strong bathochromic ICT absorption band (S 2) and in the moderate emission band (S 1). The ICT process is analyzed in terms of charge distribution and dipole moment evolutions upon photoexcitation. These results are compared with steady-state spectroscopic measurements.

  19. Syntheses of arabinose-derived pyrrolidine catalysts and their applications in intramolecular Diels-Alder reactions.

    PubMed

    Shing, Tony K M; Wu, Kwun W; Wu, Ho T; Xiao, Qicai

    2015-02-14

    Six chiral hydroxylated pyrrolidine catalysts were synthesized from commercially available D-arabinose in seven steps. Various aromatic substituents α to the amine can be introduced readily by a Grignard reaction, which enables facile optimization of the catalyst performance. The stereoselectivities of these catalysts have been assessed by comparing with those of MacMillan's imidazolidinone in a known intramolecular Diels-Alder (IMDA) reaction of a triene. Two additional IMDA reactions of symmetrical dienals with concomitant desymmetrisation further established the potential use of these novel amine catalysts. These pyrrolidines are valuable catalysts for other synthetic transformations. PMID:25503272

  20. 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

  1. Enantioselective Organocatalytic Construction of Spiroindane Derivatives by Intramolecular Friedel-Crafts-Type 1,4-Addition.

    PubMed

    Yoshida, Keisuke; Itatsu, Yukihiro; Fujino, Yuta; Inoue, Hiroki; Takao, Ken-Ichi

    2016-06-01

    The highly enantioselective organocatalytic construction of spiroindanes containing an all-carbon quaternary stereocenter by intramolecular Friedel-Crafts-type 1,4-addition is described. The reaction was catalyzed by a cinchonidine-based primary amine and accelerated by water and p-bromophenol. A variety of spiro compounds containing quaternary stereocenters were obtained with excellent enantioselectivity (up to 95 % ee). The reaction was applied to the asymmetric formal synthesis of the spirocyclic natural products (-)-cannabispirenones A and B.

  2. Intra-molecular electron transfer and electric conductance via sequential hopping: Unified theoretical description

    NASA Astrophysics Data System (ADS)

    Berlin, Yuri A.; Ratner, Mark A.

    2005-10-01

    The relation between intra-molecular electron transfer in the donor-bridge-acceptor system and zero-bias conductance of the same bridge in the metal-molecule-metal junction is analyzed for the sequential hopping regime of both processes. The electron transfer rate and molecular conductance are expressed in terms of rates characterizing each individual step of electron motion. Based on the results obtained, we derive the analytical expression that relates these two quantities in the general case of the energy landscape governing hopping transport.

  3. Advanced organic optoelectronic materials: harnessing excited-state intramolecular proton transfer (ESIPT) process.

    PubMed

    Kwon, Ji Eon; Park, Soo Young

    2011-08-23

    Recently, organic fluorescent molecules harnessing the excited-state intramolecular proton transfer (ESIPT) process are drawing great attention due to their unique photophysical properties which facilitate novel optoelectronic applications. After a brief introduction to the ESIPT process and related photo-physical properties, molecular design strategies towards tailored emission are discussed in relation to their theoretical aspects. Subsequently, recent studies on advanced ESIPT molecules and their optoelectronic applications are surveyed, particularly focusing on chemical sensors, fluorescence imaging, proton transfer lasers, and organic light-emitting diodes (OLEDs).

  4. 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.

  5. Differentiating mechanistic possibilities for the thermal, intramolecular [2 + 2] cycloaddition of allene-ynes.

    PubMed

    Siebert, Matthew R; Osbourn, Joshua M; Brummond, Kay M; Tantillo, Dean J

    2010-09-01

    Intramolecular [2 + 2] cycloaddition reactions of allene-ynes offer a quick and efficient route to fused bicyclic ring structures. Insights into the mechanism and regiochemical preferences of this reaction are provided herein on the basis of the results of quantum chemical calculations (B3LYP/6-31+G(d,p)) and select experiments; both indicate that the reaction likely proceeds through a stepwise diradical pathway where one radical center is stabilized through allylic delocalization. The influences of the length of the tether connecting the alkyne and allene and substituent effects are also discussed.

  6. Copper-Catalyzed Intramolecular Benzylic C-H Amination for the Synthesis of Isoindolinones.

    PubMed

    Yamamoto, Chiaki; Takamatsu, Kazutaka; Hirano, Koji; Miura, Masahiro

    2016-09-01

    A copper-catalyzed intramolecular amination occurs at the benzylic C-H of 2-methylbenzamides to deliver the corresponding isoindolinones of great interest in medicinal chemistry. The mild and abundant MnO2 works well as a terminal oxidant, and the reaction proceeds smoothly under potentially explosive organic peroxide-free conditions. Additionally, the directing-group-dependent divergent mechanisms are proposed: 8-aminoquinoline-containing benzamides include a Cu-mediated organometallic pathway whereas an aminyl radical-promoted Hofmann-Loffler-Freytag (HLF)-type mechanism can be operative in the case of N-naphthyl-substituted substrates. PMID:27504671

  7. 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

  8. 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

  9. Formation of H3+ due to Intramolecular Bond Rearrangement in Doubly Charged Methanol

    NASA Astrophysics Data System (ADS)

    de, Sankar; Rajput, Jyoti; Roy, A.; Ghosh, P. N.; Safvan, C. P.

    2006-11-01

    We report the formation of H3+ by proton coagulation in methanol under the impact of low energy Ar8+ projectiles. Our time-of-flight coincidence measurements with CH3OD establish that the H3+ formation arises from intramolecular bond rearrangement of the methyl group. We have performed ab initio quantum chemical calculations that show the preferred pathway for C-H3 bond cleavage. Fragmentation of organic molecules like methanol under impact of highly charged ions is suggested as an alternative mechanism of H3+ formation in outer space.

  10. 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.

  11. 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.

  12. Direct Observation and Control of Ultrafast Photoinduced Twisted Intramolecular Charge Transfer (TICT) in Triphenyl-Methane Dyes

    PubMed Central

    Li, Guifeng; Magana, Donny; Dyer, R. Brian

    2012-01-01

    Femtosecond time-resolved infrared spectroscopy was employed to study intramolecular charge transfer in triphenylmethane dyes, including malachite green (MG), malachite green carbinol base (MGCB), and leucomalachite green (LMG). A local excited state (LE) and a twisted intramolecular charge-transfer (TICT) state have been observed directly in MG. Furthermore, solvent-controlled TICT measurements in a series of linear alcohols indicate that the transition time (4–11 ps) from LE to TICT is strongly dependent on alcohol viscosity, which is due to rotational hindrance of dimethylaniline in high-viscosity solvents. For LMG, no TICT is observed due to steric hindrance caused by the sp3-hybridized central carbon atom. However, for MGCB, TICT is rescued by the addition of the electron-donating hydroxyl group to the bridge. These results for MG and its analogues provide new insight regarding the dynamics and mechanism of twisted intramolecular charge transfer (TICT) in triphenylmethane dyes. PMID:23009668

  13. Rapid intramolecular turnover of N-linked glycans in plasma membrane glycoproteins. Extension of intramolecular turnover to the core sugars in plasma membrane glycoproteins of hepatoma.

    PubMed

    Tauber, R; Park, C S; Becker, A; Geyer, R; Reutter, W

    1989-12-01

    Plasma membrane glycoproteins of rat hepatocytes undergo a rapid terminal deglycosylation in that the terminal sugars of the oligosaccharide side chains are rapidly removed from the otherwise intact glycoproteins [Tauber, R., Park, C.S. & Reutter, W. (1983) Proc. Natl Acad. Sci. USA 80, 4026-4029]. The present paper demonstrates that this rapid intramolecular turnover of plasma membrane glycoproteins is not restricted to peripheral sugars but, in contrast to liver, in hepatoma the core sugars of the oligosaccharide chains are also involved. Intramolecular turnover was measured in Morris hepatoma 7777 in five plasma membrane glycoproteins with Mr of 85,000 (hgp85), 105,000 (hgp105), 115,000 (hgp115), 125,000 (hgp125), 175,000 (hgp175) (hgp = hepatoma glycoprotein) that were isolated and purified to homogeneity by concanavalin-A--Sepharose affinity chromatography and semipreparative SDS gel electrophoresis. Analysis of the carbohydrates of hgp85, hgp105, hgp115 and hgp125 revealed the presence of N-linked oligosaccharides containing L-fucose, D-galactose, D-mannose and N-acetyl-D-glucosamine, but only of trace amounts of N-acetyl-D-galactosamine; hgp175 additionally contained significant amounts of N-acetyl-D-galactosamine, indicating the presence of both N- and O-linked oligosaccharides. As shown by digestion with endoglucosaminidase H, the N-linked oligosaccharides of hgp105, hgp115, hgp125 and hgp175 were of the complex type, whereas hgp85 also contained oligosaccharides of the high-mannose type. Half-lives of the turnover of the oligosacharide chains and of the protein backbone of the five glycoproteins were measured in the plasma membrane in pulse-chase experiments in vivo, using L-[3H]fucose as a marker of terminal sugars, D-[3H]mannose as marker of a core sugar and L-[3H]leucine for labelling the protein backbone. Protein backbones of the five glycoproteins were degraded with individual half-lives ranging over 41-90 h with a mean of 66 h. Compared to the

  14. Intramolecular pnicogen interactions in PHF-(CH2)(n)-PHF (n=2-6) systems.

    PubMed

    Sánchez-Sanz, Goar; Alkorta, Ibon; Trujillo, Cristina; Elguero, José

    2013-06-01

    A computational study of the intramolecular pnicogen bond in PHF-(CH2)n-PHF (n=2-6) systems was carried out. For each compound, two different conformations, (R,R) and (R,S), were considered on the basis of the chirality of the phosphine groups. The characteristics of the closed conformers, in which the pnicogen interaction occurs, were compared with those of the extended conformer. In several cases, the closed conformations are more stable than the extended conformations. The calculated interaction energies of the pnicogen contact, by means of isodesmic reactions, provide values between -3.4 and -26.0 kJ mol(-1). Atoms in molecules and electron localization function analysis of the electron density showed that the systems in the closed conformations with short P···P distances have a partial covalent character in this interaction. The calculated absolute chemical shieldings of the P atoms showed an exponential relationship with the P···P distance. In addition, a search in the Cambridge crystallographic database was carried out to detect those compounds with a potential intramolecular pnicogen bond in the solid phase.

  15. Stabilization of intermediate density states in globular proteins by homogeneous intramolecular attractive interactions.

    PubMed Central

    Bahar, I; Jernigan, R L

    1994-01-01

    On-lattice simulations of two-dimensional self-avoiding chains subject to homogeneous intramolecular attractive interactions were performed as a model for studying various density regimes in globular proteins. For short chains of less than 15 units, all conformations were generated and classified by density. The range of intramolecular interactions was found to increase uniformly with density, and the average number of topological contacts is directly proportional to density. The uniform interaction energy increases the probability of high density states but does not necessarily lead to dominance of the highest density state. Typically, several large peaks appear in the probability distribution of packing densities, their location and amplitude being determined by the balance between entropic effects enhancing more expanded conformations and attractive interactions favoring compact forms. Also, the homogeneous interaction energy affects the distribution of most probable interacting points in favor of the longer range interactions over the short range ones, but in addition it introduces some more detailed preferences even among short range interactions. There are some implications about the characteristics of the intermediate density states and also for the likelihood that the native state does not correspond completely to the lowest energy conformation. Images FIGURE 7 FIGURE 8 FIGURE 9 FIGURE 10 FIGURE 11 FIGURE 12 FIGURE 13 PMID:8161699

  16. 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

  17. 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.

  18. 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.

  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.

  20. 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

  1. 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

  2. Effect of Hartree-Fock exact exchange on intramolecular magnetic coupling constants of organic diradicals

    SciTech Connect

    Cho, Daeheum; Ko, Kyoung Chul; Lee, Jin Yong; Ikabata, Yasuhiro; Wakayama, Kazufumi; Yoshikawa, Takeshi; Nakai, Hiromi

    2015-01-14

    The intramolecular magnetic coupling constant (J) of diradical systems linked with five- or six-membered aromatic rings was calculated to obtain the scaling factor (experimental J/calculated J ratio) for various density functional theory (DFT) functionals. Scaling factors of group A (PBE, TPSSh, B3LYP, B97-1, X3LYP, PBE0, and BH and HLYP) and B (M06-L, M06, M06-2X, and M06-HF) were shown to decrease as the amount of Hartree-Fock exact exchange (HFx) increases, in other words, overestimation of calculated J becomes more severe as the HFx increases. We further investigated the effect of HFx fraction of DFT functional on J value, spin contamination, and spin density distributions by comparing the B3LYP analogues containing different amount of HFx. It was revealed that spin contamination and spin densities at each atom increases as the HFx increases. Above all, newly developed BLYP-5 functional, which has 5% of HFx, was found to have the scaling factor of 1.029, indicating that calculated J values are very close to that of experimental values without scaling. BLYP-5 has potential to be utilized for accurate evaluation of intramolecular magnetic coupling constant (J) of diradicals linked by five- or six-membered aromatic ring couplers.

  3. 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.

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

    PubMed

    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.

  5. 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

  6. 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

  7. 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

  8. 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.

  9. 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

  10. A spontaneously blinking fluorophore based on intramolecular spirocyclization for live-cell super-resolution imaging.

    PubMed

    Uno, Shin-Nosuke; Kamiya, Mako; Yoshihara, Toshitada; Sugawara, Ko; Okabe, Kohki; Tarhan, Mehmet C; Fujita, Hiroyuki; Funatsu, Takashi; Okada, Yasushi; Tobita, Seiji; Urano, Yasuteru

    2014-08-01

    Single-molecule localization microscopy is used to construct super-resolution images, but generally requires prior intense laser irradiation and in some cases additives, such as thiols, to induce on-off switching of fluorophores. These requirements limit the potential applications of this methodology. Here, we report a first-in-class spontaneously blinking fluorophore based on an intramolecular spirocyclization reaction. Optimization of the intramolecular nucleophile and rhodamine-based fluorophore (electrophile) provide a suitable lifetime for the fluorescent open form, and equilibrium between the open form and the non-fluorescent closed form. We show that this spontaneously blinking fluorophore is suitable for single-molecule localization microscopy imaging deep inside cells and for tracking the motion of structures in living cells. We further demonstrate the advantages of this fluorophore over existing methodologies by applying it to nuclear pore structures located far above the coverslip with a spinning-disk confocal microscope and for repetitive time-lapse super-resolution imaging of microtubules in live cells for up to 1 h. PMID:25054937

  11. Action at a distance in supercoiled DNA: effects of sequence on slither, branching, and intramolecular concentration.

    PubMed Central

    Sprous, D; Harvey, S C

    1996-01-01

    We report a computer modeling study of DNA supercoiling in model plasmids over the size range of 140-1260 bp. We used a computer model with basepair resolution. Molecular dynamics was used to produce ensembles at 300 K and to investigate intramolecular motions. The plasmid models varied by their sequence. The sequence types employed for comparison included a curve-bearing plasmid, a heterogenous sequence plasmid, and a homogenous sequence. Within the three sequence types tested at the 1260-bp plasmid size, we observed several sequence-dependent phenomena. Writhe, radius of gyration, slither motion, and branching probability were seen to be sequence dependent. Branching probability was the least in the homogenous plasmid and the greatest in the curve-bearing plasmid. The curve imposed a symmetry on the plasmid that was absent in the heterogenous sequence. Significant localizations and enhancements of intramolecular concentration were seen to a persistence length. Molecular dynamics allowed us to observe the mechanism of branch formation and reabsorption. We observed a size-dependent change in the types of motion observed in plasmids. Slither motion predominated in plasmids up to 600 bp in size, whereas global rearrangements were more important in the 1260 mer. Images FIGURE 1 FIGURE 5 FIGURE 10 PMID:8785349

  12. 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

  13. 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.

  14. 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

  15. 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

  16. 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

  17. 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.

  18. Autoactivation of the MDM2 E3 Ligase by Intramolecular Interaction

    PubMed Central

    Cheng, Qian; Song, Tanjing; Chen, Lihong

    2014-01-01

    The RING domain ubiquitin E3 ligase MDM2 is a key regulator of p53 degradation and a mediator of signals that stabilize p53. The current understanding of the mechanisms by which MDM2 posttranslational modifications and protein binding cause p53 stabilization remains incomplete. Here we present evidence that the MDM2 central acidic region is critical for activating RING domain E3 ligase activity. A 30-amino-acid minimal region of the acidic domain binds to the RING domain through intramolecular interactions and stimulates the catalytic function of the RING domain in promoting ubiquitin release from charged E2. The minimal activation sequence is also the binding site for the ARF tumor suppressor, which inhibits ubiquitination of p53. The acidic domain-RING domain intramolecular interaction is modulated by ATM-mediated phosphorylation near the RING domain or by binding of ARF. These results suggest that MDM2 phosphorylation and association with protein regulators share a mechanism in inhibiting the E3 ligase function and stabilizing p53 and suggest that targeting the MDM2 autoactivation mechanism may be useful for therapeutic modulation of p53 levels. PMID:24842904

  19. Hydroxyalkoxy radicals: importance of intramolecular hydrogen bonding on chain branching reactions in the combustion and atmospheric decomposition of hydrocarbons.

    PubMed

    Davis, Alexander C; Francisco, Joseph S

    2014-11-20

    During both the atmospheric oxidation and combustion of volatile organic compounds, sequential addition of oxygen can lead to compounds that contain multiple hydrogen-bonding sites. The presence of two or more of these sites on a hydrocarbon introduces the possibility of intramolecular H-bonding, which can have a stabilizing effect on the reactants, products, and transition states of subsequent reactions. The present work compares the absolute energies of two sets of conformations, those that contain intramolecular H-bonds and those that lack intramolecular H-bonds, for each reactant, product, and transition state species in the 1,2 through 1,7 H-migrations and Cα-Cβ, Cα-H, and Cα-OH-bond scission reactions in the n-hydroxyeth-1-oxy through n-hydroxyhex-1-oxy radicals, for n ranging from 1 to 6. The difference in energy between the two conformations represents the balance between the stabilizing effects of H-bonds and the steric cost of bringing the two H-bonding sites together. The effect of intramolecular H-bonding and the OH group is assessed by comparing the net intramolecular H-bond stabilization energies, the reaction enthalpies, and barrier heights of the n-hydroxyalkoxy radical reactions with the corresponding alkoxy radicals values. The results suggest that there is a complex dependence on the location of the two H-bonding groups, the location of the abstraction or bond scission, and the shape of the transition state that dictates the extent to which intramolecular H-bonding effects the relative importance of H-migration and bond scission reactions for each n-hydroxyalkoxy radical. These findings have important implications for future studies on hydrocarbons with multiple H-bonding sites.

  20. 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

  1. Reactivity umpolung in intramolecular ring closure of 3,4-disubstituted butenolides: diastereoselective total synthesis of paeonilide.

    PubMed

    Deore, Prashant S; Argade, Narshinha P

    2013-11-15

    Remarkable reactivity reversal stratagem in 3,4-disubstituted butenolides under acidic conditions is described. Design of a suitably substituted multifunctional butenolide followed by an acid-catalyzed chemo- and diastereoselective intramolecular ring closure via the reactivity umpolung has been demonstrated to accomplish a concise total synthesis of paeonilide. Overall, the present protocol involves one-pot reduction of an α,β-unsaturated carbon-carbon double bond and intramolecular nucleophilic insertion of oxygen function at the electron-rich γ-position of butenolide. The involved mechanistic aspects have also been discussed. PMID:24175675

  2. Laurdan solvatochromism: solvent dielectric relaxation and intramolecular excited-state reaction.

    PubMed Central

    Viard, M; Gallay, J; Vincent, M; Meyer, O; Robert, B; Paternostre, M

    1997-01-01

    Absorption, steady-state, and time-resolved fluorescence measurements have been performed on laurdan dissolved either in white viscous apolar solvents or in ethanol as a function of temperature. The heterogeneity of the absorption spectra in white oils or in ethanol is consistent with semiempirical calculations performed previously on Prodan. From steady-state and time-resolved fluorescence measurements in apolar media, an excited state reaction is evidenced. The bimodal lifetime distribution determined from the maximum entropy method (MEM) analysis is attributed to the radiative deexcitation of a "locally excited" (LE) state and of a "charge transfer" (CT) state, whereas a very short component (20 ps), the sign and the amplitude of which depend on the emission wavelength, is attributed to the kinetics of the interconvertion reaction. The observation of an isoemissive point in the temperature range from -50 degrees C to -110 degrees C in ethanol suggests an interconvertion between two average excited-state populations: unrelaxed and solvent-relaxed CT states. A further decrease in temperature (-190 degrees C), leading to frozen ethanol, induces an additional and important blue shift. This low temperature spectrum is partly attributed to the radiative deexcitation of the LE state. Time-resolved emission spectra (TRES) measurements at -80 degrees C in the ethanol liquid phase show a large spectral shift of approximately 2500 cm(-1) (stabilization energy of the excited state: 7.1 kcal x M(-1)). The time-dependent fluorescence shift (TDFS) is described for its major part by a nanosecond time constant. The initial part of the spectral shift reveals, however, a subnanosecond process that can be due to fast internal solvent reorientation and/or to intramolecular excited-state reactions. These two relaxation times are also detected in the analysis of the fluorescence decays in the middle range of emission energy. The activation energy of the longest process is

  3. Intramolecular ferro- and antiferromagnetic interactions in oxo-carboxylate bridged digadolinium(III) complexes.

    PubMed

    Cañadillas-Delgado, Laura; Fabelo, Oscar; Pasán, Jorge; Delgado, Fernando S; Lloret, Francesc; Julve, Miguel; Ruiz-Pérez, Catalina

    2010-08-21

    Two new digadolinium(III) complexes with monocarboxylate ligands, [Gd2(pac)6(H2O)4] (1) and [Gd2(tpac)6(H2O)4] (2) (Hpac = pentanoic acid and Htpac = 3-thiopheneacetic acid), have been prepared and their structures determined by X-ray diffraction on single crystals. Their structures consist of neutral and isolated digadolinium(III) units, containing six monocarboxylate ligands and four coordinated water molecules, the bridging skeleton being built by a muO(1):kappa2O(1)O(2) framework. This structural pattern has already been observed in the parent acetate-containing compound [Gd2(ac)6(H2O)4] x 4 H2O (3) whose structure and magnetic properties were reported elsewhere (L. Cañadillas-Delgado, O. Fabelo, J. Cano, J. Pasán, F. S. Delgado, M. Julve, F. Lloret and C. Ruiz-Pérez, CrystEngComm, 2009, 11, 2131). Each gadolinium(III) ion in 1 and 2 is nine-coordinated with seven carboxylate-oxygen atoms from four pac (1)/tpac (2) ligands and two water molecules (1 and 2) building a distorted monocapped square antiprism. The values of the intramolecular gadolinium-gadolinium separation are 4.1215(5) (1), 4.1255(6) (2) and 4.1589(3) A (3) and those of the angle at the oxo-carboxylate bridge (theta) are 113.16(13) (1), 112.5(2) (2) and 115.47(7) degrees (3). Magnetic susceptibility measurements in the temperature range 1.9-300 K reveal the occurrence of a weak intramolecular antiferromagnetic interaction [J = -0.032(1) (1) and -0.012(1) cm(-1) (2), the Hamiltonian being defined as H = -JS(A) x S(B)] in contrast with the intramolecular ferromagnetic coupling which occurs in 3 (J = +0.031(1) cm(-1)). The magneto-structural data of 1-3 show the relevance of the geometrical parameters at the muO(1):kappa2O(1)O(2) bridge on the nature of the magnetic coupling between two gadolinium(III) ions.

  4. 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.

  5. 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

  6. Bifunctional ferrocene-based squaramide-phosphine as an organocatalyst for highly enantioselective intramolecular Morita-Baylis-Hillman reaction.

    PubMed

    Zhang, Xiaorui; Ma, Pengfei; Zhang, Dongxu; Lei, Yang; Zhang, Shengyong; Jiang, Ru; Chen, Weiping

    2014-04-21

    This work demonstrates that, in accord with metal catalysis, ferrocene could be an excellent scaffold for organocatalysts. The simple and easily accessible bifunctional ferrocene-based squaramide-phosphine shows high enantioselectivity in the intramolecular Morita-Baylis-Hillman reaction of 7-aryl-7-oxo-5-heptenals, giving a variety of 2-aroyl-2-cyclohexenols in up to 96% ee.

  7. 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

  8. An intramolecular recombination mechanism for the formation of the rRNA gene palindrome of Tetrahymena thermophila

    SciTech Connect

    Butler, D.K.; Yasuda, L.E.; Yao, Meng-Chao

    1995-12-01

    This report discusses the formation of rRNA gene palindrome in Tetrahymena thermophila and the involvement of intramolecular recombination. This, along with the authors` previous study, is the first to define a molecular pathway of palindrome formation. 48 refs., 6 figs.

  9. Direct access to pyrazolo(benzo)thienoquinolines. Highly effective palladium catalysts for the intramolecular C-H heteroarylation of arenes.

    PubMed

    Churruca, Fátima; Hernández, Susana; Perea, María; SanMartin, Raul; Domínguez, Esther

    2013-02-18

    A short and atom-efficient strategy to obtain a series of pyrazolo(benzo)thienoquinolines is developed. Alternative catalytic systems for the key intramolecular direct heteroarylation of arenes are presented and include the first example of C-H (hetero)arylation of (hetero)arenes catalyzed by very low catalyst loadings of a palladium source. PMID:23320258

  10. Enantioselective synthesis of benzofurans and benzoxazines via an olefin cross-metathesis-intramolecular oxo-Michael reaction.

    PubMed

    Zhang, Jun-Wei; Cai, Quan; Gu, Qing; Shi, Xiao-Xin; You, Shu-Li

    2013-09-11

    Chiral phosphoric acid and Hoveyda-Grubbs II were found to catalyze an olefin cross-metathesis-intramolecular oxo-Michael cascade reaction of the ortho-allylphenols and enones to provide a variety of benzofuran and benzoxazine derivatives in moderate to good yields and enantioselectivity. PMID:23884172

  11. 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.

  12. 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.

  13. Enantioselective synthesis of benzofurans and benzoxazines via an olefin cross-metathesis-intramolecular oxo-Michael reaction.

    PubMed

    Zhang, Jun-Wei; Cai, Quan; Gu, Qing; Shi, Xiao-Xin; You, Shu-Li

    2013-09-11

    Chiral phosphoric acid and Hoveyda-Grubbs II were found to catalyze an olefin cross-metathesis-intramolecular oxo-Michael cascade reaction of the ortho-allylphenols and enones to provide a variety of benzofuran and benzoxazine derivatives in moderate to good yields and enantioselectivity.

  14. 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

  15. Enantioselective synthesis of 4-substituted tetrahydroisoquinolines via palladium-catalyzed intramolecular Friedel-Crafts type allylic alkylation of phenols.

    PubMed

    Zhao, Zheng-Le; Xu, Qing-Long; Gu, Qing; Wu, Xin-Yan; You, Shu-Li

    2015-03-14

    Palladium-catalyzed asymmetric intramolecular Friedel-Crafts type allylic alkylation reaction of phenols was developed under mild conditions. In the presence of Pd2(dba)3 with (1R,2R)-DACH-phenyl Trost ligand (L2) in toluene at 50 °C, the reaction provides various C4 substituted tetrahydroisoquinolines with moderate to excellent yields, regioselectivity and enantioselectivity. PMID:25625805

  16. Rhodium-catalyzed 1,3-acyloxy migration and subsequent intramolecular [4 + 2] cycloaddition of vinylallene and unactivated alkyne†

    PubMed Central

    Huang, Suyu; Li, Xiaoxun; Lin, Claire L.; Guzei, Ilia A.

