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Sample records for intramolecular utilizando nbcl5

  1. 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.

  2. FeCl3-Assisted Niobium-Catalyzed Cycloaddition of Nitriles and Alkynes: Synthesis of Alkyl- and Arylpyrimidines Based on Independent Functions of NbCl5 and FeCl3 Lewis Acids.

    PubMed

    Fuji, Maito; Obora, Yasushi

    2017-10-02

    NbCl5-catalyzed [2 + 2 + 2] cycloaddition of nitriles with alkynes was used to synthesize pyrimidine derivatives. In this reaction, the use of individual Lewis acids, namely NbCl5 and FeCl3, is a key strategy for achieving the reaction using a catalytic amount of NbCl5. The roles of the two Lewis acids were investigated using FT-IR spectroscopy. The results showed that NbCl5 served as an efficient Lewis acid catalyst for nitrile activation, whereas FeCl3 showed stronger Lewis acidity toward pyrimidines, releasing NbCl5 into the catalytic cycle.

  3. 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.

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

    SciTech Connect

    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

  5. Intramolecular carbonickelation of alkenes

    PubMed Central

    Lhermet, Rudy

    2013-01-01

    Summary The efficiency of the intramolecular carbonickelation of substituted allylic ethers and amines has been studied to evaluate the influence of the groups borne by the double bond on this cyclization. The results show that when this reaction takes place, it affords only the 5-exo-trig cyclization products, viz. dihydrobenzofurans or indoles. Depending on the tethered heteroatom (O or N), the outcome of the cyclization differs. While allylic ethers are relatively poor substrates that undergo a side elimination and need an intracyclic double bond to proceed, allylic amines react well and afford indoline and indole derivatives. Finally, the synthesis of the trinuclear ACE core of a morphine-like skeleton was achieved by using NiBr2bipy catalysis. PMID:23766783

  6. Quantification and analysis of intramolecular interactions.

    PubMed

    Gonthier, Jérôme F; Corminboeuf, Clémence

    2014-01-01

    Non-covalent interactions play a prominent role in chemistry and biology. While a myriad of theoretical methods have been devised to quantify and analyze intermolecular interactions, the theoretical toolbox for the intramolecular analogues is much scarcer. Yet interactions within molecules govern fundamental phenomena as illustrated by the energetic differences between structural isomers. Their accurate quantification is of utmost importance. This paper gives an overview of the most common approaches able to probe intramolecular interactions and stresses both their characteristics and limitations. We finally introduce our recent theoretical approach, which represents the first step towards the development of an intramolecular version of Symmetry-Adapted Perturbation Theory (SAPT).

  7. Intramolecular association within the SAFT framework

    NASA Astrophysics Data System (ADS)

    Avlund, Ane S.; Kontogeorgis, Georgios M.; Chapman, Walter G.

    2011-07-01

    A general theory for modelling intramolecular association within the SAFT framework is proposed. Sear and Jackson [Phys. Rev. E. 50 (1), 386 (1994)] and Ghonasgi and Chapman [J. Chem. Phys. 102 (6), 2585 (1995)] have previously extended SAFT to include intramolecular association for chains with two sites. We show that the resulting equations from the two approaches are equivalent, and use their work as a basis for developing a new general theory. The approach used by Ghonasgi and Chapman is based on mass balances and an infinite dilution result and provides the equations needed to determine the contribution to the Helmholtz free energy from association (inter- as well as intramolecularly) at equilibrium. Sear and Jackson rederived the contribution to the Helmholtz free energy from association from the theory by Wertheim [J. Stat. Phys. 42 (3-4), 459 (1986)] with inclusion of intramolecular association, and using this approach we obtain an expression for the Helmholtz free energy that is valid also at non-equilibrium states (with respect to hydrogen bonds), which is very useful when calculating derivatives.

  8. 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.

  9. The Limit of Intramolecular H-Bonding.

    PubMed

    Hubbard, Thomas A; Brown, Alisdair J; Bell, Ian A W; Cockroft, Scott L

    2016-11-23

    Hydrogen bonds are ubiquitous interactions in molecular recognition. The energetics of such processes are governed by the competing influences of pre-organization and flexibility that are often hard to predict. Here we have measured the strength of intramolecular interactions between H-bond donor and acceptor sites separated by a variable linker. A striking distance-dependent threshold was observed in the intramolecular interaction energies. H-bonds were worth less than -1 kJ mol(-1) when the interacting groups were separated by ≥6 rotating bonds, but ranged between -5 and -9 kJ mol(-1) for ≤5 rotors. Thus, only very strong external H-bond acceptors were able to compete with the stronger internal H-bonds. In addition, a constant energetic penalty per rotor of ∼5-6 kJ mol(-1) was observed in less strained situations where the molecule contained ≥4 rotatable bonds.

  10. An unusual intramolecular trans-amidation.

    PubMed

    Rivera, Heriberto; Dhar, Sachin; La Clair, James J; Tsai, Shiou-Chuan; Burkart, Michael D

    2016-06-23

    Polyketide biosynthesis engages a series of well-timed biosynthetic operations to generate elaborate natural products from simple building blocks. Mimicry of these processes has offered practical means for total synthesis and provided a foundation for reaction discovery. We now report an unusual intramolecular trans-amidation reaction discovered while preparing stabilized probes for the study of actinorhodin biosynthesis. This rapid cyclization event offers insight into the natural cyclization process inherent to the biosynthesis of type II polyketide antibiotics.

  11. Quantification of intramolecular nonbonding interactions in organochalcogens.

    PubMed

    Roy, Dipankar; Sunoj, Raghavan B

    2006-05-04

    Intramolecular nonbonding interactions between chalcogen atoms in a series of ortho substituted arylselenides (S/O...Se-Y, with Y = -Me, -CN, -Cl, and -F) are quantified using the coupled cluster CCSD(T)/cc-pVDZ level of theory. A homodesmic reaction method as well as an ortho-para approach are employed in evaluating the strength of intramolecular interactions. Comparison of the results obtained using the ab initio MP2 method and pure and hybrid density functional theories are performed with that of the coupled cluster values to assess the quality of different density functionals in evaluating the strength of nonbonding interactions. The interaction energies are found to be higher when the thioformyl group acts as the donor and the Se-F bond acts as the acceptor. In a given series with the same donor atom, the strength of the interaction follows the order Me < CN < Cl < F, exhibiting fairly high sensitivity to the group attached to selenium (Se-Y). Analysis of electron density at the S/O...Se bond critical point within the Atoms in Molecule framework shows a very good correlation with the computed intramolecular interaction energies.

  12. Intramolecular hydrogen bonding in medicinal chemistry.

    PubMed

    Kuhn, Bernd; Mohr, Peter; Stahl, Martin

    2010-03-25

    The formation of intramolecular hydrogen bonds has a very pronounced effect on molecular structure and properties. We study both aspects in detail with the aim of enabling a more rational use of this class of interactions in medicinal chemistry. On the basis of exhaustive searches in crystal structure databases, we derive propensities for intramolecular hydrogen bond formation of five- to eight-membered ring systems of relevance in drug discovery. A number of motifs, several of which are clearly underutilized in drug discovery, are analyzed in more detail by comparing small molecule and protein-ligand X-ray structures. To investigate effects on physicochemical properties, sets of closely related structures with and without the ability to form intramolecular hydrogen bonds were designed, synthesized, and characterized with respect to membrane permeability, water solubility, and lipophilicity. We find that changes in these properties depend on a subtle balance between the strength of the hydrogen bond interaction, geometry of the newly formed ring system, and the relative energies of the open and closed conformations in polar and unpolar environments. A number of general guidelines for medicinal chemists emerge from this study.

  13. Intramolecular Isotopic Studies: Chemical Enhancements and Alternatives

    NASA Astrophysics Data System (ADS)

    Hayes, J. M.

    2016-12-01

    As mass spectroscopic and NMR-based methods now appropriately flourish, chemical techniques should not be forgotten. First, the methods developed by pioneering intramolecular analysts can be reapplied to new samples. Second, they can be extended. The synthesis of intramolecular isotopic standards is particularly important and straightforward. It requires only that a chemical reaction has no secondary products. An example is provided by the addition of carbon dioxide to a Grignard reagent. The reaction proceeds with an isotope effect. The isotopic composition of the carboxyl group in the acid which is produced is thus not equal to that of the starting carbon dioxide but the unconsumed CO2 can be recovered and analyzed. A simple titration can show that all the rest of the CO2 is in the product acid. The isotopic composition of the carboxyl group can then be calculated by difference. The product is an intramolecular isotopic standard, an organic molecule in which the isotopic composition of a specific carbon position is known accurately. Both analysts and reviewers can thus gain invaluable confidence in the accuracy of instrumental results. A second example: the haloform reaction quantitatively degrades methyl ketones, producing a carboxylic acid which can be decarboxylated to determine the isotopic composition of the parent carbonyl and a haloform (CHI3, for example) that can be combusted to determine the isotopic composition of the methyl group. Ketones thus analyzed can be combined with Grignard reagents to yield carbon skeletons in which the isotopic compositions of internal and terminal -CH2- and -CH3 groups are known accurately. In general, analysts accustomed to demanding quantitative reactions should remember the power of mass balances and recognize that many organic-chemical reactions, while not quantitative, lack side products and can be driven to the total consumption of at least one reactant.

  14. Intramolecular energy transfer reactions in polymetallic

    SciTech Connect

    Petersen, J.

    1990-11-01

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

  15. 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.

  16. The stereochemical course of intramolecular Michael reactions.

    PubMed

    Kwan, Eugene E; Scheerer, Jonathan R; Evans, David A

    2013-01-04

    We present a general model for understanding the stereochemical course of intramolecular Michael reactions. We show that the addition of β-ketoester enolates to α,β-unsaturated esters and imides bearing adjacent stereocenters (X, Y = H, Me, OR) leads to high levels of asymmetric induction. Reinforcing and nonreinforcing stereochemical relationships are evaluated from the syn and anti reactant diastereomers. On the basis of synthetic, spectroscopic, and computational studies, we propose that the outcomes of these reactions can be rationalized by a dipole-minimized chair transition-state model.

  17. 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.

  18. 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.

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

    PubMed

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

    2016-03-04

    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.

  20. Helical polymers based on intramolecularly hydrogen-bonded aromatic polyamides.

    PubMed

    Lu, Yi-Xuan; Shi, Zhu-Ming; Li, Zhan-Ting; Guan, Zhibin

    2010-12-21

    Inspired by arylamide-based oligomeric foldermers that are stabilized by intramolecular hydrogen bonding, a series of polyamides with intramolecular hydrogen-bonding motifs were synthesized via polycondensation reactions. These polymers can fold into helical conformation different from their linear control. The chirality of helical conformation can further be tuned via acid-base complexation using chiral residues.

  1. The intramolecular click reaction using 'carbocontiguous' precursors.

    PubMed

    Patil, Pravin C; Luzzio, Frederick A

    2017-07-20

    The synthesis and utilization of all carbon-chain 'carbocontiguous' azidoalkynyl precursors for an intramolecular click reaction is described. The substrates contain both azidoalkyl and ethynylmethyl groups which are conjoined by a 2-(phenylsulfonylmethyl)-4,5-diphenyloxazole lynchpin and are suitably disposed for ring closure. On promotion by copper salts, a number of cyclic click products having the 1,4-disubstituted endo-fused triazole component and the 4,5-diphenyloxazole component are obtained. In one case, removal of the phenylsulfonylmethyl group from the substrate prior to cyclization gave the 1,5-disubstituted exo-fused triazole. The utilization of CuSO4/sodium ascorbate system appears to be the optimal conditions for closure/cyclization and afforded the cyclized products in yields of 84-95%.

  2. Influence of Intramolecular Charge Transfer and Nuclear Quantum Effects on Intramolecular Hydrogen Bonds in Azopyrimidines.

    PubMed

    Bártová, Kateřina; Čechová, Lucie; Procházková, Eliška; Socha, Ondřej; Janeba, Zlatko; Dračínský, Martin

    2017-10-06

    Intramolecular hydrogen bonds (IMHBs) in 5-azopyrimidines are investigated by NMR spectroscopy and DFT computations that involve nuclear quantum effects. A series of substituted 5-phenylazopyrimidines with one or two hydrogen bond donors able to form IMHBs with the azo group is prepared by azo coupling. The barrier of interconversion between two rotamers of the compounds with two possible IMHBs is determined by variable temperature NMR spectroscopy and it is demonstrated that the barrier is significantly affected by intramolecular charge transfer. Through-hydrogen-bond scalar coupling is investigated in (15)N labeled compounds and the stability of the IMHBs is correlated with experimental NMR parameters and rationalized by path integral molecular dynamics simulations that involve nuclear quantum effects. Detailed information on the hydrogen bond geometry upon hydrogen-to-deuterium isotope exchange is obtained from a comparison of experimental and calculated NMR data.

  3. Intramolecular Rovibrational Dynamics of Hydrocarbons and Argon

    NASA Astrophysics Data System (ADS)

    McIlroy, Andrew

    This dissertation describes investigations of the intramolecular dynamics of two types of systems: isolated hydrocarbon molecules, and clusters of Ar atoms with an HF molecule. Both are studied via high resolution (0.001 cm^{-1}) infrared (IR) laser spectroscopy in a slit supersonic expansion. The slit expansion provides a cold (T = 3-15 K) source of isolated gas phase molecules or complexes with sufficient pathlength to carry out IR laser absorption experiments. Furthermore, probing the expansion parallel to the slit produces Doppler broadening up to a factor of ten below that found at room temperature facilitating high resolution, state specific experiments. In the hydrocarbon v = 1 >=ts 0 CH stretch spectra, the vibrational mixing ultimately responsible for intramolecular vibrational energy redistribution (IVR) is elucidated from the observation of splitting of the individual rovibrational transitions; this is due to coupling of the CH stretch to the bath of combination and overtone states. The repetition of qualitative patterns in these data suggest that in some cases individual functional groups within a molecule may control IVR rates largely independent of the specific details of the molecule. For example, vibrational coupling of acetylenic CH stretches is shown to produce similar relaxation rates in molecules whose vibrational state densities vary by almost three orders of magnitude. The studies of Ar_{rm n}HF complexes, n = 1-4, focus on the transition from a free, gas phase HF molecule to a "solvated" HF in an Ar matrix. Models describing the observed red shifting of the HF vibration with the sequential addition of Ar atoms are investigated. Furthermore, these multibody clusters provide the opportunity to test the approximation of the potential energy surfaces (PES) of weakly bound (< 1000 cm^{-1}) systems with sums of two-body potentials. Initial calculations and experiments suggest that significant discrepancies exist between the true PES and the

  4. Ultrastructural evidence for intramolecular double stranding in iota-carrageenan.

    PubMed

    Abeysekera, R M; Bergström, E T; Goodall, D M; Norton, I T; Robards, A W

    1993-10-04

    Kinetic studies of primary processes of conformational ordering in gel-forming biopolymers have suggested that a change in mechanism from intermolecular to intramolecular multistrand formation occurs on lowering the concentration of biopolymer. We report here ultrastructural observations consistent with intramolecular double stranding in a carbohydrate polymer, iota-carrageenan, by arresting this process of primary conformational ordering by an ultra-rapid freeze fixation technique. High-resolution transmission electron microscopy (TEM) revealed isolated iota-carrageenan chains showing a range of morphologies (linear, circular, and hairpin) consistent with intramolecular stranding. Control experiments in which iota-carrageenan was frozen in the disordered form revealed longer and thinner strands.

  5. Intramolecular epitope spreading in Heymann nephritis.

    PubMed

    Shah, Pallavi; Tramontano, Alfonso; Makker, Sudesh P

    2007-12-01

    Immunization with megalin induces active Heymann nephritis, which reproduces features of human idiopathic membranous glomerulonephritis. Megalin is a complex immunological target with four discrete ligand-binding domains (LBDs) that may contain epitopes to which pathogenic autoantibodies are directed. Recently, a 236-residue N-terminal fragment, termed "L6," that spans the first LBD was shown to induce autoantibodies and severe disease. We used this model to examine epitope-specific contributions to pathogenesis. Sera obtained from rats 4 weeks after immunization with L6 demonstrated reactivity only with the L6 fragment on Western blot, whereas sera obtained after 8 weeks demonstrated reactivity with all four recombinant fragments of interest (L6 and LBDs II, III, and IV). We demonstrated that the L6 immunogen does not contain the epitopes responsible for the reactivity to the LBD fragments. Therefore, the appearance of antibodies directed at LBD fragments several weeks after the primary immune response suggests intramolecular epitope spreading. In vivo, we observed a temporal association between increased proteinuria and the appearance of antibodies to LBD fragments. These data implicate B cell epitope spreading in antibody-mediated pathogenesis of active Heymann nephritis, a model that should prove valuable for further study of autoimmune dysregulation.

  6. Intramolecular photoelectron diffraction in the gas phase

    NASA Astrophysics Data System (ADS)

    Ueda, K.; Miron, C.; Plésiat, E.; Argenti, L.; Patanen, M.; Kooser, K.; Ayuso, D.; Mondal, S.; Kimura, M.; Sakai, K.; Travnikova, O.; Palacios, A.; Decleva, P.; Kukk, E.; Martín, F.

    2013-09-01

    We report unambiguous experimental and theoretical evidence of intramolecular photoelectron diffraction in the collective vibrational excitation that accompanies high-energy photoionization of gas-phase CF4, BF3, and CH4 from the 1s orbital of the central atom. We show that the ratios between vibrationally resolved photoionization cross sections (v-ratios) exhibit pronounced oscillations as a function of photon energy, which is the fingerprint of electron diffraction by the surrounding atomic centers. This interpretation is supported by the excellent agreement between first-principles static-exchange and time-dependent density functional theory calculations and high resolution measurements, as well as by qualitative agreement at high energies with a model in which atomic displacements are treated to first order of perturbation theory. The latter model allows us to rationalize the results for all the v-ratios in terms of a generalized v-ratio, which contains information on the structure of the above three molecules and the corresponding molecular cations. A fit of the measured v-ratios to a simple formula based on this model suggests that the method could be used to obtain structural information of both neutral and ionic molecular species.

  7. Intramolecular photoelectron diffraction in the gas phase.

    PubMed

    Ueda, K; Miron, C; Plésiat, E; Argenti, L; Patanen, M; Kooser, K; Ayuso, D; Mondal, S; Kimura, M; Sakai, K; Travnikova, O; Palacios, A; Decleva, P; Kukk, E; Martín, F

    2013-09-28

    We report unambiguous experimental and theoretical evidence of intramolecular photoelectron diffraction in the collective vibrational excitation that accompanies high-energy photoionization of gas-phase CF4, BF3, and CH4 from the 1s orbital of the central atom. We show that the ratios between vibrationally resolved photoionization cross sections (v-ratios) exhibit pronounced oscillations as a function of photon energy, which is the fingerprint of electron diffraction by the surrounding atomic centers. This interpretation is supported by the excellent agreement between first-principles static-exchange and time-dependent density functional theory calculations and high resolution measurements, as well as by qualitative agreement at high energies with a model in which atomic displacements are treated to first order of perturbation theory. The latter model allows us to rationalize the results for all the v-ratios in terms of a generalized v-ratio, which contains information on the structure of the above three molecules and the corresponding molecular cations. A fit of the measured v-ratios to a simple formula based on this model suggests that the method could be used to obtain structural information of both neutral and ionic molecular species.

  8. Exciton Correlations in Intramolecular Singlet Fission

    SciTech Connect

    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, 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.

  9. Exciton Correlations in Intramolecular Singlet Fission

    DOE PAGES

    Sanders, Samuel N.; Kumarasamy, Elango; Pun, Andrew B.; ...

    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

  10. Exciton Correlations in Intramolecular Singlet Fission

    SciTech Connect

    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, 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.

  11. Molecular structures and intramolecular dynamics of pentahalides

    NASA Astrophysics Data System (ADS)

    Ischenko, A. A.

    2017-03-01

    This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.

  12. Amino acid salt catalyzed intramolecular Robinson annulation†‡

    PubMed Central

    Li, Pingfan; Yamamoto, Hisashi

    2009-01-01

    The silica gel absorbed amino acid salt catalyzed asymmetric intramolecular Robinson annulation reaction has been developed; up to 97% ee was obtained with this readily recoverable organocatalyst. PMID:19724802

  13. 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.

  14. Intramolecular energy transfer in fullerene pyrazine dyads

    SciTech Connect

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

    1998-11-26

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

  15. Photochemical Dynamics of Intramolecular Singlet Fission

    NASA Astrophysics Data System (ADS)

    Lin, Zhou; Iwasaki, Hikari; Van Voorhis, Troy

    2017-06-01

    Singlet fission (SF) converts a singlet exciton (S_1) into a pair of triplet ones (T_1) via a ``multi-exciton'' (ME) intermediate: S_1 \\longleftrightarrow ^1ME \\longleftrightarrow ^1(T_1T_1) \\longrightarrow 2T_1. In exothermic cases, e.g., crystalline pentacene or its derivatives, the quantum yield of SF can reach 200%. With SF doubling the electric current generated by an incident high-energy photon, the solar conversion efficiency in pentacene-based organic photovoltaics (OPVs) can exceed the Shockley-Queisser limit of 33.7%. The ME state is popularly considered to be a dimeric state with significant charge transfer (CT) character that is strongly coupled to both S_1 and ^1(T_1T_1), while this local model lacks strong support from full quantum dynamics studies. Intramolecular SF (ISF) occurring to covalently-bound dimers in the solution phase is an excellent model for a straightforward dynamics simulation of local excitons. In the present study, we investigate the ISF mechanisms for three covalently-bound dimers of pentacene derivatives, including ortho-, meta-, and para-bis(6,13-bis(triisopropylsilylethynyl)pentacene)benzene, in non-protic solvents. Specifically, we propagate the real-time, non-adiabatic quantum mechanical/molecular mechanical (QM/MM) dynamics on the potential energy surfaces associated with the states of S_1, ^1(T_1T_1) and CT. We explore how the energies of these ISF-relevant states and the non-adiabatic couplings between each other fluctuate with time and the instantaneous molecular configuration (e.g., intermonomer distance and orientation). We also quantitatively compare Condon and non-Condon ISF dynamics with solution-phase spectroscopic data. Our results allow us to understand the roles of CT energy levels in the ISF mechanism and propose a design strategy to maximize ISF efficiency. M. B. Smith and J. Michl, Chem. Rev. 110, 6891 (2010). W. Shockley and H. J. Queisser, J. Appl. Phys. 32, 510 (1961). T. C. Berkelbach, M. S. Hybertsen

  16. Extremely slow intramolecular diffusion in unfolded protein L.

    PubMed

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

    2010-08-03

    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.

  17. The role of intramolecular scattering in K-shell photoionization

    NASA Astrophysics Data System (ADS)

    Ayuso, D.; Ueda, K.; Miron, C.; Plésiat, E.; Argenti, L.; Patanen, M.; Kooser, K.; Mondal, S.; Kimura, M.; Sakai, K.; Travnikova, O.; Palacios, A.; Decleva, P.; Kukk, E.; Martín, F.

    2014-04-01

    We report evidence of intramolecular scattering occurring in inner shell photoionization of small molecules. Pronounced oscillations of the ratios between vibrationally resolved cross sections (v-ratios) as a function of photon energy have been observed theoretically and experimentally. Qualitative agreement with a 1st Born model confirms that they are due to intramolecular scattering: when an electron is ejected from a very localized region in the center of a polyatomic molecule, such as the C(1s) orbital in a CF4 molecule, it is diffracted by the surrounding atomic centers, encoding the geometry of the molecule [1, 2].

  18. Intramolecular donor-acceptor cyclopropane ring-opening cyclizations.

    PubMed

    Cavitt, Marchello A; Phun, Lien H; France, Stefan

    2014-02-07

    Cyclization reactions of donor-acceptor (D-A) cyclopropanes are recognized as versatile methods for construction of carbocyclic and heterocyclic scaffolds. In the literature, many examples of these polarized cyclopropanes' reactivity with nucleophiles, electrophiles, and radicals are prevalent. Although intermolecular reactivity of donor-acceptor cyclopropanes is widely reported, reviews that center on their intramolecular chemistry are rare. Thereupon, this tutorial review focalizes on new intramolecular transformations of donor-acceptor cyclopropanes for cycloisomerizations, formal cycloadditions, umpolung reactions, rearrangements and ring-opening lactonizations/lactamizations from 2009 to 2013. Furthermore, the role of D-A acceptor cyclopropanes as reactive subunits in natural product synthesis is underscored.

  19. Intramolecular nonbonded S...N interaction in rabeprazole.

    PubMed

    Hayashi, Kazuhiko; Ogawa, Shiho; Sano, Shigeki; Shiro, Motoo; Yamaguchi, Kentaro; Sei, Yoshihisa; Nagao, Yoshimitsu

    2008-06-01

    Intramolecular nonbonded S...N interactions in the crystal structures of the derivatives (7a-d) of sodium rabeprazole (1) and an intermolecular nonbonded S...N interaction between ethylmethylsulfoxide and pyridine in a solution were recognized. These results made us estimate that the intramolecular nonbonded S...N interaction existed in 1 and its derivatives in a solution, and formed the 4-membered quasi-ring in 2 (Fig. 1) followed by the increase of the reactivity of 2 to give the putative spiro sulfoxide 3, which is the key intermediate in the reaction cascade of 1 (Chart 1).

  20. Oxacycle synthesis via intramolecular reaction of carbanions and peroxides.

    PubMed

    Willand-Charnley, Rachel; Puffer, Benjamin W; Dussault, Patrick H

    2014-04-23

    The intramolecular reaction of dialkyl peroxides with carbanions, generated via chemoselective metal-heteroatom exchange or deprotonation, provides a new approach to cyclic ethers. Applied in tandem with C-C bond formation, the strategy enables a one-step annelation to form oxaospirocycles.

  1. Oxacycle Synthesis via Intramolecular Reaction of Carbanions and Peroxides

    PubMed Central

    2015-01-01

    The intramolecular reaction of dialkyl peroxides with carbanions, generated via chemoselective metal-heteroatom exchange or deprotonation, provides a new approach to cyclic ethers. Applied in tandem with C–C bond formation, the strategy enables a one-step annelation to form oxaospirocycles. PMID:24702123

  2. Synthesis of Antitumor Lycorines by Intramolecular Diels-Alder Reaction.

    PubMed

    Pérez, Dolores; Burés, Gema; Guitián, Enrique; Castedo, Luis

    1996-03-08

    Pharmacologically interesting lycorines were obtained by a short, efficient method based on an intramolecular Diels-Alder reaction between an alpha-pyrone and an alkyne, followed by loss of CO(2) in a retro Diels-Alder reaction. The cyclization precursors (pyrones 9) were obtained in good yields in two or three steps from the corresponding homophthalic acid or anhydride.

  3. Recent insights into intramolecular 13C isotope composition of biomolecules

    NASA Astrophysics Data System (ADS)

    Gilbert, A.; Yamada, K.; Julien, M.; Yoshida, N.; Remaud, G.; Robins, R.

    2016-12-01

    In 1961 Abelson & Hoering shown that the intramolecular 13C distribution in amino acids was not homogeneous, namely the carboxylic acid positions were 13C-enriched compared with the mean of the remaining C-atoms in the molecule [1]. Nearly 20 years later, Monson & Hayes were able to demonstrate that even and odd positions in acetogenic fatty acids also showed non-statistical 13C isotope distributions, and that the pattern varied depending on the organism [2]. It took a further decade for the intramolecular 13C distribution in the key metabolite, glucose, to be defined [3]. Although informative, much of this work was incomplete, a number of positions having to be deduced by difference. This limitation arose mainly due to the lack of techniques enabling the separation and quantification of 13C isotopomers of the target molecule. In the past decade, quantitative 13C NMR has been developed for the determination of the intramolecular isotope composition of a given molecule with a precision of 1‰ or better [4]. This breakthrough has made possible a comprehensive view of the determinants governing intramolecular isotope composition of biological molecules. In particular, it can be shown that intramolecular pattern in sugars is influenced by the C-assimilation pathway and by post-photosynthetic fractionation associated with carbohydrate metabolism [5]. In addition, analysis by NMR of the alkyl chain of acetogenic lipids (fatty acids, n-alkanes) shows an alternation between odd and even C-atom positions, as observed by Monson& Hayes [2], throughout the molecule [6]. Overall, it is becoming apparent that this pattern is influenced by two principal metabolic factors: (i) the 13C pattern extant in the starting compounds; (ii) isotope fractionation associated with the enzymes involved in the biosynthetic pathway. On the whole, the determination of intramolecular isotope patterns in biomolecules allows better insights into the conditions and pathways by which they are formed

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

    PubMed

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

    2009-12-07

    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.

  5. Proximity vs. strain in intramolecular ring-closing reactions

    NASA Astrophysics Data System (ADS)

    Karaman, Rafik

    2010-07-01

    The DFT and ab initio calculation results for ring-closing reactions of eight different ω-bromoalkanecarboxylate anions (1-8) reveal that the activation energy (ΔG ‡) for the intramolecular cyclization process is strongly correlated with both (i) the experimental intramolecular cyclization rate (log k intra) and (ii) the distance between the two reactive centres, whereas the slope values of the change in enthalpy (ΔH) vs. the attack angle (α) and the distance between the two reacting centres (r) were found to correlate strongly with the experimental strain energy of the cycle being formed (E s Exp). These results assist in designing pro-prodrug systems that can be utilized to improve the overall biopharmaceutical profile of current medications in order to enhance their effectiveness and ease their utility.

  6. 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

  7. Intramolecular aminocyanation of alkenes by N-CN bond cleavage.

    PubMed

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

    2014-05-12

    A metal-free, Lewis acid promoted intramolecular aminocyanation of alkenes was developed. B(C6F5)3 activates N-sulfonyl cyanamides, thus leading to a 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 (13)C suggest a fully intramolecular cyclization pattern due to the lack of label scrambling in double crossover experiments. Catalysis with Lewis acid is realized and the reaction can be conducted under air. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. 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.

  9. The Physical Chemistry of the Intramolecular Cyclodehydration Reactions of Prepolymers

    NASA Astrophysics Data System (ADS)

    Rabinovich, I. B.; Karyakin, Nikolai V.; Rusanov, Aleksandr L.; Korshak, V. V.

    1986-07-01

    The experimental data on the thermodynamics of the intramolecular cyclodehydration reactions of prepolymers in the solid phase are examined and treated systematically. The changes in the thermodynamic functions of the above processes have been analysed in detail over a wide temperature range. The temperature ranges corresponding to the formation of polyheteroarylenes which are "defect-free" to the maximum extent have been estimated. The bibliography includes 65 references.

  10. Overcoming product inhibition in catalysis of the intramolecular Schmidt reaction.

    PubMed

    Motiwala, Hashim F; Fehl, Charlie; Li, Sze-Wan; Hirt, Erin; Porubsky, Patrick; Aubé, Jeffrey

    2013-06-19

    A method for carrying out the intramolecular Schmidt reaction of alkyl azides and ketones using a substoichiometric amount of catalyst is reported. Following extensive screening, the use of the strong hydrogen-bond-donating solvent hexafluoro-2-propanol was found to be consistent with low catalyst loadings, which ranged from 2.5 mol % for favorable substrates to 25 mol % for more difficult cases. Reaction optimization, broad substrate scope, and preliminary mechanistic studies of this improved version of the reaction are described.

  11. Overcoming Product Inhibition in Catalysis of the Intramolecular Schmidt Reaction

    PubMed Central

    Motiwala, Hashim F.; Fehl, Charlie; Li, Sze-Wan; Hirt, Erin; Porubsky, Patrick; Aubé, Jeffrey

    2014-01-01

    A method for carrying out the intramolecular Schmidt reaction of alkyl azides and ketones using a substoichiometric amount of catalyst is reported. Following extensive screening, the use of the strong hydrogen bond donating solvent hexafluoro-2-propanol was found to be consistent with low catalyst loadings, which range from 2.5 mol% for favorable substrates to 25 mol% for more difficult cases. Reaction optimization, broad substrate scope, and preliminary mechanistic studies of this improved version of the reaction are described. PMID:23687993

  12. Short intramolecular hydrogen bonds: derivatives of malonaldehyde with symmetrical substituents.

    PubMed

    Hargis, Jacqueline C; Evangelista, Francesco A; Ingels, Justin B; Schaefer, Henry F

    2008-12-24

    A systematic study of various derivatives of malonaldehyde has been carried out to explore very short hydrogen bonds (r(OO) < 2.450 A). Various electron-withdrawing groups, including CN, NO(2), and BH(2), have been attached to the central carbon atom, C(2). To C(1) and C(3), strong electron donors and/or sterically hindered substituents were used to strengthen the intramolecular hydrogen bond, including but not limited to NH(2), N(CH(3))(2), and C(CH(3))(3). Seven molecules (Figure 2 ) were found to have extremely short intramolecular hydrogen bonds. The chemical systems investigated are intriguing due to their low energetic barriers for the intramolecular hydrogen atom transfers. Classical barriers were predicted using correlated methods including second-order perturbation theory and coupled cluster theory in conjunction with the Dunning hierarchy of correlation consistent basis sets, cc-pVXZ (X = D, T, Q, 5). Focal point analyses allowed for the barriers to be evaluated at the CBS limit including core correlation and zero-point vibrational energy corrections. B3LYP energies are benchmarked against highly accurate correlated energies for intramolecular hydrogen bonded systems. The focal point extrapolated method, including coupled cluster full triple excitation contributions, gives a hydrogen transfer barrier for malonaldehyde of approximately 4 kcal mol(-1). We describe two compounds with extremely low classical barriers, nitromalonamide (0.43 kcal mol(-1)) and 2-borylmalonamide (0.60 kcal mol(-1)). An empirical relationship was drawn between the B3LYP energetic barriers and the predicted coupled cluster barriers at the CBS limit. By relating these two quantities, barrier heights may be estimated for systems too large to presently use highly correlated electronic structure methods.

  13. Communication: Pseudoisomorphs in liquids with intramolecular degrees of freedom

    NASA Astrophysics Data System (ADS)

    Olsen, Andreas Elmerdahl; Dyre, Jeppe C.; Schrøder, Thomas B.

    2016-12-01

    Computer simulations show that liquids of molecules with harmonic intramolecular bonds may have "pseudoisomorphic" lines of approximately invariant dynamics in the thermodynamic phase diagram. We demonstrate that these lines can be identified by requiring scale invariance of the inherent-structure reduced-unit low-frequency vibrational spectrum evaluated for a single equilibrium configuration. This rationalizes why generalized excess-entropy scaling, density scaling, and isochronal superposition apply for many liquids with internal degrees of freedom.

  14. Bimorpholine-mediated enantioselective intramolecular and intermolecular aldol condensation.

    PubMed

    Kanger, Tõnis; Kriis, Kadri; Laars, Marju; Kailas, Tiiu; Müürisepp, Aleksander-Mati; Pehk, Tõnis; Lopp, Margus

    2007-07-06

    Monosalts of N-substituted bimorpholine derivatives are efficient organocatalysts in intramolecular and intermolecular aldol reactions. The properties of the catalysts can be tuned either by the selection of an appropriate acid for the salt formation or by the change of a substituent at the nitrogen atom. In aldol condensation, i-Pr-substituted bimorpholine is the most stereoselective catalyst affording products in high yield with enantioselectivities up to 95% ee.

  15. Ultrafast excited-state intramolecular proton transfer of aloesaponarin I.

    PubMed

    Nagaoka, Shin-ichi; Uno, Hidemitsu; Huppert, Dan

    2013-04-25

    Time-resolved emission of aloesaponarin I was studied with the fluorescence up-conversion and time-correlated single-photon-counting techniques. The rates of the excited-state intramolecular proton transfer, of the solvent and molecular rearrangements, and of the decay from the excited proton-transferred species were determined and interpreted in the light of time-dependent density functional calculations. These results were discussed in conjunction with UV protection and singlet-oxygen quenching activity of aloe.

  16. Visible-Light Photocatalytic Intramolecular Cyclopropane Ring Expansion.

    PubMed

    Luis-Barrera, Javier; Laina-Martín, Víctor; Rigotti, Thomas; Peccati, Francesca; Solans-Monfort, Xavier; Sodupe, Mariona; Mas-Ballesté, Rubén; Liras, Marta; Alemán, José

    2017-06-26

    Described herein is a new visible-light photocatalytic strategy for the synthesis of enantioenriched dihydrofurans and cyclopentenes by an intramolecular nitro cyclopropane ring expansion reaction. Mechanistic studies and DFT calculations are used to elucidate the key factors in this new ring expansion reaction, and the need for the nitro group on the cyclopropane. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Mechanism of intramolecular photostabilization in self-healing cyanine fluorophores.

    PubMed

    van der Velde, Jasper H M; Ploetz, Evelyn; Hiermaier, Matthias; Oelerich, Jens; de Vries, Jan Willem; Roelfes, Gerard; Cordes, Thorben

    2013-12-16

    Organic fluorophores, which are popular labels for microscopy applications, intrinsically suffer from transient and irreversible excursions to dark-states. An alternative to adding photostabilizers at high concentrations to the imaging buffer relies on the direct linkage to the fluorophore. However, the working principles of this approach are not yet fully understood. In this contribution, we investigate the mechanism of intramolecular photostabilization in self-healing cyanines, in which photodamage is automatically repaired. Experimental evidence is provided to demonstrate that a single photostabilizer, that is, the vitamin E derivative Trolox, efficiently heals the cyanine fluorophore Cy5 in the absence of any photostabilizers in solution. A plausible mechanism is that Trolox interacts with the fluorophore through intramolecular quenching of triplet-related dark-states, which is a mechanism that appears to be common for both triplet-state quenchers (cyclooctatetraene) and redox-active compounds (Trolox, ascorbic acid, methylviologen). Additionally, the influence of solution-additives, such as cysteamine and procatechuic acid, on the self-healing process are studied. The results suggest the potential applicability of self-healing fluorophores in stochastic optical reconstruction microscopy (STORM) with optical super-resolution. The presented data contributes to an improved understanding of the mechanism involved in intramolecular photostabilization and has high relevance for the future development of self-healing fluorophores, including their applications in various research fields.

  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. Extremely slow intramolecular diffusion in unfolded protein L

    PubMed Central

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

    2010-01-01

    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 μs 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. PMID:20643973

  20. Intramolecular bridges formed by photoswitchable click amino acids.

    PubMed

    Hoppmann, Christian; Kühne, Ronald; Beyermann, Michael

    2012-01-01

    Photoswitchable click amino acids (PSCaa) are amino acids bearing a side chain consisting of a photoswitchable unit elongated with a functional group that allows for a specific click reaction, such as an alkene that can react with the thiol group of a cysteine residue. An intramolecular click reaction results in the formation of a photoswitchable bridge, which can be used for controlling conformational domains in peptides and proteins. The ability to control conformations as well as the efficiency of the intramolecular bridging depends on the length of the PSCaa side chain and the distance to the cysteine residue to be clicked with. On comparing i,i+4 and i,i+7 spacings of PSCaa and cysteine in a model peptide without a preferred conformation, it was seen that the thiol-ene click reaction takes place efficiently in both cases. Upon induction of an α-helical structure by the addition of trifluoroethanol, the thiol click reaction occurs preferentially with the i,i+4 spacing. Even in the presence of glutathione as an additional thiol the click reaction of the PSCaa occurs intramolecularly with the cysteine rather than with the glutathione, indicating that the click reaction may be used even under reducing conditions occurring in living cells.

  1. 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.

  2. Gas-Phase Intramolecular Cyclization of Argentinated N-Allylbenzamides

    NASA Astrophysics Data System (ADS)

    Sun, Hezhi; Chai, Yunfeng; Jin, Zhe; Sun, Cuirong; Pan, Yuanjiang

    2015-05-01

    The fragmentations of argentinated N-allylbenzamides have been exhaustively studied through collision-induced dissociation and through deuterium labeling. The intriguing elimination of AgOH is certified as the consequence of intramolecular cyclization between terminal olefin and carbonyl carbon following proton transfer to carbonyl oxygen, rather than simple enolization of amide. Linear free energy correlations and density functional theory (DFT) calculations were performed to understand the competitive relationship between AgOH loss and AgH loss, which results from the 1,2-elimination of α-hydrogen (to the amido nitrogen) with the silver.

  3. Intramolecular charge transfer in donor-acceptor molecules

    SciTech Connect

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

    1990-05-17

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

  4. 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.

  5. 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.

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

    PubMed

    Lim, Hee Nam; Dong, Guangbin

    2015-12-07

    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.

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

    PubMed Central

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

    1994-01-01

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

  8. Semirubin. A novel dipyrrinone strapped by intramolecular hydrogen bonds.

    PubMed

    Huggins, M T; Lightner, D A

    2000-09-22

    (4Z)-9-(5-Carboxypentyl)-2,3,7,8-tetramethyl-(10H)-dipyrrin- 1-one (1, semirubin), a new dipyrrinone model for one-half of bilirubin, the yellow-orange neurotoxic pigment of jaundice, was synthesized following Friedel-Crafts acylation of 2,3,7, 8-tetramethyl-(10H)-dipyrrin-1-one (5) with the half-ester acid chloride of adipic acid. Unlike other dipyrrinone models for bilirubin, such as the xanthobilirubic acids, which engage only in intermolecular hydrogen bonding, 1 is unique in having been designed and found to engage in intramolecular hydrogen bonding, between the carboxylic acid and the dipyrrinone lactam and pyrrole. This important conformation-determining structural characteristic, shared by 1 and bilirubin, renders them less polar than their methyl esters and leaves them monomeric in nonpolar solvents, where their esters are dimeric. The corresponding 10-oxo analogue (3) of 1 serves as a model for 10-oxo-bilirubin, a presumed bilirubin metabolite in alternate pathways for bilirubin excretion. Like 1, 3 is found to engage in intramolecular hydrogen bonding. Unlike the methyl ester of 1, the ethyl ester of 3 is not intermolecularly hydrogen bonded in nonpolar solvents.

  9. A Study of Intramolecular Hydrogen Bonding in Levoglucosan Derivatives.

    PubMed

    Quiquempoix, Lucas; Bogdan, Elena; Wells, Neil J; Le Questel, Jean-Yves; Graton, Jérôme; Linclau, Bruno

    2017-03-24

    Organofluorine is a weak hydrogen-bond (HB) acceptor. Bernet et al. have demonstrated its capability to perturb OH···O intramolecular hydrogen bonds (IMHBs), using conformationally rigid carbohydrate scaffolds including levoglucosan derivatives. These investigations are supplemented here by experimental and theoretical studies involving six new levoglucosan derivatives, and complement the findings of Bernet et al. However, it is shown that conformational analysis is instrumental in interpreting the experimental data, due to the occurrence of non-intramolecular hydrogen-bonded populations which, although minor, cannot be neglected and appears surprisingly significant. The DFT conformational analysis, together with the computation of NMR parameters (coupling constants and chemical shifts) and wavefunction analyses (AIM, NBO), provides a full picture. Thus, for all compounds, the most stabilized structures show the OH groups in a conformation allowing IMHB with O5 and O6, when possible. Furthermore, the combined approach points out the occurrence of various IMHBs and the effect of the chemical modulations on their features. Thus, two-center or three-center IMHB interactions are observed in these compounds, depending on the presence or absence of additional HB acceptors, such as methoxy or fluorine.

  10. Heuristic RNA pseudoknot prediction including intramolecular kissing hairpins

    PubMed Central

    Sperschneider, Jana; Datta, Amitava; Wise, Michael J.

    2011-01-01

    Pseudoknots are an essential feature of RNA tertiary structures. Simple H-type pseudoknots have been studied extensively in terms of biological functions, computational prediction, and energy models. Intramolecular kissing hairpins are a more complex and biologically important type of pseudoknot in which two hairpin loops form base pairs. They are hard to predict using free energy minimization due to high computational requirements. Heuristic methods that allow arbitrary pseudoknots strongly depend on the quality of energy parameters, which are not yet available for complex pseudoknots. We present an extension of the heuristic pseudoknot prediction algorithm DotKnot, which covers H-type pseudoknots and intramolecular kissing hairpins. Our framework allows for easy integration of advanced H-type pseudoknot energy models. For a test set of RNA sequences containing kissing hairpins and other types of pseudoknot structures, DotKnot outperforms competing methods from the literature. DotKnot is available as a web server under http://dotknot.csse.uwa.edu.au. PMID:21098139

  11. A Study about Regioisomeric Hydroquinones with Multiple Intramolecular Hydrogen Bonding.

    PubMed

    Martínez-Cifuentes, Maximiliano; Cardona, Wilson; Saitz, Claudio; Weiss-López, Boris; Araya-Maturana, Ramiro

    2017-04-07

    A theoretical exploration about hydrogen bonding in a series of synthetic regioisomeric antitumor tricyclic hydroquinones is presented. The stabilization energy for the intramolecular hydrogen bond (IHB) formation in four structurally different situations were evaluated: (a) IHB between the proton of a phenolic hydroxyl group and an ortho-carbonyl group (forming a six-membered ring); (b) between the oxygen atom of a phenolic hydroxyl group and the proton of an hydroxyalkyl group (seven membered ring); (c) between the proton of a phenolic hydroxyl group with the oxygen atom of the hydroxyl group of a hydroxyalkyl moiety (seven-membered ring); and (d) between the proton of a phenolic hydroxyl group and an oxygen atom directly bonded to the aromatic ring in ortho position (five-membered ring). A conformational analysis for the rotation around the hydroxyalkyl substituent is also performed. It is observed that there is a correspondence between the conformational energies and the IHB. The strongest intramolecular hydrogen bonds are those involving a phenolic proton and a carbonyl oxygen atom, forming a six-membered ring, and the weakest are those involving a phenolic proton with the oxygen atom of the chromenone, forming five-membered rings. Additionally, the synthesis and structural assignment of two pairs of regioisomeric hydroquinones, by 2D-NMR experiments, are reported. These results can be useful in the design of biologically-active molecules.

  12. 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.

  13. Intramolecular Hydrogen Bonding Restricts Gd-Aqua-Ligand Dynamics [The Day the Water Stood Still: Intramolecular Hydrogen Bonding to Restrict Gd-Aqua Ligand Dynamics

    DOE PAGES

    Boros, Eszter; Srinivas, Raja; Kim, Hee -Kyung; ...

    2017-04-11

    Aqua ligands can undergo rapid internal rotation about the M-O bond. For magnetic resonance contrast agents, this rotation results in diminished relaxivity. Herein, we show that an intramolecular hydrogen bond to the aqua ligand can reduce this internal rotation and increase relaxivity. Molecular modeling was used to design a series of four Gd complexes capable of forming an intramolecular H-bond to the coordinated water ligand, and these complexes had anomalously high relaxivities compared to similar complexes lacking a H-bond acceptor. Molecular dynamics simulations supported the formation of a stable intramolecular H-bond, while alternative hypotheses that could explain the higher relaxivitymore » were systematically ruled out. Finally, intramolecular H-bonding represents a useful strategy to limit internal water rotational motion and increase relaxivity of Gd complexes.« less

  14. Intramolecular cyclization of a diruthenium complex: insight into the mechanism of heteroatom-directed intramolecular C-H/olefin coupling reactions.

    PubMed

    Gong, Dawei; Hu, Bowen; Shi, Jing; Chen, Dafa

    2015-07-28

    Complex 2, synthesized by the reaction of {(C5H4N)(μ2-η(5):η(1)-C9H5)}Ru3(CO)9 (1) with 1,5-hexadiene, could further transform to another diruthenium complex 3via intramolecular carbometalation. The results are relevant to the mechanism of transition-metal catalyzed heteroatom-directed intramolecular C-H/olefin coupling reactions.

  15. Intramolecular hydrophobic interactions are critical mediators of STAT5 dimerization

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

    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.

  16. Flexible Viologen Cyclophanes: Odd/Even Effects on Intramolecular Interactions.

    PubMed

    Berville, Mathilde; Choua, Sylvie; Gourlaouen, Christophe; Boudon, Corinne; Ruhlmann, Laurent; Bailly, Corinne; Cobo, Saioa; Saint-Aman, Eric; Wytko, Jennifer; Weiss, Jean

    2017-01-04

    The ability of three bis-viologen cyclophanes to act as redox-triggered contractile switches is investigated. Odd/even effects in the formation of cyclic bis-viologens are circumvented by the use of a Zincke salt intermediate and a tetrathiafulvalene template to prepare a flexible cyclophane with hexyl linkers. Comparative spectro-electrochemical studies of this macrocycle with two other pentyl- or heptyl-linked cyclic bis-viologens show that the development of intramolecular interactions in aqueous solution depends on the length of the bridges. This dependence is confirmed by EPR and DFT studies of the magnetic coupling in the diradical dication species. The anti-ferromagnetic or ferromagnetic nature of the coupling depend, respectively, on the odd or even number of methylene groups in the spacer.

  17. Direct Preparation of Carbon Nanotube Intramolecular Junctions on Structured Substrates

    NASA Astrophysics Data System (ADS)

    An, Jianing; Zhan, Zhaoyao; Sun, Gengzhi; Mohan, Hari Krishna Salila Vijayalal; Zhou, Jinyuan; Kim, Young-Jin; Zheng, Lianxi

    2016-12-01

    Leveraging the unique properties of single-walled carbon nanotube (SWNT) intramolecular junctions (IMJs) in innovative nanodevices and next-generation nanoelectronics requires controllable, repeatable, and large-scale preparation, together with rapid identification and comprehensive characterization of such structures. Here we demonstrate SWNT IMJs through directly growing ultralong SWNTs on trenched substrates. It is found that the trench configurations introduce axial strain in partially suspended nanotubes, and promote bending deformation in the vicinity of the trench edges. As a result, the lattice and electronic structure of the nanotubes can be locally modified, to form IMJs in the deformation regions. The trench patterns also enable pre-defining the formation locations of SWNT IMJs, facilitating the rapid identification. Elaborate Raman characterization has verified the formation of SWNT IMJs and identified their types. Rectifying behavior has been observed by electrical measurements on the as-prepared semiconducting-semiconducting (S-S) junction.

  18. Prodrugs design based on inter- and intramolecular chemical processes.

    PubMed

    Karaman, Rafik

    2013-12-01

    This review provides the reader a concise overview of the majority of prodrug approaches with the emphasis on the modern approaches to prodrug design. The chemical approach catalyzed by metabolic enzymes which is considered as widely used among all other approaches to minimize the undesirable drug physicochemical properties is discussed. Part of this review will shed light on the use of molecular orbital methods such as DFT, semiempirical and ab initio for the design of novel prodrugs. This novel prodrug approach implies prodrug design based on enzyme models that were utilized for mimicking enzyme catalysis. The computational approach exploited for the prodrug design involves molecular orbital and molecular mechanics (DFT, ab initio, and MM2) calculations and correlations between experimental and calculated values of intramolecular processes that were experimentally studied to assign the factors determining the reaction rates in certain processes for better understanding on how enzymes might exert their extraordinary catalysis.

  19. Direct Preparation of Carbon Nanotube Intramolecular Junctions on Structured Substrates

    PubMed Central

    An, Jianing; Zhan, Zhaoyao; Sun, Gengzhi; Mohan, Hari Krishna Salila Vijayalal; Zhou, Jinyuan; Kim, Young-Jin; Zheng, Lianxi

    2016-01-01

    Leveraging the unique properties of single-walled carbon nanotube (SWNT) intramolecular junctions (IMJs) in innovative nanodevices and next-generation nanoelectronics requires controllable, repeatable, and large-scale preparation, together with rapid identification and comprehensive characterization of such structures. Here we demonstrate SWNT IMJs through directly growing ultralong SWNTs on trenched substrates. It is found that the trench configurations introduce axial strain in partially suspended nanotubes, and promote bending deformation in the vicinity of the trench edges. As a result, the lattice and electronic structure of the nanotubes can be locally modified, to form IMJs in the deformation regions. The trench patterns also enable pre-defining the formation locations of SWNT IMJs, facilitating the rapid identification. Elaborate Raman characterization has verified the formation of SWNT IMJs and identified their types. Rectifying behavior has been observed by electrical measurements on the as-prepared semiconducting-semiconducting (S-S) junction. PMID:27905564

  20. Anharmonic dynamics of intramolecular hydrogen bonds driven by DNA breathing

    NASA Astrophysics Data System (ADS)

    Alexandrov, B. S.; Stanev, V. G.; Bishop, A. R.; Rasmussen, K. Ø.