    2012-01-01

    A Rh-catalyzed 1,3-acyloxy migration of propargyl ester followed by intramolecular [4 + 2] cycloaddition of vinylallene and unactivated alkyne was developed. This tandem reaction provides access to bicyclic compounds containing a highly functionalized isotoluene or cyclohexenone structural motif, while only aromatic compounds were observed in related transition metal-catalyzed cycloadditions. PMID:22252254

  17. Rhodium-catalyzed 1,3-acyloxy migration and subsequent intramolecular [4+2] cycloaddition of vinylallene and unactivated alkyne.

    PubMed

    Huang, Suyu; Li, Xiaoxun; Lin, Claire L; Guzei, Ilia A; Tang, Weiping

    2012-02-21

    A Rh-catalyzed 1,3-acyloxy migration of propargyl ester followed by intramolecular [4+2] cycloaddition of vinylallene and unactivated alkyne was developed. This tandem reaction provides access to bicyclic compounds containing a highly functionalized isotoluene or cyclohexenone structural motif, while only aromatic compounds were observed in related transition metal-catalyzed cycloadditions.

  18. Total synthesis of debromoflustramines B and E based on the intramolecular carbamoylketene-alkene [2 + 2] cycloaddition.

    PubMed

    Ozawa, Tsukasa; Kanematsu, Makoto; Yokoe, Hiromasa; Yoshida, Masahiro; Shishido, Kozo

    2012-10-19

    Total synthesis of debromoflustramines B and E has been accomplished by using a platinum-catalyzed addition reaction of o-aminophenylboronic acid with the allene and an intramolecular carbamoylketene-alkene [2 + 2] cycloaddition for the construction of the basic carbon framework of the target alkaloids as the key steps.

  19. Second order rate constants for intramolecular conversions: Application to gas-phase NMR relaxation times

    NASA Astrophysics Data System (ADS)

    Bauer, S. H.; Lazaar, K. I.

    1983-09-01

    The usually quoted expression for the second order rate constant, for a unimolecular reaction at the low pressure limit, is valid only for strictly irreversible processes. Its application to isomerization reactions (which are to some extent reversible) is demonstrably in error; corrected expressions have been published. Attention is directed to intramolecular conversions over low barriers, for which the inappropriateness of the unidirectional expression becomes obvious. For such isomerizations we propose a model which incorporates only operationally observable states, so that an essential conceptual ambiguity is avoided. Use of this model is illustrated for the syn⇄anti conversions of methyl nitrite, derived from a gas phase NMR coalescence curve (Mc:Tc). The present data suggest that during isomerization the alkyl nitrites may not be completely ergodic on a time scale of 10-9 s. A regional phase-space model is proposed which has the appropriate formalism to account for this behavior.

  20. Intramolecular Electron Transfer in Bis(tetraalkyl Hydrazine) and Bis(hydrazyl) Radical Cations.

    NASA Astrophysics Data System (ADS)

    Chang, Hao

    A series of multicyclic bis(hydrazine) and bis(diazenium) compounds connected by relatively rigid hydrocarbon frameworks were prepared for the study of intramolecular electron transfer. The thermodynamics of electron removal of these compounds was investigated by cyclic voltammetry. The difference between the first and second oxidation potentials for the 4 sigma-bonded species was found to be larger for the bis(hydrazyl) radical systems than for the bis(hydrazines) by ca. 0.2 V (4.6 kcal/mol). This indicates a greater degree of interaction between the two nitrogen moieties for the hydrazyl systems, which is consistent with a greater degree of electronic coupling (H _{rm AB}) in these systems. The ESR spectra of the 4 sigma -bonded bis(hydrazine) radical cations indicate localized radical cations, which corresponds to slow intramolecular electron transfer on the ESR timescale. Conversely, the ESR spectra of the corresponding bis(hydrazyl) radical cation systems show nitrogen hyperfine splittings of a(4N) of ca. 4.5 G. This indicates that intramolecular electron transfer between the two nitrogen moieties is fast on the ESR timescale; the rate of exchange, k_ {rm ex} was estimated to be well above 1.9 times 10^8 s^{-1}. The contrast in exchange rates is consistent with the large geometry change upon oxidation which is characteristic of hydrazines. The hydrazyls undergo a smaller geometry change upon oxidation, and thus are expected to exhibit smaller inner-sphere reorganization energies. The optical spectra of these radical species was investigated in hopes of observing absorption bands corresponding to intramolecular electron transfer, as predicted by Hush theory. A broad absorption band was observed in the near IR region for the saturated bis(hydrazyl) radical cation system at 1060 nm (9420 cm^{-1} ) in acetonitrile at room temperature, and was accompanied by a narrower band at 1430 nm (6993 cm^ {-1}). The width of this band was estimated to be 545 nm (6496 cm^{-1

  1. A general overview of the organocatalytic intramolecular aza-Michael reaction.

    PubMed

    Sánchez-Roselló, María; Aceña, José Luis; Simón-Fuentes, Antonio; del Pozo, Carlos

    2014-11-01

    The organocatalytic intramolecular aza-Michael reaction gives access to enantiomerically enriched nitrogen-containing heterocycles in a very simple manner. Enals, enones, conjugated esters and nitro olefins have been employed as Michael acceptors, while moderate nitrogen nucleophiles such as sulphonamides, carbamates and amides have been shown to be appropriate Michael donors in this type of reaction. Additionally, the process has been performed under both covalent and non-covalent catalysis, with diaryl prolinols, imidazolidinones, thioureas and chiral binol phosphoric acids being the most frequently used catalysts. The level of efficiency reached with this protocol is demonstrated by the implementation of numerous tandem processes, as well as the total synthesis of several natural products.

  2. A computational study of the copper(II)-catalyzed enantioselective intramolecular aminooxygenation of alkenes.

    PubMed

    Belding, Lee; Chemler, Sherry R; Dudding, Travis

    2013-10-18

    The origin of the enantioselectivity in the [Cu(R,R)-Ph-box](OTf)2-catalyzed intramolecular aminooxygenation of N-sulfonyl-2-allylanilines and 4-pentenylsulfonamides to afford chiral indolines and pyrrolidines, respectively, was investigated using density functional theory (DFT) calculations. The pyrrolidine-forming transition-state model for the major enantiomer involves a chairlike seven-membered cyclization transition state with a distorted square-planar copper center, while the transition-state model for the minor enantiomer was found to have a boatlike cyclization geometry having a distorted tetrahedral geometry about the copper center. Similar copper-geometry trends were observed in the chiral indoline-forming reactions. These models were found to be qualitatively consistent with experimental results and allow for rationalization of how substitution on the substrate backbone and N-sulfonyl substituent affect the level of enantioselectivity in these and related copper(II)-catalyzed enantioselective reactions. PMID:24032369

  3. Experimental exploration of the Mulliken-Hush relationship for intramolecular electron transfer reactions.

    PubMed

    Mukherjee, Tamal; Ito, Naoki; Gould, Ian R

    2011-03-17

    The Mulliken-Hush (M-H) relationship provides the critical link between optical and thermal electron transfer processes, and yet very little direct experimental support for its applicability has been provided. Dicyanovinylazaadamantane (DCVA) represents a simple two-state (neutral/charge-transfer) intramolecular electron transfer system that exhibits charge-transfer absorption and emission spectra that are readily measurable in solvents with a wide range of polarities. In this regard it represents an ideal model system for studying the factors that control both optical charge separation (absorption) and recombination (emission) processes in solution. Here we explore the applicability of the M-H relation to quantitative descriptions of the optical charge-transfer processes in DCVA. For DCVA, the measured radiative rate constants exhibit a linear dependence on transition energy, and transition dipole moments exhibit an inverse dependence on transition energy, consistent with the M-H relationship.

  4. 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.

  5. 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

  6. 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.

  7. Controlling energy level offsets in organic/organic heterostructures using intramolecular polar bonds

    NASA Astrophysics Data System (ADS)

    Duhm, Steffen; Salzmann, Ingo; Heimel, Georg; Oehzelt, Martin; Haase, Anja; Johnson, Robert L.; Rabe, Jürgen P.; Koch, Norbert

    2009-01-01

    The impact of intramolecular polar bonds (IPBs) on the energy level alignment in layered systems of rodlike conjugated molecules standing on the substrate was investigated for pentacene (PEN) and perfluoropentacene (PFP) on SiO2 using ultraviolet photoelectron spectroscopy. A remarkably large energy offset of 1.75 eV was found between the highest occupied molecular orbital (HOMO) levels of PEN and PFP caused by IPBs at the surface of standing PFP layers. This large HOMO-level offset results in a narrow intermolecular energy gap of approximately 0.4 eV at the interface between PEN and PFP layers. However, the absence of significant spatial overlap of PEN and PFP electron wave functions across the layers suppresses interlayer optical transitions.

  8. Tandem Intramolecular Benzyne-Furan Cycloadditions. Total Synthesis of Vineomycinone B(2) Methyl Ester.

    PubMed

    Sparks, Steven M; Chen, Chi-Li; Martin, Stephen F

    2007-08-27

    We have exploited tandem intramolecular benzyne-furan cycloadditions employing three different benzyne precursors to generate substituted bisoxabenzonorbornadienes in a single operation. The regiochemical outcomes in these Diels-Alder reactions were effectively controlled by using disposable silicon tethers to link the reacting benzynes and furan moieties. Two different methods for converting the intermediate bisoxabenzonorbornadienes to substituted anthrarufins were developed. The first tactic entails the initial cleavage of the silicon tethers followed by regioselective ring opening of the oxabicycloheptadienes and oxidation of the central ring giving the target anthrarufin, whereas the second features the regioselective ring opening of the oxabicycloheptadienes followed by protiodesilylation and oxidation. When the starting furans bear carbohydrate substitutents, this new methodology enables the rapid assembly of the glycosyl-substituted aromatic cores of complex C-aryl glycoside antibiotics from simple starting materials. The utility of this novel approach to anthrarufins and C-aryl glycosides is exemplified in a triply convergent synthesis of vineomycinone B(2) methyl ester.

  9. High-yield total synthesis of (-)-strictinin through intramolecular coupling of gallates.

    PubMed

    Michihata, Naoki; Kaneko, Yuki; Kasai, Yusuke; Tanigawa, Kotaro; Hirokane, Tsukasa; Higasa, Sho; Yamada, Hidetoshi

    2013-05-01

    This paper describes a total synthesis of (-)-strictinin, an ellagitannin that is 1-O-galloyl-4,6-O-(S)-hexahydroxydiphenoyl (HHDP)-β-D-glucose. In the study, total efficiency of the synthesis was improved to produce a 78% overall yield in 13 steps from D-glucose. In the synthesis, formation of the 4,6-(S)-HHDP bridge including the 11-membered bislactone ring was a key step, in which intramolecular aryl-aryl coupling was adopted. The coupling was oxidatively induced by CuCl2-n-BuNH2 with perfect control of the axial chirality, and the reaction conditions of this coupling were optimized thoroughly to achieve the quantitative formation of the bridge.

  10. Spectroscopy and intramolecular relaxation of methyl salicylate in its first excited singlet state

    NASA Astrophysics Data System (ADS)

    Kuper, Jerry W.; Perry, David S.

    1984-05-01

    High resolution fluorescence excitation experiments are reported for the blue emitting rotamer of methyl salicylate in its first excited singlet state. These experiments employ moderate expansions of methyl salicylate seeded in argon ( P0D=5-8 Torr cm) to achieve rotational and vibrational cooling in a pulsed supersonic jet. The rotational contour of the electronic origin at 30 055.3 cm-1 is shown to be consistent with a geometrically distorted π-π* excited state, partially polarized along the A axis and with a rotational temperature of 5-7 K. A noticeable broadening of the spectral features beyond the rotational contour begins at 500 cm-1 above the origin and then increases rapidly above 900 cm-1 reaching a width of 12 cm-1 near 1200 cm-1. The constancy of fluorescence decay lifetimes in this region indicate that intramolecular vibrational relaxation in the S1 manifold is the broadening mechanism.

  11. Dipole-mediated rectification of intramolecular photoinduced charge separation and charge recombination.

    PubMed

    Bao, Duoduo; Upadhyayula, Srigokul; Larsen, Jillian M; Xia, Bing; Georgieva, Boriana; Nuñez, Vicente; Espinoza, Eli M; Hartman, Joshua D; Wurch, Michelle; Chang, Andy; Lin, Chung-Kuang; Larkin, Jason; Vasquez, Krystal; Beran, Gregory J O; Vullev, Valentine I

    2014-09-17

    Controlling charge transfer at a molecular scale is critical for efficient light harvesting, energy conversion, and nanoelectronics. Dipole-polarization electrets, the electrostatic analogue of magnets, provide a means for "steering" electron transduction via the local electric fields generated by their permanent electric dipoles. Here, we describe the first demonstration of the utility of anthranilamides, moieties with ordered dipoles, for controlling intramolecular charge transfer. Donor-acceptor dyads, each containing a single anthranilamide moiety, distinctly rectify both the forward photoinduced electron transfer and the subsequent charge recombination. Changes in the observed charge-transfer kinetics as a function of media polarity were consistent with the anticipated effects of the anthranilamide molecular dipoles on the rectification. The regioselectivity of electron transfer and the molecular dynamics of the dyads further modulated the observed kinetics, particularly for charge recombination. These findings reveal the underlying complexity of dipole-induced effects on electron transfer and demonstrate unexplored paradigms for molecular rectifiers. PMID:25162490

  12. 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.

  13. 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

  14. Quasi-classical trajectory simulations of intramolecular vibrational energy redistribution in HONO2 and DONO2.

    PubMed

    Liu, Yong; Lohr, Lawrence L; Barker, John R

    2005-05-01

    By use of an analytic potential energy surface developed in this work for nitric acid, the quasi-classical trajectory method was used to simulate intramolecular vibrational energy redistribution (IVR). A method was developed for monitoring the average vibrational energy in the OH (or OD) mode that uses the mean-square displacement of the bond length calculated during the trajectories. This method is effective for both rotating and nonrotating molecules. The calculated IVR time constant for HONO(2) decreases exponentially with increasing excitation energy, is almost independent of rotational temperature, and is in excellent agreement with the experimental determination (Bingemann, D.; Gorman, M. P.; King, A. M.; Crim, F. F. J. Chem.Phys. 1997, 107, 661). In DONO(2), the IVR time constants show more complicated behavior with increasing excitation energy, apparently due to 2:1 Fermi-resonance coupling with lower frequency modes. This effect should be measurable in experiments.

  15. Solution conformation of gramicidin S: An intramolecular nuclear Overhauser effect study.

    PubMed

    Huang, D H; Walter, R; Glickson, J D; Krishna, N R

    1981-02-01

    The solution conformation of gramicidin S in deuterated dimethyl sulfoxide was investigated by using the intramolecular nuclear Overhauser effect experiment. Experimental Overhauser enhancements were compared with predicted values for each of the nine most-stable conformations (M1-M9) calculated by Dygert et al. on the basis of energy-minimization procedures [Dygert, M., Gō, N. & Scheraga, H. A. (1975) Macromolecules 8, 750-761]. By using statistical hypothesis testing, the three lowest-energy conformations (M1, M2, and M3) were shown to give the best fit with the experimental data. All other conformations (M4-M9) were found to be inconsistent with the experimental data. PMID:16592969

  16. Electronic and transport properties of radially deformed double-walled carbon nanotube intramolecular junction

    NASA Astrophysics Data System (ADS)

    Yang, Xiaoping; Dong, Jinming

    2004-09-01

    The electronic and transport property of a radially deformed double-walled carbon nanotube (DWNT) intramolecular junction (IMJ) has been studied by the tight-binding (TB) model combined with the first-principle calculations. The geometrical structures of the DWNT IMJ have been first optimized in energy by the universal force field (UFF) method. It is found that when heavily squashed, the DWNT will become an insulator-coated metallic wire, and the conductance near the Fermi level has been significantly changed by the radial squash. Specially, several resonance conductance peaks appear at some energies in the conduction band of the squashed DWNT IMJ. Finally, we have also investigated the conductance variation due to change of the length of the central semiconductor in the squashed DWNT IMJ. Furthermore, a promising pure carbon nanoscale electronic device is proposed based on the DWNT IMJ.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Gold-catalyzed intramolecular [3+2] cycloadditions of 1-aryl-1-allene-6-enes.

    PubMed

    Chaudhuri, Rupsha; Liao, Hsin-Yi; Liu, Rai-Shung

    2009-09-01

    Treatment of 1-aryl-1-allen-6-enes with [PPh(3)AuCl]/AgSbF(6) (5 mol %) in CH(2)Cl(2) at 25 degrees C led to intramolecular [3+2] cycloadditions, giving cis-fused dihydrobenzo[a]fluorene products efficiently and selectively. The reactions proceeded with initial formation of trans/cis mixtures of 2-alkyl-1-isopropyl-2-phenyl-1,2-dihydronaphthalene cations B, which were convertible into the desired cis-fused cycloadducts through the combined action of a gold catalyst and a Brønsted acid. Theoretic calculation supports the participation of the trans-B cation as reaction intermediate. Although HOTf showed similar activity towards several 1-aryl-1-allen-6-enes, it lacks generality for this cycloaddition reaction.

  3. 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

  4. Intramolecularly resolved Kondo resonance of high-spin Fe (II ) -porphyrin adsorbed on Au ( 111 )

    NASA Astrophysics Data System (ADS)

    Wang, Weihua; Pang, Rui; Kuang, Guowen; Shi, Xingqiang; Shang, Xuesong; Liu, Pei Nian; Lin, Nian

    2015-01-01

    Using cryogenic scanning tunneling microscopy, we measured the electronic states and Kondo resonance of single Fe (II ) -porphyrin molecules adsorbed on a Au ( 111 ) surface with intramolecular resolution. We found that the Fe (II ) ion introduces a spin-polarized molecular state near the Fermi level. Tunneling spectroscopy revealed that this state gives rise to Kondo resonance exhibiting characteristics different from those of the Fe (II ) spin state. Spin-polarized density functional theory calculations revealed that the molecule was weakly adsorbed on the surface, yet still switches its spin configuration from S =1 to2 . The spin switching was found to be driven by three effects: a structural distortion of the macrocyclic ring from planar to saddle shaped, a weak chemical bonding between the Fe and the Au surface atom underneath, and weakened Fe-N bonds due to Au ( 111 ) -molecule charge transfer.

  5. Excited-State Proton Transfer and Intramolecular Charge Transfer in 1,3-Diketone Molecules.

    PubMed

    Savarese, Marika; Brémond, Éric; Adamo, Carlo; Rega, Nadia; Ciofini, Ilaria

    2016-05-18

    The photophysical signature of the tautomeric species of the asymmetric (N,N-dimethylanilino)-1,3-diketone molecule are investigated using approaches rooted in density functional theory (DFT) and time-dependent DFT (TD-DFT). In particular, since this molecule, in the excited state, can undergo proton transfer reactions coupled to intramolecular charge transfer events, the different radiative and nonradiative channels are investigated by making use of different density-based indexes. The use of these tools, together with the analysis of both singlet and triplet potential energy surfaces, provide new insights into excited-state reactivity allowing one to rationalize the experimental findings including different behavior of the molecule as a function of solvent polarity.

  6. 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

  7. A study of intramolecular H-complexes of novel bis(heptamethine cyanine) dyes.

    PubMed

    Kim, Jun Seok; Kodagahally, Ravikumar; Strekowski, Lucjan; Patonay, Gabor

    2005-10-31

    Near-infrared (NIR) bis(heptamethine cyanine) (BHmC) dyes containing a flexible polymethylene linker between the two cyanine subunits are a novel class of compounds with versatile spectroscopic properties. The first bis-cyanine of this type is BHmC-10 (with a decamethylene bridge) that has been reported by us recently [G. Patonay, J.S. Kim, R. Kodagahally, L. Strekowski, Appl. Spectrosc., in press]. As part of this work, additional bis-cyanines BHmC-4, BHmC-6, and BHmC-8 were synthesized and their spectral properties were evaluated for the dyes free in solution and in the presence of human serum albumin (HSA). These bis-cyanines undergo H-type aggregation, mainly H-type intramolecular complexation between the two cyanine subunits, when free in aqueous solution. This H-type interaction in phosphate buffer (pH 7.2) is characterized by hypsochromic (H) absorption at 700nm, low extinction coefficient, and low fluorescence quantum yield. By contrast, an analogous monomeric cyanine exhibits strong fluorescence under similar conditions. Upon binding with HSA, the fluorescence of BHmC-6 changes negligibly, that for BHmC-8 shows a slight increase, and the fluorescence of BHmC-4 is greatly increased. It is suggested that BHmC-4 binds with HSA in the open form exclusively, while the H-type intramolecular interaction in BHmC-6 is mostly retained in the complex with HSA. Bis-cyanine BHmC-4 may be of significant bioanalytical utility due to its negligible fluorescence in aqueous solution and a strong increase in fluorescence upon binding with a protein.

  8. 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.

  9. 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

  10. 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.

  11. Formation of amides, their intramolecular reactions for the synthesis of N-heterocycles, and preparation of a marketed drug, sildenafil: a comprehensive coverage.

    PubMed

    Laha, Joydev K; Patel, Ketul V; Tummalapalli, K S Satyanarayana; Dayal, Neetu

    2016-08-11

    A unified approach to the tandem preparation of diverse nitrogen heterocycles via decarboxylative acylation of ortho-substituted amines with α-oxocarboxylic acids and subsequent intramolecular cyclizations has been developed. The key features of this work include: the first example of transition-metal-free decarboxylative amidation of α-oxocarboxylic acids with ortho-substituted amines, realization of intramolecular cyclization of amides employing nucleophiles that have previously been unexplored, mechanistic investigation of an unprecedented K2S2O8 promoted amide formation and its subsequent intramolecular cyclizations, and application to the synthesis of a best-selling marketed drug. PMID:27430326

  12. Mechanism of the intramolecular Claisen condensation reaction catalyzed by MenB, a crotonase superfamily member.

    PubMed

    Li, Huei-Jiun; Li, Xiaokai; Liu, Nina; Zhang, Huaning; Truglio, James J; Mishra, Shambhavi; Kisker, Caroline; Garcia-Diaz, Miguel; Tonge, Peter J

    2011-11-01

    MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase from the bacterial menaquinone biosynthesis pathway, catalyzes an intramolecular Claisen condensation (Dieckmann reaction) in which the electrophile is an unactivated carboxylic acid. Mechanistic studies on this crotonase family member have been hindered by partial active site disorder in existing MenB X-ray structures. In the current work the 2.0 Å structure of O-succinylbenzoyl-aminoCoA (OSB-NCoA) bound to the MenB from Escherichia coli provides important insight into the catalytic mechanism by revealing the position of all active site residues. This has been accomplished by the use of a stable analogue of the O-succinylbenzoyl-CoA (OSB-CoA) substrate in which the CoA thiol has been replaced by an amine. The resulting OSB-NCoA is stable, and the X-ray structure of this molecule bound to MenB reveals the structure of the enzyme-substrate complex poised for carbon-carbon bond formation. The structural data support a mechanism in which two conserved active site Tyr residues, Y97 and Y258, participate directly in the intramolecular transfer of the substrate α-proton to the benzylic carboxylate of the substrate, leading to protonation of the electrophile and formation of the required carbanion. Y97 and Y258 are also ideally positioned to function as the second oxyanion hole required for stabilization of the tetrahedral intermediate formed during carbon-carbon bond formation. In contrast, D163, which is structurally homologous to the acid-base catalyst E144 in crotonase (enoyl-CoA hydratase), is not directly involved in carbanion formation and may instead play a structural role by stabilizing the loop that carries Y97. When similar studies were performed on the MenB from Mycobacterium tuberculosis, a twisted hexamer was unexpectedly observed, demonstrating the flexibility of the interfacial loops that are involved in the generation of the novel tertiary and quaternary structures found in the crotonase superfamily. This

  13. Solvation dynamics and energetics of intramolecular hydride transfer reactions in biomass conversion.

    PubMed

    Mushrif, Samir H; Varghese, Jithin J; Krishnamurthy, Chethana B

    2015-02-21

    Hydride transfer changes the charge structure of the reactant and thus, may induce reorientation/reorganization of solvent molecules. This solvent reorganization may in turn alter the energetics of the reaction. In the present work, we investigate the intramolecular hydride transfer by taking Lewis acid catalyzed glucose to fructose isomerization as an example. The C2-C1 hydride transfer is the rate limiting step in this reaction. Water and methanol are used as solvents and hydride transfer is simulated in the presence of explicit solvent molecules, treated quantum mechanically and at a finite temperature, using Car-Parrinello molecular dynamics (CPMD) and metadynamics. Activation free energy barrier for hydride transfer in methanol is found to be 50 kJ mol(-1) higher than that in water. In contrast, in density functional theory calculations, using an implicit solvent environment, the barriers are almost identical. Analysis of solvent dynamics and electronic polarization along the molecular dynamics trajectory and the results of CPMD-metadynamics simulation of the hydride transfer process in the absence of any solvent suggest that higher barrier in methanol is a result of non-equilibrium solvation. Methanol undergoes electronic polarization during the hydride transfer step. However, its molecular orientational relaxation is a much slower process that takes place after the hydride transfer, over an extended timescale. This results in non-equilibrium solvation. Water, on the other hand, does not undergo significant electronic polarization and thus, has to undergo minimal molecular reorientation to provide near equilibrium solvation to the transition state and an improved equilibrium solvation to the post hydride shift product state. Hence, the hydride transfer step is also observed to be exergonic in water and endergonic in methanol. The aforementioned explanation is juxtaposed to enzyme catalyzed charge transfer reactions, where the enhanced solvation of the

  14. 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

  15. 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

  16. 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

  17. 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.

  18. 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

    2016-04-21

    Three l-tartaric acid based symmetrical A-π-D-chiral-D-π-A type structural isomeric nitrobenzylidenes (1-3) 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.

  19. Intramolecular Radical Aziridination of Allylic Sulfamoyl Azides by Cobalt(II)-Based Metalloradical Catalysis: Effective Construction of Strained Heterobicyclic Structures.

    PubMed

    Jiang, Huiling; Lang, Kai; Lu, Hongjian; Wojtas, Lukasz; Zhang, X Peter

    2016-09-12

    Cobalt(II)-based metalloradical catalysis (MRC) has been successfully applied for effective construction of the highly strained 2-sulfonyl-1,3-diazabicyclo[3.1.0]hexane structures in high yields through intramolecular radical aziridination of allylic sulfamoyl azides. The resulting [3.1.0] bicyclic aziridines prove to be versatile synthons for the preparation of a diverse range of 1,2- and 1,3-diamine derivatives by selective ring-opening reactions. As a demonstration of its application for target synthesis, the metalloradical intramolecular aziridination reaction has been incorporated as a key step for efficient synthesis of a potent neurokinin 1 (NK1 ) antagonist in 60 % overall yield. PMID:27511474

  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. 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

    2016-04-21

    Three l-tartaric acid based symmetrical A-π-D-chiral-D-π-A type structural isomeric nitrobenzylidenes (1-3) 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

  2. Stereodivergent Intramolecular C(sp(3))-H Functionalization of Azavinyl Carbenes: Synthesis of Saturated Heterocycles and Fused N-Heterotricycles.

    PubMed

    Lindsay, Vincent N G; Viart, Hélène M-F; Sarpong, Richmond

    2015-07-01

    A general approach for the formation of five-membered saturated heterocycles by intramolecular C(sp(3))-H functionalization is reported. Using N-sulfonyltriazoles as Rh(II) azavinyl carbene equivalents, a wide variety of stereodefined cis-2,3-disubstituted tetrahydrofurans were obtained with good to excellent diastereoselectivity from readily available acyclic precursors. The reaction is shown to be amenable to gram scale, and judicious choice of reaction conditions allowed for stereodivergence, providing selective access to the trans diastereomer in good yield. The resulting products were shown to be valuable intermediates for the direct preparation of fused N-heterotricycles in one step by intramolecular C-H amination or Pictet-Spengler cyclization. PMID:26096731

  3. 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.