    2012-12-01

    We study the effects of the anharmonic strand-separation dynamics of double-stranded DNA on the infrared spectra of the intramolecular base-pairing hydrogen bonds. Using the extended Peyrard-Bishop-Dauxois model for the DNA breathing dynamics coupled with the Lippincott-Schroeder potential for N-H⋯N and N-H⋯O hydrogen bonding, we identify a high-frequency (˜96 THz) feature in the infrared spectra. We show that this sharp peak arises as a result of the anharmonic base-pair breathing dynamics of DNA. In addition, we study the effects of friction on the infrared spectra. For higher temperatures (˜300 K), where the anharmonicity of DNA dynamics is pronounced, the high-frequency peak is always present irrespective of the friction strength.

  1. Measurement of electromagnetic pulse emitted during rapid intramolecular electron transfer

    NASA Astrophysics Data System (ADS)

    Beard, Matthew C.; Turner, Gordon M.; Schmuttenmaer, Charles A.

    2001-03-01

    We have measured the electromagnetic radiation emitted during intramolecular electron transfer using a method does not rely on secondary processes.^1 The motion of the electrons themselves generates the measured signal (as understood by Maxwell's equations). If the electron transfer occurs on a timescale of 0.1 to 10 picoseconds, the emitted radiation will fall in the THz or far-infrared region of the spectrum (1 THz = 33.33 wavenumbers), which is the region covered by our detector. We photoexcite a sample of partially oriented molecules and measure the emitted waveform. The polarity of the emitted field determines the direction of charge transfer unambiguously, and the shape of the field encodes the dynamics of the charge transfer -- a slower transfer rate produces a broader temporal pulse. Future work will extend this method to systems that are difficult to study by traditional means. 1. M. C. Beard, G. M. Turner, and C. A. Schmuttenmaer, J. Am. Chem. Soc. 122, 11541 (2000).

  2. 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.

  3. Intramolecular Charge Transfer States in the Condensed Phase

    NASA Astrophysics Data System (ADS)

    Williams, C. F.; Herbert, J. M.

    2009-06-01

    Time-Dependent Density Functional Theory (TDDFT) with long range corrected functionals can give accurate results for the energies of electronically excited states involving Intramolecular Charge Transfer (ICT) in large molecules. If this is combined with a Molecular Mechanics (MM) representation of the surrounding solvent this technique can be used to interpret the results of condensed phase UV-Vis Spectroscopy. Often the MM region is represented by a set of point charges, however this means that the solvent cannot repolarize to adapt to the new charge distribution as a result of ICT and so the excitation energies to ICT states are overestimated. To solve this problem an algorithm that interfaces TDDFT with the polarizable force-field AMOEBA is presented; the effect of solvation on charge transfer in species such as 4,4'dimethylaminobenzonitrile (DMABN) is discussed. M.A. Rohrdanz, K.M. Martins, and J.M. Herbert, J. Chem. Phys. 130 034107 (2008).

  4. Acquisition of accurate data from intramolecular quenched fluorescence protease assays.

    PubMed

    Arachea, Buenafe T; Wiener, Michael C

    2017-04-01

    The Intramolecular Quenched Fluorescence (IQF) protease assay utilizes peptide substrates containing donor-quencher pairs that flank the scissile bond. Following protease cleavage, the dequenched donor emission of the product is subsequently measured. Inspection of the IQF literature indicates that rigorous treatment of systematic errors in observed fluorescence arising from inner-filter absorbance (IF) and non-specific intermolecular quenching (NSQ) is incompletely performed. As substrate and product concentrations vary during the time-course of enzyme activity, iterative solution of the kinetic rate equations is, generally, required to obtain the proper time-dependent correction to the initial velocity fluorescence data. Here, we demonstrate that, if the IQF assay is performed under conditions where IF and NSQ are approximately constant during the measurement of initial velocity for a given initial substrate concentration, then a simple correction as a function of initial substrate concentration can be derived and utilized to obtain accurate initial velocity data for analysis.

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

    PubMed Central

    Demchenko, A P; Sytnik, A I

    1991-01-01

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

  6. 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.

  7. Intramolecular strain coordinates kinesin stepping behavior along microtubules

    PubMed Central

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

    2008-01-01

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

  8. Intramolecular 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

  9. Polymeric photosensitizers: effects of intramolecular energy migration on sensitization efficiences

    SciTech Connect

    Urruti, E.H.; Kilp, T.

    1984-01-01

    The occurrence of intramolecular energy migration was found to have no significant effect on the efficiency of ketyl radical formation via hydrogen abstration from cumene by benzophenone (BP) or poly(vinylbenzophenone) (PVBP). Rate constants were found to be 1.1 x 10/sup 6/ and 0.81 x 10/sup 6/ M/sup -1/ s/sup -1/ for the small molecule and the polymer, respectively. The large difference in rate constants, 9.6 x 10/sup 6/ and 22.2 x 10/sup 6/ M/sup -1/ s/sup -1/ for BP and PVBP, respectively, when tetrahydrofuran was used as a quencher is probably attributable to preferential solvation. Conversely, intramolecular energy migration was found to significantly enhance the overall efficiency of triplet energy transfer to 1-methylnaphthalene (MeN). Rate constants for formation of /sup 3/MeN were found to be 0.94 x 10/sup 9/ and 1.85 x 10/sup 9/ M/sup -1/ s/sup -1/ for BP and PVBP, respectively. An energy migration coefficient, LAMBDA, of 3.28 x 10/sup -5/ cm/sup 2/ s/sup -1/ and a frequency of energy migration, omega, of 7.88 x 10/sup 10/ x/sup -1/ were calculated for PVBP. For a series of copolymers of methyl methacrylate with vinylbenzophenone, values of LAMBDA and omega were strongly dependent on the ketone content of the polymer and decreased sharply at 40 mol % VBP or less.

  10. Highly enantioselective intramolecular 1,3-dipolar cycloaddition: a route to piperidino-pyrrolizidines.

    PubMed

    Vidadala, Srinivasa Rao; Golz, Christopher; Strohmann, Carsten; Daniliuc, Constantin-G; Waldmann, Herbert

    2015-01-07

    Enantioselective catalytic intermolecular 1,3-dipolar cycloadditions are powerful methods for the synthesis of heterocycles. In contrast, intramolecular enantioselective 1,3-dipolar cycloadditions are virtually unexplored. A highly enantioselective synthesis of natural-product-inspired pyrrolidino-piperidines by means of an intramolecular 1,3-dipolar cycloaddition with azomethine ylides is now reported. The method has a wide scope and yields the desired cycloadducts with four tertiary stereogenic centers with up to 99% ee. Combining the enantioselective catalytic intramolecular 1,3-dipolar cycloaddition with a subsequent diastereoselective intermolecular 1,3-dipolar cycloaddition yielded complex piperidino-pyrrolizidines with very high stereoselectivity in a one-pot tandem reaction.

  11. Branching Reaction in Melanogenesis: The Effect of Intramolecular Cyclization on Thiol Binding

    NASA Astrophysics Data System (ADS)

    Kishida, Ryo; Kasai, Hideaki; Aspera, Susan Meñez; Arevalo, Ryan Lacdao; Nakanishi, Hiroshi

    2017-01-01

    With the aid of density functional theory-based first principles calculations, we investigated energetics and electronic structure changes in reactions involving dopaquinone to give insights into the branching behaviors in melanogenesis. The reactions we investigated are the intramolecular cyclization and thiol binding, which are competing with each other. It was found that, in order to accomplish thiol binding, charge transfer of around one electron from thiol to dopaquinone occurs. Furthermore, intramolecular cyclization of dopaquinone increases the lowest unnoccupied molecular orbital level substantially. This result clearly shows prevention of the binding of thiol by intramolecular cyclization.

  12. DFT and AIM studies of intramolecular hydrogen bonds in dicoumarols

    NASA Astrophysics Data System (ADS)

    Trendafilova, Natasha; Bauer, Günther; Mihaylov, Tzvetan

    2004-07-01

    Density functional calculations with Becke's three parameter hybrid method using the correlation functional of Lee, Yang and Parr (B3LYP) were carried out for 3,3 '-benzylidenebis(4-hydroxycoumarin) (phenyldicoumarol, PhDC), 3,3 '-methylenebis(4-hydroxycoumarin) (dicoumarol, DC) and the parent compound, 4-hydroxycoumarin (4-HC). Different basis sets were tested in the course of the calculations: 6-31G*, 6-31+G** and 6-311G*. In full agreement with available X-ray data, B3LYP/6-31G* calculations of the lowest-energy conformer, PhDC showed two O-H⋯O asymmetrical intramolecular hydrogen bonds with O⋯O distances 2.638 and 2.696 Å. The HB energies in PhDC were estimated of -55.46 and -52.32 kJ/mol, respectively. The values obtained correlated with the calculated and experimental O⋯O distances and predicted difference in the hydrogen bonding strengths in PhDC. The total HB energy in PhDC was calculated of -107.73 kJ/mol. At the same level of theory, both O⋯O intramolecular distances in DC were calculated identical (2.696 Å) and thus two symmetrical hydrogen bondings were obtained. The single HB strength was estimated of -50.89 kJ/mol and the total one of -101.79 kJ/mol. The electron density ( ρb) and Laplacian (∇ 2ρb) properties, estimated by AIM calculations, showed that both O⋯H bonds have low ρb and positive ∇ 2ρb values (consistent with electrostatic character of the HBs), whereas both O-H bonds have covalent character (∇ 2ρb<0). Natural population analysis data for PhDC, DC and 4-HC were used to predict electrostatic interactions in the exocyclic rings. The calculated oxygen natural charges were found to correlate with the O⋯O distances in PhDC and DC. On the basis of the calculated bond ellipticity, the π-delocalization in the exocyclic rings of PhDC and DC was estimated. The results thus obtained helped to describe the nature of the intramolecular O⋯H-O bonds and the forces driving their formation

  13. 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

  14. Ground and excited state intramolecular proton transfer controlled intramolecular charge separation and recombination: A new type of charge and proton transfer reaction

    NASA Astrophysics Data System (ADS)

    Nie, Daobo; Bian, Zuqiang; Yu, Anchi; Chen, Zhuqi; Liu, Zhiwei; Huang, Chunhui

    2008-06-01

    A novel β-diketone 1-(4-(9-carbazol)phenyl)-3-phenyl-1,3-propanedione (CDBM) has been synthesized. When excited at 380 nm, this molecule shows single fluorescence. However, when excited at 338 nm, it shows dual fluorescence. A Al 3+ complex Al(CDBM) 3 has been synthesized to investigate the dual fluorescence of CDBM. It is found that this complex shows single fluorescence under all excitation. This result indicated that the dual fluorescence of CDBM may relate to the intramolecular proton transfer reaction. Based on the experimental and theoretical studies of CDBM, N-(4-cyanophenyl)carbazole (CBN) and Al(CDBM) 3, a "ground and excited state intramolecular proton transfer controlled intramolecular charge separation and recombination" mechanism is proposed to explain the unusual excitation-dependent dual fluorescence of CDBM.

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

    PubMed

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

    2016-03-11

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

  16. 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

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

    PubMed

    Kozlowska, Mariana; Goclon, Jakub; Rodziewicz, Pawel

    2016-04-18

    We used static DFT calculations to analyze, in detail, the intramolecular hydrogen bonds formed in low-molecular-weight polyethylene glycol (PEG) with two to five repeat subunits. Both red-shifted O-H⋅⋅⋅O and blue-shifting C-H⋅⋅⋅O hydrogen bonds, which control the structural flexibility of PEG, were detected. To estimate the strength of these hydrogen bonds, the quantum theory of atoms in molecules was used. Car-Parrinello molecular dynamics simulations were used to mimic the structural rearrangements and hydrogen-bond breaking/formation in the PEG molecule at 300 K. The time evolution of the H⋅⋅⋅O bond length and valence angles of the formed hydrogen bonds were fully analyzed. The characteristic hydrogen-bonding patterns of low-molecular-weight PEG were described with an estimation of their lifetime. The theoretical results obtained, in particular the presence of weak C-H⋅⋅⋅O hydrogen bonds, could serve as an explanation of the PEG structural stability in the experimental investigation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. 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.

  19. In Vivo Measurement of Intramolecular Distances Using Genetically Encoded Reporters

    PubMed Central

    Sandtner, Walter; Bezanilla, Francisco; Correa, Ana M.

    2007-01-01

    The function of membrane proteins occurs in the context of the cell membrane in living cells acting in concert with various cell components such as other proteins, cofactors, etc. The understanding of the function at the molecular level requires structural techniques, but high resolution structural studies are normally obtained in vitro and in artificial membranes or detergent. Ideally the correlation of structure and function should be carried out in the native environment but most of the techniques applicable in vivo lack the high resolution necessary to track conformational changes on a molecular level. Here we report on the successful application of an improved variant of lanthanide-based resonance energy transfer a fluorescent based technique, to Shaker potassium channels expressed in live Xenopus oocytes. Lanthanide-based resonance energy transfer is particularly suitable to measure intramolecular distances with high resolution. The improvements reported in this work are mainly based on the use of two different small genetically encoded tags (the Lanthanide Binding Tag and the hexa-histidine tag), which due to their small size can be encoded at will in many positions of interest without distorting the protein's function. The technique reported here has the additional improvement that the two tags can be placed independently in contrast to previously described techniques that rely on chemical labeling procedures of thiols. PMID:17766346

  20. Thermal selectivity of intermolecular versus intramolecular reactions on surfaces

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  1. 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

  2. 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.

  3. Inversion of experimental data to extract intermolecular and intramolecular potentials

    SciTech Connect

    Ho, T.S.; Rabitz, H. )

    1993-12-23

    We present a general nonlinear inverse method utilizing discrete experimental data to extract inter- and intramolecular potential energy surfaces. The inverse method is formulated in terms of perturbation expansions of the experimental data upon the functional variations of the underlying potential energy surface--a functional sensitivity analysis approach. A distinction is drawn between the inverse method and the conventional parameter fitting procedure in that the former treats the potential energy surfaces as continuous functions of the internuclear coordinates, whereas the latter is based on restricted forms with a small number of parameters. The possible numerical instability of molecular nonlinear inverse problems is examined in detail using singular function expansion analysis and is overcome using the Tikhonov regularization method, which incorporates the a priori smooth properties of the sought-after potential energy surfaces. Numerical studies show that the iterative inversion procedure based on this inverse method is generic, efficient, and stable and is capable of accurately rendering physically acceptable potential energy surfaces for a variety of problems--either spectroscopic or collisional and one-dimensional or multidimensional. An example employing actual laboratory data has been successfully inverted. Application of the method to small polyatomic systems of current interest and improvement of the method by including higher-order sensitivity densities are also discussed. 84 refs., 9 figs.

  4. Intramolecular proton transfer (IPT) in alkoxyamine: a theoretical investigation.

    PubMed

    Parkhomenko, Dmitriy; Bagryanskaya, Elena G; Marque, Sylvain R A; Siri, Didier

    2013-09-07

    The Intramolecular Proton Transfer (IPT) in alkoxyamines is one of the main factors determining the process of Nitroxide Mediated Polymerization (NMP). Recently, we proposed an experimental approach to study IPT and applied it to a series of alkoxyamines. It was found that IPT dramatically depends on the structure of the alkoxyamine, but it was not clear which factors are significant for IPT (M. V. Edeleva et al., J. Polym. Sci., Part A: Polym. Chem. 2009, 47, 6579-6595). To understand the mechanism and the factors determining the IPT process, in this article we investigate the geometrical parameters and thermokinetics of this reaction using the BMK/6-311++G(3df,3pd)//B3LYP/6-31+G(d,p) method. It was found that the thermokinetics and geometrical parameters of the transition state (TS) for IPT do not depend on the alkoxyamine structure. The only factor which determines the occurrence of IPT is the position of the TS energy level of the C-ON bond homolysis.

  5. Intramolecular, oxidatively induced substitution on a coordinated terpyridyl ligand

    SciTech Connect

    Huynh, M.H.V.; Lee, D.G.; White, P.S.; Meyer, T.J.

    1999-11-10

    In recent experiments, the authors demonstrated that in the Os-hydrazido complexes, trans-[Os{sup VI}(L{sub 3})(Cl){sub 2}(NN(CH{sub 2}){sub 4}O)]{sup 2+} (L{sub 3} = 2,2{prime}:6{prime},2{double{underscore}prime}-terpyridine or tris(1-pyrazolyl)-methane and N(CH{sub 2}){sub 4}O{sup {minus}} = morpholide), there are four interconvertible oxidation states with Os(VI), Os(V), Os(IV), and Os(III) accessible within the solvent limit in CH{sub 3}CN. Examples of Os(VI), Os(V), and Os(IV) have been characterized by X-ray crystallography. The authors report here a remarkable reaction between trans-[Os{sup VI}(tpy)(Cl){sub 2}(NN(CH{sub 2}){sub 4}O)]{sup 2+} (2), has been characterized crystallographically. An extraordinary electrophilic substituent effect of Os(VI) on the tpy ligand and the ability of Os(VI) to undergo reversible intramolecular Os(VI {yields} IV) electron transfer appear to play essential roles in these reactions.

  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. 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

  8. Mercury(II) 2-aminoethanethiolate clusters: intramolecular transformations and mechanisms.

    PubMed

    Bharara, Mohan S; Parkin, Sean; Atwood, David A

    2006-09-04

    The combination of HgF2 and 2-aminoethanethiol (AET, with some AET.HCl present) yielded a cyclic tetranuclear thiolate, [Hg4Cl4(SCH2CH2NH2)4] (1), with alternating Hg and S atoms. The Cl from the reaction mixture led to the formation of Hg-Cl bonds with no Hg-F in the final product. In contrast, a similar reaction with HgBr2 yielded a nonanuclear cluster, [Hg9Br15(SCH2CH2NH3)15]3+ (2), and the disulfide salt {[HgBr4][(NH3CH2CH2S-)2]} (3). Despite similar reactions, the AET groups in 2 are protonated compared to the nonprotonated amine groups in 1, which allows the ligand to chelate the Hg atom in the latter compound. The reaction with HgI2 yielded a cyclic tetranuclear compound, [Hg4I6(SCH2CH2NH2)2(SCH2CH2NH3)2](H2O/EtOH) (4), containing protonated and nonprotonated AET groups. Compound 4 at room temperature irreversibly rearranges to [Hg4I4(SCH2CH2NH2)4] (5), which is isostructural to 1. A systematic pathway for the formation of 1 along with the intramolecular conversion of 4 to 5 is proposed. These compounds demonstrate that very diverse Hg-S compounds form under similar reaction conditions.

  9. Vibrational spectroscopy and intramolecular dynamics of 1-butyne.

    PubMed

    Portnov, Alexander; Rosenwaks, Salman; Bar, Ilana

    2004-09-22

    Photodissociation of jet-cooled vibrationally excited 1-butyne, C(2)H(5)C[Triple Bond]C[Single Bond]H, coupled with mass spectrometric detection of H photofragments, facilitated measurements of action spectra and Doppler profiles, expressing the yield of the ensuing fragments versus the vibrational excitation and UV probe lasers, respectively. Both the action spectra and the simultaneously measured room temperature photoacoustic spectra in the 2nu(1), 3nu(1), and 4nu(1) C[Single Bond]H acetylenic stretch regions exhibit unresolved rotational envelopes with significant narrowing of the former due to temperature-related change in the rotational structure. The narrowing of the action spectrum in the 3nu(1) region exposed a resonance splitting, implying intramolecular vibrational energy redistribution (IVR) time of approximately 1 ps. Asymmetric rotor simulation of the band contours provided the rotational constants and estimates for the homogeneous broadening arising from IVR to the bath vibrational states. The homogenous linewidth of 4nu(1) is anomalously narrower than that of 2nu(1) and 3nu(1), indicating a longer lived 4nu(1) state despite the increasing background state density, suggestive of a lack of low-order resonances or of mode-specific coupling with the bath states. The Doppler profiles indicate that the H photofragments are released with low average translational energies, pointing to an indirect dissociation process occurring after internal conversion (IC) to the ground electronic state or after IC and isomerization to butadiene.

  10. 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.

  11. Intramolecular Diels–Alder/1,3-Dipolar Cycloaddition Cascade of 1,3,4-Oxadiazoles

    PubMed Central

    Elliott, Gregory I.; Fuchs, James R.; Blagg, Brian S. J.; Ishikawa, Hayato; Tao, Houchao; Yuan, Z.-Q.; Boger, Dale L.

    2008-01-01

    Full details of a systematic exploration of the intramolecular [4+2]/[3+2] cycloaddition cascade of 1,3,4-oxadiazoles are disclosed in which the scope and utility of the reaction are defined. PMID:16895427

  12. Fluorescence turn-on response of a conjugated polyelectrolyte with intramolecular stack structure to biomacromolecules.

    PubMed

    Lee, Wang-Eun; Jin, Young-Jae; Kim, Shin-Il; Kwak, Giseop; Kim, Joon Heon; Sakaguchi, Toshikazu; Lee, Chang-Lyoul

    2013-10-28

    An anionic conjugated polyelectrolyte based on polydiphenylacetylene showed a significant fluorescence turn-on response to positively-charged proteins through a conformational relaxation of its intramolecular stack structure.

  13. Tree-ring cellulose exhibits several distinct intramolecular 13C signals

    NASA Astrophysics Data System (ADS)

    Wieloch, Thomas; Ehlers, Ina; Frank, David; Gessler, Arthur; Grabner, Michael; Yu, Jun; Schleucher, Jürgen

    2017-04-01

    Stable carbon isotopes are a key tool in biogeosciences. Present applications including compound-specific isotope analysis measure 13C/12C ratios (δ13C) of bulk material or of whole molecules. However, it is well known that primary metabolites also show large intramolecular 13C variation - also called isotopomer variation. This variation reflects 13C fractionation by enzyme reactions and therefore encodes metabolic information. Furthermore, δ13C must be considered an average of the intramolecular 13C distribution. Here we will present (1) methodology to analyse intramolecular 13C distributions of tree-ring cellulose by quantitative 13C NMR (Chaintreau et al., 2013, Anal Chim Acta, 788, 108-113); (2) intramolecular 13C distributions of an annually-resolved tree ring chronology (Pinus nigra, 1961-1995); (3) isotope parameters and terminology for analysis of intramolecular isotope time series; (4) a method for correcting for heterotrophic C redistribution. We will show that the intramolecular 13C distribution of tree-ring cellulose shows large variation, with differences between isotopomers exceeding 10‰Ṫhus, individual 13C isotopomers of cellulose constitute distinct 13C inputs into major global C pools such as wood and soil organic matter. When glucose units with the observed intramolecular 13C pattern are broken down along alternative catabolic pathways, it must be expected that respired CO2 with strongly differing δ13C will be released; indicating that intramolecular 13C variation affects isotope signals of atmosphere-biosphere C exchange fluxes. taking this variation into account will improve modelling of the global C cycle. Furthermore, cluster analysis shows that tree-ring glucose exhibits several independent intramolecular 13C signals, which constitute distinct ecophysiological information channels. Thus, whole-molecule 13C analysis likely misses a large part of the isotope information stored in tree rings. As we have shown for deuterium (Ehlers et al

  14. Total synthesis of virgatolide B via exploitation of intramolecular hydrogen bonding.

    PubMed

    Hume, Paul A; Furkert, Daniel P; Brimble, Margaret A

    2014-06-06

    A full account of the enantioselective total synthesis of virgatolide B is reported. Key features of the synthesis include an sp(3)-sp(2) Suzuki-Miyaura cross-coupling of a β-trifluoroboratoamide with an aryl bromide, regioselective intramolecular carboalkoxylation, and a 1,3-anti-selective Mukaiyama aldol reaction. Intramolecular hydrogen bonding governed the regioselectivity of the key spiroketalization step, affording the natural product as a single regioisomer.

  15. Stereoselective Intramolecular Cyclopropanation of α-Diazoacetates via Co(II)-Based Metalloradical Catalysis.

    PubMed

    Ruppel, Joshua V; Cui, Xin; Xu, Xue; Zhang, X Peter

    2014-07-01

    Co(II) complexes of D2-symmetric chiral porphyrins have been proven to be effective metalloradical catalysts for the asymmetric intramolecular cyclopropanation of allyl α-diazoacetates. 4-(Dimethylamino)pyridine (DMAP), through positive trans effect, plays an important role in the enhancement of the asymmetric induction for the intramolecular cyclopropanation process. This metalloradical catalytic system is suitable for cyclopropanation of allyl α-diazoacetates with varied functional groups and substitution patterns, producing bicyclic products with complete diastereocontrol and good enantiocontrol.

  16. Subpicosecond time-resolved intramolecular electronic energy transfer in flexible bichromophoric Coumarin molecules

    SciTech Connect

    Kaschke, M.; Ernsting, N.P. ); Valeur, B.; Bourson, J. )

    1990-07-26

    By excite-and-probe spectroscopy with subpicosecond time resolution, the authors have measured the intramolecular electronic energy transfer in bichromophoric coumarins linked by a flexible polymethylene chain. The transfer proceeds on a time scale between 1 and 20 ps depending on the polymethylene chain length. The results can be well described by a dipole-dipole interaction model that takes into account the statistical distribution of intramolecular distances between the two chromophores.

  17. Intramolecular excimer formation in hexakis(pyrenyloxy)cyclotriphosphazene: photophysical properties, crystal structure, and theoretical investigation.

    PubMed

    Yeşilot, Serkan; Coşut, Bünyemin; Alidaği, Hüsnüye Ardiç; Hacivelioğlu, Ferda; Özpinar, Gül Altinbaş; Kiliç, Adem

    2014-03-07

    A hexakis(pyrenyloxy)cyclotriphosphazene is synthesized by the reaction of N3P3Cl6 with 2-hydroxypyrene, and its excimer emission through intramolecular interactions in solution and in the solid state has been investigated by fluorescence spectroscopy and X-ray crystallography. Thermal and electrochemical properties were investigated. A DFT benchmark study has been performed to evaluate the intramolecular interactions and molecular orbital levels by comparing with the experimental results.

  18. 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.