  4. Enamide-benzyne-[2 + 2] cycloaddition: stereoselective tandem [2 + 2]-pericyclic ring-opening-intramolecular N-tethered [4 + 2] cycloadditions.

    PubMed

    Feltenberger, John B; Hayashi, Ryuji; Tang, Yu; Babiash, Eric S C; Hsung, Richard P

    2009-08-20

    Benzyne-[2 + 2] cycloadditions with enamides are described. This effort led to the development of a highly stereoselective tandem [2 + 2] cycloaddition-pericyclic ring-opening-intramolecular-N-tethered-[4 + 2] cycloaddition for rapid assembly of nitrogen heterocycles.

  5. Ultrafast intramolecular exciton splitting dynamics in isolated low-band-gap polymers and their implications in photovoltaic materials design.

    PubMed

    Rolczynski, Brian S; Szarko, Jodi M; Son, Hae Jung; Liang, Yongye; Yu, Luping; Chen, Lin X

    2012-03-01

    Record-setting organic photovoltaic cells with PTB polymers have recently achieved ~8% power conversion efficiencies (PCE). A subset of these polymers, the PTBF series, has a common conjugated backbone with alternating thieno[3,4-b]thiophene and benzodithiophene moieties but differs by the number and position of pendant fluorine atoms attached to the backbone. These electron-withdrawing pendant fluorine atoms fine tune the energetics of the polymers and result in device PCE variations of 2-8%. Using near-IR, ultrafast optical transient absorption (TA) spectroscopy combined with steady-state electrochemical methods we were able to obtain TA signatures not only for the exciton and charge-separated states but also for an intramolecular ("pseudo") charge-transfer state in isolated PTBF polymers in solution, in the absence of the acceptor phenyl-C(61)-butyric acid methyl ester (PCBM) molecules. This led to the discovery of branched pathways for intramolecular, ultrafast exciton splitting to populate (a) the charge-separated states or (b) the intramolecular charge-transfer states on the subpicosecond time scale. Depending on the number and position of the fluorine pendant atoms, the charge-separation/transfer kinetics and their branching ratios vary according to the trend for the electron density distribution in favor of the local charge-separation direction. More importantly, a linear correlation is found between the branching ratio of intramolecular charge transfer and the charge separation of hole-electron pairs in isolated polymers versus the device fill factor and PCE. The origin of this correlation and its implications in materials design and device performance are discussed.

  6. 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

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

    DOE PAGESBeta

    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.

  8. Ortho-substituted catechol derivatives: the effect of intramolecular hydrogen-bonding pathways on chloride anion recognition.

    PubMed

    Winstanley, Keith J; Smith, David K

    2007-04-13

    This paper reports a series of chloride anion receptors containing two catechol head groups connected through their ortho-positions via a spacer chain. The linking group chosen to attach the spacer chain to the catechol units has a major impact on the anion-binding potential of the receptor. Linking groups that are capable of forming stable six-membered intramolecular hydrogen-bonded rings with the catechol O-H groups significantly inhibit the ability of the catechol units to hydrogen bond to chloride anions. However, where the linking groups are only capable of forming five- or seven-membered intramolecular hydrogen-bonded rings, then anion binding via hydrogen bonding through the catechol O-H groups becomes a possibility. This process is solvent dependent; the presence of competitive solvent (e.g., DMSO-d6) disrupts the intramolecular hydrogen-bonding pattern and enhances anion binding relative to simple unfunctionalized catechol. The most effective receptor is that in which the hydrogen-bonding linker (-CH2CONH-) is most distant from the catechol units and can only form a seven-membered intramolecular hydrogen-bonded ring. In this case, the receptor, which contains two catechol units, is a more effective chloride anion binder than simple unfunctionalized catechol, demonstrating that the two head groups, in combination with the N-H groups in the linker, act cooperatively and enhance the degree of anion binding. In summary, this paper provides insight into the hydrogen-bonding patterns in ortho-functionalized catechols and the impact these have on the potential of the catechol O-H groups to hydrogen bond to a chloride anion.

  9. 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

  10. Intramolecular 1,1-carboboration versus intermolecular FLP addition in reactions of boranes and bis(phenylethynyl)telluroether.

    PubMed

    Tsao, Fu An; Lough, Alan J; Stephan, Douglas W

    2015-03-11

    Reactions of boranes with Te(CCPh)2 proceed via initial intermolecular 1,1-carboboration followed by either an intramolecular carboboration or an FLP addition to a second molecule of the intermediate, yielding 1-bora-4-tellurocyclohexa-2,5-diene heterocycles or tricylic derivatives of 1,4-ditellurocyclohexa-2,5-diene, respectively. The latter species is also shown to convert to the former upon heating.

  11. Intramolecular radical rearrangement reactions of 2-methyleneaziridines: application to the synthesis of substituted piperidines, decahydroquinolines, and octahydroindolizines.

    PubMed

    Prévost, N; Shipman, M

    2001-07-26

    [reaction: see text] Intramolecular 5-exo cyclization of 3-(2-methyleneaziridin-1-yl)propyl radicals leads to the generation of a highly strained, bicyclic aziridinylcarbinyl radical that undergoes C-N bond fission to the ring-expanded aminyl radical. This methodology provides access to substituted 3-methylenepiperidines and, by combining it with an additional 5-exo-trig cyclization reaction, the octahydroindolizidine skeleton.

  12. Dual-face nucleoside scaffold featuring a stereogenic all-carbon quaternary center. Intramolecular silicon tethered group-transfer reaction.

    PubMed

    Tambutet, Guillaume; Becerril-Jiménez, Fabiola; Dostie, Starr; Simard, Ryan; Prévost, Michel; Mochirian, Philippe; Guindon, Yvan

    2014-11-01

    The design of a novel nucleoside scaffold that exhibits an all-carbon quaternary center is reported. This allows for both α- and β-anomers of a given 2'-deoxy-2',2'-difluoro nucleoside analog (NA) to have potential biological activity. Using an intramolecular atom-transfer reaction, an all-carbon quaternary center was obtained without the use of heavy metals and/or harsh conditions. The chemistry developed is efficient, easily scalable and leads to novel libraries of molecules.

  13. Probe development for detection of TERRA 1 intramolecular G-quadruplex formation using a fluorescent adenosine derivative.

    PubMed

    Kim, In Sun; Seo, Young Jun

    2014-03-15

    We developed a probing system to detect the intramolecular G-quadruplex of telomeric repeat-containing RNA (TERRA 1). We used a fluorescent adenosine derivative rA(py) as a fluorophore and incorporated it into the dangling position of the parallel-type G-quadruplex sequence of TERRA 1. The rA(py)-modified G-quadruplex structure exhibited a strong fluorescence emission signal, while the emission signals of the single-strand and duplex structures were much lower.

  14. Short chemoenzymatic total synthesis of ent-hydromorphone: an oxidative dearomatization/intramolecular [4+2] cycloaddition/amination sequence.

    PubMed

    Varghese, Vimal; Hudlicky, Tomas

    2014-04-22

    A short synthesis of ent-hydromorphone has been achieved in twelve steps from β-bromoethylbenzene. The key transformations involved the enzymatic dihydroxylation of the arene to the corresponding cis-dihydrodiol, Mitsunobu coupling with the ring A fragment, oxidative dearomatization of the C3 phenol, and the subsequent [4+2] cycloaddition to form ring B of the morphinan. The synthesis was completed by intramolecular amination at C9.

  15. Isothermal Fourier transform infrared microspectrosopic studies on the stability kinetics of solid-state intramolecular cyclization of aspartame sweetener.

    PubMed

    Cheng, Y D; Lin, S Y

    2000-03-01

    A novel Fourier transform infrared (FT-IR) microspectrophotometer equipped with differential scanning calorimetry (DSC) was used to investigate the kinetics of intramolecular cyclization of aspartame (APM) sweetener in the solid state under isothermal conditions. The thermal-dependent changes in the peak intensity of IR spectra at 1543, 1283, and 1259 cm(-1) were examined to explore the reaction. The results support that the intramolecular cyclization process in APM proceeded in three steps: the methoxyl group of ester was first thermolyzed to release methanol, then an acyl cation was attacked by the lone pair of electrons available on nitrogen by an S(N)1 pathway, and finally ring-closure occurred. The intramolecular cyclization of APM determined by this microscopic FT-IR/DSC system was found to follow zero-order kinetics after a brief induction period. The bond cleavage energy (259.38 kJ/mol) of thermolysis for the leaving group of -OCH(3), the bond conversion energy (328.88 kJ/mol) for the amide II NH band to DKP NH band, and the CN bond formation energy (326.93 kJ/mol) of cyclization for the DKP in the APM molecule were also calculated from the Arrhenius equation. The total activation energy of the DKP formation via intramolecular cyclization was 261.33 kJ/mol, calculated by the above summation of the bond energy of cleavage, conversion, and formation, which was near to the value determined by the DSC or TGA method. This indicates that the microscopic FT-IR/DSC system is useful as a potential tool not only to investigate the degradation mechanism of drugs in the solid state but also to directly predict the bond energy of the reaction.

  16. Tandem Intramolecular Benzyne-Furan Cycloadditions. Total Synthesis of Vineomycinone B2 Methyl Ester

    PubMed Central

    Sparks, Steven M.; Chen, Chi-Li; Martin, Stephen F.

    2007-01-01

    We have exploited tandem intramolecular benzyne–furan cycloadditions employing three different benzyne precursors to generate substituted bisoxabenzonorbornadienes in a single operation. The regiochemical outcomes in these Diels–Alder reactions were effectively controlled by using disposable silicon tethers to link the reacting benzynes and furan moieties. Two different methods for converting the intermediate bisoxabenzonorbornadienes to substituted anthrarufins were developed. The first tactic entails the initial cleavage of the silicon tethers followed by regioselective ring opening of the oxabicycloheptadienes and oxidation of the central ring giving the target anthrarufin, whereas the second features the regioselective ring opening of the oxabicycloheptadienes followed by protiodesilylation and oxidation. When the starting furans bear carbohydrate substitutents, this new methodology enables the rapid assembly of the glycosyl–substituted aromatic cores of complex C-aryl glycoside antibiotics from simple starting materials. The utility of this novel approach to anthrarufins and C-aryl glycosides is exemplified in a triply convergent synthesis of vineomycinone B2 methyl ester. PMID:18728697

  17. Twisted intramolecular charge transfer of methyl p-dimethylaminobenzoate in aqueous β-cyclodextrin solution

    NASA Astrophysics Data System (ADS)

    Jiang, Yun-Bao

    1995-02-01

    This paper reports the investigation of the twisted intramolecular charge transfer (TICT) of methyl p-dimethylaminobenzoate (MDMAB) in aqueous β-cyclodextrin (β-CD) solution by the TICT-typical dual fluorescence. In pure water, MDMAB emits only LE fluorescence, and the TICT fluorescence band is developed with the addition of β-CD. Both the LE and TICT fluorescence bands are continuously enhanced upon the increase of β-CD concentration. The intensity ratio of the TICT band to the LE band shows a hillshaped dependence on β-CD concentration, and a blue shift in both TICT and LE bands is observed with the increase of β-CD concentration, of which the blue shift in TICT band is more appreciable. Formation of a 1:1 MDMAB-β-CD inclusion complex, with an association constant of 580±80 l mol -1, is evaluated. The effect of β-CD on TICT of MDMAB is discussed, with consideration of the fact that aqueous β-CD solution is pseudoaquaorganic binary mixture and that TICT in aqueous solution acts differently than in organic solvents. A comparison is made between the TICT of MDMAB and of DMABN in aqueous β-CD solution.

  18. 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.

  19. 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.

  20. Intramolecular Homolytic Substitution with Amidyl Radicals: A Free-Radical Synthesis of Ebselen and Related Analogues.

    PubMed

    Fong, Mei C.; Schiesser, Carl H.

    1997-05-16

    Irradiation of a water-cooled benzene solution of pyridine-2-thioneoxycarbonyl (PTOC) imidate esters 9 derived from N-butyl-2-(benzylseleno)benzamide (6, R = Bu), 2-(benzylseleno)-N-hexylbenzamide (6, R = Hex), N-benzyl-2-(benzylseleno)benzamide (6, R = Bn), and 2-(benzylseleno)-N-cyclohexylbenzamide (6, R = c-Hex) with a 250-W low-pressure mercury lamp affords the corresponding 1,2-benzisoselenazol-3(2H)-ones (1) in yields of 81-91% (R = primary alkyl) and 45% (R = c-Hex). Presumably, these transformations involve formation of amidyl radicals 2 which undergo subsequent intramolecular homolytic substitution at the selenium atom with expulsion of a benzyl radical. PTOC imidate esters derived from 2-(benzylseleno)benzanilide (6, R = Ph) and 2-(benzylseleno)-N-tert-butylbenzamide (6, R = t-Bu) were unable to be prepared in this manner. 1,2-Benzisoselenazol-3(2H)-ones (1, R = Ph, Hex, i-Pr, t-Bu) could also be prepared in 76-85% yield by reaction of the corresponding 2,2'-diselenobis(benzamide) (15) with benzoyl or tert-butyl peroxide. The mechanisms of these transformations are discussed.

  1. Platinum-catalyzed intramolecular hydrohydrazination: evidence for alkene insertion into a Pt-N bond.

    PubMed

    Hoover, Jessica M; Dipasquale, Antonio; Mayer, James M; Michael, Forrest E

    2010-04-14

    Dicationic (bpy)Pt(II) complexes were found to catalyze the intramolecular hydrohydrazination of alkenes. Reaction optimization revealed Pt(bpy)Cl(2) (10 mol %) and AgOTf (20 mol %) in DMF-d(7) to be an effective catalyst system for the conversion of substituted hydrazides to five- and six-membered N-amino lactams (N-amino = N-acetamido at 120 degrees C, N-phthalimido at 80 degrees C, (-)OTf = trifluoromethanesulfonate). Of the four possible regioisomeric products, only the product of 5-exo cyclization at the proximal nitrogen is formed, without reaction at the distal nitrogen or 6-endo cyclization. The resting states were found to be a 2:1 Pt-amidate complex (25, for N-acetamido) of the deprotonated hydrazide and a Pt-alkyl complex of the cyclized pyrrolidinone (20 for N-phthalimido). Both complexes are catalytically competent. Catalysis using 25 as the precatalyst shows no rate dependence on added acid (HOTf) or base (2,6-lutidine). The available mechanistic data are all consistent with a mechanism involving N-H activation of the hydrazide, followed by insertion of the alkene into the Pt-N bond, and finally protonation of the resulting cyclized alkyl complex by hydrazide to release the hydrohydrazination product and regenerate the active Pt-amidate catalyst. PMID:20334376

  2. 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.

  3. Heat maps for intramolecular communication in an RNP enzyme encoding glutamine.

    PubMed

    Rodríguez-Hernández, Annia; Perona, John J

    2011-03-01

    Allosteric signaling within large ribonucleoproteins modulates both catalytic function and biological specificity, but the spatial extent and quantitative magnitudes of long-distance free-energy couplings have yet to be well characterized. Here, we employ pre-steady-state kinetics to generate a comprehensive mapping of intramolecular communication in the glutaminyl-tRNA synthetase:tRNA(Gln) complex. Alanine substitution at 29 positions across the protein-RNA interface reveals distinct coupling amplitudes for glutamine binding and aminoacyl-tRNA formation on the enzyme, respectively, implying the existence of multiple signaling pathways. Structural models suggest that long-range signal propagation from the tRNA anticodon is dynamically driven, whereas shorter pathways are mediated by induced-fit rearrangements. Seven protein contacts with the distal tRNA vertical arm each weaken glutamine binding affinity across distances up to 40 Å, demonstrating that negative allosteric coupling plays a key role in enforcing the selective RNA-amino acid pairing at the heart of the genetic code. PMID:21397189

  4. Direct Attack on RAS: Intramolecular Communication and Mutation-Specific Effects.

    PubMed

    Marcus, Kendra; Mattos, Carla

    2015-04-15

    The crystal structure of RAS was first solved 25 years ago. In spite of tremendous and sustained efforts, there are still no drugs in the clinic that directly target this major driver of human cancers. Recent success in the discovery of compounds that bind RAS and inhibit signaling has fueled renewed enthusiasm, and in-depth understanding of the structure and function of RAS has opened new avenues for direct targeting. To succeed, we must focus on the molecular details of the RAS structure and understand at a high-resolution level how the oncogenic mutants impair function. Structural networks of intramolecular communication between the RAS active site and membrane-interacting regions on the G-domain are disrupted in oncogenic mutants. Although conserved across the isoforms, these networks are near hot spots of protein-ligand interactions with amino acid composition that varies among RAS proteins. These differences could have an effect on stabilization of conformational states of interest in attenuating signaling through RAS. The development of strategies to target these novel sites will add a fresh direction in the quest to conquer RAS-driven cancers. Clin Cancer Res; 21(8); 1810-8. ©2015 AACR. See all articles in this CCR Focus section, "Targeting RAS-Driven Cancers." PMID:25878362

  5. Rate-equilibria relationships in intramolecular proton transfer in human carbonic anhydrase III.

    PubMed

    Silverman, D N; Tu, C; Chen, X; Tanhauser, S M; Kresge, A J; Laipis, P J

    1993-10-12

    Maximal turnover rates for the dehydration of HCO3- catalyzed by the zinc metalloenzyme carbonic anhydrase III are limited by a proton transfer to zinc-bound hydroxide in the active site. We have used site-directed mutagenesis to place a proton donor, histidine, at position 64 and used 18O exchange between CO2 and water measured by mass spectrometry to determine the rates of intramolecular proton transfer to the zinc-bound hydroxide. In a series of site-specific mutants, the values of pKa of the zinc-bound water ranged from approximately 5 to 9. The rate constants for proton transfer obeyed a Brønsted correlation and showed sharp curvature characteristic of facile proton transfers. Application of Marcus rate theory shows that this proton transfer has the small intrinsic energy barrier (near 1.5 kcal/mol) characteristic of rapid proton transfer between nitrogen and oxygen acids and bases, but has an observed overall energy barrier (near 10 kcal/mol), indicating the involvement of accompanying, energy requiring processes such as solvent reorganization or conformational change. PMID:8399223

  6. Intramolecular photoinduced electron transfer of fluorescent probes based on 1,8-naphthalimide and aniline derivatives

    NASA Astrophysics Data System (ADS)

    Burmistrova, Natalia A.; Mushtakova, Svetlana P.; Zilberg, Rufina A.; Vakulin, Ivan V.; Duerkop, Axel

    2015-03-01

    The effect of conformation and electronic structure of fluorescent probes based on 1,8-naphthalimide and aniline derivatives (4-methoxyaniline and N,N-dimethyl-p-phenylenediamine) on the intramolecular photoinduced electron transfer (PET) was investigated by density functional theory calculations (B3LYP/6-31G (d, p)). We established restricted rotation around spacer bonds of the model compounds and their protonated and oxidized forms do not block the convergence of the nitrogen atoms involved in the electron transfer at a distance of ~3Å, which is adequately for PET. Computed values of protonation free energy for the gas-phase (ΔG298 r) show that the investigated fluorescent probes are predominantly protonated on the nitrogen atoms of the donor moiety. Electron population and localization of the frontier orbitals (LUMO, HOMO, HOMO-1) on the donor and acceptor moieties are transformed under protonation and one-electron oxidation of fluorescent probes. The results show that appearance or disappearance of the PET can be predicted by the energy difference between the frontier orbitals and the nature of their location of donor and acceptor moieties, which is in agreement with the PET theory and observed experimental data.

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

    PubMed

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

    2016-01-29

    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.

  8. Intramolecular co-action of two independent photosensory modules in the fern phytochrome 3.

    PubMed

    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.

  9. Dynamical traps lead to the slowing down of intramolecular vibrational energy flow

    PubMed Central

    Manikandan, Paranjothy; Keshavamurthy, Srihari

    2014-01-01

    The phenomenon of intramolecular vibrational energy redistribution (IVR) is at the heart of chemical reaction dynamics. Statistical rate theories, assuming instantaneous IVR, predict exponential decay of the population with the properties of the transition state essentially determining the mechanism. However, there is growing evidence that IVR competes with the reaction timescales, resulting in deviations from the exponential rate law. Dynamics cannot be ignored in such cases for understanding the reaction mechanisms. Significant insights in this context have come from the state space model of IVR, which predicts power law behavior for the rates with the power law exponent, an effective state space dimensionality, being a measure of the nature and extent of the IVR dynamics. However, whether the effective IVR dimensionality can vary with time and whether the mechanism for the variation is of purely quantum or classical origins are issues that remain unresolved. Such multiple power law scalings can lead to surprising mode specificity in the system, even above the threshold for facile IVR. In this work, choosing the well-studied thiophosgene molecule as an example, we establish the anisotropic and anomalous nature of the quantum IVR dynamics and show that multiple power law scalings do manifest in the system. More importantly, we show that the mechanism of the observed multiple power law scaling has classical origins due to a combination of trapping near resonance junctions in the network of classical nonlinear resonances at short to intermediate times and the influence of weak higher-order resonances at relatively longer times. PMID:25246538

  10. 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

  11. 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

  12. Intramolecular excited-state interactions of surfactant-active osmium(II) photosensitizers

    SciTech Connect

    Sasksteder, L.; Demas, J.N. ); DeGraff, B.A. )

    1989-05-17

    A new class of luminescent surfactant-active complexes, cis-OsL{sub 2}(CO)NC(CH{sub 2}){sub n}CH{sub 3}{sup 2+} (n = 0-19; L = 2,2{prime}-bipyridine and 1,10-phenanthroline), were synthesized and characterized. They represent another example of an intramolecular perturbation of excited-state properties by what would normally be considered an electronically passive alkyl ligand. The effect is smaller in the Os(II) case and has a different n dependence than was observed in the fac-ReL(CO){sub 3}NC(CH{sub 2}){sub n}CH{sub 3}{sup +} system. The differences arise from varied geometric constraints on the foldback and the orbital parentage of the emitting state. Foldback must be directly to ligands involved in the emission process in order to perturb the emission. The osmium(II) center highly activates the bound nitrile to thermal nucleophilic attack, and luminescent adducts are formed with alcohols and aliphatic and aromatic amines. Such activation has not been previously observed in complexes with {alpha}-diimine ligands. The complexes also photodecompose by labilization of the nitrile. 37 refs., 5 figs.

  13. 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

  14. Intramolecular singlet-singlet energy transfer in antenna-substituted azoalkanes.

    PubMed

    Pischel, Uwe; Huang, Fang; Nau, Werner M

    2004-03-01

    Two novel azoalkane bichromophores and related model compounds have been synthesised and photophysically characterised. Dimethylphenylsiloxy (DPSO) or dimethylnaphthylsiloxy (DNSO) serve as aromatic donor groups (antenna) and the azoalkane 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) as the acceptor. The UV spectral window of DBO (250-300 nm) allows selective excitation of the donor. Intramolecular singlet-singlet energy transfer to DBO is highly efficient and proceeds with quantum yields of 0.76 with DPSO and 0.99 with DNSO. The photophysical and spectral properties of the bichromophoric systems suggest that energy transfer occurs through diffusional approach of the donor and acceptor within a van der Waals contact at which the exchange mechanism is presumed to dominate. Furthermore, akin to the behaviour of electron-transfer systems in the Marcus inverted region, a rate of energy transfer 2.5 times slower was observed for the system with the more favourable energetics, i.e. singlet-singlet energy transfer from DPSO proceeded slower than from DNSO, although the process is more exergonic for DPSO (-142 kJ mol(-1) for DPSO versus-67 kJ mol(-1) for DNSO).

  15. 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.

  16. 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.

  17. The mucin-degradation strategy of Ruminococcus gnavus: The importance of intramolecular trans-sialidases

    PubMed Central

    Crost, Emmanuelle H.; Tailford, Louise E.; Monestier, Marie; Swarbreck, David; Henrissat, Bernard; Crossman, Lisa C.; Juge, Nathalie

    2016-01-01

    ABSTRACT We previously identified and characterized an intramolecular trans-sialidase (IT-sialidase) in the gut symbiont Ruminococcus gnavus ATCC 29149, which is associated to the ability of the strain to grow on mucins. In this work we have obtained and analyzed the draft genome sequence of another R. gnavus mucin-degrader, ATCC 35913, isolated from a healthy individual. Transcriptomics analyses of both ATCC 29149 and ATCC 35913 strains confirmed that the strategy utilized by R. gnavus for mucin-degradation is focused on the utilization of terminal mucin glycans. R. gnavus ATCC 35913 also encodes a predicted IT-sialidase and harbors a Nan cluster dedicated to sialic acid utilization. We showed that the Nan cluster was upregulated when the strains were grown in presence of mucin. In addition we demonstrated that both R. gnavus strains were able to grow on 2,7-anyhydro-Neu5Ac, the IT-sialidase transglycosylation product, as a sole carbon source. Taken together these data further support the hypothesis that IT-sialidase expressing gut microbes, provide commensal bacteria such as R. gnavus with a nutritional competitive advantage, by accessing and transforming a source of nutrient to their own benefit. PMID:27223845

  18. A manganese catalyst for highly reactive yet chemoselective intramolecular C(sp(3))-H amination.

    PubMed

    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(sp(3))-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((t)BuPc)], that is an outlier to the reactivity-selectivity paradigm. It is unique in its capacity to functionalize all types of C(sp(3))-H bond intramolecularly, while displaying excellent chemoselectivity in the presence of π functionality. Mechanistic studies indicate that [Mn((t)BuPc)] transfers bound nitrenes to C(sp(3))-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((t)BuPc)] aminates even 1° aliphatic and propargylic C-H bonds, demonstrating reactivity and selectivity unusual for previously known catalysts. PMID:26587714

  19. 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

  20. 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

  1. 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

  2. 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

  3. Vibrational study of intramolecular hydrogen bonding in o-hydroxybenzoyl compounds

    NASA Astrophysics Data System (ADS)

    Palomar, J.; De Paz, J. L. G.; Catalán, J.

    1999-07-01

    The vibrational study of a set of o-hydroxybenzoyl compounds (salicylaldehyde, o-hydroxyacetophenone, methyl salicylate and salicylamide) and their parent compounds (phenol, benzaldehyde, acetophenone, methyl benzoate and benzamide) has been performed by infrared (IR) measurements and by quantum chemical calculations using B3LYP density functional in conjunction with 6-31G ∗∗ and 6-311++G(3df, 2p) basis sets. The assignment of the infrared bands results unequivocal for most cases, including those signals in which the motion of the intramolecular hydrogen bond (IMHB) is involved. The analysis of the IR spectra for the deuterated derivatives was proved to be a very useful tool for this purpose. A model based on isotopically substituted benzenes was used for classifying the phenyl ring movements of the molecules studied. The results obtained show the suitability and limitation of the harmonic treatment using B3LYP method to describe the characteristic IMHB vibrations. Vibrational data are analyzed in order to obtain information about the nature of the hydrogen bonding interaction in this family of compounds. Finally, the available empirical relationships to approximate the IMHB energy from experimental spectroscopic data are revised in view of the new theoretical results.

  4. 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.

  5. 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

  6. 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

  7. Contribution of inter- and intramolecular energy transfers to heat conduction in liquids

    NASA Astrophysics Data System (ADS)

    Torii, Daichi; Nakano, Takeo; Ohara, Taku

    2008-01-01

    The molecular dynamics expression of heat flux, originally derived by Irving and Kirkwood [J. Chem. Phys. 18, 817 (1950)] for pairwise potentials, is generalized in this paper for systems with many-body potentials. The original formula consists of a kinetic part and a potential part, and the latter term is found in the present study to be expressible as a summation of contributions from all the many-body potentials defined in the system. The energy transfer among a set of sites for which a many-body potential is defined is discussed and evaluated by the rate of increase in the kinetic energy of each site due to the potential, and its accumulation over all the potentials in the system is shown to make up the potential part of the generalized expression. A molecular dynamics simulation for liquid n-octane was performed to demonstrate the applicability of the new expression obtained in this study to measure the heat flux and to elucidate the contributions of inter- and intramolecular potentials to heat conduction.

  8. Tandem sequence of phenol oxidation and intramolecular addition as a method in building heterocycles.

    PubMed

    Ratnikov, Maxim O; Farkas, Linda E; Doyle, Michael P

    2012-11-16

    A tandem phenol oxidation-Michael addition furnishing oxo- and -aza-heterocycles has been developed. Dirhodium caprolactamate [Rh(2)(cap)(4)] catalyzed oxidation by T-HYDRO of phenols with alcohols, ketones, amides, carboxylic acids, and N-Boc protected amines tethered to their 4-position afforded 4-(tert-butylperoxy)cyclohexa-2,5-dienones that undergo Brønsted acid catalyzed intramolecular Michael addition in one-pot to produce oxo- and -aza-heterocycles in moderate to good yields. The scope of the developed methodology includes dipeptides Boc-Tyr-Gly-OEt and Boc-Tyr-Phe-Me and provides a pathway for understanding the possible transformations arising from oxidative stress of tyrosine residues. A novel method of selective cleavage of O-O bond in hindered internal peroxide using TiCl(4) has been discovered in efforts directed to the construction of cleroindicin F, whose synthesis was completed in 50% yield over just 3 steps from tyrosol using the developed methodology.

  9. Controlling Intramolecular Conformation through Nonbonding Interaction for Soft-Conjugated Materials: Molecular Design and Optoelectronic Properties.

    PubMed

    Cheng, Yuanfang; Qi, Yuanyuan; Tang, Yuting; Zheng, Chao; Wan, Yifang; Huang, Wei; Chen, Runfeng

    2016-09-15

    To address the intrinsic contradiction between high optoelectronic properties and good processability in organic π-conjugated molecules, we propose that soft-conjugated molecules (SCMs), conformationally locked by intramolecular nonbonding interactions, can benefit from both nonplanar molecular structures in solution for processing and rigid coplanar structures in the solid state for enhanced optoelectronic properties. Computational results reveal that nonbonding pairs of S···N, N···H, and F···S are strong enough to prevail over thermal fluctuations, steric effects, and other repulsive interactions to force the adjacent aromatic rings to be planar; thus, constructed SCMs display delocalized frontier molecular orbitals with frontier orbital energy levels, band gaps, reorganization energies, and photophyscial properties comparable to those of rigid-conjugated molecules because of their stable planar soft-conjugation at both ground and excited states. The understanding gained from the theoretical investigations of SCMs provides keen insights into construction and modification of soft-conjugations to harmonize the optoelectronic property and processability in conjugated molecules for advanced optoelectronic applications. PMID:27569364

  10. 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.

  11. 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.

  12. Estimation of N-H...O=C intramolecular hydrogen bond energy in polypeptides.

    PubMed

    Deshmukh, Milind M; Gadre, Shridhar R

    2009-07-01

    The previously proposed molecular tailoring approached (MTA) [Deshmukh, M. M.; Gadre, S. R.; Bartolotti, L. J. J. Phys. Chem. A 2006, 110, 12519] for the estimation of intramolecular O-H...O hydrogen bond energy is extended to that for the N-H...O=C bond within polypeptides. The methodology is initially tested on a tetrapeptide containing two types of N-H...O=C hydrogen bonds and is found to distinguish between them. The estimated values are in good agreement with the trends predicted by the geometrical parameters. Furthermore, this methodology is applied to partially as well as fully substituted, capped polyglycines that contain five glycine residues (acetyl-(gly)(5)-NH(2)) to check the effect of substituents on the energetics of hydrogen bonds. The estimated N-H...O=C bond energy values lie in the range of 4-6 kcal/mol. These estimated values are not only in concurrence with the geometric parameters but also able to reflect the subtle effects of substituents for the substituted polypeptides studied in the present work.

  13. 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.

  14. 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.

  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 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. 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.

  18. Measurement of the intramolecular isotope effect on aliphatic hydroxylation by Chromobacterium violaceum phenylalanine hydroxylase.

    PubMed

    Panay, Aram J; Fitzpatrick, Paul F

    2010-04-28

    The non-heme iron enzyme phenylalanine hydroxylase from Chromobacterium violaceum has previously been shown to catalyze the hydroxylation of benzylic and aliphatic carbons in addition to the normal aromatic hydroxylation reaction. The intrinsic isotope effect for hydroxylation of 3-cyclochexylalanine by the enzyme was determined in order to gain insight into the reactivity of the iron center. With 3-[(2)H(11)-cyclohexyl]alanine as the substrate, the isotope effect on the k(cat) value was 1, consistent with an additional step in the overall reaction being significantly slower than hydroxylation. Consequently, the isotope effect was determined as an intramolecular effect by measuring the amount of deuterium lost in the hydroxylation of 3-[1,2,3,4,5,6-(2)H(6)-cyclohexyl]alanine. The ratio of 4-HO-cyclohexylalanine that retained deuterium to that which lost one deuterium atom was 2.8. This gave a calculated value of 12.6 for the ratio of the primary deuterium kinetic isotope effect to the secondary isotope effect. This value is consistent with hydrogen atom abstraction by an electrophilic Fe(O) center and a contribution of quantum-mechanical tunneling to the reaction.

  19. 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.

  20. 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

  1. 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

  2. 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

  3. Formation of H3^+ in methanol : an intramolecular bond rearrangement study

    NASA Astrophysics Data System (ADS)

    de, Sankar; Rajput, Jyoti; Roy, A.; Safvan, C. P.; Ghosh, P. N.

    2007-06-01

    We report here results of TOF multi-hit coincidence experiment [1] that provide evidence for intramolecular reactions involving proton coagulation in methanol [2] after interaction with 1.2 MeV Ar^8+ projectiles produced from the ECR ion source in the LEIBF laboratory of Inter-University Accelerator Centre, India. Quite remarkably, we have observed the formation of H3^+ due to movement of protons within the multiply charged parent molecular ion through two-body process (CH3OH^2+->H3^+ + COH^+) and such bond formation occurs before the Coulomb repulsion makes the fragment ions to fly apart. Analysis of the fragmentation pattern of CH3OH^2+ has been carried out using ab initio quantum chemical techniques. Structural calculations indicate that the formation of H3^+ is the preferred pathway in the overall fragmentation dynamics of the ground state of this alcohol. The field generated from highly charged ions induces the system to rearrange its structure following a minimum energy pathway and form hydrogen molecular ions. Repeating the experiment with CH3OD confirm our bond rearrangement phenomenon and establish that H3^+ formation occurs only within the methyl group of the alcohol. Ref: [1] S. De et. al. NIMB, 243, 435 (2006) [2] Sankar De et. al. PRL, 97, 213201 (2006)

  4. [Asymmetric intramolecular conjugate addition of chiral enolates via non-equilibrium].

    PubMed

    Monguchi, Daiki

    2006-08-01

    Optically active alpha,alpha-disubstituted alpha-amino acids belong to an important class of unnatural amino acids. Since the synthesis of such amino acids involves the creation of a quaternary stereocenter, methods for their synthesis have been extensively studied. We have reported that N-t-butoxycarbonyl(Boc)-N-methoxymethyl(MOM)-amino acid derivatives undergo asymmetric alpha-alkylation in up to 93% ee. Original chiral information on an amino acid is preserved in axially chiral enolate intermediates, and thus asymmetric induction is achieved without the aid of external chiral sources (i.e., memory of chirality). Recently, we have reported a new protocol for the asymmetric cyclization of amino acid derivatives, which enables straightforward synthesis of cyclic amino acids with a tetrasubstituted carbon center from the usual alpha-amino acids in up to 98% ee. Here we report the asymmetric construction of highly substituted chiral nitrogen heterocycles via intramolecular conjugate addition of chiral enolates generated from N-Boc-N-alkylylamino acid derivatives. This method is applicable to the asymmetric construction of pyrrolidine, piperidine, tetrahydroisoquinoline, and indoline derivatives with contiguous quaternary and tertiary stereocenters.

  5. Controlling Intramolecular Conformation through Nonbonding Interaction for Soft-Conjugated Materials: Molecular Design and Optoelectronic Properties.

    PubMed

    Cheng, Yuanfang; Qi, Yuanyuan; Tang, Yuting; Zheng, Chao; Wan, Yifang; Huang, Wei; Chen, Runfeng

    2016-09-15

    To address the intrinsic contradiction between high optoelectronic properties and good processability in organic π-conjugated molecules, we propose that soft-conjugated molecules (SCMs), conformationally locked by intramolecular nonbonding interactions, can benefit from both nonplanar molecular structures in solution for processing and rigid coplanar structures in the solid state for enhanced optoelectronic properties. Computational results reveal that nonbonding pairs of S···N, N···H, and F···S are strong enough to prevail over thermal fluctuations, steric effects, and other repulsive interactions to force the adjacent aromatic rings to be planar; thus, constructed SCMs display delocalized frontier molecular orbitals with frontier orbital energy levels, band gaps, reorganization energies, and photophyscial properties comparable to those of rigid-conjugated molecules because of their stable planar soft-conjugation at both ground and excited states. The understanding gained from the theoretical investigations of SCMs provides keen insights into construction and modification of soft-conjugations to harmonize the optoelectronic property and processability in conjugated molecules for advanced optoelectronic applications.

  6. 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.

  7. Intramolecular excimer kinetics of fluorescent dipyrenyl lipids: 1. DMPC/cholesterol membranes.

    PubMed Central

    Cheng, K H; Ruymgaart, L; Liu, L I; Somerharju, P; Sugar, I P

    1994-01-01

    The intramolecular dynamics of the excimer forming dipyrenyl lipids (DipynPC) of different chain lengths (n) in ethanol and in dimyristoylphosphatidycholine (DMPC) membranes was investigated by the use of frequency-domain fluorescence intensity decay technique. Based on a 3-state model, the extent of aggregation and rotational rate of the two intralipid pyrene moieties in the dipyrenyl lipids were estimated from the frequency-domain data. In ethanol (20 degrees C), the rotational rate for DipynPC increased progressively as n was varied from 4 to 12. At the gel (L beta)-to-liquid crystalline (L alpha) phase transition of DMPC (approximately 23 degrees C), the rotational rate increased and aggregation decreased significantly for Dipy10PC, whereas only the rotational rate was changed for Dipy4PC. In the presence of 30 mol% cholesterol, significant increases in both the rotational rate and aggregation were observed for Dipy10PC in both L beta and L alpha phases. However, for the case of Dipy4PC, an increase in the rotational rate but a decrease in the aggregation were noticed only in the L beta phase, and no similar changes were detected in the L alpha phase. Our results indicate differential effects of cholesterol on the conformational dynamics of acyl chains at different depths of the membranes. PMID:7948704

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. N-H-Type Excited-State Proton Transfer in Compounds Possessing a Seven-Membered-Ring Intramolecular Hydrogen Bond.

    PubMed

    Chen, Yi-An; Meng, Fan-Yi; Hsu, Yen-Hao; Hung, Cheng-Hsien; Chen, Chi-Lin; Chung, Kun-You; Tang, Wei-Feng; Hung, Wen-Yi; Chou, Pi-Tai

    2016-10-01

    A series of compounds containing 5-(2-aminobenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one (o-ABDI) as the core chromophore with a seven-membered-ring N-H-type intramolecular hydrogen bond have been synthesized and characterized. The acidity of the N-H proton and thus the hydrogen-bond strength can be fine-tuned by replacing one of the amino hydrogen atoms by a substituent R, the acidity increasing with increasing electron-withdrawing strength of R, that is, in the order Hintramolecular proton transfer (ESIPT) that results in proton-transfer emission solely in the red region. Reversible ESIPT, and hence dual emission, involving the normal and proton-transfer tautomers was resolved for the acetyl- and benzyl-substituted counterparts. For o-ABDI, which has the weakest acidity, ESIPT is prohibited due to its highly endergonic reaction. The results clearly demonstrate the harnessing of ESIPT by modifying the proton acidity and hydrogen-bonding strength in a seven-membered-ring intramolecular hydrogen-bonding system. For all the compounds studied, the emission quantum yields are weak (ca. 10(-3) ) in dichloromethane, but strong in the solid form, ranging from 3.2 to 47.4 %. PMID:27539818

  15. 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

  16. Intramolecular hydrogen bonds involving organic fluorine in the derivatives of hydrazides: an NMR investigation substantiated by DFT based theoretical calculations.

    PubMed

    Mishra, Sandeep Kumar; Suryaprakash, N

    2015-06-21

    The rare examples of intramolecular hydrogen bonds (HB) of the type the N-H∙∙∙F-C, detected in a low polarity solvent in the derivatives of hydrazides, by utilizing one and two-dimensional solution state multinuclear NMR techniques, are reported. The observation of through-space couplings, such as, (1h)JFH, and (1h)JFN, provides direct evidence for the existence of intra-molecular HB. Solvent induced perturbations and the variable temperature NMR experiments unambiguously establish the presence of intramolecular HB. The existence of multiple conformers in some of the investigated molecules is also revealed by two dimensional HOESY and (15)N-(1)H HSQC experiments. The (1)H DOSY experimental results discard any possibility of self or cross dimerization of the molecules. The derived NMR experimental results are further substantiated by Density Function Theory (DFT) based Non Covalent Interaction (NCI), and Quantum Theory of Atom in Molecule (QTAIM) calculations. The NCI calculations served as a very sensitive tool for detection of non-covalent interactions and also confirm the presence of bifurcated HBs.

  17. Utilization of an intramolecular hydrogen bond to increase the CNS penetration of an NK(1) receptor antagonist.

    PubMed

    Ashwood, V A; Field, M J; Horwell, D C; Julien-Larose, C; Lewthwaite, R A; McCleary, S; Pritchard, M C; Raphy, J; Singh, L

    2001-07-01

    This paper describes the synthesis and physical and biological effects of introducing different substituents at the alpha-position of the tryptophan containing neurokinin-1 receptor antagonist [(R)-2-(1H-indol-3-yl)-1-methyl-1-((S)-1-phenyl-ethylcarbamoyl)-ethyl]-carbamic acid benzofuran-2-ylmethyl ester (CI 1021). The described compounds all exhibit less than 5 nM binding affinities for the human neurokinin-1 receptor and selectivity over the tachykinin NK(2) and NK(3) receptor subtypes. Application of variable temperature nuclear magnetic resonance spectroscopy studies of the amide and urethane protons was utilized to determine the existence of an intramolecular hydrogen bond. This intramolecular hydrogen bond increases the apparent lipophilicity to allow increased central nervous system penetration and pharmacological activity (gerbil foot tap test) in the case of the highest affinity compound [(S)-1-dimethylaminomethyl-2-(1H-indol-3-yl)-1-((S)-1-phenyl-ethylcarbamoyl)-ethyl]-carbamic acid benzofuran-2-ylmethyl ester (PD 174424) over those analogues that could not form an intramolecular hydrogen bond. PMID:11428921

  18. 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.

  19. Pyrrolidine and piperidine formation via copper(II) carboxylate-promoted intramolecular carboamination of unactivated olefins: diastereoselectivity and mechanism.

    PubMed

    Sherman, Eric S; Fuller, Peter H; Kasi, Dhanalakshmi; Chemler, Sherry R

    2007-05-11

    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 gamma- and delta-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.

  20. 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.

  1. Post-transition State Dynamics for Propene Ozonolysis: Intramolecular and Unimolecular Dynamics of Molozonide

    SciTech Connect

    Vayner, Grigoriy; Addepalli, Srirangam V.; Song, Kihyung; Hase, William L.

    2006-07-07

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. A direct chemical dynamics simulation, at the B3LYP/6-31G(d) level of theory, was used to study the post-transition state intramolecular and unimolecular dynamics for the O₃+propene reaction. Comparisons of B3LYP/6-31G(d) with CCSD(T)/cc-pVTZ and other levels of theory show that the former gives accurate structures and energies for the reaction’s stationary points. The direct dynamics simulations are initiated at the anti and syn O₃+propene transition states (TSs) and the TS symmetries are preserved in forming the molozonide intermediates. Anti↔syn molozonide isomerization has a very low barrier of 2–3 kcal/mol and its Rice-Ramsperger-Kassel-Marcus (RRKM) lifetime is 0.3 ps. However, the trajectory isomerization is slower and it is unclear whether this anti↔syn equilibration is complete when the trajectories are terminated at 1.6 ps. The syn (anti) molozonides dissociate to CH₃CHO+H₂COO and H₂CO+syn (anti) CH₃CHOO. The kinetics for the latter reactions are in overall good agreement with RRKM theory, but there is a symmetry preserving non-RRKM dynamical constraint for the former. Dissociation of anti molozonide to CH₃CHO+H₂COO is enhanced and suppressed, respectively, for the trajectory ensembles initiated at the anti and syn O₃+propene TSs. The dissociation of syn molozonide to CH₃CHO+H₂COO may also be enhanced for trajectories initiated at the syn O₃+propene TS. At the time the trajectories are terminated at 1.6 ps, the ratio of the trajectory and RRKM values of the CH₃CHO+H₂COO product yield is 1.6 if the symmetries of the initiation and dissociation TSs are the same and 0.6 if their symmetries are different. There are coherences in the

  2. 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.

  3. Dependence of effective molarity on linker length for an intramolecular protein-ligand system.

    PubMed

    Krishnamurthy, Vijay M; Semetey, Vincent; Bracher, Paul J; Shen, Nan; Whitesides, George M

    2007-02-01

    This paper reports dissociation constants and "effective molarities" (M(eff)) for the intramolecular binding of a ligand covalently attached to the surface of a protein by oligo(ethylene glycol) (EG(n)) linkers of different lengths (n = 0, 2, 5, 10, and 20) and compares these experimental values with theoretical estimates from polymer theory. As expected, the value of M(eff) is lowest when the linker is too short (n = 0) to allow the ligand to bind noncovalently at the active site of the protein without strain, is highest when the linker is the optimal length (n = 2) to allow such binding to occur, and decreases monotonically as the length increases past this optimal value (but only by a factor of approximately 8 from n = 2 to n = 20). These experimental results are not compatible with a model in which the single bonds of the linker are completely restricted when the ligand has bound noncovalently to the active site of the protein, but they are quantitatively compatible with a model that treats the linker as a random-coil polymer. Calorimetry revealed that enthalpic interactions between the linker and the protein are not important in determining the thermodynamics of the system. Taken together, these results suggest that the manifestation of the linker in the thermodynamics of binding is exclusively entropic. The values of M(eff) are, theoretically, intrinsic properties of the EG(n) linkers and can be used to predict the avidities of multivalent ligands with these linkers for multivalent proteins. The weak dependence of M(eff) on linker length suggests that multivalent ligands containing flexible linkers that are longer than the spacing between the binding sites of a multivalent protein will be effective in binding, and that the use of flexible linkers with lengths somewhat greater than the optimal distance between binding sites is a justifiable strategy for the design of multivalent ligands.

  4. Functional Characterization of Propeptides in Plant Subtilases as Intramolecular Chaperones and Inhibitors of the Mature Protease.

    PubMed

    Meyer, Michael; Leptihn, Sebastian; Welz, Max; Schaller, Andreas

    2016-09-01

    Subtilisin-like serine proteases (SBTs) are extracellular proteases that depend on their propeptides for zymogen maturation and activation. The function of propeptides in plant SBTs is poorly understood and was analyzed here for the propeptide of tomato subtilase 3 (SBT3PP). SBT3PP was found to be required as an intramolecular chaperone for zymogen maturation and secretion of SBT3 in vivo Secretion was impaired in a propeptide-deletion mutant but could be restored by co-expression of the propeptide in trans SBT3 was inhibited by SBT3PP with a Kd of 74 nm for the enzyme-inhibitor complex. With a melting point of 87 °C, thermal stability of the complex was substantially increased as compared with the free protease suggesting that propeptide binding stabilizes the structure of SBT3. Even closely related propeptides from other plant SBTs could not substitute for SBT3PP as a folding assistant or autoinhibitor, revealing high specificity for the SBT3-SBT3PP interaction. Separation of the chaperone and inhibitor functions of SBT3PP in a domain-swap experiment indicated that they are mediated by different regions of the propeptide and, hence, different modes of interaction with SBT3. Release of active SBT3 from the autoinhibited complex relied on a pH-dependent cleavage of the propeptide at Asn-38 and Asp-54. The remarkable stability of the autoinhibited complex and pH dependence of the secondary cleavage provide means for stringent control of SBT3 activity, to ensure that the active enzyme is not released before it reaches the acidic environment of the trans-Golgi network or its final destination in the cell wall. PMID:27451395

  5. Intramolecular localization of the functional units of Sepia officinalis hemocyanin by immunoelectron microscopy.

    PubMed

    Lamy, J; You, V; Taveau, J C; Boisset, N; Lamy, J N

    1998-12-11

    The quaternary structure of Sepia officinalis hemocyanin (Hc) as studied in immunoelectron microscopy with rabbit IgGs and Fab fragments raised against functional units (FU) Soc, Sod, Soe, Sof, Sog, and Soh and fragment Soab. The architecture of immunocomplexes shows that (i) epitopes characteristic of FUs Soc and Sog and of fragment Soab are located in the two external tiers of FUs, (ii) FUs Soh and Soe or Sod are located in arches. These results were confirmed using immunocomplexes made up of Sepia Hc and IgGs or Fab fragments purified from antisera raised against FUs of Octopus vulgaris and Octopus dofleini. Frozen-hydrated immunocomplexes containing one Hc molecule and at least one FU-specific Fab fragment were observed in the electron microscope and submitted to image processing. When the Hc molecule is viewed along its 5-fold axis (i) anti-Soc Fab fragments project on a radius passing through the arch's pillar, (ii) anti-Sof Fabs project slightly out of the arches, and (iii) anti-Soh Fabs project between neighboring arches. When applied to a recent three-dimensional (3D) reconstruction volume, these results allow us to deduce the intramolecular location of five of the eight FUs. For the last three FUs limited uncertainties remain: (i) Soc can be located in two positions in the external tier of FUs; (ii) Soa and Sob can both occupy three positions in the external tiers; and (iii) because of an immunological cross-reactivity Sod may be located in the wall and Soe in the arch, or vice versa. An analysis of the quaternary structure considering the possible locations of the 80 FUs and postulating a single type of subunit shows that 80 possibilities of paths still exist for the polypeptide chain. To solve definitely these 80 possibilities only five questions remain to be answered. PMID:9837726

  6. A new pair for inter- and intra-molecular FRET measurement

    SciTech Connect

    Yang Xiaofei; Xu Pingyong; Xu Tao . E-mail: xutao@sun5.ibp.ac.cn

    2005-05-13

    Fluorescence resonance energy transfer between mutant green fluorescent proteins provides powerful means to monitor in vivo protein-protein proximity and intracellular signaling. However, the current widely applied FRET pair of this class (CFP/YFP) requires excitation by expensive UV lasers, thereby hindering FRET imaging on many confocal microscopes. Further challenges arise from the large spectral overlap of CFP/YFP emission. Another FRET pair GFP/DsRed could obviate such limitations. However, the use of DsRed as a FRET acceptor is hampered by several critical problems, including a slow and incomplete maturation and obligate tetramerization. A tandem dimer mutant of DsRed (TDimer2) has similar spectral properties as those of DsRed. The rapid maturation and non-oligomerization make TDimer2 a promising substitute for DsRed in FRET experiments. Here, we have explored the possibility of using TDimer2 as a FRET acceptor for the donor EGFP. FRET was demonstrated between the EGFP-TDimer2 chimeric fusion protein. By substituting CFP/YFP in the Ca{sup 2+}-sensor cameleon with EGFP/TDimer2, dynamic changes in cytosolic free Ca{sup 2+} concentrations were observed with 488 nm excitation under conventional wide-field microscopy. The EGFP/TDimer2 pair was further successfully employed to monitor inter-molecular interaction between Syntaxin and SNAP25. These results reveal EGFP/TDimer2 as a promising FRET pair in monitoring intra-molecular conformation change as well as inter-molecular interaction.

  7. Inter- and intramolecular quenching of the singlet excited state of porphyrins by ferrocene

    SciTech Connect

    Giasson, R.; Lee, E.J.; Xiaohong Zhao; Wrighton, M.S. )

    1993-03-18

    Inter- and intramolecular quenching of the lowest singlet excited state of three porphyrins by ferrocene derivatives is reported. 5,15-Bis(4-tolyl)-2,3,7,8,12,13,17,18-octamethylporphyrin (1) and two derivatives of 1 where one of the tolyl methyl groups was replaced by a ferrocenylvinyl group, 2, or by a ferrocenylethyl group, 3, were prepared. Porphyrin 2 was isolated as a mixture of cis (73%) and trans (27%) isomers. Singlet excited state properties were studied by steady-state emission spectroscopy and by emission lifetime measurements. The relative quantum yields of fluorescence for 2 and 3 compared to 1 are 0.38 and 0.84, respectively. Fluorescence decay lifetimes of 1 and 3 are 15 and 14 ns, respectively. Fluorescence of 2 is revealed to be due to the emission of two species (cis and trans isomers) with lifetimes of 4 and 13 ns. The shorter fluorescence lifetimes and smaller fluorescence quantum yields for 2 and 3 compared to 1 are attributed to quenching of the singlet excited state of the porphyrin by the ferrocenyl centers. However, the fraction of quenching by electron transfer and energy transfer could not be quantitatively measured. The rate constant for quenching is no more than 10[sup 8] s[sup [minus]1], consistent with electron-transfer quenching. Intermolecular quenching rate constants for the quenching of the porphyrin singlet excited state by ferrocene derivatives were also found to be consistent with an electron transfer quenching mechanism. 28 refs., 3 figs., 1 tab.

  8. ``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.

  9. 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

  10. A synthetic picture of intramolecular dynamics of proteins. Towards a contemporary statistical theory of biochemical processes.

    PubMed

    Kurzyński, M

    1998-01-01

    An increasing body of experimental evidence indicates the slow character of internal dynamics of native proteins. The important consequence of this is that theories of chemical reactions, used hitherto, appear inadequate for description of most biochemical reactions. Construction of a contemporary, truly advanced statistical theory of biochemical processes will need simple but realistic models of microscopic dynamics of biomolecules. In this review, intended to be a contribution towards this direction, three topics are considered. First, an intentionally simplified picture of dynamics of native proteins which emerges from recent investigations is presented. Fast vibrational modes of motion, of periods varying from 10(-14) to 10(-11) s, are contrasted with purely stochastic conformational transitions. Significant evidence is adduced that the relaxation time spectrum of the latter spreads in the whole range from 10(-11) to 10(5) s or longer, and up to 10(-7) s it is practically quasi-continuous. Next, the essential ideas of the theory of reaction rates based on stochastic models of intramolecular dynamics are outlined. Special attention is paid to reactions involving molecules in the initial conformational substrates confirmed to the transition state, which is realized in actual experimental situations. And finally, the two best experimentally justified classes of models of conformational transition dynamics, symbolically referred to as "protein glass" and "protein machine", are described and applied to the interpretation of a few simple biochemical processes, perhaps the most important result reported is the demonstration of the possibility of predominance of the short initial condition-dependent stage of protein involved reactions over the main stage described by the standard kinetics. This initial stage, and not the latter, is expected to be responsible for the coupling of component reactions in the complete enzymatic cycles as well as more complex processes of

  11. Solvent effect on intramolecular electron transfer rates of mixed-valence biferrocene monocation derivatives.

    PubMed

    Masuda, Y; Shimizu, C

    2006-06-01

    Intramolecular electron transfer (ET) rates in various solvents of mixed-valence biferrocene monocation (Fe(II), Fe(III)) and the 1',1' ''-diiodo and 1',1' ''-diethyl derivatives (respectively abbreviated as BFC(+), I(2)BFC(+), and Et(2)BFC(+)) were determined by means of the spin-lattice relaxation times of the protons, taking into account the local magnetic field fluctuation caused by the electron hopping between the two ferrocene units. We also determined the ET rates of a mixed-valence diferrocenylacetylene monocation (DFA(+)) in order to examine the effect of the insertion of an acetylene bridge between the two ferrocene units. The insertion of the bridge decreased the ET rate, while the effect of substitution on the cyclopentadienyl rings on the rate was minor. The observed rates for each mixed-valence monocation in various solvents did not correlate with the reorganization energies, but we did find a significant contribution of the solvent dynamics. The observed rates were considerably higher than those expected on the basis of the Sumi-Marcus-Nalder model in which the solvents were regarded as dielectric continua. The slope of the logarithm plot of the pre-exponential factors in various solvents for each mixed-valence monocation versus the inverse of the longitudinal dielectric relaxation times of the solvents was significantly smaller than unity, and the slope for DFA(+) was larger than those for BFC(+), I(2)BFC(+), and Et(2)BFC(+). These results were ascribed to a partial contribution of the dielectric friction to the dynamics along the solvent coordinate; the extent of the contribution decreased with a reduction in the ET distance. For the dynamics along the solvent coordinate of the ET reactions in methanol, the observed rates indicated an important contribution by the minor dielectric relaxation components with faster relaxation times, rather than the major component with an extraordinarily long relaxation time.