  19. Intramolecular charge transfer with fluorazene and N-phenylpyrrole.

    PubMed

    Druzhinin, Sergey I; Kovalenko, Sergey A; Senyushkina, Tamara A; Demeter, Attila; Zachariasse, Klaas A

    2010-02-04

    The reaction from the initially prepared locally excited (LE) precursor to the intramolecular charge transfer (ICT) state of the planarized fluorazene (FPP) is investigated and compared with its flexible counterpart N-phenylpyrrole (PP). The fluorescence spectra of FPP and PP at 25 degrees C in solvents of different polarity reveal that the onset of a LE --> ICT reaction occurs at lower polarity (tetrahydrofuran, epsilon = 7.39) for FPP than for PP (1,2-dichloroethane, epsilon = 10.4). In accordance with this observation, the ICT reaction enthalpy -DeltaH is larger for FPP than for PP, 16.7 versus 6.7 kJ/mol in ethyl cyanide (EtCN). The larger ICT efficiency of FPP is related to the smaller energy gap between the two lowest excited singlet states DeltaE(S(1),S(2)): 3680 cm(-1) for FPP and 4070 cm(-1) for PP in n-hexane, as would be expected in the context of the PICT model. From picosecond fluorescence decays in EtCN at -45 degrees C it is found that the LE --> ICT reaction rate constant k(a) of FPP is with 9.8 x 10(10) s(-1) considerably larger than that of PP with 3.9 x 10(10) s(-1). From femtosecond transient absorption spectra in acetonitrile (MeCN) at 22 degrees C, an ICT reaction time of 1.6 ps is obtained for FPP, shorter than the 4.0 ps determined for PP. The results show that a perpendicular twist of the pyrrole and phenyl subgroups is not required for an efficient ICT reaction with PP, the planarization of FPP even making this reaction faster. The similarity of the ESA spectra of FPP with those of PP in MeCN, with ICT absorption maxima at 365 nm (FPP) and 370 nm (PP), leads to the conclusion that both ICT states have a planar structure.

  20. Counteranion-dependent mechanisms of intramolecular proton transfer in aprotic solution.

    PubMed

    Lesnichin, Stepan B; Tolstoy, Peter M; Limbach, Hans-Heinrich; Shenderovich, Ilja G

    2010-09-21

    Using the freon mixture CDF(3)/CDClF(2) as solvent we have been able to measure the (1)H and (15)N NMR spectra of the doubly (15)N labeled 2,2'-bipyridinium cation (BpyH(+)) at temperatures down to 115 K. The obtained NMR parameters strongly depend on the type of counteranions indicating the formation of ion pairs. In the case of the bulky poorly coordinating tetrakis[3,5-bis(trifluoromethyl)phenyl]-borate as the counteranion a strong intramolecular NHN hydrogen bond was observed in BpyH(+) exhibiting a degenerate intramolecular proton transfer which is of the order of 10(6) s(-1) even at 120 K. By contrast, the weak hydrogen bond acceptor tetrafluoroborate favors a weak intermolecular FHN interaction and quenches the intramolecular proton transfer. The intramolecular proton transfer requires in this case a dissociation of the ion pair which is hindered by the Coulomb interaction. A slow intramolecular proton transfer was observed in the case of dichloroacetate which forms a strong intermolecular OHN hydrogen bond to BpyH(+). The mechanism of this transfer presumably involves a preliminary intermolecular proton transfer from nitrogen towards oxygen followed by a hydrogen bond switch to the neighboring nitrogen to which the proton is then transferred.

  1. Conductance and activation energy for electron transport in series and parallel intramolecular circuits.

    PubMed

    Hsu, Liang-Yan; Wu, Ning; Rabitz, Herschel

    2016-11-30

    We investigate electron transport through series and parallel intramolecular circuits in the framework of the multi-level Redfield theory. Based on the assumption of weak monomer-bath couplings, the simulations depict the length and temperature dependence in six types of intramolecular circuits. In the tunneling regime, we find that the intramolecular circuit rule is only valid in the weak monomer coupling limit. In the thermally activated hopping regime, for circuits based on two different molecular units Ma and Mb with distinct activation energies Eact,a > Eact,b, the activation energies of Ma and Mb in series are nearly the same as Eact,a while those in parallel are nearly the same as Eact,b. This study gives a comprehensive description of electron transport through intramolecular circuits from tunneling to thermally activated hopping. We hope that this work can motivate additional studies to design intramolecular circuits based on different types of building blocks, and to explore the corresponding circuit laws and the length and temperature dependence of conductance.

  2. The structural basis of androgen receptor activation: intramolecular and intermolecular amino-carboxy interactions.

    PubMed

    Schaufele, Fred; Carbonell, Xavier; Guerbadot, Martin; Borngraeber, Sabine; Chapman, Mark S; Ma, Aye Aye K; Miner, Jeffrey N; Diamond, Marc I

    2005-07-12

    Nuclear receptors (NRs) are ligand-regulated transcription factors important in human physiology and disease. In certain NRs, including the androgen receptor (AR), ligand binding to the carboxy-terminal domain (LBD) regulates transcriptional activation functions in the LBD and amino-terminal domain (NTD). The basis for NTD-LBD communication is unknown but may involve NTD-LBD interactions either within a single receptor or between different members of an AR dimer. Here, measurement of FRET between fluorophores attached to the NTD and LBD of the AR established that agonist binding initiated an intramolecular NTD-LBD interaction in the nucleus and cytoplasm. This intramolecular folding was followed by AR self-association, which occurred preferentially in the nucleus. Rapid, ligand-induced intramolecular folding and delayed association also were observed for estrogen receptor-alpha but not for peroxisome proliferator activated receptor-gamma2. An antagonist ligand, hydroxyflutamide, blocked the NTD-LBD association within AR. NTD-LBD association also closely correlated with the transcriptional activation by heterologous ligands of AR mutants isolated from hormone-refractory prostate tumors. Intramolecular folding, but not AR-AR affinity, was disrupted by mutation of an alpha-helical ((23)FQNLF(27)) motif in the AR NTD previously described to interact with the AR LBD in vitro. This work establishes an intramolecular NTD-LBD conformational change as an initial component of ligand-regulated NR function.

  3. 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.

  4. The influence of intramolecular hydrogen bonds on the adsorption properties of aromatic alcohols and thiols

    NASA Astrophysics Data System (ADS)

    Varfolomeeva, V. V.; Terent'ev, A. V.; Buryak, A. K.

    2008-06-01

    The thermodynamic characteristics of adsorption equilibria of primary aromatic alcohols and thiols on graphitized carbon black at 300 K were determined by the molecular-statistical method. The influence of intramolecular effects under the action of the force field of the sorbent on the conformation of the molecules studied was considered in comparison with n-alkylbenzenes having similar structures. An increase in the chain length by one-CH2 group was shown to influence the formation of intramolecular H-bonds in alcohol and thiol molecules. In adsorption, a considerable fraction of molecules assumed configurations close to planar. An exception was the nonplanar conformation of the 2-phenylethanol molecule stabilized by the intramolecular H-bond.

  5. 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

    2015-10-05

    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.

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

    PubMed

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

    2012-02-01

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

  7. 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.

  8. Synthesis of the carbon framework of scholarisine A by intramolecular oxidative coupling.

    PubMed

    Watanabe, Tsugunori; Kato, Nobuki; Umezawa, Naoki; Higuchi, Tsunehiko

    2013-03-25

    Scholarisine A, isolated from the leaves of Alstonia scholaris, is a monoterpene indole alkaloid with an unprecedented cage-like structure. In this paper, preparation of the distinctive cage-like core skeleton of scholarisine A is described. The key feature of this synthetic strategy is an intramolecular oxidative coupling reaction at the late stage to construct a 10-oxa-tricyclo[5.3.1.0(3, 8)]undecan-9-one structure fused with indolenine. Intramolecular oxidative coupling by using N-iodosuccinimide gave the carbon framework of scholarisine A in moderate yield, which is the first example of intramolecular oxidative-coupling reaction between non-activated enolate and indole. This study lays the foundation for continued investigations towards the total synthesis of scholarisine A. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Intramolecular Benzoin Reaction Catalyzed by Benzaldehyde Lyase from Pseudomonas Fluorescens Biovar I.

    PubMed

    Hernández, Karel; Parella, Teodor; Petrillo, Giovanna; Usón, Isabel; Wandtke, Claudia M; Joglar, Jesús; Bujons, Jordi; Clapés, Pere

    2017-05-02

    Intramolecular benzoin reactions catalyzed by benzaldehyde lyase from Pseudomonas fluorescens biovar I (BAL) are reported. The structure of the substrates envisaged for this reaction consists of two benzaldehyde derivatives linked by an alkyl chain. The structural requirements needed to achieve the intramolecular carbon-carbon bond reaction catalyzed by BAL were established. Thus, a linker consisting of a linear alkyl chain of three carbon atoms connected through ether-type bonds to the 2 and 2' positions of two benzaldehyde moieties, which could be substituted with either Cl, Br, or OCH3 at either the 3 and 3' or 5 and 5' positions, were suitable substrates for BAL. Reactions with 61-84 % yields of the intramolecular product and ee values between 64 and 98 %, were achieved. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Rare-earth metal diisopropylamide-catalyzed intramolecular hydroamination.

    PubMed

    Spallek, Tatiana; Anwander, Reiner

    2016-10-18

    Rare-earth metal diisopropylamide complexes LiLn(NiPr2)4(THF) (Ln = Sc, Y, La), [LiY(NiPr2)4]n, NaLn(NiPr2)4(THF) (Ln = Sc, Y), Sc(NiPr2)3(THF) and Ce(NiPr2)4 were screened as catalysts for the intramolecular hydroamination/cyclization (IHC) of 1-amino-2,2-dimethyl-4-pentene, 1-amino-2,2-diphenyl-4-pentene, and 1-amino-2,2-diphenyl-5-hexene at ambient and moderately increased temperature of 60 °C in C6D6. The lithium ate complexes displayed the most efficient precatalysts with high conversion rates at 60 °C for the phenyl-substituted substrates and Ln = Y and La, affording turnover frequencies Nt as high as 164 h(-1). The catalytic activity could be increased by employing THF-free complex [LiY(NiPr2)4]n (Nt = 45.8 h(-1) at 26 °C; 34.1 h(-1) for LiY(NiPr2)4(THF)). In situ generation of putative LiY(NiPr2)4(THF) from YCl3(THF)3.3 and four equivalents of LiNiPr2 (LDA) in C6D6 generated a catalyst revealing Nt comparable to pre-isolated crystallized LiY(NiPr2)4(THF) but yielding even higher substrate conversion. The IHC reactions were also examined for rare-earth metal bis(trimethylsilyl)amide catalysts Ln[N(SiMe3)2]3 (Ln = Sc, Y, La) as well as for LDA using the same reaction conditions, revealing overall superior activity of the silylamide derivatives but poor performance of LDA compared to the rare-earth metal diisopropylamide complexes LiLn(NiPr2)4(THF). Cyclization of 1-amino-2,2-diphenyl-5-hexene to the 6-membered heterocycle 2-methyl-4,4-diphenylpiperidine by lanthanum derivative LiLa(NiPr2)4(THF) was accompanied by a competitive isomerization reaction affording max. 20% of 1-amino-2,2-diphenyl-4-hexene after 2 h at 60 °C. Crystalline tetravalent Ce(NiPr2)4 showed a better IHC performance than crystalline trivalent Sc(NiPr2)3(THF) as preliminary examined for 1-amino-2,2-diphenyl-4-pentene at 26 °C (Nt = 5.6 and 0.9 h(-1), respectively), but cyclization came to a halt after 2 h, probably due to decomposition of the catalyst.

  11. 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.

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

    NASA Astrophysics Data System (ADS)

    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.

  13. Stereoselective Intramolecular Cyclopropanation of α-Diazoacetates via Co(II)-Based Metalloradical Catalysis

    PubMed Central

    Ruppel, Joshua V.; Cui, Xin; Xu, Xue

    2014-01-01

    Co(II) complexes of D2-symmetric chiral porphyrins have been proven to be effective metalloradical catalysts for the asymmetric intramolecular cyclopropanation of allyl α-diazoacetates. 4-(Dimethylamino)pyridine (DMAP), through positive trans effect, plays an important role in the enhancement of the asymmetric induction for the intramolecular cyclopropanation process. This metalloradical catalytic system is suitable for cyclopropanation of allyl α-diazoacetates with varied functional groups and substitution patterns, producing bicyclic products with complete diastereocontrol and good enantiocontrol. PMID:24910778

  14. Examination of the Mechanism of Rh2(II)-Catalyzed Carbazole Formation Using Intramolecular Competition Experiments

    PubMed Central

    Stokes, Benjamin J.; Richert, Kathleen J.; Driver, Tom G.

    2009-01-01

    The use of a rhodium(II) carboxylate catalyst enables the mild and stereoselective formation of carbazoles from biaryl azides. Intramolecular competition experiments of triaryl azides suggested the source of the selectivity. A primary intramolecular kinetic isotope effect was not observed and correlation of the product ratios with Hammett σ+-values produced a plot with two intersecting lines with opposite ρ-values. These data suggest that electronic donation by the biaryl π-system accelerates the formation of rhodium nitrenoid and that C–N bond formation occurs through a 4π-electron-5-atom electrocyclization. PMID:19663433

  15. Intramolecular, reductive cyclization of beta-ketoisothiocyanates promoted by using samarium diiodide.

    PubMed

    Cho, Min Seok; Lee, In Sang; Kang, Sung Ho; Kim, Yong Hae

    2005-02-18

    A novel samarium diiodide (SmI2) promoted intramolecular cyclization of beta-ketoisothiocyanate, derived from alpha,beta-unsaturated esters and ammonium thiocyanate led to alpha-hydroxythiolactams and/or thiolactams in high yields. Treatment of beta-ketoisothiocyanate with two equivalents of SmI2 gave a mixture of alpha-hydroxythiolactam and thiolactam. Four equivalents of SmI2 afforded only thiolactam in high yields. The intramolecular cyclization took place with high to complete stereoselectivity. A mechanism to explain this transformation is proposed.

  16. 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.

  17. Molecular Coplanarity and Self-Assembly Promoted by Intramolecular Hydrogen Bonds.

    PubMed

    Zhu, Congzhi; Mu, Anthony U; Lin, Yen-Hao; Guo, Zi-Hao; Yuan, Tianyu; Wheeler, Steven E; Fang, Lei

    2016-12-16

    Active conformational control is realized in a conjugated system using intramolecular hydrogen bonds to achieve tailored molecular, supramolecular, and solid-state properties. The hydrogen bonding functionalities are fused to the backbone and precisely preorganized to enforce a fully coplanar conformation of the π-system, leading to short π-π stacking distances, controllable molecular self-assembly, and solid-state growth of one-dimensional nano-/microfibers. This investigation demonstrates the efficiency and significance of an intramolecular noncovalent approach in promoting conformational control and self-assembly of organic molecules.

  18. Intramolecular features of individual C 60 molecules on Si(100) observed by STM

    NASA Astrophysics Data System (ADS)

    Yao, Xiaowei; Ruskell, Todd G.; Workman, Richard K.; Sarid, Dror; Chen, Dong

    1996-12-01

    Intramolecular features (IMF) of a variety of individual C 60 molecules adsorbed on an Si(100)-(2 × 1) surface have been imaged by scanning tunneling microscopy under ultrahigh vacuum conditions. Features of individual C 60 molecules clearly show the local density of states superimposed on their cage structure. Both physisorbed (pre-annealed) and chemisorbed (post-annealed) species have been imaged on the same surface, exhibiting characteristics that depend on their bonding nature. Intramolecular features of a physisorbed C 60 molecule and of two chemisorbed molecules are presented.

  19. 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

  20. Photoinduced Intramolecular Cyclopentanation vs Photoprotolytic Oxametathesis in Polycyclic Alkenes Outfitted with Conformationally Constrained Aroylmethyl Chromophores‡

    PubMed Central

    Valiulin, Roman A.; Arisco, Teresa M.; Kutateladze, Andrei G.

    2012-01-01

    Intramolecular photoinduced cyclizations are investigated in photoprecursors assembled in a modular fashion via a Diels-Alder reaction of acetylenic dienophiles with subsequent Michael additions of aromatic ketones to install a chromophore capable of initiating Paternò-Büchi cycloadditions or radical cyclization cascades. The protolytic oxametathesis in these systems allows for rapid access to novel polycyclic scaffolds decorated by formyl groups and carboxylates suitable for subsequent modifications. In conformationally constrained photoprecursors a radical rearrangement takes place resulting in intramolecular 1,3-diradical cyclopentanation of the double bond. PMID:23106813

  1. Spectral and photophysical properties of intramolecular charge transfer fluorescence probe: 4'-Dimethylamino-2,5-dihydroxychalcone

    NASA Astrophysics Data System (ADS)

    Xu, Zhicheng; Bai, Guan; Dong, Chuan

    2005-12-01

    The spectral and photophysical properties of a new intramolecular charge transfer (ICT) probe, namely 4'-dimethylamino-2,5-dihydroxychalcone (DMADHC) were studied in different solvents by using steady-state absorption and emission spectroscopy. Whereas the absorption spectrum undergoes minor change with increasing polarity of the solvents, the fluorescence spectrum experiences a distinct bathochromic shift in the band position and the fluorescence quantum yield increases reaching a maximum before decrease with increasing the solvent polarity. The magnitude of change in the dipole moment was calculated based on the Lippert-Mataga equation. These results give the evidence about the intramolecular charge transfer character in the emitting singlet state of this compound.

  2. Large molecules on surfaces: deposition and intramolecular STM manipulation by directional forces

    NASA Astrophysics Data System (ADS)

    Grill, Leonhard

    2010-03-01

    Intramolecular manipulation of single molecules on a surface with a scanning tunnelling microscope enables the controlled modification of their structure and, consequently, their physical and chemical properties. This review presents examples of intramolecular manipulation experiments with rather large molecules, driven by directional, i.e. chemical or electrostatic, forces between tip and molecule. It is shown how various regimes of forces can be explored and characterized with one and the same manipulation of a single molecule by changing the tip-surface distance. Furthermore, different deposition techniques under ultrahigh vacuum conditions are discussed because the increasing functionality of such molecules can lead to fragmentation during the heating step, making their clean deposition difficult.

  3. 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…

  4. 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.

  5. Functionalized azabicycloalkane amino acids by nitrone 1,3-dipolar intramolecular cycloaddition.

    PubMed

    Manzoni, Leonardo; Arosio, Daniela; Belvisi, Laura; Bracci, Antonio; Colombo, Matteo; Invernizzi, Donatella; Scolastico, Carlo

    2005-05-13

    [reaction: see text] An efficient and operationally simple method for the synthesis of functionalized azaoxobicyclo[X.3.0]alkane amino acids has been devised. The key step is an intramolecular nitrone cycloaddition on 5-allyl- or 5-homoallylproline that was found to be completely regio- and stereoselective.

  6. 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

    2014-01-07

    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.

  7. Chiral N,N'-dioxide-FeCl3 complex-catalyzed asymmetric intramolecular Cannizzaro reaction.

    PubMed

    Wu, Wangbin; Liu, Xiaohua; Zhang, Yuheng; Ji, Jie; Huang, Tianyu; Lin, Lili; Feng, Xiaoming

    2015-07-25

    An environmentally benign catalyst, the N,N'-dioxide-FeCl3 complex, has been developed for the asymmetric intramolecular Cannizzaro reaction. Aryl and alkyl glyoxal monohydrates were applied to obtain α-hydroxy acid esters with excellent results. Deuterium-label and control experiments shed light on the reaction mechanism.

  8. Pressure dependence of intramolecular mode frequencies in solid N2, O2, and CO2

    NASA Technical Reports Server (NTRS)

    Etters, R. D.; Helmy, A.

    1983-01-01

    A microscopic description of the pressure dependence of intramolecular vibrational modes in simple molecular crystals has been formulated using a classical perturbation theory. Quantitative agreement with experiment is demonstrated and it is shown that frequency changes at phase transitions are large enough to be observed optically.

  9. Chemoselective intramolecular Wittig reactions for the synthesis of oxazoles and benzofurans.

    PubMed

    Fan, Yu-Shiou; Das, Utpal; Hsiao, Ming-Yu; Liu, Meng-Hsien; Lin, Wenwei

    2014-12-05

    A chemoselective approach was developed for the synthesis of highly functionalized oxazoles and benzofurans using an intramolecular Wittig reaction as the key step. By choosing proper trapping reagent or method of addition of reagents, chemoselectivity can be controlled toward either oxazole or benzofuran derivatives.

  10. Regio-Selective Intramolecular Hydrogen/Deuterium Exchange in Gas-Phase Electron Transfer Dissociation.

    PubMed

    Hamuro, Yoshitomo

    2017-05-01

    Protein backbone amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) typically utilizes enzymatic digestion after the exchange reaction and before MS analysis to improve data resolution. Gas-phase fragmentation of a peptic fragment prior to MS analysis is a promising technique to further increase the resolution. The biggest technical challenge for this method is elimination of intramolecular hydrogen/deuterium exchange (scrambling) in the gas phase. The scrambling obscures the location of deuterium. Jørgensen's group pioneered a method to minimize the scrambling in gas-phase electron capture/transfer dissociation. Despite active investigation, the mechanism of hydrogen scrambling is not well-understood. The difficulty stems from the fact that the degree of hydrogen scrambling depends on instruments, various parameters of mass analysis, and peptide analyzed. In most hydrogen scrambling investigations, the hydrogen scrambling is measured by the percentage of scrambling in a whole molecule. This paper demonstrates that the degree of intramolecular hydrogen/deuterium exchange depends on the nature of exchangeable hydrogen sites. The deuterium on Tyr amide of neurotensin (9-13), Arg-Pro-Tyr-Ile-Leu, migrated significantly faster than that on Ile or Leu amides, indicating the loss of deuterium from the original sites is not mere randomization of hydrogen and deuterium but more site-specific phenomena. This more precise approach may help understand the mechanism of intramolecular hydrogen exchange and provide higher confidence for the parameter optimization to eliminate intramolecular hydrogen/deuterium exchange during gas-phase fragmentation. Graphical Abstract ᅟ.

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

    PubMed

    Wang, Jian; Tang, Shi; Zhu, Qiang

    2016-07-01

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

  12. Enantioselective organocatalytic intramolecular ring-closing Friedel-Crafts-type alkylation of indoles.

    PubMed

    Li, Chang-Feng; Liu, Hiu; Liao, Jie; Cao, Yi-Ju; Liu, Xiao-Peng; Xiao, Wen-Jing

    2007-05-10

    An enantioselective organocatalytic intramolecular ring-closing Friedel-Crafts-type alkylation of indolyl alpha,beta-unsaturated aldehydes has been developed. This powerful new strategy allows enantioselective access to THPIs and THBCs in a straightforward and atom-economical manner.

  13. 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.

  14. 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…

  15. 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…

  16. Capped guanidino-α-cyclodextrin first synthesis based on intramolecular Staudinger-Aza-Wittig (SAW) reaction.

    PubMed

    Couturier, C; Dumarcay-Charbonnier, F; Lambert, A; Barth, D; Marsura, A

    2014-11-01

    An intramolecularly promoted SAW reaction between a phosphinimide and an isocyanate intermediate led to an original bridged trisubstituted ((A,C),E)-α-cyclodextrin. The latter was in a second step converted into a new capped (ACE)-(guanidino)-α-cyclodextrin.

  17. A novel synthesis of 4H-chromen-4-ones via intramolecular wittig reaction

    PubMed

    Kumar; Bodas

    2000-11-30

    The acylphosphoranes formed in a sequential manner from the reaction of the silyl ester of O-acyl(aroyl)salicylic acids and (trimethylsilyl)methylenetriphenylphosphorane undergo intramolecular Wittig cyclization on the ester carbonyl to afford the 4H-chromen-4-ones in good to excellent yields.

  18. Intramolecular hydrogen bonding as a synthetic tool to induce chemical selectivity in acid catalyzed porphyrin synthesis.

    PubMed

    Megiatto, Jackson D; Patterson, Dustin; Sherman, Benjamin D; Moore, Thomas A; Gust, Devens; Moore, Ana L

    2012-05-14

    A straightforward procedure based on the formation of intramolecular hydrogen bonds to impart selectivity in the preparation of multi-functionalized porphyrins has been developed. To illustrate the concept, the synthesis of a biomimetic artificial photosynthetic model able to undergo electron and proton transfer reactions upon irradiation is reported. This journal is © The Royal Society of Chemistry 2012

  19. Regio-Selective Intramolecular Hydrogen/Deuterium Exchange in Gas-Phase Electron Transfer Dissociation

    NASA Astrophysics Data System (ADS)

    Hamuro, Yoshitomo

    2017-05-01

    Protein backbone amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) typically utilizes enzymatic digestion after the exchange reaction and before MS analysis to improve data resolution. Gas-phase fragmentation of a peptic fragment prior to MS analysis is a promising technique to further increase the resolution. The biggest technical challenge for this method is elimination of intramolecular hydrogen/deuterium exchange (scrambling) in the gas phase. The scrambling obscures the location of deuterium. Jørgensen's group pioneered a method to minimize the scrambling in gas-phase electron capture/transfer dissociation. Despite active investigation, the mechanism of hydrogen scrambling is not well-understood. The difficulty stems from the fact that the degree of hydrogen scrambling depends on instruments, various parameters of mass analysis, and peptide analyzed. In most hydrogen scrambling investigations, the hydrogen scrambling is measured by the percentage of scrambling in a whole molecule. This paper demonstrates that the degree of intramolecular hydrogen/deuterium exchange depends on the nature of exchangeable hydrogen sites. The deuterium on Tyr amide of neurotensin (9-13), Arg-Pro-Tyr-Ile-Leu, migrated significantly faster than that on Ile or Leu amides, indicating the loss of deuterium from the original sites is not mere randomization of hydrogen and deuterium but more site-specific phenomena. This more precise approach may help understand the mechanism of intramolecular hydrogen exchange and provide higher confidence for the parameter optimization to eliminate intramolecular hydrogen/deuterium exchange during gas-phase fragmentation.