  12. Evidence for intramolecular OH⋯π hydrogen bonding in unsaturated alcohols from UV photoelectron spectroscopy

    NASA Astrophysics Data System (ADS)

    Kowski, Klaus; Lüttke, Wolfgang; Rademacher, Paul

    2001-06-01

    The gas phase He(I) photoelectron (PE) spectra of several unsaturated alcohols ( 1- 11) have been measured and analysed with respect to intramolecular OH⋯π hydrogen bonding. Evidence for such a hydrogen bond has been detected in the spectra of 2-allylphenol ( 1) and 2-phenylethan-1-ol ( 3). 1 exists as a conformational mixture of a hydrogen bonded form 1a and an open form 1b in a composition of roughly 2:1. A strong ionization band (IP v=10.01 eV; where IP v is the vertical ionization potential) is assigned to the ethylenic CC double bond in the major conformer ( 1a) and a weak band (IP v=9.72 eV) to that of the minor conformer ( 1b). The latter IP coincides with the corresponding ionization of allylbenzene. In the series of ω-phenylalkan-1-ols, compound 3 exhibits an unusually low nπ(O) ionization indicating hydrogen bonding between the OH group and the π electron system of the phenyl ring. The higher homologs 4 and 5 prefer 'open' conformations without such interaction. The PE spectra of alkenols such as but-3-en-1-ol ( 7) and pent-4-en-1-ol ( 8) as well as of alkynols such as but-3-yn-1-ol ( 10) and pent-4-yn-1-ol ( 11) are consistent with OH⋯π hydrogen bonded conformers. The methanol/ethylene hetero-dimer has a T-shaped structure, as indicated by B3LYP/6-311++G(d) calculations, with a binding energy of 5.65 kJ mol -1.

  13. 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

  14. 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.

  15. Enhanced rate of intramolecular electron transfer in an engineered purple CuA azurin

    PubMed Central

    Farver, Ole; Lu, Yi; Ang, Majorie C.; Pecht, Israel

    1999-01-01

    The recent expression of an azurin mutant where the blue type 1 copper site is replaced by the purple CuA site of Paracoccus denitrificans cytochrome c oxidase has yielded an optimal system for examining the unique electron mediation properties of the binuclear CuA center, because both type 1 and CuA centers are placed in the same location in the protein while all other structural elements remain the same. Long-range electron transfer is induced between the disulfide radical anion, produced pulse radiolytically, and the oxidized binuclear CuA center in the purple azurin mutant. The rate constant of this intramolecular process, kET = 650 ± 60 s−1 at 298 K and pH 5.1, is almost 3-fold faster than for the same process in the wild-type single blue copper azurin from Pseudomonas aeruginosa (250 ± 20 s−1), in spite of a smaller driving force (0.69 eV for purple CuA azurin vs. 0.76 eV for blue copper azurin). The reorganization energy of the CuA center is calculated to be 0.4 eV, which is only 50% of that found for the wild-type azurin. These results represent a direct comparison of electron transfer properties of the blue and purple CuA sites in the same protein framework and provide support for the notion that the binuclear purple CuA center is a more efficient electron transfer agent than the blue single copper center because reactivity of the former involves a lower reorganization energy. PMID:9927665

  16. Intramolecular charge transfer and thermal exciplex dissociation with p-aminobenzonitriles in toluene

    SciTech Connect

    Leinhos, U.; Kuehnle, W.; Zachariasse, K.A. )

    1991-03-07

    The rate constants of the reversible intramolecular excited-state charge-transfer (CT) reaction of 4-(dimethylamino)benzonitrile (DMABN;I) in toluene were determined as a function of temperature, from double-exponential fluorescence decays measured by time-correlated single-photon counting. The same decay times were found for the locally excited (LE) and the CT state, as shown by global analysis. For the CT state, the stabilization enthalpy {Delta}H ({minus}6 kJ mol{sup {minus}1}) and the change in entropy {Delta}S ({minus}24 J K{sup {minus}1} M{sup {minus}1}) were determined. A correlation of the charge-transfer time of DMABN with the longitudinal dielectric relaxation time was not observed. The presence of dimers or solute/solvent complexes in the ground state was excluded by {sup 1}H NMR experiments. A reversible excited-state reaction was shown to occur in toluene for the planar molecules 1-methyl-5-cyanoindoline (NMCI; II) and 1-methyl-6-cyano-1,2,3,4-tetrahydroquinoline (NMCQ;III) as well as for 3,5-dimethyl-4-(dimethylamino)benzonitrile (DMADBN;IV), based on the wavelength dependence of the double-exponential fluorescence decays. Such a dependence was not found for N-methyl-4-aminobenzonitrile (MABN; IH), 4-aminobenzonitrile (ABN; IHH), and 3,5-dimethyl-4-aminobenzonitrile (ADBN; IVHH), which is attributed to an increase in energy of the CT state relative to the LE state in these secondary and primary aromatic amines.

  17. 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.

  18. Intramolecular vibrational redistribution in aromatic molecules. I. Eigenstate resolved CH stretch first overtone spectra of benzene

    NASA Astrophysics Data System (ADS)

    Callegari, A.; Merker, U.; Engels, P.; Srivastava, H. K.; Lehmann, K. K.; Scoles, G.

    2000-12-01

    We have used infrared-infrared double resonance spectroscopy to record a rovibrational eigenstate resolved spectrum of benzene in the region of the CH stretch first overtone. This experiment is the first of a series aimed at investigating intramolecular vibrational energy redistribution (IVR) in aromatic molecules. The experiment has been carried out in a supersonic molecular beam apparatus using bolometric detection. A tunable resonant cavity was used to enhance the on-beam intensity of the 1.5 μm color center laser used to pump the overtone, and a fixed frequency [R(30)] 13CO2 laser was used to saturate the coinciding ν18 rQ(2) transition of benzene. After assigning the measured lines of the highly IVR fractionated spectrum to their respective rotational quantum number J, analysis of the data reveals that the dynamics occurs on several distinct time scales and is dominated by anharmonic coupling with little contribution from Coriolis coupling. After the fast (˜100 fs) redistribution of the energy among the previously observed "early time resonances" [R. H. Page, Y. R. Shen, and Y. T. Lee, J. Chem. Phys. 88, 4621 (1988) and 88, 5362 (1988)], a slower redistribution (10-20 ps) takes place, which ultimately involves most of the symmetry allowed vibrational states in the energy shell. Level spacing statistics reveal that IVR produces a highly mixed, but nonstatistical, distribution of vibrational excitation, even at infinite time. We propose that this nonintuitive phenomenon may commonly occur in large molecules when the bright state energy is localized in a high-frequency mode.

  19. 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.

  20. C₅-symmetric chiral corannulenes: desymmetrization of bowl inversion equilibrium via "intramolecular" hydrogen-bonding network.

    PubMed

    Kang, Jiheong; Miyajima, Daigo; Itoh, Yoshimitsu; Mori, Tadashi; Tanaka, Hiroki; Yamauchi, Masahito; Inoue, Yoshihisa; Harada, Soichiro; Aida, Takuzo

    2014-07-30

    Because of a rapid conformational inversion, bowl-shaped C5-symmetric corannulenes, though geometrically chiral, have not been directly resolved into their enantiomers. However, if this inversion equilibrium can be desymmetrized, chiral corannulenes enriched in either enantiomer can be obtained. We demonstrated this possibility using pentasubstituted corannulenes 4 and 5 carrying amide-appended thioalkyl side chains. Compound 4 displays chiroptical activity in a chiral hydrocarbon such as limonene. Because compound 5 carries a chiral center in the side chains, its enantiomers 5R and 5S show chiroptical activity even in achiral solvents such as CHCl3 and methylcyclohexane. In sharp contrast, when the side chains bear no amide functionality (1 and 2R), no chiroptical activity emerges even in limonene or with a chiral center in the side chains. Detailed investigations revealed that the peripheral amide units in 4 and 5 are hydrogen-bonded only "intramolecularly" along the corannulene periphery, affording cyclic amide networks with clockwise and anticlockwise geometries. Although this networking gives rise to four stereoisomers, only two, which are enantiomeric to one another, are suggested computationally to exist in the equilibrated system. In a chiral environment (chiral solvent or side chain), their thermodynamic stabilities are certainly unequal, so the bowl-inversion equilibrium can be desymmetrized. However, this is not the case when the system contains a protic solvent that can deteriorate the hydrogen-bonding network. When the enantiomeric purity of limonene as the solvent is varied, the chiroptical activity of the corannulene core changes nonlinearly with its enantiomeric excess (majority rule). PMID:25046475

  1. Relationship between chemical structure and supramolecular effective molarity for formation of intramolecular H-bonds.

    PubMed

    Sun, Hongmei; Hunter, Christopher A; Navarro, Cristina; Turega, Simon

    2013-09-01

    Effective molarity (EM) is a key parameter that determines the efficiency of a range of supramolecular phenomena from the folding of macromolecules to multivalent ligand binding. Coordination complexes formed between zinc porphyrins equipped H-bond donor sites and pyridine ligands equipped with H-bond acceptor sites have allowed systematic quantification of EM values for the formation of intramolecular H-bonds in 240 different systems. The results provide insights into the relationship of EM to supramolecular architecture, H-bond strength, and solvent. Previous studies on ligands equipped with phosphonate diester and ether H-bond acceptors were inconclusive, but the experiments described here on ligands equipped with phosphine oxide, amide, and ester H-bond acceptors resolve these ambiguities. Chemical double-mutant cycles were used to dissect the thermodynamic contributions of individual H-bond interactions to the overall stabilities of the complexes and hence determine the values of EM, which fall in the range 1-1000 mM. Solvent has little effect on EM, and the values measured in toluene and 1,1,2,2-tetrachloroethane are similar. For H-bond acceptors that have similar geometries but different H-bond strengths (amide and ester), the values of EM are very similar. For H-bond acceptors that have different geometries but similar H-bond strengths (amide and phosphonate diester), there is little correlation between the values of EM. These results imply that supramolecular EMs are independent of solvent and intrinsic H-bond strength but depend on supramolecular architecture and geometric complementarity.

  2. Excited state intramolecular charge transfer reaction in nonaqueous electrolyte solutions: Temperature dependence

    NASA Astrophysics Data System (ADS)

    Pradhan, Tuhin; Gazi, Harun Al Rasid; Biswas, Ranjit

    2009-08-01

    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 (LiClO4) 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 (-ΔGr) 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, LiClO4 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 (-ΔGr), the former in ethanol and ACN increases only linearly with the increase in driving force (-ΔGr). 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.

  3. Mechanically induced intramolecular electron transfer in a mixed-valence molecular shuttle

    PubMed Central

    Barnes, Jonathan C.; Fahrenbach, Albert C.; Dyar, Scott M.; Frasconi, Marco; Giesener, Marc A.; Zhu, Zhixue; Liu, Zhichang; Hartlieb, Karel J.; Carmieli, Ranaan; Wasielewski, Michael R.; Stoddart, J. Fraser

    2012-01-01

    The kinetics and thermodynamics of intramolecular electron transfer (IET) can be subjected to redox control in a bistable [2]rotaxane comprised of a dumbbell component containing an electron-rich 1,5-dioxynaphthalene (DNP) unit and an electron-poor phenylene-bridged bipyridinium (P-BIPY2+) unit and a cyclobis (paraquat-p-phenylene) (CBPQT4+) ring component. The [2]rotaxane exists in the ground-state co-conformation (GSCC) wherein the CBPQT4+ ring encircles the DNP unit. Reduction of the CBPQT4+ leads to the CBPQT2(•+) diradical dication while the P-BIPY2+ unit is reduced to its P-BIPY•+ radical cation. A radical-state co-conformation (RSCC) results from movement of the CBPQT2(•+) ring along the dumbbell to surround the P-BIPY•+ unit. This shuttling event induces IET to occur between the pyridinium redox centers of the P-BIPY•+ unit, a property which is absent between these redox centers in the free dumbbell and in the 1∶1 complex formed between the CBPQT2(•+) ring and the radical cation of methyl-phenylene-viologen (MPV•+). Using electron paramagnetic resonance (EPR) spectroscopy, the process of IET was investigated by monitoring the line broadening at varying temperatures and determining the rate constant (kET = 1.33 × 107 s-1) and activation energy (ΔG‡ = 1.01 kcal mol-1) for electron transfer. These values were compared to the corresponding values predicted, using the optical absorption spectra and Marcus–Hush theory. PMID:22685213

  4. 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

  5. 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.

  6. Direct electrochemistry and intramolecular electron transfer of ascorbate oxidase confined on L-cysteine self-assembled gold electrode.

    PubMed

    Patil, Bhushan; Kobayashi, Yoshiki; Fujikawa, Shigenori; Okajima, Takeyoshi; Mao, Lanqun; Ohsaka, Takeo

    2014-02-01

    A direct electrochemistry and intramolecular electron transfer of multicopper oxidases are of a great importance for the fabrication of these enzyme-based bioelectrochemical-devices. Ascorbate oxidase from Acremonium sp. (ASOM) has been successfully immobilized via a chemisorptive interaction on the l-cysteine self-assembled monolayer modified gold electrode (cys-SAM/AuE). Thermodynamics and kinetics of adsorption of ASOM on the cys-SAM/AuE were studied using cyclic voltammetry. A well-defined redox wave centered at 166±3mV (vs. Ag│AgCl│KCl(sat.)) was observed in 5.0mM phosphate buffer solution (pH7.0) at the fabricated ASOM electrode, abbreviated as ASOM/cys-SAM/AuE, confirming a direct electrochemistry, i.e., a direct electron transfer (DET) between ASOM and cys-SAM/AuE. The direct electrochemistry of ASOM was further confirmed by taking into account the chemical oxidation of ascorbic acid (AA) by O2 via an intramolecular electron transfer in the ASOM as well as the electrocatalytic oxidation of AA at the ASOM/cys-SAM/AuE. Thermodynamics and kinetics of the adsorption of ASOM on the cys-SAM/AuE have been elaborated along with its direct electron transfer at the modified electrodes on the basis of its intramolecular electron transfer and electrocatalytic activity towards ascorbic acid oxidation and O2 reduction. ASOM saturated surface area was obtained as 2.41×10(-11)molcm(-2) with the apparent adsorption coefficient of 1.63×10(6)Lmol(-1). The ASOM confined on the cys-SAM/AuE possesses its essential enzymatic function. PMID:24189123

  7. An abnormally slow proton transfer reaction in a simple HBO derivative due to ultrafast intramolecular-charge transfer events.

    PubMed

    Alarcos, Noemí; Gutierrez, Mario; Liras, Marta; Sánchez, Félix; Douhal, Abderrazzak

    2015-07-01

    We report on the steady-state, picosecond and femtosecond time-resolved studies of a charge and proton transfer dye 6-amino-2-(2'-hydroxyphenyl)benzoxazole (6A-HBO) and its methylated derivative 6-amino-2-(2'-methoxyphenyl)benzoxazole (6A-MBO), in different solvents. With femtosecond resolution and comparison with the photobehaviour of 6A-MBO, we demonstrate for 6A-HBO in solution, the photoproduction of an intramolecular charge-transfer (ICT) process at S1 taking place in ∼140 fs or shorter, followed by solvent relaxation in the charge transferred species. The generated structure (syn-enol charge transfer conformer) experiences an excited-state intramolecular proton-transfer (ESIPT) reaction to produce a keto-type tautomer. This subsequent proton motion occurs in 1.2 ps (n-heptane), 14 ps (DCM) and 35 ps (MeOH). In MeOH, it is assisted by the solvent molecules and occurs through tunneling for which we got a large kinetic isotope effect (KIE) of about 13. For the 6A-DBO (deuterated sample in CD3OD) the global proton-transfer reaction takes place in 200 ps, showing a remarkable slow KIE regime. The slow ESIPT reaction in DCM (14 ps), not through tunnelling as it is not sensitive to OH/OD exchange, has however to overcome an energy barrier using intramolecular as well as solvent coordinates. The rich ESIPT dynamics of 6A-HBO in the used solutions is governed by an ICT reaction, triggered by the amino group, and it is solvent dependent. Thus, the charge injection to a 6A-HBO molecular frame makes the ICT species more stable, and the phenol group less acidic, slowing down the subsequent ESIPT reaction. Our findings bring new insights into the coupling between ICT and ESIPT reactions on the potential-energy surfaces of several barriers.

  8. Bacterial conversion of hydroxylamino aromatic compounds by both lyase and mutase enzymes involves intramolecular transfer of hydroxyl groups.

    PubMed

    Nadeau, Lloyd J; He, Zhongqi; Spain, Jim C

    2003-05-01

    Hydroxylamino aromatic compounds are converted to either the corresponding aminophenols or protocatechuate during the bacterial degradation of nitroaromatic compounds. The origin of the hydroxyl group of the products could be the substrate itself (intramolecular transfer mechanism) or the solvent water (intermolecular transfer mechanism). The conversion of hydroxylaminobenzene to 2-aminophenol catalyzed by a mutase from Pseudomonas pseudoalcaligenes JS45 proceeds by an intramolecular hydroxyl transfer. The conversions of hydroxylaminobenzene to 2- and 4-aminophenol by a mutase from Ralstonia eutropha JMP134 and to 4-hydroxylaminobenzoate to protocatechuate by a lyase from Comamonas acidovorans NBA-10 and Pseudomonas sp. strain 4NT were proposed, but not experimentally proved, to proceed by the intermolecular transfer mechanism. GC-MS analysis of the reaction products formed in H(2)(18)O did not indicate any (18)O-label incorporation during the conversion of hydroxylaminobenzene to 2- and 4-aminophenols catalyzed by the mutase from R. eutropha JMP134. During the conversion of 4-hydroxylaminobenzoate catalyzed by the hydroxylaminolyase from Pseudomonas sp. strain 4NT, only one of the two hydroxyl groups in the product, protocatechuate, was (18)O labeled. The other hydroxyl group in the product must have come from the substrate. The mutase in strain JS45 converted 4-hydroxylaminobenzoate to 4-amino-3-hydroxybenzoate, and the lyase in Pseudomonas strain 4NT converted hydroxylaminobenzene to aniline and 2-aminophenol but not to catechol. The results indicate that all three types of enzyme-catalyzed rearrangements of hydroxylamino aromatic compounds proceed via intramolecular transfer of hydroxyl groups.

  9. Direct electrochemistry and intramolecular electron transfer of ascorbate oxidase confined on L-cysteine self-assembled gold electrode.

    PubMed

    Patil, Bhushan; Kobayashi, Yoshiki; Fujikawa, Shigenori; Okajima, Takeyoshi; Mao, Lanqun; Ohsaka, Takeo

    2014-02-01

    A direct electrochemistry and intramolecular electron transfer of multicopper oxidases are of a great importance for the fabrication of these enzyme-based bioelectrochemical-devices. Ascorbate oxidase from Acremonium sp. (ASOM) has been successfully immobilized via a chemisorptive interaction on the l-cysteine self-assembled monolayer modified gold electrode (cys-SAM/AuE). Thermodynamics and kinetics of adsorption of ASOM on the cys-SAM/AuE were studied using cyclic voltammetry. A well-defined redox wave centered at 166±3mV (vs. Ag│AgCl│KCl(sat.)) was observed in 5.0mM phosphate buffer solution (pH7.0) at the fabricated ASOM electrode, abbreviated as ASOM/cys-SAM/AuE, confirming a direct electrochemistry, i.e., a direct electron transfer (DET) between ASOM and cys-SAM/AuE. The direct electrochemistry of ASOM was further confirmed by taking into account the chemical oxidation of ascorbic acid (AA) by O2 via an intramolecular electron transfer in the ASOM as well as the electrocatalytic oxidation of AA at the ASOM/cys-SAM/AuE. Thermodynamics and kinetics of the adsorption of ASOM on the cys-SAM/AuE have been elaborated along with its direct electron transfer at the modified electrodes on the basis of its intramolecular electron transfer and electrocatalytic activity towards ascorbic acid oxidation and O2 reduction. ASOM saturated surface area was obtained as 2.41×10(-11)molcm(-2) with the apparent adsorption coefficient of 1.63×10(6)Lmol(-1). The ASOM confined on the cys-SAM/AuE possesses its essential enzymatic function.

  10. 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

  11. 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.

  12. Phenylalanine and tyrosine methyl ester intramolecular interactions and conformational analysis by (1)H NMR and infrared spectroscopies and theoretical calculations.

    PubMed

    Cormanich, Rodrigo A; Ducati, Lucas C; Tormena, Cláudio F; Rittner, Roberto

    2014-04-01

    Amino acid conformational analysis in solution are scarce, since these compounds present a bipolar zwitterionic structure ((+)H3NCHRCOO(-)) in these media. Also, intramolecular hydrogen bonds have been classified as the sole interactions governing amino acid conformational behavior in the literature. In the present work we propose phenylalanine and tyrosine methyl ester conformational studies in different solvents by (1)H NMR and infrared spectroscopies and theoretical calculations. Both experimental and theoretical results are in agreement and suggest that the conformational behavior of the phenylalanine and tyrosine methyl esters are similar and are dictated by the interplay between steric and hyperconjugative interactions.

  13. Implications of dynamic imine chemistry for the sustainable synthesis of nitrogen heterocycles via transimination followed by intramolecular cyclisation.

    PubMed

    Laha, Joydev K; Tummalapalli, K S Satyanarayana; Jethava, Krupal P

    2016-02-28

    An exploration of a tandem approach to the sustainable synthesis of N-heterocycles from readily available N-aryl benzylamines or imines and ortho-substituted anilines is described, which demonstrates, for the first time, an important synthetic application of dynamic imine chemistry. The key features to the successful development of this protocol include the utilisation of N-aryl benzylamines as imine precursors in transimination, the occurrence of transimination in acetonitrile in the absence of any catalysts, an intramolecular nucleophilic addition occurring in the newly formed imine causing irreversible transimination, and the tandem event occurring under green conditions.

  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. A Monte Carlo density functional theory for the competition between inter and intramolecular association in inhomogeneous fluids.

    PubMed

    Marshall, Bennett D; García-Cuéllar, Alejandro J; Chapman, Walter G

    2013-05-28

    A Monte Carlo density functional theory is developed for chain molecules which both intra and intermolecularly associate. The approach can be applied over a range of chain lengths. The theory is validated for the case of an associating 4-mer fluid in a planar hard slit pore. Once validated, the new theory is used to study the effect of chain length and temperature on the competition between intra and intermolecular association near a hard wall. We show that this competition enhances intramolecular association near wall contact and inverts the chain length dependence of the fraction bonded intermolecularly in the inhomogeneous region.

  16. Constructing thioether-tethered cyclic peptides via on-resin intra-molecular thiol-ene reaction.

    PubMed

    Zhao, Bingchuan; Zhang, Qingzhou; Li, Zigang

    2016-08-01

    Thiol-ene reactions have been used in a variety of applications that mostly involve an inter-molecular pathway. Herein, we report a facile method to construct thioether-tethered cyclic peptides via an intra-molecular thiol-ene reaction. This reaction is efficient, selective, and has good residue compatibility. Short peptides with thioether tethers were constructed and were used to construct longer cyclic peptides. This synthetic method may be useful for constructing bioactive peptides. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd. PMID:27378284

  17. 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

  18. 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.

  19. Tandem cross enyne metathesis (CEYM)-intramolecular Diels-Alder reaction (IMDAR). An easy entry to linear bicyclic scaffolds.

    PubMed

    Miró, Javier; Sánchez-Roselló, María; Sanz, Álvaro; Rabasa, Fernando; Del Pozo, Carlos; Fustero, Santos

    2015-01-01

    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

  20. Intramolecular proton transfer through the adjoining π-conjugated system in Shiff base: application for colorimetric sensing of fluoride anion.

    PubMed

    Yu, Xudong; Zhang, Ping; Li, Yajuan; Zhen, Xiaoli; Geng, Lijun; Wang, Yanqiu; Ma, Zichuan

    2014-07-01

    In this paper, a new kind of phenol-based chemsensor L2 comprised of a Schiff base and azo groups was rationally designed and synthesized. It could selectively recognize fluoride anion among tested anions such as F(-), AcO(-), H2PO4(-), Cl(-), Br(-), and I(-) with obvious color changes from yellow to fuchsia. The intramolecular PT (proton transfer) in L1 and L2 was responsible for the sensing ability, which was certified by the (1)H NMR and Uv-vis experiments. PMID:24857515

  1. Inter- versus intra-molecular cyclization of tripeptides containing tetrahydrofuran amino acids: a density functional theory study on kinetic control.

    PubMed

    Kumar, N V Suresh; Priyakumar, U Deva; Singh, Harjinder; Roy, Saumya; Chakraborty, Tushar Kanti

    2012-07-01

    Density functional B3LYP method was used to investigate the preference of intra- and inter-molecular cyclizations of linear tripeptides containing tetrahydrofuran amino acids. Two distinct model pathways were conceived for the cyclization reaction, and all possible transition states and intermediates were located. Analysis of the energetics indicate intermolecular cyclization being favored by both thermodynamic and kinetic control. Geometric and NBO analyses were performed to explain the trends obtained along both the reaction pathways. Conceptual density functional theory-based reactive indices also show that reaction pathways leading to intermolecular cyclization of the tripeptides are relatively more facile compared to intramolecular cyclization.

  2. 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

  3. 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.

  4. Unusually rigid macrocyclic tris(picolinolato)-4-tert-butylcalix[4]arene: Its intramolecular interaction effect on picolinoylation

    NASA Astrophysics Data System (ADS)

    Lee, Haeri; Noh, Tae Hwan; Kim, Eun Ji; Jung, Ok-Sang

    2012-11-01

    The reaction of 4-tert-butylcalix[4]arene (calix[4]) with picolinoyl chloride affords only the unprecedented rigid tris(pico)-product calix[4]-(pico)3(OH) (pico = picolinoylato) with an upper-rim and two lower-rim pico groups, via a subtle combination of steric hindrance and intrinsically weak intramolecular interactions. The chemical shift of one of the upper-rim pico group's aromatic protons appears, unusually, 5.18 ppm in chloroform, which is the quite up-field chemical shift of the reported aromatic proton signals.

  5. Rhodium-Catalyzed Stereoselective Intramolecular [5 + 2] Cy-cloaddition of 3-Acyloxy-1,4-enyne and Alkene

    PubMed Central

    Shu, Xing-zhong; Schienebeck, Casi M.; Li, Xiaoxun; Zhou, Xin; Song, Wangze; Chen, Lianqing; Guzei, Ilia A.; Tang, Weiping

    2015-01-01

    The first rhodium-catalyzed intramolecular [5 + 2] cycloaddition of 3-acyloxy-1,4-enyne and alkene was developed. The cycloaddition is highly diastereoselective in most cases. Various cis-fused bicyclo[5.3.0]decadienes were prepared stereoselectively. The chirality in the propargylic ester starting materials could be transferred to the bicyclic products with high efficiency. Electron-deficient phosphine ligand greatly facilitated the cycloaddition. Up to three new stereogenic centers could be generated. The resulting diene in the products could be hydrolyzed to enones, which allowed the introduction of more functional groups to the seven-membered ring. PMID:26440751

  6. 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

  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. 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.

  9. Quantum theory of concerted electronic and nuclear fluxes associated with adiabatic intramolecular processes.

    PubMed

    Bredtmann, Timm; Diestler, Dennis J; Li, Si-Dian; Manz, Jörn; Pérez-Torres, Jhon Fredy; Tian, Wen-Juan; Wu, Yan-Bo; Yang, Yonggang; Zhai, Hua-Jin

    2015-11-28

    An elementary molecular process can be characterized by the flow of particles (i.e., electrons and nuclei) that compose the system. The flow, in turn, is quantitatively described by the flux (i.e., the time-sequence of maps of the rate of flow of particles though specified surfaces of observation) or, in more detail, by the flux density. The quantum theory of concerted electronic and nuclear fluxes (CENFs) associated with electronically adiabatic intramolecular processes is presented. In particular, it is emphasized how the electronic continuity equation can be employed to circumvent the failure of the Born-Oppenheimer approximation, which always predicts a vanishing electronic flux density (EFD). It is also shown that all CENFs accompanying coherent tunnelling between equivalent "reactant" and "product" configurations of isolated molecules are synchronous. The theory is applied to three systems of increasing complexity. The first application is to vibrating, aligned H2(+)((2)Σg(+)), or vibrating and dissociating H2(+)((2)Σg(+), J = 0, M = 0). The EFD maps manifest a rich and surprising structure in this simplest of systems; for example, they show that the EFD is not necessarily synchronous with the nuclear flux density and can alternate in direction several times over the length of the molecule. The second application is to coherent tunnelling isomerization in the model inorganic system B4, in which all CENFs are synchronous. The contributions of core and valence electrons to the EFD are separately computed and it is found that core electrons flow with the nuclei, whereas the valence electrons flow obliquely to the core electrons in distinctive patterns. The third application is to the Cope rearrangement of semibullvalene, which also involves coherent tunnelling. An especially interesting discovery is that the so-called "pericyclic" electrons do not behave in the manner typically portrayed by the traditional Lewis structures with appended arrows. Indeed, it is

  10. Acylmethyl(aryl)tellurium(IV,II) derivatives: intramolecular secondary bonding and steric rigidity.

    PubMed

    Chauhan, Ashok K S; Singh, Puspendra; Srivastava, Ramesh C; Duthie, Andrew; Voda, Andreea

    2008-08-14

    Electrophilic substitution of acylmethanes (methyl ketones), RCOCH3 (R = i-Pr, 1; Et, 2; Me, 3) with aryltellurium trichlorides, ArTeCl3 (Ar = 1-C10H7, Np, A; 2,4,6-Me3C6H2, Mes, B; 4-MeOC6H4, Anisyl, C) under mild conditions affords the corresponding acylmethyl(aryl)tellurium dichlorides (RCOCH2)ArTeCl2. Reduction of the dichlorides, gives tellurides, (i-PrCOCH2)ArTe, 1A-1C, which give the corresponding dihalides, (i-PrCOCH2)ArTeX2 (X = Cl, 1Aa-1Ca; Br, 1Ab-1Cb; I, 1Ac-1Cc) when reacted in situ with SO2Cl2, Br2 or I2. The unsymmetric tellurides are labile towards disproportionation and attempts to obtain them lead to the isolation of Ar2Te2 except in the case of (i-PrCOCH2)MesTe (1B), which represents an interesting example of a kinetically stable aryl(alkyl)telluride. All the dihalomesityltellurium(IV) derivatives show separate 1H and 13C NMR signals for the ortho methyls irrespective of the sizes of R and X ligands. The telluride, 1B with free rotation about Te-C(mesityl) bond shows, like the unsymmetric diorganotellurium(IV) dihalides, only one 125Te NMR signal. The 1,4-chelating behavior of the acyl ligand among diorganotellurium(IV) compounds is inferred from the X-ray diffraction data for 1Aa, 1Ac, 1Ba, 1Bb, 1cA and 1Cc which are indicative of the presence of intramolecular Te...O secondary bonding interactions (SBIs) at least in the solid state. As a consequence, steric repulsion in case of the mesityltellurium(IV) derivatives, 1Ba and 1Bb, reaches the threshold so as to cause loss of two-fold rotational symmetry of the mesityl group about the Te-C(mesityl) bond axis. Intermolecular C-HO...O H-bonding interactions appears to stabilize such an orientation of the aryl ligand at least in the solid state. PMID:18648706

  11. Ion-responsive Intramolecular Charge-transfer Absorption Using a Pyridinium Benzocrown Ether Conjugate.

    PubMed

    Kuwabara, Tetsuo; Tao, Xuanyi; Guo, Haocheng; Katsumata, Masayo; Ueta, Ikuo; Takahashi, Masaki; Suzuki, Yasutada

    2015-01-01

    A pyridinium benzocrown ether conjugated compound, 1, and its analogue with a non-crown ether unit, 2, have been prepared. Both compounds showed similar absorption spectra with two absorption bands at around 260 and 330 nm in acetonitrile. The bands at the longer wavelength side are associated with intramolecular charge transfer (ICT) absorption, in which the dialkoxyphenyl unit in benzocrown ether and the pyridinium unit act as the donor and acceptor, respectively. The addition of a guest, such as Li(+) or Mg(2+), caused a blue shift in the ICT absorption band for 1, but not for 2. This is explained by the formation of a 1:1 host-guest inclusion complex of 1 with the guest. The guest-induced absorption variation of 1 can be used for alkali and alkaline metal ion sensing. Compound 1 could detect divalent cations, especially for Mg(2+), rather than univalent ones (Li(+), Na(+), K(+), Rb(+), and Cs(+)), although Li(+) was detected with high sensitivity among the alkali metal ions. Compound 3, which has a pyridyl unit at the para position on the pyridinium of 1, showed a similar trend to that of 1 with lower sensitivity than that of 1. The fact that the Mg(2+)/Li(+) sensitivity ratio of 1 and 3 was estimated to be 8.63 and 5.08, respectively, suggests a higher Mg(2+)-preference of 1 rather than 3, while the Ca(2+)/Na(+) ones were 4.98 and 4.85, respectively, when compared ions with similar ionic radii. The sensitivity values of 1 were roughly proportional to their binding constants, as shown by the binding constants with Li(+), Na(+), Mg(2+), and Ca(2+) with values of 2100, 910, 11500, and 2000 M(-1) for 1, respectively. The binding constants of 3 were estimated to be 1710, 650, 3000, and 1400 M(-1) for Li(+), Na(+), Mg(2+), and Ca(2+), respectively, but could not be obtained for alkaline metal ions. The limit concentration for the detection of 1 for Mg(2+) was estimated to be 0.0156 mM, which was the smallest value in this system.

  12. Acylmethyl(aryl)tellurium(IV,II) derivatives: intramolecular secondary bonding and steric rigidity.

    PubMed

    Chauhan, Ashok K S; Singh, Puspendra; Srivastava, Ramesh C; Duthie, Andrew; Voda, Andreea

    2008-08-14

    Electrophilic substitution of acylmethanes (methyl ketones), RCOCH3 (R = i-Pr, 1; Et, 2; Me, 3) with aryltellurium trichlorides, ArTeCl3 (Ar = 1-C10H7, Np, A; 2,4,6-Me3C6H2, Mes, B; 4-MeOC6H4, Anisyl, C) under mild conditions affords the corresponding acylmethyl(aryl)tellurium dichlorides (RCOCH2)ArTeCl2. Reduction of the dichlorides, gives tellurides, (i-PrCOCH2)ArTe, 1A-1C, which give the corresponding dihalides, (i-PrCOCH2)ArTeX2 (X = Cl, 1Aa-1Ca; Br, 1Ab-1Cb; I, 1Ac-1Cc) when reacted in situ with SO2Cl2, Br2 or I2. The unsymmetric tellurides are labile towards disproportionation and attempts to obtain them lead to the isolation of Ar2Te2 except in the case of (i-PrCOCH2)MesTe (1B), which represents an interesting example of a kinetically stable aryl(alkyl)telluride. All the dihalomesityltellurium(IV) derivatives show separate 1H and 13C NMR signals for the ortho methyls irrespective of the sizes of R and X ligands. The telluride, 1B with free rotation about Te-C(mesityl) bond shows, like the unsymmetric diorganotellurium(IV) dihalides, only one 125Te NMR signal. The 1,4-chelating behavior of the acyl ligand among diorganotellurium(IV) compounds is inferred from the X-ray diffraction data for 1Aa, 1Ac, 1Ba, 1Bb, 1cA and 1Cc which are indicative of the presence of intramolecular Te...O secondary bonding interactions (SBIs) at least in the solid state. As a consequence, steric repulsion in case of the mesityltellurium(IV) derivatives, 1Ba and 1Bb, reaches the threshold so as to cause loss of two-fold rotational symmetry of the mesityl group about the Te-C(mesityl) bond axis. Intermolecular C-HO...O H-bonding interactions appears to stabilize such an orientation of the aryl ligand at least in the solid state.

  13. Intramolecular electron transfer in sulfite oxidizing enzymes: elucidating the role of a conserved active site arginine†

    PubMed Central

    Emesh, Safia; Rapson, Trevor D.; Rajapakshe, S. Asha; Kappler, Ulrike; Bernhardt, Paul V.; Tollin, Gordon; Enemark, John H.

    2009-01-01

    All reported sulfite oxidizing enzymes have a conserved arginine in their active site which hydrogen bonds to the equatorial oxygen ligand on the Mo atom. Previous studies on the pathogenic R160Q mutant of human sulfite oxidase (HSO) have shown that Mo-heme intramolecular electron transfer (IET) is dramatically slowed when positive charge is lost at this position. In order to better understand the function that this conserved positively charged residue plays in IET, we have studied the equivalent uncharged substitutions, R55Q and R55M, as well as the positively charged substitution, R55K, in bacterial sulfite dehydrogenase (SDH). The heme and molybdenum cofactor (Moco) subunits are tightly associated in SDH, which makes it an ideal system for increasing the understanding of residue function in IET without the added complexity of the inter-domain movement that occurs in HSO. Unexpectedly, the uncharged SDH variants (R55Q and R55M) showed increased IET rate constants relative to the wildtype (3–4 fold) when studied by laser flash photolysis. The gain in function observed in SDHR55Q and SDHR55M suggests that the reduction of IET seen in HSOR160Q is not due to a required role of this residue in the IET pathway itself, but to the fact that it plays an important role in heme orientation during the inter-domain movement necessary for IET in HSO (as seen in viscosity experiments). The pH profiles of SDHwt, SDHR55M, and SDHR55Q show that the arginine substitution also alters the behavior of the Mo-heme IET equilibrium (Keq) and rate constants (ket) of both variants with respect to SDHWT enzyme. SDHWT has a ket that is independent of pH and a Keq that increases as pH decreases, whereas both SDHR55M and SDHR55Q have a ket that increases as pH decreases, and SDHR55M has a Keq that is pH independent. IET in the SDHR55Q variant is inhibited by sulfate in laser flash photolysis experiments, a behavior that differs from SDHWT, but which also occurs in HSO. IET in SDHR55K is

  14. Controlling the ambiphilic nature of σ-arylpalladium intermediates in intramolecular cyclization reactions.

    PubMed

    Solé, Daniel; Fernández, Israel

    2014-01-21

    the metal center with the carbonyl group. Second, the additive phenol exchanges the iodide ligand to give an arylpalladium(II) phenoxide complex, which has a beneficial effect on the arylation. The formation of this transient intermediate not only stabilizes the arylpalladium moiety, thus preventing the nucleophilic attack at the carbonyl group, but also assists the enolization reaction, which takes place in a more favorable intramolecular manner. The azapalladacycle intermediate is, in the words of J. R. R. Tolkien, "the one ring to bring them all and in the darkness to bind them." With this intermediate, we can easily achieve the synthesis of a variety of heterocyclic systems by selectively promoting electrophilic α-arylation or nucleophilic addition reactions from the same precursors. PMID:23957464

  15. Intramolecular energy transfer and excitation coupling in metal-to-ligand charge transfer (MLCT) excited states

    NASA Astrophysics Data System (ADS)

    Riesen, Hans; Krausz, Elmars

    1995-02-01

    Several new spectroscopic studies relating to the coupling and dynamics in the spin-forbidden 3MLCT excited states of the chromophores [Ru(bpy)3]2+ and [Os(bpy)3]2+ (bpy equals 2,2'-bipyridine) in the racemic crystal lattices [Ru(bpy)3](PF6)2, [Ru(bpy)3](ClO4)2 and [Zn(bpy)3](ClO4)2 are presented. In the first of these lattices there are three closely related chromophoric sites at low temperatures, each with trigonal (C3) symmetry. In the two, isomorphic perchlorate salts there is a single chromophoric site, which has C2 symmetry. Using time resolved luminescence line narrowing, we have been able to directly measure the excitation transfer rate between two equivalent metal-ligand units in the [Ru(bpy)3]2+ chromophore doped in the [Zn(bpy)3](ClO4)2 lattice. The rate obtained (approximately equals 1 X 108 sec-1) is in excellent accord with estimates made from the observed linewidth in Stark swept transient hole-burning experiments made on the same system and confirm the single ligand, localized nature of the lowest emitting excited states and thus the very weak intramolecular coupling between metal ligand sub-units within this chromophore. The corresponding coupling in the [Os(bpy)3]2+ system is stronger and, in contrast to the ruthenium analogue, gives rise to additional features in the optical spectra in the origin region of the lowest 3MLCT excited states. The magnitude of the coupling can be probed and assessed by preparing modified chromophoric materials, in which one or two of the bpy ligands are perdeuterated (bpy-d8). This selective deuteration breaks the (near) degeneracy of excitations involving crystallographically equivalent ligands by approximately equals 30 - 40 cm-1 and this competes with or completely overrides the exciton coupling process. The exciton coupling is found to be approximately equals 2.4 cm-1 for [Os(bpy)3]2+ doped in [Ru(bpy)3](PF6)2 and can be understood within a mini-exciton description. Stronger couplings for the same chromophore in

  16. d-Orbital Effects on Stereochemical Non-Rigidity: Twisted Ti IV Intramolecular Dynamics

    SciTech Connect

    Davis, Anna V.; Firman, Timothy K.; Hay, Benjamin P.; Raymond, Kenneth N.

    2006-07-26

    The isomerization dynamics of tris-catecholate complexes have been investigated by variable temperature NMR methods, demonstrating that the intramolecular racemization of ? and ? enantiomers of d0 TiIV is facile and faster than that of d10 GaIII and GeIV analogs. Activation parameters for the racemization of K2[Ti23] (H22 = 2,3-dihydroxy-N,N?-diisopropylterephthalamide) were determined from lineshape analysis of 1H NMR spectra (methanol-d4: ?H? = 47(1) kJ/mol; ?S? = -34(4) J/molK; ?G?298 = 57(3) kJ/mol; DMF-d7: ?H? = 55(1) kJ/mol; ?S? = -16(4) J/molK; ?G?298 = 59(3) kJ/mol; D2O (pD* = 8.6, 20% MeOD): ?H? = 48(3) kJ/mol; ?S? = -28(10) J/molK; ?G?298 = 56(3) kJ/mol). The study of K2[Ti43] (H24 = 2,3-dihydroxy-N-tert-butyl-N?-benzylterephthalamide) reveals two distinct isomerization processes: faster racemization of mer-[Ti43]2- by way of a Bailar twist mechanism (D3h transition state) (Tc ? 242 K, methanol-d4), and a slower mer/fac-[Ti43]2- isomerization by way of a R?y-Dutt mechanism (C2v transition state) (Tc ? 281 K, methanol-d4). The solution behavior of the TiIV complexes mirrors that reported previously for analogous GaIII complexes, while that of analogous GeIV complexes was too inert to be detected by 1H NMR up to 400 K. These experimental findings are augmented by DFT calculations of the ML3 grounds states and Bailar and R?y-Dutt transition states, which correctly predict the relative kinetic barriers of the three metal ions, in addition to faithfully reproducing the ground state structures. Orbital calculations support the conclusion that participation of the TiIV d0 orbitals in ligand bonding contributes to the greater stabilization of the prismatic TiIV transition states. Battelle operates the Pacific Northwest National Laboratory for the U.S. Department of Energy.

  17. 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

  18. 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

  19. 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

  20. Role of Intramolecular Aromatic π-π Interactions in the Self-Assembly of Di-l-Phenylalanine Dipeptide Driven by Intermolecular Interactions: Effect of Alanine Substitution.

    PubMed

    Reddy, Samala Murali Mohan; Shanmugam, Ganesh

    2016-09-19

    Although the role of intermolecular aromatic π-π interactions in the self-assembly of di-l-phenylalanine (l-Phe-l-Phe, FF), a peptide that is known for hierarchical structure, is well established, the influence of intramolecular π-π interactions on the morphology of the self-assembled structure of FF has not been studied. Herein, the role of intramolecular aromatic π-π interactions is investigated for FF and analogous alanine (Ala)-containing dipeptides, namely, l-Phe-l-Ala (FA) and l-Ala-l-Phe (AF). The results reveal that these dipeptides not only form self-assemblies, but also exhibit remarkable differences in structural morphology. The morphological differences between FF and the analogues indicate the importance of intramolecular π-π interactions, and the structural difference between FA and AF demonstrates the crucial role of the nature of intramolecular side-chain interactions (aromatic-aliphatic or aliphatic-aromatic), in addition to intermolecular interactions, in deciding the final morphology of the self-assembled structure. The current results emphasise that intramolecular aromatic π-π interaction may not be essential to induce self-assembly in smaller peptides, and π (aromatic)-alkyl or alkyl-π (aromatic) interactions may be sufficient. This work also illustrates the versatility of aromatic and a combination of aromatic and aliphatic residues in dipeptides in the formation of structurally diverse self-assembled structures.

  1. Time-dependent density functional theory (TD-DFT) study on the excited-state intramolecular proton transfer (ESIPT) in 2-hydroxybenzoyl compounds: Significance of the intramolecular hydrogen bonding

    NASA Astrophysics Data System (ADS)

    Lan, Xin; Yang, Dapeng; Sui, Xiao; Wang, Dandan

    2013-02-01

    The excited-state properties of intramolecular hydrogen bonding (IMHB) in methyl salicylate (MS) and its effects on the excited-state intramolecular proton transfer (ESIPT) have been investigated using theoretical methods. From the geometric optimization and IR spectra in the ground and excited states calculated by density functional theory (DFT) and time-dependent DFT (TD-DFT) methods respectively, the IMHB is demonstrated to be significantly strengthened upon excitation to excited state S1. Thereby, the ESIPT is facilitated by the excited-state IMHB strengthening since ESIPT takes place through IMHB. In addition, the absorption and fluorescence peaks of the S1 state are also calculated using the TD-DFT method. It is noted that the calculated spectra are in good agreement with the experimental results, which has confirmed the ESIPT mechanism of MS first proposed by Weller. Moreover, other four 2-hydroxybenzoyl compounds forming strong IMHB are investigated to understand the effect of substituent R on the ESIPT process. We find that the hydrogen bond strength can be controlled by the inductive field effect of the substituent. Thus it is inferred that the ESIPT reaction can be facilitated by the inductive effect of electron-donating substituent.

  2. Intramolecular ipso-halocyclization of 4-(p-unsubstituted-aryl)-1-alkynes leading to spiro[4,5]trienones: scope, application, and mechanistic investigations.

    PubMed

    Tang, Bo-Xiao; Zhang, Yue-Hua; Song, Ren-Jie; Tang, Dong-Jun; Deng, Guo-Bo; Wang, Zhi-Qiang; Xie, Ye-Xiang; Xia, Yuan-Zhi; Li, Jin-Heng

    2012-03-16

    A new, general method for the synthesis of spiro[4,5]trienones is described by the intramolecular ipso-halocyclization of 4-(p-unsubstituted-aryl)-1-alkynes. In the presence of halide electrophiles, a variety of 4-(p-unsubstituted-aryl)-1-alkynes underwent the intramolecular ipso-halocyclization with water smoothly, affording the corresponding halo-substituted spiro[4,5]trienones in moderate to good yields. The obtained spiro[4,5]trienones can be applied in constructing the azaquaternary tricyclic skeleton via Pd-catalyzed Heck reaction. Notably, the prepared spiro[4,5]trienones and azaquaternary tricycles are of importance in the areas of pharmaceuticals and agrochemicals. The mechanism of the intramolecular ipso-halocyclization reaction is also discussed according to the (18)O-labeling experiments and DFT calculations. PMID:22360308

  3. Control of intramolecular electron transfer by protonation: Oligomers of ruthenium porphyrins bridged by 4,4[prime]-azopyridine

    SciTech Connect

    Marvaud, V.; Launay, J.P. )

    1993-04-14

    The association of pentaammineruthenium(II) with the reducible ligand 4,4[prime]-azopyridine leads to a pH-induced redox reaction in which ruthenium is oxidized to the III state, while 4,4[prime]-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, the authors have prepared shish kebab oligomers by first inserting a ruthenium chloro carbonyl complex in tetrakis(3,5-di-tert-butyl-4-hydroxyphenyl)porphyrin. The resulting Ru(CO)(porphyrin) complex is photochemically decarbonylated in the presence of bridging ligands (4,4[prime]-azopyridine or pyrazine). Oligomers 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 oligomer chain. In the case of 4,4[prime]-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. 17 refs., 8 figs. 2 tabs.

  4. 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

  5. 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.

  6. Mechanistic Studies of Wacker-Type Intramolecular Aerobic Oxidative Amination of Alkenes Catalyzed by Pd(OAc)2/Pyridine

    PubMed Central

    Ye, Xuan; Liu, Guosheng; Popp, Brian V.; Stahl, Shannon S.

    2011-01-01

    Wacker-type oxidative cyclization reactions have been the subject of extensive research for several decades, but few systematic mechanistic studies of these reactions have been reported. The present study features experimental and DFT computational studies of Pd(OAc)2/pyridine-catalyzed intramolecular aerobic oxidative amination of alkenes. The data support a stepwise catalytic mechanism that consists of (1) steady-state formation of a PdII-amidate-alkene chelate with release of one equivalent of pyridine and AcOH from the catalyst center, (2) alkene insertion into a Pd–N bond, (3) reversible β-hydride elimination, (4) irreversible reductive elimination of AcOH, and (5) aerobic oxidation of palladium(0) to regenerate the active trans-Pd(OAc)2(py)2 catalyst. Evidence is obtained for two energetically viable pathways for the key C–N bond-forming step, featuring a pyridine-ligated and a pyridine-dissociated PdII species. Analysis of natural charges and bond lengths of the alkene-insertion transition state suggest that this reaction is best described as an intramolecular nucleophilic attack of the amidate ligand on the coordinated alkene. PMID:21250706

  7. 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

  8. 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.

  9. 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

  10. Gas-Phase Intramolecular Protein Crosslinking via Ion/Ion Reactions: Ubiquitin and a Homobifunctional sulfo-NHS Ester

    NASA Astrophysics Data System (ADS)

    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.

  11. 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.

  12. 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.

  13. Susceptibility towards intramolecular disulphide-bond formation affects conformational stability and folding of human basic fibroblast growth factor.

    PubMed Central

    Estapé, D; van den Heuvel, J; Rinas, U

    1998-01-01

    The conformational stability and the folding properties of the all-beta-type protein human basic fibroblast growth factor (hFGF-2) were studied by means of fluorescence spectroscopy. The results show that the instability of the biological activity of hFGF-2 is also reflected in a low conformational stability of the molecule. The reversibility of the unfolding and refolding process was established under reducing conditions. Determination of the free-energy of unfolding in the presence of reducing agents revealed that the conformational stability of hFGF-2 (DeltaGH2Oapp congruent with21 kJ. mol-1, 25 degreesC) is low compared with other globular proteins under physiological conditions (20-60 kJ.mol-1). However, the conformational stability of hFGF-2 is particularly low under non-reducing conditions. This instability is attributed to intramolecular disulphide-bond formation, rendering the molecule more susceptible to denaturant-induced unfolding. In addition, denaturant-induced unfolding of hFGF-2 renders the protein more susceptible to irreversible oxidative denaturation. Experimental evidence is provided that the irreversibility of the unfolding and refolding process in the absence of reducing agents is linked to the formation of an intramolecular disulphide bond involving cysteines 96 and 101. PMID:9761733

  14. 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

  15. Vibrational assignment, structure and intramolecular hydrogen bond study of 3-amino-1-phenyl-2-buten-1-one.

    PubMed

    Raissi, Haidar; Yarali, Atieh; Farzad, Farzaneh; Nowroozi, Alireza

    2006-03-01

    Fourier transform infrared and Fourier transform Raman spectra of 3-amino-1-phenyl-2-buten-1-one and its deuterated analogue were recorded in the regions 400-4,000 and 150-4,000 cm(-1), respectively. Furthermore, the molecular structure and vibrational frequencies of title compound were investigated by a series of density functional theoretical, DFT, and ab initio calculations at the post-Hartree-Fock (MP2) level. Although, the calculated frequencies are generally in agreement with the observed spectra but the DFT results are in much better quantitative agreement with the observed spectra than the MP2 results. The observed wavenumbers were analyzed and assigned to different normal modes of vibration of the molecule. The calculated geometrical parameters show a strong intramolecular hydrogen bond with a N...O distance of 2.621-2.668 A. This bond length is shorter than that of its parent, 4-amino-3-penten-2-one (with two methyl groups in the beta-position), which is in agreement with spectroscopic results. The topological properties of the electron density contributions for intramolecular hydrogen bond in 3-amino-1-phenyl-2-buten-1-one and 4-amino-3-penten-2-one have been analyzed in term of the Bader theory of atoms in molecules (AIM). These results also support the stronger hydrogen bond in the title compound with respect to the parent molecule.

  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. Molecular dynamics study of chemically engineered green fluorescent protein mutants: comparison of intramolecular fluorescence resonance energy transfer rate.

    PubMed

    Mitchell, Felicity L; Frank, Filipp; Marks, Gabriel E; Suzuki, Miho; Douglas, Kenneth T; Bryce, Richard A

    2009-04-01

    Because of its unusual spectroscopic properties, green fluorescent protein (GFP) has become a useful tool in molecular genetics, biochemistry and cell biology. Here, we computationally characterize the behavior of two GFP constructs, designed as bioprobes for enzymatic triggering using intramolecular fluorescence resonance energy transfer (FRET). These constructs differ in the location of an intramolecular FRET partner, an attached chemical chromophore (either near an N-terminal or C-terminal site). We apply the temperature replica exchange molecular dynamics method to the two flexible constructs in conjunction with a generalized Born implicit solvent model. The calculated rate of FRET was derived from the interchromophore distance, R, and orientational factor, kappa(2). In agreement with experiment, the construct with the C-terminally attached dye was predicted to have higher energy transfer rate than observed for the N-terminal construct. The molecular basis for this observation is discussed. In addition, we find that the orientational factor, kappa(2), deviates from the commonly assumed value, the implications of which are also considered.

  18. Effect of Intramolecular High-Frequency Vibrational Mode Excitation on Ultrafast Photoinduced Charge Transfer and Charge Recombination Kinetics.