  20. Regio-Selective Intramolecular Hydrogen/Deuterium Exchange in Gas-Phase Electron Transfer Dissociation

    NASA Astrophysics Data System (ADS)

    Hamuro, Yoshitomo

    2017-02-01

    Protein backbone amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) typically utilizes enzymatic digestion after the exchange reaction and before MS analysis to improve data resolution. Gas-phase fragmentation of a peptic fragment prior to MS analysis is a promising technique to further increase the resolution. The biggest technical challenge for this method is elimination of intramolecular hydrogen/deuterium exchange (scrambling) in the gas phase. The scrambling obscures the location of deuterium. Jørgensen's group pioneered a method to minimize the scrambling in gas-phase electron capture/transfer dissociation. Despite active investigation, the mechanism of hydrogen scrambling is not well-understood. The difficulty stems from the fact that the degree of hydrogen scrambling depends on instruments, various parameters of mass analysis, and peptide analyzed. In most hydrogen scrambling investigations, the hydrogen scrambling is measured by the percentage of scrambling in a whole molecule. This paper demonstrates that the degree of intramolecular hydrogen/deuterium exchange depends on the nature of exchangeable hydrogen sites. The deuterium on Tyr amide of neurotensin (9-13), Arg-Pro-Tyr-Ile-Leu, migrated significantly faster than that on Ile or Leu amides, indicating the loss of deuterium from the original sites is not mere randomization of hydrogen and deuterium but more site-specific phenomena. This more precise approach may help understand the mechanism of intramolecular hydrogen exchange and provide higher confidence for the parameter optimization to eliminate intramolecular hydrogen/deuterium exchange during gas-phase fragmentation.

  1. Enantioselective synthesis of planar-chiral benzosiloloferrocenes by Rh-catalyzed intramolecular C-H silylation.

    PubMed

    Shibata, Takanori; Shizuno, Tsubasa; Sasaki, Tomoya

    2015-05-07

    The first synthesis of planar-chiral benzosiloloferrocenes was achieved by the intramolecular reaction of 2-(dimethylhydrosilyl)arylferrocenes. The enantioselective cross dehydrogenative coupling of an sp(2) C-H bond of ferrocene with a Si-H bond proceeded efficiently with the use of a Rh-chiral diene catalyst.

  2. 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

  3. Intramolecular C-H···O hydrogen bonding in 1,4-dihydropyridine derivatives.

    PubMed

    Petrova, Marina; Muhamadejev, Ruslan; Vigante, Brigita; Cekavicus, Brigita; Plotniece, Aiva; Duburs, Gunars; Liepinsh, Edvards

    2011-09-19

    The diastereotopy of the methylene protons at positions 2 and 6 in 1,4-dihydropiridine derivatives with various substituents has been investigated. NMR spectroscopy and quantum chemistry calculations show that the CH···O intramolecular hydrogen bond is one of the factors amplifying the chemical shift differences in the 1H-NMR spectra.

  4. Aromatic ring strain in arylselenenyl bromides: role in facile synthesis of selenenate esters via intramolecular cyclization.

    PubMed

    Selvakumar, K; Singh, Harkesh B; Butcher, Ray J

    2010-09-10

    The synthesis and reactivity of 2,6-disubstituted arylselenium compounds derived from 2-bromo-5-tert-butylisophthalic acid (43) are described. The syntheses of bis(5-tert-butylisophthalic acid dimethyl ester)diselenide (46) and bis(5-tert-butylisophthalic acid diisopropyl ester)diselenide (47) have been achieved by the reaction of the corresponding ester precursors with disodium diselenide. Reduction of diselenide 46 with lithium aluminum hydride affords 2,2'-bis(5-tert-butylbenzene-1,3-dimethanol)diselenide (53). Diselenides 46 and 47 exhibit intramolecular Se...O interaction. Compound 53 does not show any intramolecular Se...O interaction. The anomalous Se...O nonbonded coordination observed in the single-crystal X-ray structures of compounds 46, 47 and 53 is compared and contrasted. The corresponding selenenyl bromides 54 and 55, derived from the reaction of diselenides 46 and 47 with bromine, are quite stable in the solid state. However, they undergo hydrolysis and subsequent intramolecular cyclization upon heating or after having been kept in solution over a period of time to give the corresponding selenenate esters 56 and 57. The X-ray crystallographic study and density functional theory calculations on 54 at the B3LYP/6-31G(d) level of theory indicate a significant distortion in planarity of the aromatic ring. Glutathione peroxidase-like activities of diselenides 46 and 47 and their selenenate esters 56 and 57 have been studied both by thiophenol and bioassay methods. The very low glutathione peroxidase-like activity of the diselenides (46 and 47) and their selenenate esters (56 and 57) in the thiophenol assay is attributed to the presence of the relatively strong Se...O intramolecular interaction in the selenenyl sulfide intermediates. The interaction retards the catalytic activity through both thiol exchange and an intramolecular cyclization reaction.

  5. Elucidating hydrogenase surfaces and tracing the intramolecular tunnels for hydrogenase inhibition in microalgal species

    PubMed Central

    Dixit, Kritika; Rahman, Md.Akhlaqur; Nath, Adi; Sundaram, Shanthy

    2016-01-01

    Intramolecular tunnels are majorly attracting attention as possible pathways for entry of inhibitors like oxygen and carbon monoxide to the active sites of the enzymes, hydrogenases. The results of homology modeling of the HydSL protein, a NiFe-hydrogenase from Chlamydomonas reinhardtii and Chlorella vulgaris are presented in this work. Here we identify and describe molecular tunnels observed in HydSL hydrogenase enzyme systems. The possible determinant of the oxygen stability of already studied hydrogenases could be the lack of several intramolecular tunnels. The possible tunnels were traced out using MOLE 2 software, which showed several intramolecular pathways that may be connecting the active sites of the enzyme. The RMSD value showed a great deal of significance in the enzyme homology. This is the first report of its kind in which mapping of the intramolecular tunnels in the four-hydrogenase enzymes disclosed potential variations between designed models and acknowledged structures. We are seeking out the explanations for oxygen sensitivity of studied hydrogenases within the structure of intramolecular tunnels. Local and Global RMSD (Root mean square deviation) was calculated for models and templates, which showed value of 1.284 indicating a successful homology model. The tunnel tracing study by Mole 2 indicated two tunnels joined into one in C. reinhardtii model whereas C. vulgaris model showed one tunnel almost like two tunnels. Templates of both the A. vinosum and D. vulgaris hydrogenase consisted of six tunnels. For HydSL from Chlamydomonas and Chlorella Species the maximal potential was set to 250 kcal/mol (1,046 kJ/mol) and the positive potential areas were marked. Electrostatic studies define electrostatic potential (ESP) that help shuttle protons to the active site. PMID:28149051

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

    PubMed

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

    2009-01-01

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

  7. Identification of Two Tyrosine Residues Required for the Intramolecular Mechanism Implicated in GIT1 Activation

    PubMed Central

    Totaro, Antonio; Astro, Veronica; Tonoli, Diletta; de Curtis, Ivan

    2014-01-01

    GIT1 is an ArfGAP and scaffolding protein regulating cell adhesion and migration. The multidomain structure of GIT1 allows the interaction with several partners. Binding of GIT1 to some of its partners requires activation of the GIT1 polypeptide. Our previous studies indicated that binding of paxillin to GIT1 is enhanced by release of an intramolecular interaction between the amino-terminal and carboxy-terminal portions that keeps the protein in a binding-incompetent state. Here we have addressed the mechanism mediating this intramolecular inhibitory mechanism by testing the effects of the mutation of several formerly identified GIT1 phosphorylation sites on the binding to paxillin. We have identified two tyrosines at positions 246 and 293 of the human GIT1 polypeptide that are needed to keep the protein in the inactive conformation. Interestingly, mutation of these residues to phenylalanine did not affect binding to paxillin, while mutation to either alanine or glutamic acid enhanced binding to paxillin, without affecting the constitutive binding to the Rac/Cdc42 exchange factor βPIX. The involvement of the two tyrosine residues in the intramolecular interaction was supported by reconstitution experiments showing that these residues are important for the binding between the amino-terminal fragment and carboxy-terminal portions of GIT1. Either GIT1 or GIT1-N tyrosine phosphorylation by Src and pervanadate treatment to inhibit protein tyrosine phosphatases did not affect the intramolecular binding between the amino- and carboxy-terminal fragments, nor the binding of GIT1 to paxillin. Mutations increasing the binding of GIT1 to paxillin positively affected cell motility, measured both by transwell migration and wound healing assays. Altogether these results show that tyrosines 246 and 293 of GIT1 are required for the intramolecular inhibitory mechanism that prevents the binding of GIT1 to paxillin. The data also suggest that tyrosine phosphorylation may not be

  8. 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.

  9. Ratiometric Fluorescent Probe for Vicinal Dithiol-Containing Proteins in Living Cells Designed via Modulating the Intramolecular Charge Transfer-Twisted Intramolecular Charge Transfer Conversion Process.

    PubMed

    Wang, Yuanyuan; Zhong, Yaogang; Wang, Qin; Yang, Xiao-Feng; Li, Zheng; Li, Hua

    2016-10-18

    Vicinal dithiol-containing proteins (VDPs) play a significant role in maintaining the cellular redox homeostasis and are implicated in many diseases. To provide new chemical tools for VDPs imaging, we report here a ratiometric fluorescent probe CAsH2 for VDPs using 7-diethylaminiocoumarin as the fluorescent reporter and cyclic 1,3,2-dithiarsenolane as the specific ligand. CAsH2 shows peculiar dual fluorescence emission from the excited intramolecular charge transfer (ICT) and twisted intramolecular charge transfer (TICT) states in aqueous media. However, upon selective binding of protein vicinal dithiols to the trivalent arsenical of CAsH2, the probe was brought from the polar water media into the hydrophobic protein domain, causing the excited state ICT to TICT conversion to be restricted; as a result, an increase from the ICT emission band and a decrease from the TICT emission band were observed simultaneously. The designed probe shows high selectivity toward VDPs over other proteins and biological thiols. Preliminary experiments show that CAsH2 can be used for the ratiometric imaging of endogenous VDPs in living cells. So far as we know, this is a rare example of the ratiometric fluorescent probe designed via modulating the ICT-TICT conversion process, which provides a new way to construct various protein-specific ratiometric fluorescent probes.

  10. 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

    2015-11-05

    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.

  11. 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.

  12. 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.

  13. FACILE PREPARATION OF NANOPARTICLES BY INTRAMOLECULAR CROSSLINKING OF ISOCYANATE FUNCTIONALIZED COPOLYMERS

    PubMed Central

    Beck, J. Benjamin; Killops, Kato L.; Kang, Taegon; Sivanandan, Kulandaivelu; Bayles, Andrea; Mackay, Michael E.; Wooley, Karen L.; Hawker, Craig J.

    2009-01-01

    A new synthetic approach to the preparation of intramolecularly collapsed nanoparticles under mild, room temperature conditions has been developed from commercially available vinyl monomers. Reaction of isocyanate functionalized linear copolymers with a diamine in dilute solution leads to the efficient formation of nanoparticles where the diameter of the nanoparticle can be varied by controlling both the molecular weight and mole percentage of isocyanate repeat units. Physical properties for the intramolecularly collapsed nanoparticles were fully consistent with a three-dimensional structure and analysis of the collapse reaction revealed that approximately 75% of the isocyanate groups along the backbone underwent crosslinking with 25% being available for further reaction with mono-functional amines. This stepwise consumption of the isocyanates allows the chemical and physical properties of the nanoparticles to be further tuned and significantly opens up the range of nanoparticles that can be prepared using this mild and highly efficient chemistry. PMID:20717499

  14. Design of superbasic guanidines: the role of multiple intramolecular hydrogen bonds.

    PubMed

    Barić, Danijela; Dragičević, Ivan; Kovačević, Borislav

    2013-04-19

    New organic superbases have been designed using the concept of multiple intramolecular hydrogen bonds. Substituents capable of forming strong intramolecular H-bonds were selected on the basis of the energy of stabilization that occurs upon the formation of a complex between N,N',N"-trimethylguanidine and small model molecules. The proton affinities and the corresponding pK(a) values in acetonitrile of the new superbases are examined by Density Functional Theory (DFT). It is shown that N,N',N"-substitution of guanidine with appropriate substituents results in new organic superbases with gas phase proton affinities between 286 and 293 kcal mol(-1), thus being 15 to 20 kcal mol(-1) more basic than parental superbase N,N',N"-tris[(3-dimethylamino)propyl]-guanidine (tris-DMPG), whereas estimated pK(a) values in acetonitrile range between 29.5 and 33.2.

  15. Ultrahigh Thermal Rectification in Pillared Graphene Structure with Carbon Nanotube-Graphene Intramolecular Junctions.

    PubMed

    Yang, Xueming; Yu, Dapeng; Cao, Bingyang; To, Albert C

    2017-01-11

    In this letter, graded pillared graphene structures with carbon nanotube-graphene intramolecular junctions are demonstrated to exhibit ultrahigh thermal rectification. The designed graded two-stage pillared graphene structures are shown to have rectification values of 790.8 and 1173.0% at average temperatures 300 and 200 K, respectively. The ultrahigh thermal rectification is found to be a result of the obvious phonon spectra mismatch before and after reversing the applied thermal bias. This outcome is attributed to both the device shape asymmetry and the size asymmetric boundary thermal contacts. We also find that the significant and stable standing waves that exist in graded two-stage pillared graphene structures play an important role in this kind of thermal rectifier, and are responsible for the ultrahigh thermal rectification of the two-stage ones as well. Our work demonstrates that pillared graphene structure with SWCNT-graphene intramolecular junctions is an excellent and promising phononic device.

  16. Blue shifted intramolecular C-H···O improper hydrogen bonds in conformers of zidovudine

    NASA Astrophysics Data System (ADS)

    Chen, Fangfang; Selvam, Lalitha; Wang, Feng

    2010-06-01

    Blue shifted C-H stretch vibrations caused by C-H···O intramolecular improper hydrogen bonds in zidovudine (or AZT) conformers are employed to differentiate its conformers. Two sugar-sugar C-H···O (5') improper hydrogen bonds, existing in conformers of AZT with apparent drug potency, are related to their unique sugar puckering, showing C (3')- exo or - endo orientations. Aqueous solution causes a global red shift in IR spectra, but remains reduced blue shifted C-H stretch frequencies. Molecular electrostatic potentials (MEPs) of the conformers and orbitals such as 40a of AZT-B and 37a of AZT-C, which are found to be responsible for the intramolecular improper hydrogen bonds, are also given in this study.

  17. 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

  18. 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.

  19. Copper-catalyzed intramolecular alkene carboetherification: synthesis of fused-ring and bridged-ring tetrahydrofurans.

    PubMed

    Miller, Yan; Miao, Lei; Hosseini, Azade S; Chemler, Sherry R

    2012-07-25

    Fused-ring and bridged-ring tetrahydrofuran scaffolds are found in a number of natural products and biologically active compounds. A new copper-catalyzed intramolecular carboetherification of alkenes for the synthesis of bicyclic tetrahydrofurans is reported herein. The reaction involves Cu-catalyzed intramolecular addition of alcohols to unactivated alkenes and subsequent aryl C-H functionalization provides the C-C bond. Mechanistic studies indicate a primary carbon radical intermediate is involved and radical addition to the aryl ring is the likely C-C bond-forming mechanism. Preliminary catalytic enantioselective reactions are promising (up to 75% ee) and provide evidence that copper is involved in the alkene addition step, likely through a cis-oxycupration mechanism. Catalytic enantioselective alkene carboetherification reactions are rare and future development of this new method into a highly enantioselective process is promising. During the course of the mechanistic studies a protocol for alkene hydroetherification was also developed.

  20. Enantioselective Intramolecular Hydroarylation of Alkenes via Directed C–H Bond Activation

    PubMed Central

    Harada, Hitoshi; Thalji, Reema K.; Bergman, Robert G.; Ellman, Jonathan A.

    2008-01-01

    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)2]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. PMID:18681407

  1. 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.

  2. Empirical corrections to density functional theory highlight the importance of nonbonded intramolecular interactions in alkanes.

    PubMed

    Wodrich, Matthew D; Jana, Daniel F; Schleyer, Paul von Ragué; Corminboeuf, Clémence

    2008-11-13

    Energies of alkanes computed with many popular and even newer density functionals are flawed by systematic errors, which become considerable with larger molecules. The same energies, however, are well described by post-Hartree-Fock methods. Similar DFT shortcomings are well documented for cases involving descriptions of intermolecular van der Waals complexes. One solution to the density functional problem is the addition of an empirical correction term, which more accurately models the known R (-6) dependence of van der Waals energies. Here, we present the first empirical correction to DFT parametrized to reproduce experimental energies associated with intramolecular interactions in alkanes. Our training set used only three reactions involving simple linear and branched alkanes and provides a remarkable improvement over conventional DFT methods and empirical corrections optimized for intermolecular interactions. In contrast to many standard density functionals, the intramolecular empirical correction correctly predicts the lowest energy alkane isomer in addition to performing satisfactorily for describing the interaction energies of intermolecular complexes.

  3. 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.

  4. Substantial Intramolecular Charge Transfer Induces Long Emission Wavelengths and Mega Stokes Shifts in 6-Aminocoumarins

    DOE PAGES

    Liu, Xiaogang; Cole, Jacqueline M.; Xu, Zhaochao

    2017-06-01

    Coumarins are deployed in numerous bioimaging and biosensing applications. Among various coumarin derivatives, 6-aminocoumarins attract increasing attention for their red-shifted emissions, mega Stokes shifts, and significant solvatochromism. These spectral characteristics together with weak emission intensities have historically been ascribed to the formation of the twisted intramolecular charge transfer (TICT) state in 6-aminocoumarins. In this work, we demonstrate that it is actually substantial intramolecular charge transfer (ICT) that is responsible for these fluorescent properties. Based on this new understanding, we reanalyzed the sensing mechanism of a 6-aminocouarmin based fluorescent probe and obtained close agreement with experimental data. Lastly, our results leadmore » to a deeper understanding of the photophysics of 6-aminocoumarins and will inspire the rational development of novel fluorescent probes.« less

  5. Highly Efficient Thermally Activated Delayed Fluorescence from an Excited-State Intramolecular Proton Transfer System

    PubMed Central

    2017-01-01

    Thermally activated delayed fluorescence (TADF) materials have shown great potential for highly efficient organic light-emitting diodes (OLEDs). While the current molecular design of TADF materials primarily focuses on combining donor and acceptor units, we present a novel system based on the use of excited-state intramolecular proton transfer (ESIPT) to achieve efficient TADF without relying on the well-established donor–acceptor scheme. In an appropriately designed acridone-based compound with intramolecular hydrogen bonding, ESIPT leads to separation of the highest occupied and lowest unoccupied molecular orbitals, resulting in TADF emission with a photoluminescence quantum yield of nearly 60%. High external electroluminescence quantum efficiencies of up to 14% in OLEDs using this emitter prove that efficient triplet harvesting is possible with ESIPT-based TADF materials. This work will expand and accelerate the development of a wide variety of TADF materials for high performance OLEDs. PMID:28776019

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

    PubMed

    Ito, Soichi; Nagami, Takanori; Nakano, Masayoshi

    2016-08-11

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Klymchenko, Andriy S.; Demchenko, Alexander P.

    2002-12-01

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

  9. Multifaceted ultrafast intramolecular charge transfer dynamics of 4-(dimethylamino)benzonitrile (DMABN).

    PubMed

    Park, Myeongkee; Kim, Chul Hoon; Joo, Taiha

    2013-01-17

    Intramolecular charge transfer (ICT) of DMABN has been the subject of extensive investigations. Through the measurements of highly time-resolved fluorescence spectra (TRFS) over the whole emission region, we have examined the ICT dynamics of DMABN in acetonitrile free from the solvation dynamics and vibronic relaxation. The ICT dynamics was found to be characterized by a broad range of time scales; nearly instantaneous (<30 fs), 160 fs, and 3.3 ps. TRFS revealed that an ICT state with partially twisted geometry, ICT(P), is formed within a few hundred femtoseconds either directly from the initial photoexcited state or via the locally excited (LE) state. The ICT(P) state undergoes further relaxation along the intramolecular nuclear coordinate to reach the twisted ICT (TICT) state with the time constant of 4.8 ps. A conformational diversity along the rotation of the dimethylamino group was speculated to account for the observed diffusive dynamics.

  10. Pseudo-cyclic face-to-face rigid structure caused by the intramolecular ion pair effect.

    PubMed

    Zhang, Sheng-Ling; Huang, Zhi-Shu; Gu, Lian-Quan

    2009-04-14

    Six 3-methylpyridine zwitterions and six quinoline zwitterions were synthesized through the reaction of 4-hydroxycoumarins, p-benzoquinone and the corresponding N-aromatics. The novel pseudo-cyclic face-to-face rigid structure of the zwitterion was elucidated by (1)H-NMR at different temperatures, and assumed to be caused by both the intramolecular ion pair attraction and the steric interaction.

  11. Cobalt-catalyzed intramolecular C-H amination with arylsulfonyl azides.

    PubMed

    Ruppel, Joshua V; Kamble, Rajesh M; Zhang, X Peter

    2007-11-08

    Cobalt complexes of porphyrins are effective catalysts for intramolecular C-H amination with arylsulfonyl azides. The cobalt-catalyzed process can proceed efficiently under mild and neutral conditions in low catalyst loading without the need of other reagents or additives, generating nitrogen gas as the only byproduct. The catalytic system can be applied to primary, secondary, and tertiary C-H bonds and is suitable for a broad range of arylsulfonyl azides, leading to high-yielding syntheses of various benzosultams.

  12. Intramolecular Dynamics: A Study of Molecules at High Levels of Vibrational Excitation.

    DTIC Science & Technology

    1988-05-27

    molecular modes , which occurs in molecules that are excited above the dissociation threshold,.- however, causes the course and rate of laser-induced...8217 mode -selective’ or ’bond-specific’ photochemistry, despite the high selectivity _ of infrared excitation. Whereas the equilibration of energy for...atoms. Most of these molecules have more than one Raman active mode and thus allow direct observation of the intramolecular U distribution of

  13. Designed intramolecular blocking of the spin crossover of an Fe(ii) complex.

    PubMed

    Bartual-Murgui, C; Vela, S; Roubeau, O; Aromí, G

    2016-09-13

    A ligand derived from 1,3bpp (2-(pyrazol-1-yl)-6-(pyrazol-3-yl)-pyridine) has been prepared to prove that the spin crossover (SCO) of an Fe(ii) complex can be blocked by means of intramolecular interactions not related to the crystal field. Calculations show that the blocking is caused by the energy penalty incurred by the rotation of a phenyl ring, needed to avoid steric hindrance upon SCO.

  14. Samarium(II)-mediated spirocyclization by intramolecular aryl radical addition onto an aromatic ring.

    PubMed

    Iwasaki, Hiroki; Eguchi, Toru; Tsutsui, Nozomi; Ohno, Hiroaki; Tanaka, Tetsuaki

    2008-09-19

    Samarium(II)-mediated spirocyclization by intramolecular addition of aryl radicals onto an aromatic ring was achieved by the reaction of N-(2-iodophenyl)-N-alkylbenzamides with SmI2 in the presence of HMPA, yielding spirocyclic indolin-2-one derivatives. The ether congeners afford spirocyclic benzofuran derivatives in moderate yields by aryl radical addition onto a benzene ring without having an electron-withdrawing group. The reaction with other aryl groups such as naphthalene and indole rings is also described.

  15. Synthesis of derivatives of indole and quinoline by the intramolecular catalytic cyclization of allylanilines

    SciTech Connect

    Abdrakmanov, I.B.; Mustafin, A.G.; Tolstikov, G.A.; Fakhretdinov, R.N.; Dzhemilev, U.M.

    1986-09-01

    An effective method for the isolation of 3-methyl-2-ethylindole and 2,4-dimethyl-quinoline by the intramolecular cyclization of N-(1-methyl-2-butenyl)- and 2-(1-methyl-2-butenyl)anilines under the action of the catalyst PdCl/sub 2/ (DMSO)/sub n/ was developed. The influence of the nature of the solvent, the temperature, and the concentration of the catalyst on the yield and the ratio of the reaction products was investigated.

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

    PubMed Central

    2015-01-01

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

  17. A concomitant allylic azide rearrangement/intramolecular azide-alkyne cycloaddition sequence.

    PubMed

    Vekariya, Rakesh H; Liu, Ruzhang; Aubé, Jeffrey

    2014-04-04

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

  18. Intramolecular Diels–Alder Reactions of Cycloalkenones: Stereoselectivity, Lewis Acid Acceleration, and Halogen Substituent Effects

    PubMed Central

    2015-01-01

    The intramolecular Diels–Alder reactions of cycloalkenones and terminal dienes occur with high endo stereoselectivity, both thermally and under Lewis-acidic conditions. Through computations, we show that steric repulsion and tether conformation govern the selectivity of the reaction, and incorporation of either BF3 or α-halogenation increases the rate of cycloaddition. With a longer tether, isomerization from a terminal diene to the more stable internal diene results in a more facile cycloaddition. PMID:24410341

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

    PubMed

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

    2016-12-12

    KN(SiMe3 )2 reacts with [Re(CO)3 (phen)(PMe3 )]OTf via reversible addition to the phen ligand and irreversible deprotonation of the PMe3 ligand followed by intramolecular attack to phen by the deprotonated phosphane, whereas MeLi irreversibly adds to phen. The addition of MeLi has been shown to be intermolecular, unlike previously known nucleophilic additions to pyridines. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Influence of the intramolecular potential of adsorbed hydrogen on frequency shift calculations

    NASA Astrophysics Data System (ADS)

    Larin, Alexander V.

    1995-01-01

    The influence of the choice of the intramolecular potential on the resulting frequency shift of the fundamental vibrational transition in the dihydrogen molecule adsorbed on zeolite NaA is estimated. It is shown that an improved Morse potential and the potential calculated by Kołtsos and Wolniewicz lead to the same frequency shift value. Application of the Buckingham method for the frequency shift calculation to this case is discussed.

  1. An experimental and computational study on intramolecular charge transfer: a tetrathiafulvalene-fused dipyridophenazine molecule.

    PubMed

    Jia, Chunyang; Liu, Shi-Xia; Tanner, Christian; Leiggener, Claudia; Neels, Antonia; Sanguinet, Lionel; Levillain, Eric; Leutwyler, Samuel; Hauser, Andreas; Decurtins, Silvio

    2007-01-01

    To study the electronic interactions in donor-acceptor (D-A) ensembles, D and A fragments are coupled in a single molecule. Specifically, a tetrathiafulvalene (TTF)-fused dipyrido[3,2-a:2',3'-c]phenazine (dppz) compound having inherent redox centers has been synthesized and structurally characterized. Its electronic absorption, fluorescence emission, photoinduced intramolecular charge transfer, and electrochemical behavior have been investigated. The observed electronic properties are explained on the basis of density functional theory.

  2. Direct time-resolved spectroscopic investigation of intramolecular hydrogen atom transfer of deoxyblebbistatin

    NASA Astrophysics Data System (ADS)

    Li, Ming-De; Zhu, Ruixue; Lee Phillips, David

    2017-09-01

    The photophysics and photochemistry of deoxyblebbistatin was investigated using femtosecond time-resolved transient absorption spectroscopy. An ultrafast intramolecular hydrogen atom transfer (IHAT) appears to take place via the first singlet excited state of deoxyblebbistatin within 8 ps. Absorption and fluorescence photochemical results indicate the IHAT process leads to mainly conversion of deoxyblebbistatin into an enol form final product which was observed and characterized by resonance Raman spectroscopy.

  3. Intramolecular azide to alkene cycloadditions for the construction of pyrrolobenzodiazepines and azetidino-benzodiazepines.

    PubMed

    Hemming, Karl; Chambers, Christopher S; Jamshaid, Faisal; O'Gorman, Paul A

    2014-10-17

    The coupling of proline- and azetidinone-substituted alkenes to 2-azidobenzoic and 2-azidobenzenesulfonic acid gives precursors that undergo intramolecular azide to alkene 1,3-dipolar cycloadditions to give imine-, triazoline- or aziridine-containing pyrrolo[1,4]benzodiazepines (PBDs), pyrrolo[1,2,5]benzothiadiazepines (PBTDs), and azetidino[1,4]benzodiazepines. The imines and aziridines are formed after loss of nitrogen from a triazoline cycloadduct. The PBDs are a potent class of antitumour antibiotics.

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

    PubMed

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

    2015-10-21

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

  5. Influence of "remote" intramolecular hydrogen bonds on the stabilities of phenoxyl radicals and benzyl cations.

    PubMed

    Foti, Mario C; Amorati, Riccardo; Pedulli, Gian Franco; Daquino, Carmelo; Pratt, Derek A; Ingold, K U

    2010-07-02

    Remote intramolecular hydrogen bonds (HBs) in phenols and benzylammonium cations influence the dissociation enthalpies of their O-H and C-N bonds, respectively. The direction of these intramolecular HBs, para --> meta or meta --> para, determines the sign of the variation with respect to molecules lacking remote intramolecular HBs. For example, the O-H bond dissociation enthalpy of 3-methoxy-4-hydroxyphenol, 4, is about 2.5 kcal/mol lower than that of its isomer 3-hydroxy-4-methoxyphenol, 5, although group additivity rules would predict nearly identical values. In the case of 3-methoxy-4-hydroxybenzylammonium and 3-hydroxy-4-methoxybenzylammonium ions, the CBS-QB3 level calculated C-N eterolytic dissociation enthalpy is about 3.7 kcal/mol lower in the former ion. These effects are caused by the strong electron-withdrawing character of the -O(*) and -CH(2)(+) groups in the phenoxyl radical and benzyl cation, respectively, which modulates the strength of the HB. An O-H group in the para position of ArO(*) or ArCH(2)(+) becomes more acidic than in the parent molecules and hence forms stronger HBs with hydrogen bond acceptors (HBAs) in the meta position. Conversely, HBAs, such as OCH(3), in the para position become weaker HBAs in phenoxyl radicals and benzyl cations than in the parent molecules. These product thermochemistries are reflected in the transition states for, and hence in the kinetics of, hydrogen atom abstraction from phenols by free radicals (dpph(*) and ROO(*)). For example, the 298 K rate constant for the 4 + dpph(*) reaction is 22 times greater than that for the 5 + dpph(*) reaction. Fragmentation of ring-substituted benzylammonium ions, generated by ESI-MS, to form the benzyl cations reflects similar remote intramolecular HB effects.

  6. Addition of boranes to N-aryl-salicylaldimines: intramolecular hydrogenation of imines.

    PubMed

    Barnes, Stephanie S; Vogels, Christopher M; Decken, Andreas; Westcott, Stephen A

    2011-05-07

    Addition of boranes to N-aryl-salicylaldimines takes place initially at the reactive phenolic O-H bond to give an activated boron-containing imine and dihydrogen. In some cases a subsequent intramolecular hydrogenation step is observed and the C=N imine bond is reduced to the corresponding amine. Reactions with dimesitylborane in THF are unique in that the reduced amine product is the major product observed in solution.

  7. 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

  8. Domino Knoevenagel condensation/intramolecular aldol cyclization route to diverse indolizines with densely functionalized pyridine units.

    PubMed

    Kim, Myungock; Jung, Youngeun; Kim, Ikyon

    2013-10-18

    A highly efficient [4 + 2] annulation route to polysubstituted indolizines is described employing a domino Knoevenagel condensation/intramolecular aldol cyclization process as a key step. Construction of pyridine rings in indolizine skeleton was rapidly achieved from several pyrrole-2-carboxaldehydes in good to excellent yields, leading to indolizines with various substituents at the 5, 6, and 7 positions depending on the reacting active methylene partners.

  9. Iron(II)-catalyzed intramolecular aminohydroxylation of olefins with functionalized hydroxylamines.

    PubMed

    Liu, Guan-Sai; Zhang, Yong-Qiang; Yuan, Yong-An; Xu, Hao

    2013-03-06

    A diastereoselective aminohydroxylation of olefins with a functionalized hydroxylamine is catalyzed by new iron(II) complexes. This efficient intramolecular process readily affords synthetically useful amino alcohols with excellent selectivity (dr up to > 20:1). Asymmetric catalysis with chiral iron(II) complexes and preliminary mechanistic studies reveal an iron nitrenoid is a possible intermediate that can undergo either aminohydroxylation or aziridination, and the selectivity can be controlled by careful selection of counteranion/ligand combinations.

  10. 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

  11. Enantioselective intramolecular propargylic amination using chiral copper-pybox complexes as catalysts.

    PubMed

    Shibata, Masashi; Nakajima, Kazunari; Nishibayashi, Yoshiaki

    2014-07-25

    Intramolecular propargylic amination of propargylic acetates bearing an amino group at the suitable position in the presence of chiral copper-pybox complexes proceeds enantioselectively to give optically active 1-ethynyl-isoindolines (up to 98% ee). The method described in this communication provides a useful synthetic approach to the enantioselective preparation of nitrogen containing heterocyclic compounds with an ethynyl group at the α-position.

  12. FeCl3 mediated intramolecular olefin-cation cyclization of cinnamates for the synthesis of highly substituted indenes.

    PubMed

    Dethe, Dattatraya H; Murhade, Ganesh M

    2013-09-21

    Highly substituted indene derivatives were readily prepared in excellent yields with high regioselectivity under very mild reaction conditions by the FeCl3 mediated intramolecular olefin-cationic cyclization of cinnamates.

  13. Enantioselective cis-β-lactam synthesis by intramolecular C-H functionalization from enoldiazoacetamides and derivative donor-acceptor cyclopropenes

    PubMed Central

    Deng, Yongming; Yim, David N.; Zavalij, Peter Y.

    2015-01-01

    β-Lactam derivatives are produced through intermediate donor-acceptor cyclopropene intermediates in high yield, exclusive cis-diastereoselectivity, and high enantiocontrol in a chiral dirhodium carboxylate catalyzed intramolecular C-H functionalization reaction of enoldiazoacetamides. PMID:26029355

  14. Iron(II) triflate as a catalyst for the synthesis of indoles by intramolecular C-H amination.

    PubMed

    Bonnamour, Julien; Bolm, Carsten

    2011-04-15

    A practical iron-catalyzed intramolecular C-H amination reaction and its application in the synthesis of indole derivatives are presented. As a catalyst, commercially available iron(II) triflate is used.

  15. Pd-catalyzed enantioselective intramolecular α-arylation of α-substituted cyclic ketones: facile synthesis of functionalized chiral spirobicycles.

    PubMed

    Fan, Lulu; Takizawa, Shinobu; Takeuchi, Yoshiki; Takenaka, Kazuhiro; Sasai, Hiroaki

    2015-05-07

    Catalytic synthesis of chiral spirocyclic ketones was accomplished via the Pd-catalyzed intramolecular α-arylation of α-substituted cyclic ketones. The obtained spirocyclic ketone could be converted into a bifunctional organocatalyst.

  16. Kinetics of intramolecular chemical exchange by initial growth rates of spin saturation transfer difference experiments (SSTD NMR).

    PubMed

    Quirós, M Teresa; Angulo, Jesús; Muñoz, María Paz

    2015-06-25

    We report here the Initial Growth Rates SSTD NMR method, as a new powerful tool to obtain the kinetic parameters of intramolecular chemical exchange in challenging small organic and organometallic molecules.

  17. A Diastereoselective Intramolecular Pauson-Khand Approach to the Construction of the BC Ring System in Tuberostemoninol

    PubMed Central

    Jia, Xiangna; Williams, Robert M

    2009-01-01

    Herein we describe an asymmetric approach to the synthesis of a BC-ring synthon in tuberostemoninol via an intramolecular Pauson-Khand reaction stereocontrolled by a commercially available chiral glycinate. PMID:19779590

  18. Asymmetric synthesis of planar chiral ferrocenes by enantioselective intramolecular C-H arylation of N-(2-haloaryl)ferrocenecarboxamides.

    PubMed

    Liu, Lantao; Zhang, An-An; Zhao, Rui-Juan; Li, Feng; Meng, Tuan-Jie; Ishida, Naoki; Murakami, Masahiro; Zhao, Wen-Xian

    2014-10-17

    The palladium-catalyzed intramolecular C-H arylation reaction of N-(2-bromoaryl)ferrocenecarboxamides furnishes planar chiral ferrocene derivatives. TADDOL-derived phosphoramide ligands induce enantioselectivities ranging from 91:9 to 98:2 er.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

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

    PubMed

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

    2011-11-08

    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.

  4. 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.

  5. Identification of an Intramolecular Interaction Important for the Regulation of GIT1 Functions

    PubMed Central

    Totaro, Antonio; Paris, Simona; Asperti, Claudia

    2007-01-01

    G-protein coupled receptor kinase-interacting protein (GIT) proteins include an N-terminal Arf GTPase-activating protein domain, and a C terminus that binds proteins regulating adhesion and motility. Given their ability to form large molecular assemblies, the GIT1 protein must be tightly regulated. However, the mechanisms regulating GIT1 functions are poorly characterized. We found that carboxy-terminal–truncated fragments of GIT1 bind their partners with higher efficiency compared with the full-length GIT1. We have explored the hypothesis that GIT1 is regulated by an intramolecular mechanism, and we identified two distinct intramolecular interactions between the N and C terminus of GIT1. The release of these interactions increases binding of GIT1 to paxillin and liprin-α, and it correlates with effects on cell spreading. Analysis of cells plated on fibronectin has shown that different deletion mutants of GIT1 either enhance or inhibit spreading, depending on their subcellular localization. Moreover, although the association between βPIX and GIT1 is insufficient to activate GIT1 binding to paxillin, binding of a PAK1 fragment including the βPIX-binding domain enhances paxillin binding to βPIX/GIT1, indicating that p21-activated kinase can activate the binding of paxillin to GIT1 by a kinase-independent mechanism. The release of the identified intramolecular interaction seems to be an important mechanism for the regulation of GIT1 functions. PMID:17898078

  6. 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.

  7. Time-Resolved Signatures across the Intramolecular Response in Substituted Cyanine Dyes

    NASA Astrophysics Data System (ADS)

    Nairat, Muath; Webb, Morgan; Esch, Michael; Lozovoy, Vadim V.; Levine, Benjamin G.; Dantus, Marcos

    2017-06-01

    The optically populated excited state wave packet propagates along multidimensional intramolecular coordinates soon after photoexcitation. This action occurs alongside an intermolecular response from the surrounding solvent. Disentangling the multidimensional convoluted signal enables the possibility to separate and understand the initial intramolecular relaxation pathways over the excited state potential energy surface. Here we track the initial excited state dynamics by measuring the fluorescence yield from the first excited state as a function of time delay between two color femtosecond pulses for several cyanine dyes, having different electronic configurations. We find that when the high frequency pulse precedes the low frequency one and for timescales up to 200 fs, the excited state can be depleted through stimulated emission with efficiency that is dependent on the molecular electronic structure. A similar observation at even shorter times was made by scanning the chirp (frequencies ordering) of a femtosecond pulse. These changes reflect the rate at which the nuclear coordinates of the excited state leave the Franck-Condon (FC) region and progress towards achieving equilibrium. Through functional group substitution, we explore these dynamic changes as a function of dipolar change following photoexcitation. We show that with proper knowledge and control over the phase of the excitation pulses, we can extract the relative energy relaxation rates through which the early intramolecular modes are populated at the FC geometry soon after excitation

  8. 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.

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

    PubMed

    Baranović, Goran; Biliškov, Nikola; Vojta, Danijela

    2012-08-16

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

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

    PubMed

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

    2016-06-15

    Disulfide bond plays crucial roles in stabilization of protein structure and in fine-tuning protein functions. To explore an approach for rational heme protein design, we herein rationally introduced a pair of cysteines (F46C/M55C) into the scaffold of myoglobin (Mb), mimicking those in native neuroglobin. Molecular modeling suggested that it is possible for Cys46 and Cys55 to form an intramolecular disulfide bond, which was confirmed experimentally by ESI-MS analysis, DTNB reaction and CD spectrum. Moreover, it was shown that the spontaneously formed disulfide bond of Cys46-Cys55 fine-tunes not only the heme active site structure, but also the protein functions. The substitution of Phe46 with Ser46 in F46S Mb destabilizes the protein while facilitates H2O2 activation. Remarkably, the formation of an intramolecular disulfide bond of Cys46-Cys55 in F46C/M55C Mb improves the protein stability and regulates the heme site to be more favorable for substrate binding, resulting in enhanced peroxidase activity. This study provides valuable information of structure-function relationship for heme proteins regulated by an intramolecular disulfide bond, and also suggests that construction of such a covalent bond is useful for design of functional heme proteins. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. Intramolecular disulfide bonds between conserved cysteines in wheat gliadins control their deposition into protein bodies.

    PubMed

    Shimoni, Y; Galili, G

    1996-08-02

    Following synthesis, wheat gliadin storage proteins are deposited into protein bodies inside the endomembrane system in a way that enables not only their efficient accumulation and dehydration during seed maturation, but also their rapid rehydration and degradation during germination. In the present report, we studied the mechanism of gliadin deposition and whether it was controlled by the conformation of these proteins. Although gliadins are generally known to be insoluble in aqueous solutions, sucrose gradient analysis showed that a considerable amount of these proteins appeared as relatively soluble monomers in developing grains. In vitro reduction of the intramolecular disulfide bonds that are present in natural monomeric gliadins caused their precipitation into insoluble aggregates. In addition, pulse-chase experiments in the absence or presence of reducing agents showed that formation of intramolecular disulfide bonds also played a major role in folding and deposition of the gliadins in vivo. Our results imply that following sequestration into the endoplasmic reticulum, the gliadins fold into relatively soluble monomers, which are incompetent for rapid aggregation and gradually assemble into protein bodies. This pattern of deposition apparently depends on the conformation of the gliadins, which is stabilized by intramolecular disulfide bonds formed between the conserved cysteines. The contribution of this study to the understanding of the evolution and function of gliadins is discussed.

  12. Intramolecular direct dehydrohalide coupling promoted by KO(t)Bu: total synthesis of Amaryllidaceae alkaloids anhydrolycorinone and oxoassoanine.

    PubMed

    De, Subhadip; Ghosh, Santanu; Bhunia, Subhajit; Sheikh, Javeed Ahmad; Bisai, Alakesh

    2012-09-07

    A transition-metal-free intramolecular dehydrohalide coupling via intramolecular homolytic aromatic substitution (HAS) with aryl radicals has been developed in the presence of potassium tert-butoxide and an organic molecule as the catalyst. The methodology has been applied to a concise synthesis of Amaryllidaceae alkaloids viz. oxoassoanine (1b), anhydrolycorinone (1d), and other related structures. Interestingly, the method also works only in the presence of potassium tert-butoxide.

  13. Silver(I)‐Catalyzed Intramolecular Cyclizations of Epoxide‐Propargylic Esters to 1,4‐Oxazine Derivatives

    PubMed Central

    Li, Peng‐Hua; Yang, Jin‐Ming; Wei, Yin

    2016-01-01

    Abstract An interesting silver(I)‐catalyzed, one‐pot intramolecular cyclization of epoxide‐propargylic esters is described. A variety of 1,4‐oxazine derivatives were obtained through a novel domino sequence, including three‐membered ring‐opening, 3,3‐sigmatropic rearrangement, 6‐exo‐cycloisomerization and subsequent intramolecular elimination in moderate yields under mild conditions. PMID:28168146

  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

    NASA Astrophysics Data System (ADS)

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

    2004-07-01

    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 (CH2)m with m up to 6 as well as (CH2OCH2)n (n=1,2) and CH2SCH2. After light absorption into the azulene S1 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 S3 absorption band at 300 nm and/or the anthracene S1 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 τIVR for short bridges increase with the chain length. For longer bridges consisting of more than three elements, however, τIVR 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 ballistic and, therefore

  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. Intramolecular photoassociation and photoinduced charge transfer in bridged diaryl compounds. 7. A semiempirical MO study of intramolecular charge transfer in the excited singlet states of dinaphthylamines

    SciTech Connect

    Chen, D.; Sadygov, R.; Lim, E.C. )

    1994-02-24

    A semiempirical MO study of the intramolecular charge transfer (CT) in the excited singlet states of dinaphthylamines has been carried out with the program systems MOPAC and ARGUS. The excited-state energies for various conformations of the molecules were obtained, in both the absence and the presence of a polarizable medium, by adding the transition energies calculated with the INDO I/S method to the ground-state energies calculated by means of the AM1 method. The CT state corresponds to a twisted geometry in which one naphthalene moiety is conjugated with the amino bridge, while the other moiety is perpendicular to the first. The gas-phase energy of this twisted intramolecular CT (TICT) state is only slightly greater than that of the lowest excited singlet (S[sub 1]) state of smaller dipole moment. In solvent of large dielectric constant, the TICT state is therefore predicted to be the lowest excited singlet state of the module. The computed oscillator strength of the absorption to the TICT state is much smaller than that to the lowest-energy excited state of an isolated molecule, so that the increase CT character of the S[sub 1] state in polar solvents is expected to lead to a decrease in the radiative decay rate of the state. These results are consistent with the experimental observation of a large fluorescence Stokes shift, and a reduction in the S[sub 1] radiative decay rate, of the compounds in polar solvents relative to nonpolar solvents. 14 refs., 9 figs., 4 tabs.

  18. 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.

  19. Inhibition of intramolecular electron transfer in ascorbate oxidase by Ag+: redox state dependent binding.

    PubMed

    Santagostini, Laura; Gullotti, Michele; Hazzard, James T; Maritano, Silvana; Tollin, Gordon; Marchesini, Augusto

    2005-02-01

    Intramolecular electron transfer within zucchini squash ascorbate oxidase is inhibited in a novel manner in the presence of an equimolar concentration of Ag(+). At pH 5.5 in acetate buffer reduction of the enzyme by laser flash photolytically generated 5-deazariboflavin semiquinone occurs at the Type I Cu with a rate constant of 5 x 10(8) M(-1)s(-1). Subsequent to this initial reduction step, equilibration of the reducing equivalent between the Type I Cu and the trinuclear Type II, III copper cluster (TNC) occurs with rate constant of 430 s(-1). The 41% of the reduced Type I Cu is oxidized by this intramolecular electron transfer reaction. When these reactions are performed in the presence of Ag(+) equimolar to dimeric AO, the bimolecular reduction of the enzyme by the 5-deazariboflavin semiquinone is not affected. As in the case of the native enzyme, intramolecular electron transfer between the Type I Cu and the TNC occurs, which continues until 25% of the reducing equivalent has been transferred. At that point, the reducing equivalent is observed to more slowly return to the Type I Cu, resulting a second reduction phase whose rate constant (100 s(-1)) is protein and Ag(+) concentration independent. The data suggest that partial reduction of the TNC results in Ag(+) binding to the enzyme which causes the apparent midpoint potential of the TNC as a whole to decrease thereby reversing the direction of electron flow. These results are consistent with the inhibitory effect of Ag(+) on the steady-state activity of ascorbate oxidase [S. Maritano, E. Malusa, A. Marchesini, presented at The Meeting on Metalloproteins, SERC Daresbury Laboratory, Warrington, England, 1992; A. Marchesini, XIX Convegno Nazionale SICA, Italian Society of Agricultural Chemistry, Reggio Calabria, Italy, September 2001.].

  20. Communications: Is quantum chemical treatment of biopolymers accurate? Intramolecular basis set superposition error (BSSE).

    PubMed

    Balabin, Roman M

    2010-06-21

    The accuracy of quantum chemical treatment of biopolymers by means of density functional theory is brought into question in terms of intramolecular basis set superposition error (BSSE). Secondary structure forms--beta-strands (C5; fully extended conformation), repeated gamma-turns (C7), 3(10)-helices (C10), and alpha-helices (C13)--of homopolypeptides (polyglycine and polyalanine) are used as representative examples. The studied molecules include Ace(Gly)(5)NH(2), Ace(Gly)(10)NH(2), Ace(Ala)(5)NH(2), and Ace(Ala)(10)NH(2). The counterpoise correction procedure was found to produce reliable estimations for the BSSE values (other methods of BSSE correction are discussed). The calculations reported here used the B3LYP, PBE0 (PBE1PBE), and BMK density functionals with different basis sets [from 6-31G(d) to 6-311+G(3df,3pd)] to estimate the influence of basis set size on intramolecular BSSE. Calculation of BSSE was used to determine the deviation of the current results from the complete basis set limit. Intramolecular BSSE was found to be nonadditive with respect to biopolymer size, in contrast to claims in recent literature. The error, which is produced by a basis set superposition, was found to exceed 4 kcal mol(-1) when a medium-sized basis set was used. This indicates that this error has the same order of magnitude as the relative energy differences of secondary structure elements of biopolymers. This result makes all recent reports on the gas-phase stability of homopolypeptides and their analogs questionable.

  1. Intramolecular quadruplex conformation of human telomeric DNA assessed with 125I-radioprobing

    PubMed Central

    He, Yujian; Neumann, Ronald D.; Panyutin, Igor G.

    2004-01-01

    A repeated non-coding DNA sequence d(TTAGGG)n is present in the telomeric ends of all human chromosomes. These repeats can adopt multiple inter and intramolecular non-B-DNA conformations that may play an important role in biological processes. Two intramolecular structures of the telomeric oligonucleotide dAGGG(TTAGGG)3, antiparallel and parallel, have been solved by NMR and X-ray crystallography. In both structures, the telomeric sequence adopts an intramolecular quadruplex structure that is stabilized by G-4 quartets, but the ways in which the sequence folds into the quadruplex are different. The folds of the human telomeric DNA were described as an anti-parallel basket-type and a parallel propeller-type. We applied 125I-radioprobing to determine the conformation of the telomeric quadruplex in solution, in the presence of either Na+ or K+ ions. The probability of DNA breaks caused by decay of 125I is inversely related to the distance between the radionuclide and the sugar unit of the DNA backbone; hence, the conformation of the DNA backbone can be deduced from the distribution of breaks. The probability of breaks measured in the presence of Na+ and K+ were compared with the distances in basket-type and propeller-type quadruplexes obtained from the NMR and crystal structures. Our radioprobing data demonstrate that the antiparallel conformation was present in solution in the presence of both K+ and Na+. The preferable conformation in the Na+-containing solution was the basket-type antiparallel quadruplex whereas the presence of K+ favored the chair-type antiparallel quadruplex. Thus, we believe that the two antiparallel and the parallel conformations may coexist in solution, and that their relative proportion is determined by the type and concentration of ions. PMID:15475390

  2. 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.

  3. 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.

  4. Some Brief Notes on Theoretical and Experimental Investigations of Intramolecular Hydrogen Bonding.

    PubMed

    Sobczyk, Lucjan; Chudoba, Dorota; Tolstoy, Peter M; Filarowski, Aleksander

    2016-12-02

    A review of selected literature data related to intramolecular hydrogen bonding in ortho-hydroxyaryl Schiff bases, ortho-hydroxyaryl ketones, ortho-hydroxyaryl amides, proton sponges and ortho-hydroxyaryl Mannich bases is presented. The paper reports on the application of experimental spectroscopic measurements (IR and NMR) and quantum-mechanical calculations for investigations of the proton transfer processes, the potential energy curves, tautomeric equilibrium, aromaticity etc. Finally, the equilibrium between the intra- and inter-molecular hydrogen bonds in amides is discussed.

  5. Synthesis of anionic phosphorus-containing heterocycles by intramolecular cyclizations involving N-functionalized phosphinecarboxamides.

    PubMed

    Robinson, Thomas P; Goicoechea, Jose M

    2015-04-07

    We report that the 2-phosphaethynolate anion (PCO(-)) reacts with propargylamines in the presence of a proton source to afford novel N-derivatized phosphinecarboxamides bearing alkyne functionalities. Deprotonation of these species gives rise to novel five- and six-membered anionic heterocycles resulting from intramolecular nucleophilic attack of the resulting phosphide at the alkyne functionality (via 5-exo-dig or 6-endo-dig cyclizations, respectively). The nature of the substituents on the phosphinecarboxamide can be used to influence the outcome of these reactions. This strategy represents a unique approach to phosphorus-containing heterocylic systems that are closely related to known organic molecules with interesting bio-active properties.

  6. 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.

  7. 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.

  8. 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.

  9. Preparation of various C-2 branched carbohydrates using intramolecular radical reactions.

    PubMed

    Choe, S W; Jung, M E

    2000-12-01

    A new and efficient method for the facile synthesis of C-2 branched carbohydrates has been developed using an intramolecular radical cyclization fragmentation reaction. The desired C-2 branched glucopyranosides were isolated in 40-84% yield. Additionally, an unexpected furanoside was obtained from a tributyltin iodide-promoted rearrangement of the radical intermediate. The C-2 formyl glycal was also isolated in good yield using tris(trimethylsilyl)silane (TTMSS) as the reducing agent. This method was extended to synthesize a beta C-2 branched glucopyranoside, a C-2 branched galactoside and a C-2 cyano glucopyranoside.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

    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 (H2) and deuterium (D2) 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 H2 between 100 and 200 K.