    PubMed

    Nazarov, Alexey E; Barykov, Vadim Yu; Ivanov, Anatoly I

    2016-03-31

    A model of photoinduced ultrafast charge separation and ensuing charge recombination into the ground state has been developed. The model includes explicit description of the formation and evolution of nonequilibrium state of both the intramolecular vibrations and the surrounding medium. An effect of the high-frequency intramolecular vibrational mode excitation by a pumping pulse on ultrafast charge separation and charge recombination kinetics has been investigated. Simulations, in accord with experiment, have shown that the effect may be both positive (the vibrational mode excitation increases the charge-transfer rate constant) and negative (opposite trend). The effect on charge separation kinetics is predicted to be bigger than that on the charge recombination rate but nevertheless the last is large enough to be observable. The amplitude of both effects falls with decreasing vibrational relaxation time constant, but the effects are expected to be observable up to the time constants as short as 200 fs. Physical interpretation of the effects has been presented. Comparisons with the experimental data have shown that the simulations, in whole, provide results close to that obtained in the experiment. The reasons of the deviations have been discussed. PMID:26953595

  19. Imaging and energetics of single SSB-ssDNA molecules reveal intramolecular condensation and insight into RecOR function.

    PubMed

    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. PMID:26381353

  20. 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

  1. Diffracted X-ray tracking for monitoring intramolecular motion in individual protein molecules using broad band X-ray.

    PubMed

    Ichiyanagi, Kouhei; Sekiguchi, Hiroshi; Hoshino, Masato; Kajiwara, Kentaro; Hoshisashi, Kentaro; Chang, Jae-won; Tokue, Maki; Matsushita, Yufuku; Nishijima, Masaki; Inoue, Yoshihisa; Senba, Yasunori; Ohashi, Haruhiko; Ohta, Noboru; Yagi, Naoto; Sasaki, Yuji C

    2013-10-01

    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 (ΔE/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.

  2. Excited state intramolecular proton transfer and charge transfer dynamics of a 2-(2'-hydroxyphenyl)benzoxazole derivative in solution.

    PubMed

    Kim, Chul Hoon; Park, Jaehun; Seo, Jangwon; Park, Soo Young; Joo, Taiha

    2010-05-13

    Excited state intramolecular proton transfer (ESIPT) and subsequent intramolecular charge transfer (ICT) dynamics of a 2-(2'-hydroxyphenyl)benzoxazole derivative conjugated with an electron withdrawing group (HBOCE) in solutions and a polymer film has been investigated by femtosecond time-resolved fluorescence (TRF) and TRF spectra measurements without the conventional spectral reconstruction method. TRF with high enough resolution (<100 fs) reveals that the ESIPT dynamics of HBOCE in liquids proceeds by at least two time constants of approximately 250 fs and approximately 1.2 ps. The relative amplitude of the slower picosecond component is smaller in the polymer film than that in solution. Conformational heterogeneity in the ground state originating from the dispersion of the dihedral angle between the phenolic and benzoxazole groups is invoked to account for the dispersive ESIPT dynamics in liquids. From the TRF spectra of both the enol and keto isomers, we have identified the ICT reaction of the keto isomer occurring subsequent to the ESIPT. The ICT proceeds also by two time constants of near instantaneous and 2.7 ps. Since the ICT dynamics of HBOCE is rather close to the polar solvation dynamics, we argue that the ICT is barrierless and determined mostly by the solvent fluctuation.

  3. 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

  4. Photoinduced intramolecular electron transfer reactions in fullerene-phenothiazine linked compounds: effects of magnetic field and spacer chain length

    NASA Astrophysics Data System (ADS)

    Yonemura, Hiroaki; Noda, Masakazu; Hayashi, Kazuya; Tokudome, Hiromasa; Moribe, Shinya; Yamada, Sunao

    Spectroscopic and electrochemical properties of two fullerene(C60)-phenothiazine(PH) linked compounds with different spacer chain length have been compared in benzonitrile (polar solvent) and in benzene (non-polar solvent). Transient absorption and fluorescence spectra indicated that photoinduced intramolecular electron transfer occurred in benzonitrile, but not in benzene. The results are due to solvent effect on energy levels of the photogenerated biradical. The driving forces for the electron transfer were determined by measuring the redox potentials of the C60 and PH moieties. Thermodynamic parameters for the electron transfer processes were evaluated and compared. In benzonitrile, the lifetime of the photogenerated biradical was very long, in spite of being around the top region in Marcus theory. The decay rate of the biradicals was retarded in the presence of magnetic fields. The decay rate constant decreased quickly with increasing the magnetic field and became constant above about 0.2 T. The magnetic field effects verified that the triplet biradical was generated by the intramolecular electron transfer from PH to the triplet excited state of C60 . The long lifetime is most probably ascribed to the spin multiplicities of the biradical.

  5. Studies on the biosynthesis of paraherquamide A and VM99955. A theoretical study of intramolecular Diels-Alder cycloaddition.

    PubMed

    Domingo, Luis R; Zaragozá, Ramón J; Williams, Robert M

    2003-04-01

    Intramolecular Diels-Alder reactions of 2-azadiene models have been studied quantum chemically at the B3LYP/6-31G level in order to elucidate the stereochemical features of the cyclization step involved in the biosynthesis of paraherquamide A and VM99955. These cycloadditions take place through concerted transition states associated with [4 + 2] processes. Analysis of the energies along the competitive paths reveals that while the cycloadditions of the oxindoles present a large anti selectivity, the indoles show a low syn selectivity for the formation of the C20 stereogenic center that is larger for the reduced tertiary amide form. The presence of the C14 methyl of the beta-methylproline ring produces a low hindrance along the reaction coordinate for the syn approach of the isoprene framework, in agreement with the low facial selectivity found experimentally. An analysis of the electrophilicity and activation parameters for experimental models of the inter- and intramolecular Diels-Alder reactions reveals several significant factors controlling these biosynthetic cyclizations. The results are in reasonable agreement with the available experimental data.

  6. Long-range intramolecular electronic communication in bis(ferrocenylethynyl) complexes incorporating conjugated heterocyclic spacers: synthesis, crystallography, and electrochemistry.

    PubMed

    Shah, Hakikulla H; Al-Balushi, Rayya A; Al-Suti, Mohammed K; Khan, Muhammad S; Woodall, Christopher H; Molloy, Kieran C; Raithby, Paul R; Robinson, Thomas P; Dale, Sara E C; Marken, Frank

    2013-05-01

    A new series of bis(ferrocenylethynyl) complexes, 3-7, and a mono(ferrocenylethynyl) complex, 8, have been synthesized incorporating conjugated heterocyclic spacer groups, with the ethynyl group facilitating an effective long-range intramolecular interaction. The complexes were characterized by NMR, IR, and UV-vis spectroscopy as well as X-ray crystallography. The redox properties of these complexes were investigated using cyclic voltammetry and spectroelectrochemistry. Although there is a large separation of ∼14 Å between the two redox centers, ΔE(1/2) values in this series of complexes ranged from 50 to 110 mV. The appearance of intervalance charge-transfer bands in the UV-vis-near-IR region for the monocationic complexes further confirmed effective intramolecular electronic communication. Computational studies are presented that show the degree of delocalization across the Fc-C≡C-C≡C-Fc (Fc = C5H5FeC5H4) highest occupied molecular orbital. PMID:23593988

  7. Characterizing the Intramolecular H-bond and Secondary Structure in Methylated GlyGlyH+ with H2 Predissociation Spectroscopy

    NASA Astrophysics Data System (ADS)

    Leavitt, Christopher M.; Wolk, Arron B.; Kamrath, Michael Z.; Garand, Etienne; van Stipdonk, Michael J.; Johnson, Mark A.

    2011-11-01

    We report vibrational predissociation spectra of the four protonated dipeptides derived from glycine and sarcosine, GlyGlyH+•(H2)1,2, GlySarH+•(D2)2, SarGlyH+•(H2)2, and SarSarH+•(D2)2, generated in a cryogenic ion trap. Sharp bands were recovered by monitoring photoevaporation of the weakly bound H2 (D2) molecules in a linear action regime throughout the 700-4200 cm-1 range using a table-top laser system. The spectral patterns were analyzed in the context of the low energy structures obtained from electronic structure calculations. These results indicate that all four species are protonated on the N-terminus, and feature an intramolecular H-bond involving the amino group. The large blue-shift in the H-bonded N-H fundamental upon incorporation of a methyl group at the N-terminus indicates that this modification significantly lowers the strength of the intramolecular H-bond. Methylation at the amide nitrogen, on the other hand, induces a significant rotation (~110o) about the peptide backbone.

  8. 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

  9. Palladium(II)-catalyzed intramolecular carboxypalladation-olefin insertion cascade: direct access to indeno[1,2-b]furan-2-ones.

    PubMed

    Vinoth, Perumal; Vivekanand, Thavaraj; Suryavanshi, Padmakar A; Menéndez, J Carlos; Sasai, Hiroaki; Sridharan, Vellaisamy

    2015-05-14

    A catalytic, atom-economical, domino 5-endo-dig cyclization-intramolecular olefin insertion sequence was developed under mild conditions. Aryl alkynoic acids bearing a tethered enone partner afforded the indeno[1,2-b]furan-2-ones, the core skeleton present in a number of biologically significant molecules including the natural product solanacol, under ligand-free, palladium-catalyzed reaction conditions in high yields. The competitive β-hydride elimination in the final step leading to the conjugated analogs was avoided by the addition of lithium bromide. A plausible mechanism for this domino sequence is proposed involving intramolecular carboxypalladation and olefin insertion steps.

  10. Magnetic field effects on the decay rate of photogenerated biradical from intramolecular electron transfer of triplet excited fullerene in a fullerene phenothiazine linked compound

    NASA Astrophysics Data System (ADS)

    Yonemura, Hiroaki; Tokudome, Hiromasa; Yamada, Sunao

    2001-10-01

    Transient absorption spectra of a fullerene (C 60)-phenothiazine (PH) linked compound indicated that the intramolecular electron transfer occurred in benzonitrile, while not in benzene. In benzonitrile, the lifetime (118 ns) of photogenerated biradical was very long, in spite of being around the top region in Marcus theory. The lifetime of the biradical was enhanced by 1.8 times in the presence of magnetic fields (>0.2 T). The magnetic field effects verified that the triplet biradical was generated from the intramolecular electron transfer from PH to the triplet C 60. The long lifetime is most likely ascribed to spin multiplicities of the biradical.

  11. Toward an understanding of the acceleration of Diels-Alder reactions by a pseudo-intramolecular process achieved by molecular recognition. A DFT study.

    PubMed

    Domingo, Luis R; Aurell, M José; Arnó, Manuel; Saez, José A

    2007-05-25

    The pseudo-intramolecular Diels-Alder (DA) reaction between a 2-substituted furan (1) and a N-maleimide derivative (2) has been analyzed using DFT methods. Formation of two hydrogen bonds between the appendages on furan and maleimide derivatives favors thermodynamically the formation of a molecular complex (MC1) through an efficient molecular recognition process. The large enthalpy stabilization associated with the molecular recognition overcomes the unfavorable activation entropy associated with the bimolecular process. As a consequence, the subsequent DA reaction is clearly accelerated through a pseudo-intramolecular process.

  12. Intramolecular resonance-assisted hydrogen bonds: a theoretical description by means of atomic charges and charge fluxes.

    PubMed

    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 the strength of H

  13. Intramolecular and intermolecular hydrogen-bonding effects on photophysical properties of 2'-aminoacetophenone and its derivatives in solution.

    PubMed

    Shimada, Hirofumi; Nakamura, Akihito; Yoshihara, Toshitada; Tobita, Seiji

    2005-04-01

    Effects of intra- and intermolecular hydrogen-bonds on the photophysical properties of 2'-aminoacetophenone derivatives (X-C6H4-COCH3) having a substituted amino group (X) with different hydrogen-bonding ability to the carbonyl oxygen (X: NH2(AAP), NHCH3(MAAP), N(CH3)2(DMAAP), NHCOCH3(AAAP), NHCOCF3(TFAAP)) are investigated by means of steady-state and time-resolved fluorescence spectroscopy and time-resolved thermal lensing. Based on the photophysical parameters obtained in aprotic solvents with different polarity and protic solvents with different hydrogen-bonding ability, the characteristic photophysical behavior of the 2'-aminoacetophenone derivatives is discussed in terms of hydrogen-bonding and n,pi*-pi,pi* vibronic coupling. The dominant deactivation process of AAP and MAAP in nonpolar aprotic solvents is the extremely fast internal conversion (k(ic)= 1.0 x 10(11) s(-1) for AAP and 3.9 x 10(10) s(-1) for MAAP in n-hexane). The internal conversion rates of both compounds decrease markedly with increasing solvent polarity, suggesting that vibronic interactions between close-lying S1(pi,pi*) and S2(n,pi*) states lead to the large increase in the non-radiative decay rate of the lowest excited singlet state. It is also suggested that for MAAP, which has a stronger hydrogen-bond as compared to AAP, an intramolecular hydrogen-bonding induced deactivation is involved in the dissipation of the S1 state. For DMAAP, which cannot possess an intramolecular hydrogen-bond, the primary relaxation mechanism of the S1 state in nonpolar aprotic solvents is the intersystem crossing to the triplet state, whereas in protic solvents very efficient internal conversion due to intermolecular hydrogen-bonding is induced. In contrast, the fluorescence spectra of AAAP and TFAAP, which have an amino group with a much stronger hydrogen-bonding ability, give strongly Stokes-shifted fluorescence, indicating that these compounds undergo excited-state intramolecular proton transfer reaction

  14. Synthesis of CPZEN-45: Construction of the 1,4-Diazepin-2-one Core by the Cu-Catalyzed Intramolecular Amidation of a Vinyl Iodide.

    PubMed

    Nakamura, Hugh; Yoshida, Takuma; Tsukano, Chihiro; Takemoto, Yoshiji

    2016-05-01

    CPZEN-45 was developed as an antibiotic against Mycobacterium tuberculosis by the chemical modification of caprazamycins. CPZEN-45 has been synthesized in this study by the Cu-catalyzed intramolecular amidation of a complex vinyl iodide precursor bearing uridine and sugar moieties with a secondary amide, allowing for the construction of its 1,4-diazepin-2-one core.

  15. 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…

  16. 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.

  17. 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.

  18. Tandem carbon-carbon bond insertion and intramolecular aldol reaction of benzyne with aroylacetones: novel formation of 4,4'-disubstituted 1,1'-binaphthols.

    PubMed

    Okuma, Kentaro; Itoyama, Ryoichi; Sou, Ayumi; Nagahora, Noriyoshi; Shioj, Kosei

    2012-11-21

    An efficient route to 4-aryl-2-naphthols from arynes and aroylacetones was developed by carbon-carbon bond insertion followed by an intramolecular aldol reaction and dehydration. Benzyne derived from 2-(trimethylsilyl)phenyl triflate reacted with benzoylacetones in refluxing acetonitrile to give 4-aryl-2-naphthols and 3-aryl-1-naphthols.

  19. Synthesis of Differentially Protected myo- and chiro-Inositols from D-Xylose; Stereoselectivity in Intramolecular SmI(2)-Promoted Pinacol Reactions.

    PubMed

    Luchetti, Giovanni; Ding, Kejia; Kornienko, Alexander; d'Alarcao, Marc

    2008-10-01

    Methods for the enantioselective conversion of D-xylose to differentially protected myo-inositol and L-chiro-inositol have been developed. The key transformation is a highly diastereoselective intramolecular SmI(2)-promoted pinacol coupling. The stereoselectivity was extremely dependent on the conditions, suggesting a change in mechanism. Preliminary mechanistic experiments and possible explanations for this behavior are discussed.

  20. Indium-mediated asymmetric intramolecular allenylation of N-tert-butanesulfinyl imines: efficient and practical access to chiral 3-allenyl-4-aminochromanes.

    PubMed

    Su, Lin; Zhu, Ting-Shun; Xu, Ming-Hua

    2014-08-15

    An efficient method for the preparation of highly optically active 3-allenyl- and 3-vinyl-4-aminochromanes by In-mediated intramolecular cyclization has been developed. The synthetic utilities of the approach were demonstrated by the construction of various chiral polycyclic heterocycles, especially the interesting spiroheterocyclic compound 9 and steroid analogue 10.

  1. CMPO-calix[4]arenes with spacer containing intramolecular hydrogen bonding: effect of local rigidification on solvent extraction toward f-block elements.

    PubMed

    Chu, Hongzhu; He, Lutao; Jiang, Qian; Fang, Yuyu; Jia, Yiming; Yuan, Xiangyang; Zou, Shuliang; Li, Xianghui; Feng, Wen; Yang, Yuanyou; Liu, Ning; Luo, Shunzhong; Yang, Yanqiu; Yang, Liang; Yuan, Lihua

    2014-01-15

    To understand intramolecular hydrogen bonding in effecting liquid-liquid extraction behavior of CMPO-calixarenes, three CMPO-modified calix[4]arenes (CMPO-CA) 5a-5c with hydrogen-bonded spacer were designed and synthesized. The impact of spacer rotation that is hindered by introduction of intramolecular hydrogen bonding upon extraction of La(3+), Eu(3+), Yb(3+), Th(4+), and UO2(2+) has been examined. The results show that 5b and 5c containing only one hydrogen bond with a less hindered rotation spacer extract La(3+) more efficiently than 5a containing two hydrogen bonds with a more hindered rotation spacer, demonstrating the importance of local rigidification of spacer in the design of extractants in influencing the coordination environment. The large difference in extractability between La(3+) and Yb(3+) (or Eu(3+)) by 5b (or 5c), and the small difference by 5a, suggests intramolecular hydrogen bonding do exert pronounced influence upon selective extraction of light and heavy lanthanides. Log-log plot analysis indicates a 1:1, 2:1 and 1:1 stoichiometry (ligand/metal) for the extracted complex formed between 5b and La(3+), Th(4+), UO2(2+), respectively. Additionally, their corresponding acyclic analogs 7a-7c exhibit negligible extraction toward these metal ions. These results reveal the possibility of selective extraction via tuning local chelating surroundings of CMPO-CA by aid of intramolecular hydrogen bonding.

  2. 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

  3. One-Pot Synthesis of Polysubstituted Spirofluorene-Indene via Ru(II)-Catalyzed [3 + 2] Annulation and Intramolecular Friedel-Crafts Cyclization.

    PubMed

    Zhu, Yu-Qin; Dong, Lin

    2015-10-16

    Ru(II)-catalyzed one-pot synthesis of polysubstituted spirofluorene-indenes via [3 + 2] annulation and then intramolecular Friedel-Crafts alkylation has been achieved. The simple method provides a broad scope of aryl ketones and internal alkynes, achieving PAHs skeletons in moderate to good yields. PMID:26419666

  4. Regiospecific synthesis of bicyclo- and heterobicyclo-gem-difluorocyclobutenes using functionalized fluoroallenes and a novel Mo-catalyzed intramolecular [2 + 2] cycloaddition reaction.

    PubMed

    Shen, Qilong; Hammond, Gerald B

    2002-06-12

    The first synthesis of functionalized gem-difluoroallenes 4 served as platform for an unprecedented molybdenum-catalyzed intramolecular allene-alkyne [2 + 2]-cycloaddition that produced 6, a hitherto unknown class of bicyclo- and heterobicyclo-CF2-containing cyclobutenes.

  5. Stereospecific and stereoselective rhodium(I)-catalyzed intramolecular [2+2+2] cycloaddition of allene-ene-ynes: construction of bicyclo[4.1.0]heptenes.

    PubMed

    Ohta, Yuu; Yasuda, Shigeo; Yokogawa, Yuka; Kurokawa, Kei; Mukai, Chisato

    2015-01-19

    Treatment of the allene-ene-yne substrates with [{RhCl(CO)2}2] effected the intramolecular [2+2+2]-type ring-closing reaction to produce various of tri- and tetracyclic derivatives containing a cyclopropane ring. The reaction is highly stereoselective as well as stereospecific with good to excellent yields.

  6. Excited-state intramolecular hydrogen bonding of compounds based on 2-(2-hydroxyphenyl)-1,3-benzoxazole in solution: a TDDFT study.

    PubMed

    Li, Hui; Liu, Yufang; Yang, Yonggang; Yang, Dapeng; Sun, Jinfeng

    2014-12-10

    The excited-state properties of intramolecular hydrogen bonding in the compounds based on 2-(2-hydroxyphenyl)-1,3-benzoxazole (6 and its tautomers 6a and 6b) have been investigated using theoretical methods. According to the geometric optimization and IR spectra in the ground and excited states calculated by density functional theory (DFT) and time-dependent DFT (TD-DFT) methods respectively, the type of intramolecular hydrogen bonding N⋯HO in 6 and 6a is demonstrated to be significantly strengthened, while NH⋯O in the tautomers 6a and 6b are proved to be sharply weakened upon excitation to excited state S1. The calculated absorption peaks of 6 are in good accordance with the experimental results. Moreover, other compounds based on 6 that R1 and R2 are both substituted as well as that only R1 is substituted are investigated to understand the effect of substituent on intramolecular hydrogen bonding. It is found that the hydrogen bond strength can be controlled by the inductive field effect of the substituent. In addition, the intramolecular charge transfers (ICT) of the S1 state for 6 and its tautomers 6a and 6b were theoretically investigated by analyses of molecular orbital.

  7. [Investigation of the intramolecular cyclization of the thiophene substituted cyclohexane skeleton gamma-oxocarboxylic acid and synthesis of some N-heteroaryl isoindole derivatives].

    PubMed

    Csende, Ferenc

    2011-01-01

    From thiophene and cis-hexahydrophthalic anhydride the corresponding gamma-oxocarboxylic acid was obtained by the Friedel-Crafts reaction, which resulted in new heterocycles with acetic anhydride, Lawesson reagent or urea by intramolecular cyclization. Saturated N-heteroaryl isoindoles were prepared directly by the fusion reaction of heteroaromatic amines with the oxocarboxylic acid. PMID:21800711

  8. A new approach to cyclic hydroxamic acids: Intramolecular cyclization of N-benzyloxy carbamates with carbon nucleophiles

    PubMed Central

    Liu, Yuan; Jacobs, Hollie K.

    2011-01-01

    N-Alkyl-N-benzyloxy carbamates, 2, undergo facile intramolecular cyclization with a variety of carbon nucleophiles to give functionalized 5- and 6-membered protected cyclic hydroxamic acids, 3, in good to excellent yields. This method can be extended to prepare seven-membered cyclic hydroxamic acids in moderate yields. The sulfone intermediates 3 from this study can be alkylated while the corresponding phosphonates have been shown to undergo HWE reaction. The α,β-unsaturated synthon, 8, prepared by thermal elimination of sulfoxide 3m, undergoes Michael addition with secondary amines. The usefulness of this approach to prepare polydentate chelators has been demonstrated by the synthesis of bis cyclic hydroxamic acids 12, 14, and 15. PMID:21499514

  9. Carotenoid to chlorophyll energy transfer in the peridinin–chlorophyll-a–protein complex involves an intramolecular charge transfer state

    PubMed Central

    Zigmantas, Donatas; Hiller, Roger G.; Sundström, Villy; Polívka, Tomáš

    2002-01-01

    Carotenoids are, along with chlorophylls, crucial pigments involved in light-harvesting processes in photosynthetic organisms. Details of carotenoid to chlorophyll energy transfer mechanisms and their dependence on structural variability of carotenoids are as yet poorly understood. Here, we employ femtosecond transient absorption spectroscopy to reveal energy transfer pathways in the peridinin–chlorophyll-a–protein (PCP) complex containing the highly substituted carotenoid peridinin, which includes an intramolecular charge transfer (ICT) state in its excited state manifold. Extending the transient absorption spectra toward near-infrared region (600–1800 nm) allowed us to separate contributions from different low-lying excited states of peridinin. The results demonstrate a special light-harvesting strategy in the PCP complex that uses the ICT state of peridinin to enhance energy transfer efficiency. PMID:12486228

  10. Developing a Diastereoselective Intramolecular [4 + 3] Cycloaddition of Nitrogen-Stabilized Oxyallyl Cations Derived from N-Sulfonyl-Substituted Allenamides

    PubMed Central

    Lohse, Andrew G.; Hsung, Richard P.; Leider, Mitchell D.; Ghosh, Sunil K.

    2011-01-01

    Efforts toward achieving a practical and diastereoselective intramolecular [4 + 3] cycloaddition of nitrogen-stabilized oxyallyl cations with tethered dienes are described. Epoxidation of N-sulfonyl substituted allenamides with dimethyldioxirane (DMDO) generates nitrogen-stabilized oxyallyl cations that would readily undergo stereoselective [4 + 3] cycloaddition with dienes. Selectivity is found to depend on the tethering length as well as the stability of the oxyallyl cation intermediate, whether generated from N-carbamoyl- or N-sulfonyl-substituted allenamides. The use of chiral N-sulfonyl-substituted allenamide provided minimal diastereoselectivity in the cycloaddition, while high diastereoselectivity can be achieved with a stereocenter present on the tether. These studies provide further support for the synthetic utility of allenamides. PMID:21449577

  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.

  12. 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.

  13. 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.

  14. Excited state intramolecular proton transfer in electron-rich and electron-poor derivatives of 10-hydroxybenzo[h]quinoline.

    PubMed

    Piechowska, Joanna; Huttunen, Kirsi; Wróbel, Zbigniew; Lemmetyinen, Helge; Tkachenko, Nikolai V; Gryko, Daniel T

    2012-10-01

    Eight previously inaccessible derivatives of 10-hydroxybenzo[h]quinoline were prepared via a straightforward strategy comprising formation of the benzo[h]quinoline skeleton followed by C-H acetoxylation at position 10. The occurrence of excited state intramolecular proton transfer (ESIPT) was detected in all cases since emission was observed only from the excited keto-tautomer. Studies on derivatives bearing both electron-donating and electron-withdrawing groups adjacent to the pyridine ring allowed us to identify some design patterns giving rise to NIR emission and large Stokes shifts. For a derivative of 10-hydroxybenzo[c]acridine, emission at 745 nm was observed, one of the lowest energy fluorescence ever reported for ESIPT system. On the basis of time-resolved measurements, proton transfer was found to be extremely fast with time constants in the range (0.08-0.45 ps). PMID:22946783

  15. 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.

  16. Cooperative intramolecularly hydrogen-bonded motif in the structure of 2:2 complex of TBD with 4-nitrocatechol

    NASA Astrophysics Data System (ADS)

    Ng, S. W.; Naumov, P.; Chantrapromma, S.; Raj, S. S. S.; Fun, H.-K.; Ibrahim, A. R.; Wojciechowski, G.; Brzezinski, B.

    2001-07-01

    In the crystal of the 2:2 complex of 1,5,7-triazabicyclo[4.4.0]dec-5-ene with 4-nitrocatechol the proton from 1-hydroxyl group of 4-nitrocatechol moiety is transferred to TBD to form ion-pair; two adjacent ion-pairs are linked across a center of inversion. The structure exhibits a cooperative, intramolecularly hydrogen-bonded motif. The hydrogen bonds are relatively long and, and they display only minor proton polarizability. The structure of the complex is retained in chloroform solution, as shown by FT-IR and 1H NMR measurement; in acetonitrile, the compound partially dissociates. The partial dissociation is implied by the presence of free cations, and also by that of the (O⋯H⋯O) - hydrogen bonds formed between two mono-deprotonated 4-nitrocatechol molecules.

  17. Slow intramolecular vibrational redistribution: the latest results for trifluoropropyne, a comparison with the other terminal acetylenes and the mechanism*

    NASA Astrophysics Data System (ADS)

    Malinovsky, A. L.; Makarov, A. A.; Ryabov, E. A.

    2012-05-01

    We studied the dynamics of intramolecular vibrational redistribution (IVR) from the initially excited mode ν1≈3330 cm-1 (acetylene-type H-C bond) in H{-}C\\equivC{-}CF_3 molecules in the gaseous phase by means of time-resolved anti-Stokes spontaneous Raman scattering. The time constant of this process was estimated as 2.3 ns—this is the slowest IVR time reported so far for the room-temperature gases. We have compared this result with earlier results on the other terminal acetylene molecules, and give an explanation of this low IVR rate. Our suggestion for it follows from an assumption that the most probable doorway state leading to IVR from \

  18. 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.

  19. Iron-mediated inter- and intramolecular reductive cross-coupling of unactivated alkyl chlorides with aryl bromides.

    PubMed

    Li, Zhuang; Sun, Hong-Mei; Shen, Qi

    2016-03-28

    An efficient one-pot intermolecular reductive cross-coupling of unactivated primary and secondary alkyl chlorides bearing β-hydrogens with aryl bromides is described. A combination of magnesium turnings and a catalytic amount of the commercially available iron(iii) complex Fe(PPh3)2Cl3 was used, and the conditions were also successfully extended to an intramolecular reaction for the first time. Both types of cross-coupling reactions proceed under mild conditions, involving the in situ generation of aryl Grignard reagents, and show good applicability to a variety of readily available unactivated alkyl chlorides, which have previously been challenging substrates in iron-catalyzed reductive cross-coupling reactions. PMID:26940697

  20. Intramolecular Tsuji-Trost-type Allylation of Carboxylic Acids: Asymmetric Synthesis of Highly π-Allyl Donative Lactones.

    PubMed

    Suzuki, Yusuke; Seki, Tomoaki; Tanaka, Shinji; Kitamura, Masato

    2015-08-01

    Tsuji-Trost-type asymmetric allylation of carboxylic acids has been realized by using a cationic CpRu complex with an axially chiral picolinic acid-type ligand (Cl-Naph-PyCOOH: naph = naphthyl, py = pyridine). The carboxylic acid and allylic alcohol intramolecularly condense by the liberation of water without stoichiometric activation of either nucleophile or electrophile part, thereby attaining high atom- and step-economy, and low E factor. This success can be ascribed to the higher reactivity of allylic alcohols as compared with the allyl ester products in soft Ru/hard Brønstead acid combined catalysis, which can function under slightly acidic conditions unlike the traditional Pd-catalyzed system. Detailed analysis of the stereochemical outcome of the reaction using an enantiomerically enriched D-labeled substrate provides an intriguing view of enantioselection. PMID:26199057

  1. 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.

  2. 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.

  3. Synthesis of trifluoromethylated isoxazoles and their elaboration through inter- and intra-molecular C-H arylation.

    PubMed

    Poh, Jian-Siang; García-Ruiz, Cristina; Zúñiga, Andrea; Meroni, Francesca; Blakemore, David C; Browne, Duncan L; Ley, Steven V

    2016-07-01

    We report conditions for the preparation of a range of trifluoromethylated isoxazole building blocks through the cycloaddition reaction of trifluoromethyl nitrile oxide. It was found that controlling the rate (and therefore concentration) of the formation of the trifluoromethyl nitrile oxide was Critical for the preferential formation of the desired isoxazole products versus the furoxan dimer. Different conditions were optimised for both aryl- and alkyl-substituted alkynes. In addition, the reactivity at the isoxazole 4-position has been briefly explored for these building blocks. Conditions for intermolecular C-H arylation, lithiation and electrophile quench, and alkoxylation were all identified with brief substrate scoping that signifies useful tolerance to a range of functionalities. Finally, complementary processes for structural diversification through either intramolecular cyclisation or intermolecular cross-coupling were developed.

  4. Low-threshold wavelength-switchable organic nanowire lasers based on excited-state intramolecular proton transfer.

    PubMed

    Zhang, Wei; Yan, Yongli; Gu, Jianmin; Yao, Jiannian; Zhao, Yong Sheng

    2015-06-01

    Coherent light signals generated at the nanoscale are crucial to the realization of photonic integrated circuits. Self-assembled nanowires from organic dyes can provide both a gain medium and an effective resonant cavity, which have been utilized for fulfilling miniaturized lasers. Excited-state intramolecular proton transfer (ESIPT), a classical molecular photoisomerization process, can be used to build a typical four-level system, which is more favorable for population inversion. Low-power driven lasing in proton-transfer molecular nanowires with an optimized ESIPT energy-level process has been achieved. With high gain and low loss from the ESIPT, the wires can be applied as effective FP-type resonators, which generated single-mode lasing with a very low threshold. The lasing wavelength can be reversibly switched based on a conformation conversion of the excited keto form in the ESIPT process.

  5. Base-dependent stereodivergent intramolecular aza-Michael reaction: asymmetric synthesis of 1,3-disubstituted isoindolines.

    PubMed

    Fustero, Santos; Herrera, Lidia; Lázaro, Ruben; Rodríguez, Elsa; Maestro, Miguel A; Mateu, Natalia; Barrio, Pablo

    2013-08-26

    The nucleophilic addition (A(N)) / intramolecular aza-Michael reaction (IMAMR) process on Ellman's tert-butylsulfinyl imines, bearing a Michael acceptor in the ortho position, is studied. This reaction affords 1,3-disubstituted isoindolines with a wide range of substituents in good yields and diastereoselectivities. Interestingly, careful choice of the base for the aza-Michael step allows either the cis or the trans diastereoisomers to be exclusively obtained. This stereodivergent cyclization has enabled the synthesis of C2-symmetric bisacetate-substituted isoindolines. In addition, bisacetate isoindolines bearing two well-differentiated ester moieties are also noteworthy because they may allow for the orthogonal synthesis of β,β'-dipeptides using a single nitrogen atom as a linchpin.

  6. Intramolecular [2 + 2] photocycloaddition/thermal fragmentation: formally "allowed" and "forbidden"pathways toward 5-8-5 ring systems.

    PubMed

    Bader, Scott J; Snapper, Marc L

    2005-02-01

    The thermal fragmentation of highly functionalized, linear polycyclobutanes with a cis,syn,cis-relative stereochemistry is shown to offer a rapid entry into the dicyclopenta[a,d]cyclooctenyl (5-8-5) ring system. The thermolysis of polyfused cyclobutanes with a cis,syn,cis- or a cis,anti,cis-relationship proceeds in a formally "symmetry-allowed" manner through the intermediacy of a cis,trans-cyclooctadiene. When a bridging tether used to establish the cis,syn,cis-stereochemistry in the intramolecular [2 + 2] photocyclization is present in the thermolysis step, however, the result of a formally "symmetry-forbidden" fragmentation is observed yielding cis,cis-cyclooctadiene-containing 5-8-5 products. In general, the stereochemical observations noted in these fragmentations offer new opportunities for accessing a variety of stereochemical relationships in these 5-8-5 ring systems.

  7. [Intramolecular hygrogen bonds in conformers of 2'-deoxycytidine: results of quantum-chemical analysis of electron density topology].

    PubMed

    Zhurakivs'kyĭ, R O; Hovorun, D M

    2006-01-01

    As many as 13 types of intramolecular hygrogen bonds are determined in 89 conformers of 2'-deoxycytidine nucleoside by means of quantum-chemical analysis (at DFT B3LYP/6-31G(d,p) theory level) of electron density topology with Atoms-in-Molecules (AIM) theory. The total number of H-bonds is 168 and their types are C1'H...O2, C2'H2...O5', C2'H2...O2, C3'H...O2, C5'H1...O2, C5'H2...O2, C6H...O4', C6H...O5', C3'H...HC6, O3'H...O5', O5'H...O3', O5'H...O4' and O5'H...O2. Conformational, geometric and electron-topological properties of H-bonds are presented.

  8. The intramolecular mechanism for the second proton transfer in triosephosphate isomerase (TIM): a QM/FE approach.

    PubMed

    Alagona, Giuliano; Ghio, Caterina; Kollman, Peter A

    2003-01-15

    The intramolecular mechanism we earlier proposed [Alagona, G.; Desmeules, P.; Ghio, C.; Kollman, P. A. J Am Chem Soc 1984, 106, 3623] for the second proton transfer of the reaction catalyzed by triosephosphate isomerase (TIM) is examined ab initio at the HF and MP2/6-31+G** levels in vacuo for two conformers of the enediolate phosphate (ENEP), with the ethereal oxygen of the phosphate group either syn (X), as in the crystal structure, or anti (Y) with respect to the enediolate carbonyl O. The barrier height for the intramolecular proton transfer occurring in enediolate is very sensitive to electron correlation corrections. The MP2 internal energy barrier is much lower than the HF one, while the free energy (FE) barrier is even more favorable, indicating that the enzyme presence is not requested to speed up that step. An investigation of the dynamical aspects of the mechanism, along the pathway from ENEP A (with H on O(1)) to TS and from TS to ENEP B (with H on O(2)), was, however, carried out in the presence of the enzyme field while using a neutral His-95 with its proton on Ndelta. To perform the FE simulations, it was necessary to parametrize in the AMBER force-field the ENEP A, TS and B species, whose partial charges have been determined with the RESP procedure, with the X and Y arrangements of the phosphate head. Actually, the FE/QM approach produced a low barrier and a substantial balance between A and B, especially at the MP2 level. The trajectories, analyzed paying a particular attention to the positions assumed by His-95 and by the other active site residues, put forward somewhat different H-bond patterns around the X or Y enediolate phosphate.

  9. Mechanism of intramolecular electron transfer in the photoexcited Zn-substituted cytochrome c: theoretical and experimental perspective.

    PubMed

    Tokita, Yuichi; Shimura, Jusuke; Nakajima, Hiroshi; Goto, Yoshio; Watanabe, Yoshihito

    2008-04-16

    Photoinduced electron transfer (ET) in zinc-substituted cytochrome c (Zn-cyt c) has been utilized in many studies on the long-range ET in protein. Attempting to understand its ET mechanism in terms of electronic structure of the molecule, we have calculated an all-electron wave function for the ground-state of Zn-cyt c on the basis of density functional theory (DFT). The four molecular orbitals (MOs) responsible for excitation by UV-vis light (Gouterman's 4-orbitals) are assigned on the basis of the excited states of chromophore model for Zn-porphine complex calculated with the time-dependent DFT method. ET rates between each Gouterman's 4-orbitals and other MOs were estimated using Fermi's golden rule. It appeared that the two occupied MOs of the 4-orbitals show exclusively higher ET rate from/to particular MOs that localize on outermost amino acid residues (Lys 7 or Asn 54), respectively, whereas ET rates involving the two unoccupied MOs of the 4-orbitals are much slower. These results imply that the intramolecular ET in photoexcited Zn-cyt c is governed by the hole transfer through occupied MOs. The couplings of MOs between zinc porphyrin core and specific amino acid residues on the protein surface have been demonstrated in Zn-cyt c immobilized on an Au electrode via carboxylic acid group-terminated self-assembled monolayer. The Zn-cyt c-modified electrode showed photocurrents responsible for photoillumination. The action spectrum of the photocurrent was identical with the absorption spectrum of Zn-cyt c, indicating photoinduced electron conduction via occupied MOs. The voltage dependence of the photocurrent appeared to be linear and bidirectional like a photoconductor, which strongly supports the intramolecular ET mechanism in Zn-cyt c proposed on the basis of the theoretical calculations.

  10. High-Accurate Intermolecular Potential Energy Surface of HCN-H_2 Complex with Intramolecular Vibrational Mode of HCN Included

    NASA Astrophysics Data System (ADS)

    Zhai, Yu; Li, Hui

    2016-06-01

    ydrogen is one of the most abundant interstellar species. Observation of rotational and vibrational spectra of H_2 containing complexes is of great importance because they are possible candidates for radio-astronomical detection. CO, HCN, HCCH are as isoelectronic molecules of N_2, each with a strong triple bond. It had been a big challenge to predict reliable theoretical rovibrational spectra of complexes including such species because the higher order electron correlation energy plays a non-negligible role in improving the accuracy. However, recent works on CO-H_2 have shown that it is possible to reproduce the experimental spectra quantitatively. In this work, we calculate a five-dimension potential energy surface (PES) of HCN-H_2 complex which explicitly include the intramolecular asymmetric stretching vibrational mode(C-H,Q_3) coordinate at CCSD(T)/aug-cc-pVQZ+3s3p2d1f1g level, corrected with electron correlation energy from the triple and quadruple excitation. Vibrational average over intramolecular vibration mode is made with HCN monomer at ground and the first excited vibrational states respectively, and the averaged data are fitted to two four-dimension Morse/Long-Range (MLR) potential energy functions. Based on the MLR PESs, for the first time, we calculated the spectra of HCN-{para}H_2} and {HCN-{ortho}H_2}. The results for HCN-{ortho}H_2} are in good agreement with the published experimental data with root-mean-square-difference (RMSD) only 0.01wn, which validates the accuracy of the PESs. J. Chem. Phys., 139, 164315 (2013); Science, 336, 1147 (2012). J. Chem. Phys., 115, 5137 (2001).

  11. Vibrational spectra and intramolecular vibrational redistribution in highly excited deuterobromochlorofluoromethane CDBrClF: Experiment and theory

    NASA Astrophysics Data System (ADS)

    Beil, Andreas; Hollenstein, Hans; Monti, Oliver L. A.; Quack, Martin; Stohner, Jürgen

    2000-08-01

    The rovibrational spectra of deuterobromochlorofluoromethane (CDBrClF) were measured at intermediate (0.1 cm-1) and high resolution (0.0024 cm-1 full bandwidth, half-maximum) by interferometric Fourier transform infrared spectroscopy in the range from the far infrared at 200 cm-1 to the near infrared (12 000 cm-1) covering all the fundamentals and CD stretching overtones up to polyad N=5. The spectra are completely analyzed in terms of their vibrational assignments to fundamentals, combinations and overtones. At high excitation the analysis reveals the dominant anharmonic coupling between four high frequency vibrational modes; the CD stretching (ν1), two CD bending (ν2,ν3), and the CF stretching mode (ν4). The analysis is carried out using effective model Hamiltonians including three and four vibrational degrees of freedom. We also present vibrational variational calculations on a grid in a four-dimensional normal coordinate subspace. The potential energy and the dipole moment function are calculated ab initio on this grid using self-consistent field second order Møller-Plesset perturbation theory (MP2). Experimental and theoretical results for band positions and integrated intensities as well as effective spectroscopic parameters are found to be in good agreement. The important anharmonic coupling between the CD chromophore and the CF stretching vibration can be described by an effective cubic Fermi resonance coupling constant ksff'≈(50±10) cm-1, which leads to intramolecular vibrational redistribution between the CD and CF chromophores on the femtosecond time scale. Time dependent intramolecular vibrational redistribution processes in CDBrClF are derived in various representations, including time dependent probability densities ("wave packets") in coordinate space and finally time dependent entropy.

  12. Intramolecular Interactions between the Protease and Structural Domains Are Important for the Functions of Serine Protease Autotransporters▿ †

    PubMed Central

    Tsang, Casey; Malik, Huma; Nassman, Deana; Huang, Antony; Tariq, Fayha; Oelschlaeger, Peter; Stathopoulos, Christos

    2010-01-01

    Autotransporter (AT) is a protein secretion pathway found in Gram-negative bacteria featuring a multidomain polypeptide with a signal sequence, a passenger domain, and a translocator domain. An AT subfamily named serine protease ATs of the family Enterobacteriaceae (SPATEs) is characterized by the presence of a conserved serine protease motif in the passenger domain which contributes to bacterial pathogenesis. The goal of the current study is to determine the importance of the passenger domain conserved residues in the SPATE proteolytic and adhesive functions using the temperature-sensitive hemagglutinin (Tsh) protein as our model. To begin, mutations of 21 fully conserved residues in the four passenger domain conserved motifs were constructed by PCR-based site-directed mutagenesis. Seventeen mutants exhibited a wild-type secretion level; among these mutants, eight displayed reduced proteolytic activities in Tsh-specific oligopeptide and mucin cleavage assays. These eight mutants also demonstrated lower affinities to extracellular matrix proteins, collagen IV, and fibronectin. These eight conserved residues were analyzed by molecular graphics modeling to demonstrate their intramolecular interactions with the catalytic triad and other key residues. Additional mutations were made to confirm the above interactions in order to demonstrate their significance to the SPATE functions. Altogether our data suggest that certain conserved residues in the SPATE passenger domain are important for both the proteolytic and adhesive activities of SPATE by maintaining the proper protein structure via intramolecular interactions between the protease and β-helical domains. Here, we provide new insight into the structure-function relationship of the SPATEs and the functional roles of their conserved residues. PMID:20479079

  13. 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

  14. Intramolecular telomeric G-quadruplexes dramatically inhibit DNA synthesis by replicative and translesion polymerases, revealing their potential to lead to genetic change.

    PubMed

    Edwards, Deanna N; Machwe, Amrita; Wang, Zhigang; Orren, David K

    2014-01-01

    Recent research indicates that hundreds of thousands of G-rich sequences within the human genome have the potential to form secondary structures known as G-quadruplexes. Telomeric regions, consisting of long arrays of TTAGGG/AATCCC repeats, are among the most likely areas in which these structures might form. Since G-quadruplexes assemble from certain G-rich single-stranded sequences, they might arise when duplex DNA is unwound such as during replication. Coincidentally, these bulky structures when present in the DNA template might also hinder the action of DNA polymerases. In this study, single-stranded telomeric templates with the potential to form G-quadruplexes were examined for their effects on a variety of replicative and translesion DNA polymerases from humans and lower organisms. Our results demonstrate that single-stranded templates containing four telomeric GGG runs fold into intramolecular G-quadruplex structures. These intramolecular G quadruplexes are somewhat dynamic in nature and stabilized by increasing KCl concentrations and decreasing temperatures. Furthermore, the presence of these intramolecular G-quadruplexes in the template dramatically inhibits DNA synthesis by various DNA polymerases, including the human polymerase δ employed during lagging strand replication of G-rich telomeric strands and several human translesion DNA polymerases potentially recruited to sites of replication blockage. Notably, misincorporation of nucleotides is observed when certain translesion polymerases are employed on substrates containing intramolecular G-quadruplexes, as is extension of the resulting mismatched base pairs upon dynamic unfolding of this secondary structure. These findings reveal the potential for blockage of DNA replication and genetic changes related to sequences capable of forming intramolecular G-quadruplexes. PMID:24454683

  15. Quantifying stickiness: thermodynamic characterization of intramolecular domain interactions to guide the design of förster resonance energy transfer sensors.

    PubMed

    Lindenburg, Laurens H; Malisauskas, Mantas; Sips, Tari; van Oppen, Lisanne; Wijnands, Sjors P W; van de Graaf, Stan F J; Merkx, Maarten

    2014-10-14

    The introduction of weak, hydrophobic interactions between fluorescent protein domains (FPs) can substantially increase the dynamic range (DR) of Förster resonance energy transfer (FRET)-based sensor systems. Here we report a comprehensive thermodynamic characterization of the stability of a range of self-associating FRET pairs. A new method is introduced that allows direct quantification of the stability of weak FP interactions by monitoring intramolecular complex formation as a function of urea concentration. The commonly used S208F mutation stabilized intramolecular FP complex formation by 2.0 kCal/mol when studied in an enhanced cyan FP (ECFP)-linker-enhanced yellow FP (EYFP) fusion protein, whereas a significantly weaker interaction was observed for the homologous Cerulean/Citrine FRET pair (ΔG0(o-c) = 0.62 kCal/mol). The latter effect could be attributed to two mutations in Cerulean (Y145A and H148D) that destabilize complex formation with Citrine. Systematic analysis of the contribution of residues 125 and 127 at the dimerization interface in mOrange.linker.mCherry fusion proteins yielded a toolbox of new mOrange-mCherry combinations that allowed tuning of their intramolecular interaction from very weak (ΔG0(o-c) = .0.39 kCal/mol) to relatively stable (ΔG0(o-c) = 2.2 kCal/mol). The effects of these mutations were also studied by monitoring homodimerization of mCherry variants using fluorescence anisotropy. These mutations affected intramolecular and intermolecular domain interactions similarly, although FP interactions were found to be stronger in the latter. The knowledge thus obtained allowed successful construction of a red-shifted variant of the bile acid FRET sensor BAS-1 by replacement of the self-associating Cerulean-Citrine pair by mOrange.mCherry variants with a similar intramolecular affinity. Our findings thus allow a better understanding of the subtle but important role of intramolecular domain interactions in current FRET sensors and help

  16. A fluorescence-based method for direct measurement of submicrosecond intramolecular contact formation in biopolymers: an exploratory study with polypeptides.

    PubMed

    Hudgins, Robert R; Huang, Fang; Gramlich, Gabriela; Nau, Werner M

    2002-01-30

    A fluorescent amino acid derivative (Fmoc-DBO) has been synthesized, which contains 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) as a small, hydrophilic fluorophore with an extremely long fluorescence lifetime (325 ns in H2O and 505 ns in D2O under air). Polypeptides containing both the DBO residue and an efficient fluorescence quencher allow the measurement of rate constants for intramolecular end-to-end contact formation. Bimolecular quenching experiments indicated that Trp, Cys, Met, and Tyr are efficient quenchers of DBO (k(q) = 20, 5.1, 4.5, and 3.6 x 10(8) M(-1) x s(-1) in D2O), while the other amino acids are inefficient. The quenching by Trp, which was selected as an intrinsic quencher, is presumed to involve exciplex-induced deactivation. Flexible, structureless polypeptides, Trp-(Gly-Ser)n-DBO-NH2, were prepared by standard solid-phase synthesis, and the rates of contact formation were measured through the intramolecular fluorescence quenching of DBO by Trp with time-correlated single-photon counting, laser flash photolysis, and steady-state fluorometry. Rate constants of 4.1, 6.8, 4.9, 3.1, 2.0, and 1.1 x 10(7) s(-1) for n = 0, 1, 2, 4, 6, and 10 were obtained. Noteworthy was the relatively slow quenching for the shortest peptide (n = 0). The kinetic data are in agreement with recent transient absorption studies of triplet probes for related peptides, but the rate constants are significantly larger. In contrast to the flexible structureless Gly-Ser polypeptides, the polyproline Trp-Pro4-DBO-NH2 showed insignificant fluorescence quenching, suggesting that a high polypeptide flexibility and the possibility of probe-quencher contact is essential to induce quenching. Advantages of the new fluorescence-based method for measuring contact formation rates in biopolymers include high accuracy, fast time range (100 ps-1 micros), and the possibility to perform measurements in water under air.

  17. Naphthalene diols: a new class of antioxidants intramolecular hydrogen bonding in catechols, naphthalene diols, and their aryloxyl radicals.

    PubMed

    Foti, Mario C; Johnson, Erin R; Vinqvist, Melinda R; Wright, James S; Barclay, L Ross C; Ingold, K U

    2002-07-26

    1,8-Naphthalenediol, 5, and its 4-methoxy derivative, 6, were found to be potent H-atom transfer (HAT) compounds on the basis of their rate constants for H-atom transfer to the 2,2-di(4-t-octylphenyl)-1-picrylhydrazyl radical (DOPPH*), k(ArOH/DOPPH)*, or as antioxidants during inhibited styrene autoxidation, k(ArOH/ROO)*, initiated with AIBN. The rate constants showed that 5 and 6 are more active HAT compounds than the ortho-diols, catechol, 1, 2,3-naphthalenediol, 2, and 3,5-di-tert-butylcatechol, 3. Compound 6 has almost twice the antioxidant activity, k(ArOH/ROO)* = 6.0 x 10(6) M(-)(1) s(-1), of that of the vitamin E model compound, 2,2,5,7,8-pentamethyl-6-chromanol, 4. Calculations of the O-H bond dissociation enthalpies compared to those of phenols, (deltaBDEs), of 1-6 predict a HAT order of reactivity of 2 < 1 < 3 approximately 4 < 5 < 6 in general agreement with kinetic results. Calculations on the diols show that intramolecular H-bonding stabilizes the radicals formed on H-atom transfer more than it does the parent diols, and this effect contributes to the increased HAT activity of 5 and 6 compared to the activities of the catechols. For example, the increased stabilization due to the intramolecular H-bond of 5 radical over 5 parent of 8.6 kcal/mol was about double that of 2 radical over 2 parent of 4.6 kcal/mol. Linear free energy plots of log k(ArOH/DOPPH)* and log k(ArOH/ROO)* versus deltaBDEs for compounds 1-6 along with available literature values for nonsterically hindered monophenols placed the compounds on common scales. The derived Evans-Polanyi constants from the plots for the two reactions, alpha(DOPPH)* = 0.48 > alpha(ROO)* = 0.32, gave the expected order, since the ROO* reaction is more exothermic than the DOPPH* reaction. Compound 6 is sufficiently reactive to react directly with oxygen, and it lies off the log k(ArOH/ROO)* versus deltaBDE plot.

  18. F···HO intramolecular hydrogen bond as the main transmission mechanism for (1h)J(F,H(O)) coupling constant in 2'-fluoroflavonol.

    PubMed

    Fonseca, Tânia A O; Ramalho, Teodorico C; Freitas, Matheus P

    2012-08-01

    Flavonoids are useful compounds in medicinal chemistry and exhibit conformational isomerism, which is ruled by intramolecular interactions. One of the main intramolecular forces governing the stability of conformations is the hydrogen bond. Hydrogen bond involving fluorine covalently bonded to carbon has been found to be rare, but it appears in 2'-fluoroflavonol, although the F···HO hydrogen bond cannot be considered the main effect governing the conformational stability of this compound. Because (19)F is magnetically active and suitable for NMR studies, the (1h)J(F,H(O)) coupling constant can be used as a probe for such an interaction in 2'-fluoroflavonol. In fact, the (1h)J(F,H(O)) coupling was computationally analyzed in this work, and the F···HO hydrogen bond was found to be its main transmission mechanism, which modulates this coupling in 2'-fluoroflavonol, rather than overlap of proximate electronic clouds, such as in 2-fluorophenol.

  19. 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

  20. Formation of an Intramolecular Periplasmic Disulfide Bond in TcpP Protects TcpP and TcpH from Degradation in Vibrio cholerae

    PubMed Central

    Morgan, Sarah J.; French, Emily L.; Thomson, Joshua J.; Seaborn, Craig P.; Shively, Christian A.

    2015-01-01

    ABSTRACT TcpP and ToxR coordinately regulate transcription of toxT, the master regulator of numerous virulence factors in Vibrio cholerae. TcpP and ToxR are membrane-localized transcription factors, each with a periplasmic domain containing two cysteines. In ToxR, these cysteines form an intramolecular disulfide bond and a cysteine-to-serine substitution affects activity. We determined that the two periplasmic cysteines of TcpP also form an intramolecular disulfide bond. Disruption of this intramolecular disulfide bond by mutation of either cysteine resulted in formation of intermolecular disulfide bonds. Furthermore, disruption of the intramolecular disulfide bond in TcpP decreased the stability of TcpP. While the decreased stability of TcpP-C207S resulted in a nearly complete loss of toxT activation and cholera toxin (CT) production, the second cysteine mutant, TcpP-C218S, was partially resistant to proteolytic degradation and maintained ∼50% toxT activation capacity. TcpP-C218S was also TcpH independent, since deletion of tcpH did not affect the stability of TcpP-C218S, whereas wild-type TcpP was degraded in the absence of TcpH. Finally, TcpH was also unstable when intramolecular disulfides could not be formed in TcpP, suggesting that the single periplasmic cysteine in TcpH may assist with disulfide bond formation in TcpP by interacting with the periplasmic cysteines of TcpP. Consistent with this finding, a TcpH-C114S mutant was unable to stabilize TcpP and was itself unstable. Our findings demonstrate a periplasmic disulfide bond in TcpP is critical for TcpP stability and virulence gene expression. IMPORTANCE The Vibrio cholerae transcription factor TcpP, in conjunction with ToxR, regulates transcription of toxT, the master regulator of numerous virulence factors in Vibrio cholerae. TcpP is a membrane-localized transcription factor with a periplasmic domain containing two cysteines. We determined that the two periplasmic cysteines of TcpP form an