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

    PubMed

    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 (H2) and deuterium (D2) 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 H2 between 100 and 200 K.

  13. Construction of a Chiral Silicon Center by Rhodium-Catalyzed Enantioselective Intramolecular Hydrosilylation.

    PubMed

    Naganawa, Yuki; Namba, Tomoya; Kawagishi, Mayu; Nishiyama, Hisao

    2015-06-22

    Rhodium-catalyzed enantioselective desymmetrizing intramolecular hydrosilylation of symmetrically disubstituted hydrosilanes is described. The original axially chiral phenanthroline ligand (S)-BinThro (Binol-derived phenanthroline) was found to work as an effective chiral catalyst for this transformation. A chiral silicon stereogenic center is one of the chiral motifs gaining much attention in asymmetric syntheses and the present protocol provides cyclic five-membered organosilanes incorporating chiral silicon centers with high enantioselectivities (up to 91 % ee). The putative active Rh(I) catalyst takes the form of an N,N,O-tridentate coordination complex, as determined by several complementary experiments.

  14. 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.

  15. Imidazole-annulated tetrathiafulvalenes exhibiting pH-tuneable intramolecular charge transfer and redox properties.

    PubMed

    Wu, Jincai; Dupont, Nathalie; Liu, Shi-Xia; Neels, Antonia; Hauser, Andreas; Decurtins, Silvio

    2009-03-02

    In order to study the electronic interactions in donor-acceptor ensembles as a function of pH, an efficient synthetic route to three imidazole-annulated tetrathiafulvalene (TTF) derivatives 1-3 is reported. Their electronic absorption spectra, in view of photoinduced intramolecular charge transfer, and their electrochemical behavior were investigated, and pK(a) values for the two protonation processes on the acceptor unit were determined in organic solvents by photometric titration. The influence of the TTF moiety on these values is discussed.

  16. General form of intramolecular nuclear spin isomers mixing in C3v -symmetry

    NASA Astrophysics Data System (ADS)

    Il'ichov, L. V.

    2017-10-01

    Molecules with identical nuclei exist in nature in the form of nuclear spin isomers. In general, spin isomers are not the eigenstates of total molecular Hamiltonian. It also contains parts able to transform spin isomers one into another. Recently, nuclear spin isomers relaxation induced by such a quantum mixing was successfully demonstrated in experiment. That motivates the search for general intramolecular interactions able to mix spin isomers. In the work, the general forms of the possible mixing interactions are found for C3v-type of molecules using generalized Jordan-Schwinger approach to the theory of quantum angular momentum.

  17. Rhodium-catalyzed intramolecular hydroarylation of 1-halo-1-alkynes: regioselective synthesis of semihydrogenated aromatic heterocycles.

    PubMed

    Murase, Hirohiko; Senda, Kousuke; Senoo, Masato; Hata, Takeshi; Urabe, Hirokazu

    2014-01-03

    The regioselective intramolecular hydroarylation of (3-halo-2-propynyl)anilines, (3-halo-2-propynyl) aryl ethers, or (4-halo-3-butynyl) aryl ethers was efficiently catalyzed by Rh2(OCOCF3)4 to give semihydrogenated aromatic heterocycles, such as 4-halo-1,2-dihydroquinolines, 4-halo-3-chromenes, or 4-(halomethylene)chromans, in good to excellent yields. Some synthetic applications taking advantage of the halo-substituents of the products are also illustrated. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Palladium-Mediated Catalysis Leads to Intramolecular Narcissistic Self-Sorting on a Cavitand Platform.

    PubMed

    Nagymihály, Zoltán; Caturello, Naidel A M S; Takátsy, Anikó; Aragay, Gemma; Kollár, László; Albuquerque, Rodrigo Q; Csók, Zsolt

    2017-01-06

    Palladium-catalyzed aminocarbonylation reactions have been used to directly convert a tetraiodocavitand intermediate into the corresponding carboxamides and 2-ketocarboxamides. When complex mixtures of the amine reactants are employed in competition experiments using polar solvents, such as DMF, no "mixed" products possessing structurally different amide fragments are detected either by (1)H or (13)C NMR. Only highly symmetrical cavitands are sorted out of a large number of potentially feasible products, which represents a rare example of intramolecular, narcissistic self-sorting. Our experimental results along with thermodynamic energy analysis suggest that the observed self-sorting is a symmetry-driven, kinetically controlled process.

  19. 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.

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

    PubMed

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

    2016-07-01

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

  1. Concise total synthesis of albaflavenone utilizing sequential intramolecular aldol condensation: determination of absolute configuration.

    PubMed

    Kobayashi, Toyoharu; Kon, Yutaro; Abe, Hideki; Ito, Hisanaka

    2014-12-19

    The first total synthesis of albaflavenone, a novel antibiotic sesquiterpene, has been accomplished via the concise construction of its zizaene skeleton utilizing sequential intramolecular aldol condensation followed by chemo- and diastereoselective reduction of the conjugated carbon-carbon double bond. This synthetic work was completed in nine steps from 2-cyclopenten-1-one as a starting material without the use of protecting groups and with high stereocontrol. In addition, the absolute configuration of naturally occurring albaflavenone was determined to be 1R,2S and 8S.

  2. GTP binding to the ROC domain of DAP-kinase regulates its function through intramolecular signalling.

    PubMed

    Carlessi, Rodrigo; Levin-Salomon, Vered; Ciprut, Sara; Bialik, Shani; Berissi, Hanna; Albeck, Shira; Peleg, Yoav; Kimchi, Adi

    2011-09-01

    Death-associated protein kinase (DAPk) was recently suggested by sequence homology to be a member of the ROCO family of proteins. Here, we show that DAPk has a functional ROC (Ras of complex proteins) domain that mediates homo-oligomerization and GTP binding through a defined P-loop motif. Upon binding to GTP, the ROC domain negatively regulates the catalytic activity of DAPk and its cellular effects. Mechanistically, GTP binding enhances an inhibitory autophosphorylation at a distal site that suppresses kinase activity. This study presents a new mechanism of intramolecular signal transduction, by which GTP binding operates in cis to affect the catalytic activity of a distal domain in the protein.

  3. Syntheses of strychnine, norfluorocurarine, dehydrodesacetylretuline, and valparicine enabled by intramolecular cycloadditions of Zincke aldehydes.

    PubMed

    Martin, David B C; Nguyen, Lucas Q; Vanderwal, Christopher D

    2012-01-06

    A full account of the development of the base-mediated intramolecular Diels-Alder cycloadditions of tryptamine-derived Zincke aldehydes is described. This important complexity-generating transformation provides the tetracyclic core of many indole monoterpene alkaloids in only three steps from commercially available starting materials and played a key role in short syntheses of norfluorocurarine (five steps), dehydrodesacetylretuline (six steps), valparicine (seven steps), and strychnine (six steps). Reasonable mechanistic possibilities for this reaction, a surprisingly facile dimerization of the products, and an unexpected cycloreversion to regenerate Zincke aldehydes under specific conditions are also discussed.

  4. Time-dependent Hartree approaches for the study of intramolecular dynamics in dimer systems

    NASA Astrophysics Data System (ADS)

    Roy, Pierre-Nicholas; Light, John C.

    2000-06-01

    We apply and the time-dependent Hartree (TDH) method to the study of intramolecular dynamics in dimer systems. The HCl dimer is chosen as test case. Model calculations are performed on reduced dimensional representation of this system namely two-, three-, and four-dimensional ones. We assess the validity of different implementations of the TDH method including the account of direct correlations between coordinate pairs, and mixed quantum-classical and quantum-Gaussian wave packets treatments. The latter yields very good results compared to the fully quantal treatment.

  5. 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.

  6. Gold(I)-catalyzed intramolecular amination of allylic alcohols with alkylamines.

    PubMed

    Mukherjee, Paramita; Widenhoefer, Ross A

    2011-03-18

    A 1:1 mixture of (1)AuCl [1 = P(t-Bu)(2)o-biphenyl] and AgSbF(6) catalyzes the intramolecular amination of allylic alcohols with alkylamines to form substituted pyrrolidine and piperidine derivatives. Gold(I)-catalyzed cyclization of (R,Z)-8-(N-benzylamino)-3-octen-2-ol (96% ee, 95% de) led to isolation of (R,E)-1-benzyl-2-(1-propenyl)piperidine in 99% yield with 96% ee, consistent with the net syn addition of the amine relative to the departing hydroxyl group.

  7. 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.

  8. Conformations, energies, and intramolecular hydrogen bonds in dicarboxylic acids: implications for the design of synthetic dicarboxylic acid receptors.

    PubMed

    Nguyen, Thanh Ha; Hibbs, David E; Howard, Siân T

    2005-09-01

    The various conformers of the dicarboxylic acids HO2C--(CH2)n--CO2H, n = 1-4, were obtained using density functional methods (DFT), both in the gas phase and in the aqueous phase using a polarized continuum model (PCM). Several new conformers were identified, particularly for the two larger molecules glutaric (n = 3) and adipic acid (n =4). The PCM results show that the stability of most conformers were affected, many becoming unstable in the aqueous phase; and the energy ordering of conformers is also different. The results suggest that conformational preferences could be important in determining the design and stability of appropriate synthetic receptors for glutaric and adipic acid. Geometry changes between gas and aqueous phases were most marked in those conformers containing an intramolecular hydrogen bond. Additional calculations have probed the strength of intramolecular hydrogen bonds in these dicarboxylic acids. In the cases of glutaric and adipic acid, the strength of the intramolecular hydrogen bond were estimated to be around 28-29 kJ/mol, without any vibrational energy correction. The intramolecular hydrogen bond energies in malonic and succinic acid were also estimated from the calculated H-bond distances using an empirical relationship. Intramolecular H-bond redshifts of 170-250 cm(-1) have been estimated from the results of the harmonic frequency analyses.

  9. An excited-state intramolecular photon transfer fluorescence probe for localizable live cell imaging of cysteine

    NASA Astrophysics Data System (ADS)

    Liu, Wei; Chen, Wen; Liu, Si-Jia; Jiang, Jian-Hui

    2017-03-01

    Small molecule probes suitable for selective and specific fluorescence imaging of some important but low-concentration intracellular reactive sulfur species such as cysteine (Cys) pose a challenge in chemical biology. We present a readily available, fast-response fluorescence probe CHCQ-Ac, with 2-(5‧-chloro-2-hydroxyl-phenyl)-6-chloro-4(3 H)-quinazolinone (CHCQ) as the fluorophore and acrylate group as the functional moiety, that enables high-selectivity and high-sensitivity for detecting Cys in both solution and biological system. After specifically reacted with Cys, the probe undergoes a seven-membered intramolecular cyclization and released the fluorophore CHCQ with excited-state intramolecular photon transfer effect. A highly fluorescent, insoluble aggregate was then formed to facilitate high-sensitivity and high-resolution imaging. The results showed that probe CHCQ-Ac affords a remarkably large Stokes shift and can detect Cys under physiological pH condition with no interference from other analytes. Moreover, this probe was proved to have excellent chemical stability, low cytotoxicity and good cell permeability. Our design of this probe provides a novel potential tool to visualize and localize cysteine in bioimaging of live cells that would greatly help to explore various Cys-related physiological and pathological cellular processes in cell biology and diagnostics.

  10. 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.

  11. 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

  12. 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

    2016-01-11

    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.

  13. 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

  14. Intra-molecular triplet energy transfer is a general approach to improve organic fluorophore photostability.

    PubMed

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

    2016-02-01

    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.

  15. Visible absorbing croconium dyes with intramolecular hydrogen bonding: A combined experimental and computational study

    NASA Astrophysics Data System (ADS)

    Prabhakar, Ch.; Promila; Tripathi, Anuj; Bhanuprakash, K.; Jayathirtharao, V.

    2017-10-01

    Croconium molecules CR1-CR4 with break-in conjugation (Csbnd N Bonding) was synthesized by condensation of croconic acid and arylamines. By using combined experimental and theoretical methods like UV-visible spectra, DFT and TDDFT studies, we have characterized electronic absorption properties. The reported molecules are having absorption in visible region ranging from 450 to 550 nm with large extinction coefficient (2.5-5.0 × 104 M-1 cm-1). We find that CR2 and CR4 are showing 50 to 100 nm red shifted absorption than CR1 and CR3. This red shift is possibly due to presence of intramolecular hydrogen bonding in CR2 and CR4. Further this is supported by DFT studies, in case of CR2 and CR4 shows strong intramolecular hydrogen bonding between oxygen of carboxylate group (at ortho position of phenyl ring) and hydrogen of nitrogen attached to the central croconate ring. It is also observed that, there is small diradicaloid character in these molecules. This study is helpful in design and synthesis of new croconium dyes which are useful in materials applications.

  16. Structural and biochemical characterizations of an intramolecular tandem coiled coil protein.

    PubMed

    Shin, Donghyuk; Kim, Gwanho; Kim, Gyuhee; Zheng, Xu; Kim, Yang-Gyun; Lee, Sangho

    2014-12-12

    Coiled coil has served as an excellent model system for studying protein folding and developing protein-based biomaterials. Most designed coiled coils function as oligomers, namely intermolecular coiled coils. However, less is known about structural and biochemical behavior of intramolecular coiled coils where coiled coil domains are covalently linked in one polypeptide. Here we prepare a protein which harbors three coiled coil domains with two short linkers, termed intramolecular tandem coiled coil (ITCC) and characterize its structural and biochemical behavior in solution. ITCC consists of three coiled coil domains whose sequences are derived from Coil-Ser and its domain swapped dimer. Modifications include positioning E (Glu) residue at "e" and K (Lys) at "g" positions throughout heptad repeats to enhance ionic interaction among its constituent coiled coil domains. Molecular modeling of ITCC suggests a compact triple helical bundle structure with the second and the third coiled coil domains forming a canonical coiled coil. ITCC exists as a mixture of monomeric and dimeric species in solution. Small-angle X-ray scattering reveals ellipsoidal molecular envelopes for both dimeric and monomeric ITCC in solution. The theoretically modeled structures of ITCC dock well into the envelopes of both species. Higher ionic strength shifts the equilibrium into monomer with apparently more compact structure while secondary structure remains unchanged. Taken together, our results suggest that our designed ITCC is predominantly monomeric structure through the enhanced ionic interactions, and its conformation is affected by the concentration of ionic species in the buffer.

  17. Intramolecular clasp of the cellulosomal Ruminococcus flavefaciens ScaA dockerin module confers structural stability☆

    PubMed Central

    Slutzki, Michal; Jobby, Maroor K.; Chitayat, Seth; Karpol, Alon; Dassa, Bareket; Barak, Yoav; Lamed, Raphael; Smith, Steven P.; Bayer, Edward A.

    2013-01-01

    The cellulosome is a large extracellular multi-enzyme complex that facilitates the efficient hydrolysis and degradation of crystalline cellulosic substrates. During the course of our studies on the cellulosome of the rumen bacterium Ruminococcus flavefaciens, we focused on the critical ScaA dockerin (ScaADoc), the unique dockerin that incorporates the primary enzyme-integrating ScaA scaffoldin into the cohesin-bearing ScaB adaptor scaffoldin. In the absence of a high-resolution structure of the ScaADoc module, we generated a computational model, and, upon its analysis, we were surprised to discover a putative stacking interaction between an N-terminal Trp and a C-terminal Pro, which we termed intramolecular clasp. In order to verify the existence of such an interaction, these residues were mutated to alanine. Circular dichroism spectroscopy, intrinsic tryptophan and ANS fluorescence, and NMR spectroscopy indicated that mutation of these residues has a destabilizing effect on the functional integrity of the Ca2+-bound form of ScaADoc. Analysis of recently determined dockerin structures from other species revealed the presence of other well-defined intramolecular clasps, which consist of different types of interactions between selected residues at the dockerin termini. We propose that this thematic interaction may represent a major distinctive structural feature of the dockerin module. PMID:24251102

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

    DOE PAGES

    Fuemmeler, Eric G.; Sanders, Samuel N.; Pun, Andrew B.; ...

    2016-05-05

    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). But, the mechanism of iSF is unclear. Here, using multireference electronic structure calculations and transient absorption spectroscopy, we establish that iSF can occur viamore » a direct coupling mechanism that is independent of CT states. Moreover, 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.« less

  19. Reversible intramolecular triplet-triplet energy transfer in benzophenone-N-methylphthalimide dyad.

    PubMed

    Sakamoto, Masanori; Kim, Sung Sik; Fujitsuka, Mamoru; Majima, Tetsuro

    2008-02-21

    In the present paper, we synthesized a series of benzophenone (BP)-N-methylphthalimide (MePI) dyads (Cn, n = 3, 6, and 9, where n denotes the number of methylene in the linker) and investigated the photochemical properties and intramolecular triplet-triplet energy transfer from BP(T1) to MePI. Formation of two different intramolecular complexes was found, that is, a ground-state complex and a singlet exciplex. The formation of the triplet-equilibrium between MeBP and MePI was observed. The triplet-equilibrium constant (1.0 and 1.1 for C6 and C9, respectively) and forward ((3.8 +/- 1.3) x 107 and (3.9 +/- 1.2) x 107 s-1 for C6 and C9, respectively) and back ((3.8 +/- 1.3) x 107 and (3.6 +/- 1.2) x 107 s-1 for C6 and C9, respectively) energy transfer rates were estimated from the result of transient absorption measurements. From the van't Hoff plots, enthalpy and entropy change for the equilibrium formation were estimated.

  20. Probing intramolecular interactions in arylselenides using a property descriptor based approach.

    PubMed

    Roy, Dipankar; Patel, Chandan; Liebman, Joel F; Sunoj, Raghavan B

    2008-09-18

    Although a large volume of experimental evidence is available on the existence of intramolecular nonbonding interactions between chalcogen atoms in main group organometallic compounds, the primary focus has been on the contact distances involving the chalcogen atoms. The important class of intramolecular Se...X (where X is O, S, N) nonbonding interaction in a series of organoselenium compounds is quantified using a new scheme based on a molecular property descriptor. In the present study, we have employed the nucleus-independent chemical shift [NICS(0)] values, as a property descriptor to evaluate the strength of exocyclic nonbonding interactions in a series of aryl selenides. The ab initio MP2 as well as density functional theory methods have been used in conjunction with Dunning's cc-pVDZ basis set. The quantified values of Se...X nonbonding interactions are compared with other schemes based on thermochemical equations such as homodesmic and ortho-para methods. The changes in NICS(0) values at the aryl ring center are found to be sensitive to the strength of exocyclic Se...X interaction.

  1. 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

  2. Intramolecular Hydrogen Bonding Involving Organic Fluorine: NMR Investigations Corroborated by DFT-Based Theoretical Calculations.

    PubMed

    Mishra, Sandeep Kumar; Suryaprakash, N

    2017-03-07

    The combined utility of many one and two dimensional NMR methodologies and DFT-based theoretical calculations have been exploited to detect the intramolecular hydrogen bond (HB) in number of different organic fluorine-containing derivatives of molecules, viz. benzanilides, hydrazides, imides, benzamides, and diphenyloxamides. The existence of two and three centered hydrogen bonds has been convincingly established in the investigated molecules. The NMR spectral parameters, viz., coupling mediated through hydrogen bond, one-bond NH scalar couplings, physical parameter dependent variation of chemical shifts of NH protons have paved the way for understanding the presence of hydrogen bond involving organic fluorine in all the investigated molecules. The experimental NMR findings are further corroborated by DFT-based theoretical calculations including NCI, QTAIM, MD simulations and NBO analysis. The monitoring of H/D exchange with NMR spectroscopy established the effect of intramolecular HB and the influence of electronegativity of various substituents on the chemical kinetics in the number of organic building blocks. The utility of DQ-SQ technique in determining the information about HB in various fluorine substituted molecules has been convincingly established.

  3. Demonstration of intramolecular energy transfer in asymmetric bimetallic ruthenium(ii) complexes.

    PubMed

    Bar, Manoranjan; Maity, Dinesh; Das, Shyamal; Baitalik, Sujoy

    2016-11-01

    A new family of bimetallic Ru(ii) complexes derived from an asymmetric bridging ligand (tpy-Hbzim-dipy) consisting of both bipyridine and terpyridine chelating sites covalently connected via phenyl-imidazole spacer were designed in this work to demonstrate intramolecular energy transfer from one component to the other in asymmetric dyads. To fine tune the photo-redox properties, both bidentate and tridentate terminal ligands in the complexes were varied systematically. Both steady state and time-resolved luminescence spectral results indicated photo-induced intramolecular energy transfer from the excited MLCT state of the [(bpy/phen)2Ru(II)(dipy-Hbzim-tpy)] component to the MLCT state of the tpy-containing unit [(dipy-Hbzim-tpy)Ru(II)(tpy-PhCH3/H2pbbzim)] in dyads with rate constant values on the order of 10(6)-10(7) s(-1). Temperature-dependent luminescence studies indicated an enhancement in the luminescence intensity and excited state lifetimes upon decreasing the temperature.

  4. Understanding perovskite formation through the intramolecular exchange method in ambient conditions

    NASA Astrophysics Data System (ADS)

    Szostak, Rodrigo; Castro, Jhon A. P.; Marques, Adriano S.; Nogueira, Ana F.

    2017-04-01

    Among the methods to prepare hybrid organic-inorganic perovskite films, the intramolecular exchange method was the first one that made possible to prepare perovskite solar cells with efficiencies higher than 20%. However, perovskite formation by this method is not completely understood, especially in ambient conditions. In this work, perovskite films were prepared by the intramolecular exchange method in ambient conditions. The spin coating speed and the frequency of the MAI solution dripping onto PbI2(DMSO) were varied during the deposition steps. With the combination of these two parameters, a rigid control of the solvent drying was possible. Thus, depending on the chosen conditions, the intermediate MAPb3I8·2DMSO was formed with residual PbI2. Otherwise, direct formation of perovskite film was attained. A mechanism for the direct formation of bulk perovskite was proposed. We also investigated how the posterior thermal annealing affects the crystallinity and defects in perovskite films. With prolonged thermal annealing, the excess of MAI can be avoided, increasing the efficiency and decreasing the hysteresis of the solar cells. The best perovskite solar cell achieved a stabilized power output of 12.9%. The findings of this work pave the way for realizing the fabrication of efficient perovskite solar cells in ambient atmosphere, a very desirable condition for cost-efficient large scale manufacturing of this technology.

  5. Growth factor control of epidermal growth factor receptor kinase activity via an intramolecular mechanism.

    PubMed

    Koland, J G; Cerione, R A

    1988-02-15

    The mechanism by which the protein kinase activity of the epidermal growth factor (EGF) receptor is activated by binding of growth factor was investigated. Detergent-solubilized receptor in monomeric form was isolated by sucrose density gradient centrifugation and both its kinase and autophosphorylation activities monitored. In a low ionic strength medium and with MnCl2 as an activator, the activity of the monomeric receptor was EGF-independent. However, with 0.25 M ammonium sulfate present, the MnCl2-stimulated kinase activity was strikingly EGF-dependent. In contrast, the kinase activity expressed in the presence of MgCl2 showed growth factor control in the absence of added salt. Under the conditions of these experiments there was apparently little tendency for growth factor to induce aggregation of the receptor, indicating that the allosteric activation of the receptor kinase by EGF occurred via an intramolecular mechanism. Whereas detergent-solubilized receptor was the subject of these studies, the kinase activity of cell surface receptors might also be controlled by an intramolecular mechanism. These results indicate that an individual receptor molecule has the potential to function as a transmembrane signal transducer.

  6. Intramolecular hydrogen bond in 3-imino-propenylamine isomers: AIM and NBO studies

    NASA Astrophysics Data System (ADS)

    Raissi, H.; Jalbout, Abraham F.; Abbasi, B.; Fazli, F.; Farzad, F.; Nadim, E.; Leon, Aned De

    The molecular structure and intramolecular hydrogen bond energy of 18 conformers of 3-imino-propenyl-amine were investigated at MP2 and B3LYP levels of theory using the standard 6-311++G** basis set. The atom in molecules or AIM theory of Bader, which is based on the topological properties of the electron density (rho), was used additionally and the natural bond orbital (NBO) analysis was also carried out. Furthermore calculations for all possible conformations of 3-imino-propenyl-amin in water solution were also carried out at B3LYP/6-311++G** and MP2/6-311++G** levels of theory. The calculated geometrical parameters and conformational analyses in gas phase and water solution show that the imine-amine conformers of this compound are more stable than the other conformers. B3LYP method predicts the IMA-1 as global minimum. This stability is mainly due to the formation of a strong N bond H···N intramolecular hydrogen bond, which is assisted by pi-electrons resonance, and this pi-electrons are established by NH2 functional group. Hydrogen bond energies for all conformers of 3-imino-propenyl-amine were obtained from the related rotamers methods.

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

    PubMed Central

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

    1994-01-01

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

  8. 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

  9. 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

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

    PubMed

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

    2015-01-01

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

  11. Cohesin, condensin, and the intramolecular centromere loop together generate the mitotic chromatin spring.

    PubMed

    Stephens, Andrew D; Haase, Julian; Vicci, Leandra; Taylor, Russell M; Bloom, Kerry

    2011-06-27

    Sister chromatid cohesion provides the mechanistic basis, together with spindle microtubules, for generating tension between bioriented chromosomes in metaphase. Pericentric chromatin forms an intramolecular loop that protrudes bidirectionally from the sister chromatid axis. The centromere lies on the surface of the chromosome at the apex of each loop. The cohesin and condensin structural maintenance of chromosomes (SMC) protein complexes are concentrated within the pericentric chromatin, but whether they contribute to tension-generating mechanisms is not known. To understand how pericentric chromatin is packaged and resists tension, we map the position of cohesin (SMC3), condensin (SMC4), and pericentric LacO arrays within the spindle. Condensin lies proximal to the spindle axis and is responsible for axial compaction of pericentric chromatin. Cohesin is radially displaced from the spindle axis and confines pericentric chromatin. Pericentric cohesin and condensin contribute to spindle length regulation and dynamics in metaphase. Together with the intramolecular centromere loop, these SMC complexes constitute a molecular spring that balances spindle microtubule force in metaphase.

  12. Synthesis of triazafluoranthenones via silver(I)-mediated nonoxidative and oxidative intramolecular palladium-catalyzed cyclizations.

    PubMed

    Koutentis, Panayiotis A; Loizou, Georgia; Lo Re, Daniele

    2011-07-15

    Silver(I) fluoride (AgF)-mediated intramolecular nonoxidative and oxidative palladium-catalyzed cyclizations of 1,3-diphenyl- and 8-iodo-1,3-diphenylbenzo[e][1,2,4]triazin-7(1H)-ones 6a (R = H) and 7a (R = I) afford a new 'alkaloid like' ring system 2-phenyl-6H-[1,2,4]triazino[5,6,1-jk]carbazol-6-one 8a (triazafluoranthenone) in 86 and 100% yields, respectively. Furthermore, these cyclization protocols were used to prepare triazafluoranthenone analogues 8b-e bearing dialkylamino, methoxy, and phenylsulfanyl substituents at C-5, which were also independently synthesized from triazafluoranthenone 8a by regioselective nucleophilic addition. Similar AgF-mediated intramolecular nonoxidative and oxidative palladium-catalyzed cyclizations of 8,10-dihydro-1-iodo-10-phenylphenazin-2(7H)-ones 13 gave the new 'alkaloid like' ring system 8H-indolo[1,2,3-mn]phenazin-8-one 14 in 80 and 18% yields, respectively.

  13. 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

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

    PubMed

    Sprous, D; Harvey, S C

    1996-04-01

    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.

  15. The Tandem CARDs of NOD2: Intramolecular Interactions and Recognition of RIP2

    PubMed Central

    Fridh, Veronica; Rittinger, Katrin

    2012-01-01

    Caspase recruitment domains (CARDs) are homotypic protein interaction modules that link the stimulus-dependent assembly of large signaling platforms such as inflammasomes to the activation of downstream effectors that often include caspases and kinases and thereby play an important role in the regulation of inflammatory and apoptotic signaling pathways. NOD2 belongs to the NOD-like (NLR) family of intracellular pattern recognition receptors (PRR) and induces activation of the NF-κB pathway in response to the recognition of bacterial components. This process requires the specific recognition of the CARD of the protein kinase RIP2 by the tandem CARDs of NOD2. Here we demonstrate that the tandem CARDs of NOD2 are engaged in an intramolecular interaction that is important for the structural stability of this region. Using a combination of ITC and pull-down experiments we identify distinct surface areas that are involved in the intramolecular tandem CARD interaction and the interaction with the downstream effector RIP2. Our findings indicate that while CARDa of NOD2 might be the primary binding partner of RIP2 the two CARDs of NOD2 do not act independently of one another but may cooperate to from a binding surface that is distinct from that of single CARDs. PMID:22470564

  16. Intramolecular electron transport in quinoprotein alcohol dehydrogenase of Acetobacter methanolicus: a redox-titration study

    PubMed

    Frébortova; Matsushita; Arata; Adachi

    1998-01-27

    Quinohemoprotein-cytochrome c complex alcohol dehydrogenase (ADH) of acetic acid bacteria consists of three subunits, of which subunit I contains pyrroloquinoline quinone (PQQ) and heme c, and subunit II contains three heme c components. The PQQ and heme c components are believed to be involved in the intramolecular electron transfer from ethanol to ubiquinone. To study the intramolecular electron transfer in ADH of Acetobacter methanolicus, the redox potentials of heme c components were determined with ADH complex and the isolated subunits I and II of A. methanolicus, as well as hybrid ADH consisting of the subunit I/III complex of Gluconobacter suboxydans ADH and subunit II of A. methanolicus ADH. The redox potentials of hemes c in ADH complex were -130, 49, 188, and 188 mV at pH 7.0 and 24, 187, 190, and 255 mV at pH 4.5. In hybrid ADH, one of these heme c components was largely changed in the redox potential. Reduced ADH was fully oxidized with potassium ferricyanide, while ubiquinone oxidized the enzyme partially. The results indicate that electrons extracted from ethanol at PQQ site are transferred to ubiquinone via heme c in subunit I and two of the three hemes c in subunit II. Copyright 1998 Elsevier Science B.V.

  17. Intramolecular Halogen Atom Coordinated H Transfer via Ion-Neutral Complex in the Gas Phase Dissociation of Protonated Dichlorvos Derivatives

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaoping; Cheng, Shuai

    2017-10-01

    Intramolecular halogen atom coordinated H transfer reaction in the gas phase dissociation of protonated dichlorvos derivatives has been explored by electrospray ionization tandem mass spectrometry. Upon collisional activation, protonated dichlorvos underwent dissociation reaction via cleavage of the P-O bond to give reactive ion-neutral complex (INC) intermediate, [dimethoxylphosphinoylium + dichloroacetaldehyde]. Besides direct dissociation of the complex, intramolecular chlorine atom coordinated H transfer reaction within the complex takes place, leading to the formation of protonated dimethyl chlorophosphate. To investigate the fragmentation mechanism, deuterium-labeled experiments and several other halogen-substituted (Br and F) analogs of dichlorvos were prepared and evaluated, which display a similar intramolecular halogen transfer. Density functional theory (DFT)-based calculations were performed and the computational results also support the mechanism. [Figure not available: see fulltext.

  18. Intramolecular Halogen Atom Coordinated H Transfer via Ion-Neutral Complex in the Gas Phase Dissociation of Protonated Dichlorvos Derivatives

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaoping; Cheng, Shuai

    2017-07-01

    Intramolecular halogen atom coordinated H transfer reaction in the gas phase dissociation of protonated dichlorvos derivatives has been explored by electrospray ionization tandem mass spectrometry. Upon collisional activation, protonated dichlorvos underwent dissociation reaction via cleavage of the P-O bond to give reactive ion-neutral complex (INC) intermediate, [dimethoxylphosphinoylium + dichloroacetaldehyde]. Besides direct dissociation of the complex, intramolecular chlorine atom coordinated H transfer reaction within the complex takes place, leading to the formation of protonated dimethyl chlorophosphate. To investigate the fragmentation mechanism, deuterium-labeled experiments and several other halogen-substituted (Br and F) analogs of dichlorvos were prepared and evaluated, which display a similar intramolecular halogen transfer. Density functional theory (DFT)-based calculations were performed and the computational results also support the mechanism.

  19. 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

  20. Intramolecular vibrations in low-frequency normal modes of amino acids: L-alanine in the neat solid state.

    PubMed

    Zhang, Feng; Wang, Houng-Wei; Tominaga, Keisuke; Hayashi, Michitoshi

    2015-03-26

    This paper presents a theoretical analysis of the low-frequency phonons of L-alanine by using the solid-state density functional theory at the Γ point. We are particularly interested in the intramolecular vibrations accessing low-frequency phonons via harmonic coupling with intermolecular vibrations. A new mode-analysis method is introduced to quantify the vibrational characteristics of such intramolecular vibrations. We find that the torsional motions of COO(-) are involved in low-frequency phonons, although COO(-) is conventionally assumed to undergo localized torsion. We also find the broad distributions of intramolecular vibrations relevant to important functional groups of amino acids, e.g., the COO(-) and NH3(+) torsions, in the low-frequency phonons. The latter finding is illustrated by the concept of frequency distribution of vibrations. These findings may lead to immediate implications in other amino acid systems.

  1. 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

  2. Intramolecular catalytic asymmetric carbon-hydrogen insertion reactions. Synthetic advantages in total synthesis in comparison with alternative approaches.

    PubMed

    Doyle, Michael P; Ratnikov, Maxim; Liu, Yu

    2011-06-07

    The synthetic potential of highly directional formal insertion of a carbene between carbon and hydrogen of a carbon-hydrogen bond has recently been developed for intramolecular reactions that lead to compounds of biological and medicinal interest. Stereoselective and regiocontrolled intramolecular processes from diazoacetate reactants, catalyzed by dirhodium(II) compounds with chiral carboxamidate ligands, provide efficient and selective access to compounds as diverse as enterolactone, baclofen, imperanene, xylolactone, and rolipram. A comparison of the C-H insertion methodology with alternative approaches is presented.

  3. Ruthenium-catalyzed intramolecular [2+2+2] cycloaddition and tandem cross-metathesis of triynes and enediynes.

    PubMed

    Yuan, Wei; Wei, Yin; Shi, Min

    2013-04-01

    [2+2+2] Cycloadditions can be applied to specifically build up derivatives of benzene and cyclohexadiene and, therefore, have attracted much attention. Herein, we present an intramolecular [2+2+2] cycloaddition of triynes catalyzed by the first-generation Grubbs ruthenium complex (Ru gen-1), which can efficiently afford benzene derivatives in good yields under mild conditions. Moreover, we also report on a novel tandem cross-metathesis transformation of intramolecular enediynes also catalyzed by Ru gen-1, which has not been observed previously in related reports. On the basis of deuterium labeling experiments, a possible reaction mechanism is presented.

  4. 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.

  5. Extraction, separation, and intramolecular carbon isotope characterization of athabasca oil sands acids in environmental samples.

    PubMed

    Ahad, Jason M E; Pakdel, Hooshang; Savard, Martine M; Simard, Marie-Christine; Smirnoff, Anna

    2012-12-04

    Here we report a novel approach to extract, isolate, and characterize high molecular weight organic acids found in the Athabasca oil sands region using preparative capillary gas chromatography (PCGC) followed by thermal conversion/elemental analysis-isotope ratio mass spectrometry (TC/EA-IRMS). A number of different "naphthenic acids" surrogate standards were analyzed as were samples from the bitumen-rich unprocessed McMurray Formation, oil sands process water, groundwater from monitoring wells, and surface water from the Athabasca River. The intramolecular carbon isotope signature generated by online pyrolysis (δ(13)C(pyr)) showed little variation (±0.6‰) within any given sample across a large range of mass fractions separated by PCGC. Oil sand, tailings ponds, and deep McMurray Formation groundwater were significantly heavier (up to ∼9‰) compared to surface water and shallow groundwater samples, demonstrating the potential use of this technique in source apportionment studies.

  6. Intramolecular hydrogen migration in alkylperoxy and hydroperoxyalkylperoxy radicals: accurate treatment of hindered rotors.

    PubMed

    Sharma, Sandeep; Raman, Sumathy; Green, William H

    2010-05-13

    We have calculated the thermochemistry and rate coefficients for stable molecules and reactions in the title reaction families using CBS-QB3 and B3LYP/CBSB7 methods. The accurate treatment of hindered rotors for molecules having multiple internal rotors with potentials that are not independent of each other can be problematic, and a simplified scheme is suggested to treat them. This is particularly important for hydroperoxyalkylperoxy radicals (HOOQOO). Two new thermochemical group values are suggested in this paper, and with these values, the group additivity method for calculation of enthalpy as implemented in reaction mechanism generator (RMG) gives good agreement with CBS-QB3 predictions. The barrier heights follow the Evans-Polanyi relationship for each type of intramolecular hydrogen migration reaction studied.

  7. Ultrafast Non-Förster Intramolecular Donor-Acceptor Excitation Energy Transfer.

    PubMed

    Athanasopoulos, Stavros; Alfonso Hernandez, Laura; Beljonne, David; Fernandez-Alberti, Sebastian; Tretiak, Sergei

    2017-04-06

    Ultrafast intramolecular electronic energy transfer in a conjugated donor-acceptor system is simulated using nonadiabatic excited-state molecular dynamics. After initial site-selective photoexcitation of the donor, transition density localization is monitored throughout the S2 → S1 internal conversion process, revealing an efficient unidirectional donor → acceptor energy-transfer process. Detailed analysis of the excited-state trajectories uncovers several salient features of the energy-transfer dynamics. While a weak temperature dependence is observed during the entire electronic energy relaxation, an ultrafast initially temperature-independent process allows the molecular system to approach the S2-S1 potential energy crossing seam within the first ten femtoseconds. Efficient energy transfer occurs in the absence of spectral overlap between the donor and acceptor units and is assisted by a transient delocalization phenomenon of the excited-state wave function acquiring Frenkel-exciton character at the moment of quantum transition.

  8. Solvent-dependent intramolecular charge transfer delocalization/localization in multibranched push-pull chromophores.

    PubMed

    Li, Yang; Zhou, Meng; Niu, Yingli; Guo, Qianjin; Xia, Andong

    2015-07-21

    The effect of the solvent polarity on excitation delocalization/localization in multibranched push-pull chromophores has been thoroughly explored by combining steady state absorption and fluorescence, as well as femtosecond transient spectral measurements. We found that the excited-state relaxations of the push-pull chromophores are highly dependent on both solvent polarity and the polar degree of the excited intramolecular charge transfer states. The symmetry of multibranched chromophores is preserved in less polar solvents, leading to excitation delocalization over all of the branches because of the negligible solvent reaction field. In contrast, symmetry is broken for multibranched chromophores in more polar solvents because of intense solvent reaction field, and the excitation is consequently localized on one of the dipolar molecular branches. The results provide a fundamental understanding of solvent-dependent excitation delocalization/localization properties of the multibranched chromophores for the potential applications in nonlinear optics and energy-harvesting applications.

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

    PubMed

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

    2014-05-22

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

  10. Electron diffraction analysis for the molecules with degenerate large amplitude motions: Intramolecular dynamics in arsenic pentafluoride

    NASA Astrophysics Data System (ADS)

    Kochikov, Igor V.; Kovtun, Dmitry M.; Tarasov, Yury I.

    2017-03-01

    There exists a noticeable disagreement in the difference of axial and equatorial bond lengths in D3h symmetry arsenic and phosphorus pentafluorides between the GED data and high level quantum chemical results. In order to resolve this disagreement, a new structural analysis of the original experiment of (Clippard & Bartell, Inorg. Chem., 9 (1970) 805-811) was undertaken on the basis of modern approach incorporating spectroscopic evidence and quantum chemical information and allowing for intramolecular large-amplitude motion. The results of the analysis prove the internal insufficiency of the experimental material in the description of the accurate positions of the peaks on the radial distribution function. Additional experimental investigation of pentahalide molecules, especially at high temperatures, is of interest.

  11. 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.

  12. 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

  13. Immunoglobulin V gene replacement is caused by the intramolecular DNA deletion mechanism.

    PubMed Central

    Usuda, S; Takemori, T; Matsuoka, M; Shirasawa, T; Yoshida, K; Mori, A; Ishizaka, K; Sakano, H

    1992-01-01

    Circular DNA resulting from V gene replacement was studied with an A-MuLV transformed cell line containing ablts. This cell line undergoes V gene replacement at elevated temperatures in the immunoglobulin (Ig) heavy chain (H) gene. Examination of circular DNA revealed that a heptamer-related sequence (TACTGTG) within the coding region of VDJ was joined to the recombination signal sequence (RSS) of a germline VH segment. This provides direct evidence for a intramolecular DNA deletion mechanism for V gene replacement. In the pre-B cell line as well as in in vivo lymphocytes, unusual circular DNAs were found which were structurally similar to the V gene replacement circles. They represented excision products of the deletion type recombination between one complete RSS and a heptamer-like sequence in the Ig H region. PMID:1311252

  14. 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

    2016-05-04

    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.

  15. Iridium-Catalyzed Intramolecular Asymmetric Allylic Dearomatization Reaction of Pyridines, Pyrazines, Quinolines, and Isoquinolines.

    PubMed

    Yang, Ze-Peng; Wu, Qing-Feng; Shao, Wen; You, Shu-Li

    2015-12-23

    The first Ir-catalyzed intramolecular asymmetric allylic dearomatization reaction of pyridines, pyrazines, quinolines, and isoquinolines has been developed. Enabled by in situ formed chiral Ir-catalyst, the dearomatized products were isolated in high levels of yield (up to 99% yield) and enantioselectivity (up to 99% ee). It is worth noting that the Me-THQphos ligand is much more efficient than other tested ligands for the dearomatization of pyrazines and certain quinolines. Mechanistic studies of the dearomatization reaction were carried out, and the results suggest the feasibility of an alternative process which features the formation of a quinolinium as the key intermediate. The mechanistic findings render this reaction a yet unknown type in the chemistry of Reissert-type reactions. In addition, the utility of this method was showcased by a large-scale reaction and formal synthesis of (+)-gephyrotoxin.

  16. Vibrational energy flow in highly excited molecules: Role of intramolecular vibrational redistribution

    SciTech Connect

    Nesbitt, D.J. |; Field, R.W.

    1996-08-01

    A pedagogical overview of intramolecular vibrational redistribution (IVR) phenomena in vibrationally excited molecules is presented. In the interest of focus and simplicity, the topics covered deal primarily with IVR in the ground electronic state, relying on examples from the literature to illustrate key points. The experimental topics discussed attempt to sample systematically three different energy regimes on the full potential surface corresponding to (i) `low`, e.g., moderate- to high-resolution vibrational spectroscopies, (ii) `intermediate`, e.g., stimulated emission pumping and high overtone spectroscopies, and (iii) `high`, e.g., photofragment/predissociation dynamical spectroscopies. The interplay between experiment and theory is highlighted here because it has facilitated enormous advances in the field over the past decade. 183 refs., 13 figs., 2 tabs.

  17. Catalysis effect of micro-hydration on the intramolecular proton transfer in cytosine

    NASA Astrophysics Data System (ADS)

    Valadbeigi, Younes; Soleiman-Beigi, Mohammad; Sahraei, Reza

    2015-06-01

    Structural and thermodynamic properties of nine isomers of cytosine were studied in gas and aqueous phases and in micro-hydrated environment employing B3LYP and MP2 methods. Also, isomerizations of cytosine were studied in gas phase and the activation energies (Ea) and Gibbs free energies (ΔG#) of the internal Osbnd H rotations and proton transfer processes were calculated. The calculated Osbnd H rotational barriers were smaller than 50 kJ/mol while the activation energies of intramolecular proton transfers were in the range of 110-190 kJ/mol. Effect of mono- and di-hydration of the cytosine isomers on the transition state structures and the energy barriers was investigated.

  18. Dual fluorescence and fast intramolecular charge transfer with 4-(diisopropylamino)benzonitrile in alkane solvents

    NASA Astrophysics Data System (ADS)

    Demeter, Attila; Druzhinin, Sergey; George, Mathew; Haselbach, Edwin; Roulin, Jean-Luc; Zachariasse, Klaas A.

    2000-06-01

    Dual fluorescence and fast intramolecular charge transfer (ICT) is observed with 4-(diisopropylamino)benzonitrile (DIABN) in alkane solvents. The rate constant ka for the reaction from the locally excited (LE) to the ICT state has a value of 3.4×10 11 s -1 in n-hexane at 25°C, with an activation energy Ea of 6 kJ mol -1. Efficient intersystem crossing with a yield of 0.94 takes place from the ICT state. With 4-(dimethylamino)benzonitrile, in contrast, dual fluorescence is not observed in alkanes. The charge transfer reaction of DIABN is mainly favoured by its small energy gap Δ E( S1, S2), in accordance with the PICT model for ICT in aminobenzonitriles.

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

    PubMed Central

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

    2002-01-01

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

  20. 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.

  1. Intramolecular SEAr of phosphorus derivatives: computational approach to the synthesis of π-extended heterocycles.

    PubMed

    Larrañaga, Olatz; Romero-Nieto, Carlos; de Cozar Ruano, Abel

    2017-09-18

    The reaction mechanism associated with the synthesis of phosphorus-based heteropolyaromatic architectures by intramolecular SEAr have been investigated by DFT calculations at the B3LYP-D3/6-311+G(D) level of theory. The purpose of this study is to provide essential information for the future development of improved polycyclic organophosphorus materials. To that end, we have studied the impact of the initial reactant and/or the intermediates' structure into the mechanistic features and energetic profiles of the phosphorus cyclization process. Moreover, we have analysed in detail the reactivity parameters within a conceptual DFT framework and extracted underlying reactivity trends. Thus, our findings provide important insights for a rational design of polycyclic phosphorus compounds. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Excited-state intramolecular proton-transfer (ESIPT)-inspired solid state emitters.

    PubMed

    Padalkar, Vikas S; Seki, Shu

    2016-01-07

    Solid state emitters based on excited state intramolecular proton transfer (ESIPT) have been attracting considerable interest since the past few years in the field of optoelectronic devices because of their desirable unique photophysical properties. The photophysical properties of the solid state ESIPT fluorophores determine their possible applicability in functional materials. Less fluorescence quantum efficiencies and short fluorescence lifetime in the solid state are the shortcomings of the existing ESIPT solid state emitters. Designing of ESIPT chromophores with high fluorescence quantum efficiencies and a long fluorescence lifetime in the solid state is a challenging issue because of the unclear mechanism of the solid state emitters in the excited state. Reported design strategies, detailed photophysical properties, and their applications will help in assisting researchers to overcome existing challenges in designing novel solid state ESIPT fluorophores for promising applications. This review highlights recently developed solid state ESIPT emitters with focus on molecular design strategies and their photophysical properties, reported in the last five years.

  3. The Unique Domain Forms a Fuzzy Intramolecular Complex in Src Family Kinases.

    PubMed

    Arbesú, Miguel; Maffei, Mariano; Cordeiro, Tiago N; Teixeira, João M C; Pérez, Yolanda; Bernadó, Pau; Roche, Serge; Pons, Miquel

    2017-03-16

    The N-terminal regulatory region of c-Src including the SH4, Unique, and SH3 domains adopts a compact, yet highly dynamic, structure that can be described as an intramolecular fuzzy complex. Most of the long-range interactions within the Unique domain are also observed in constructs lacking the structured SH3, indicating a considerable degree of preorganization of the disordered Unique domain. Here we report that members of the Src family of kinases (SFK) share well-conserved sequence features involving aromatic residues in their Unique domains. This observation contrasts with the supposed lack of sequence homology implied by the name of these domains and suggests that the other members of SFK also have a regulatory region involving their Unique domains. We argue that the Unique domain of each SFK is sensitive to specific input signals, encoded by each specific sequence, but the entire family shares a common mechanism for connecting the disordered and structured domains.

  4. 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.

  5. Detailed tuning of structure and intramolecular communication are dispensable for processive motion of myosin VI.

    PubMed

    Elting, Mary Williard; Bryant, Zev; Liao, Jung-Chi; Spudich, James A

    2011-01-19

    Dimeric myosin VI moves processively hand-over-hand along actin filaments. We have characterized the mechanism of this processive motion by measuring the impact of structural and chemical perturbations on single-molecule processivity. Processivity is maintained despite major alterations in lever arm structure, including replacement of light chain binding regions and elimination of the medial tail. We present kinetic models that can explain the ATP concentration-dependent processivities of myosin VI constructs containing either native or artificial lever arms. We conclude that detailed tuning of structure and intramolecular communication are dispensable for processive motion, and further show theoretically that one proposed type of nucleotide gating can be detrimental rather than beneficial for myosin processivity. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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

    PubMed Central

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

    2015-01-01

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

  7. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  9. Intramolecular triple helix as a model for regular polyribonucleotide (CAA)(n).

    PubMed

    Efimov, Alexander V; Spirin, Alexander S

    2009-10-09

    The regular (CAA)(n) polyribonucleotide, as well as the omega leader sequence containing (CAA)-rich core, have recently been shown to form cooperatively melted and compact structures. In this report, we propose a structural model for the (CAA)(n) sequence in which the polyribonucleotide chain is folded upon itself, so that it forms an intramolecular triple helix. The triple helix is stabilized by hydrogen bonding between bases thus forming coplanar triads, and by stacking interactions between the base triads. A distinctive feature of the proposed triple helix is that it does not contain the canonical double-helix elements. The difference from the known triple helices is that Watson-Crick hydrogen bond pairings do not take place in the interactions between the bases within the base triads.

  10. 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

  11. Intramolecular interactions in the triplet excited states of benzophenone-thymine dyads.

    PubMed

    Belmadoui, Noureddine; Encinas, Susana; Climent, Maria J; Gil, Salvador; Miranda, Miguel A

    2005-12-23

    Time-resolved and product studies on the synthesized dyads 1 and 2 have provided evidence that the benzophenone-to-thymine orientation strongly influences intramolecular photophysical and photochemical processes. The prevailing reaction mechanism has been established as a Paterno-Büchi cycloaddition to give oxetanes 3-6; however, the ability of benzophenone to achieve a formal hydrogen abstraction from the methyl group of thymidine has also been evidenced by the formation of photoproducts 7 and 8. These processes have been observed only in the case of the cisoid dyad 1. Adiabatic photochemical cycloreversion of the oxetane ring is achieved upon direct photolysis to give the starting dyad 1 in its excited triplet state. The photobiological implications of the above results are discussed with respect to benzophenone-photosensitized damage of thymidine.

  12. Photoinduced intramolecular electron transfer in a 2,7-diaminofluorene chromophore decorated with two benzophenone subunits.

    PubMed

    Jin, Ming; Malval, Jean-Pierre; Morlet-Savary, Fabrice; Chaumeil, Hélène; Defoin, Albert; Batat, Pinar; Jonusauskas, Gediminas

    2009-04-21

    An extensive photophysical analysis of a 2,7-bis-(N-4-methoxyphenyl-N-phenylamino)fluorene derivative covalently linked with two benzophenone moieties is presented. A systematic comparison with a model chromophore without benzophenone was performed. For both chromophores, the electronic properties of the ground states are completely equivalent indicating that benzophenone subunits do not exhibit any electronic interaction with the diaminofluorene core. However, at the singlet excited state, the presence of benzophenones induces the occurrence of additional non-radiative de-excitation pathways. Even the intersystem crossing rate is significantly increased with respect to that of the model one. A photoinduced intramolecular electron transfer (PIET) from diaminofluorene to benzophenone subunits is proposed as the most efficient quenching process. At low polar solvent, the emission of an exciplex confirms the PIET process and the occurrence of a partial charge separation between donor and acceptor parts.

  13. Intramolecular charge transfer in the excited state of 4-dimethylaminobenzaldehyde and 4-dimethylaminoacetophenone

    NASA Astrophysics Data System (ADS)

    Fujiwara, Takashige; Lee, Jae-Kwang; Zgierski, Marek Z.; Lim, Edward C.

    2009-10-01

    TDDFT calculations and time-resolved transient absorption (TA) studies of the low-lying excited states of 4-dimethylaminobenzaldehyde (4-DMABA) and 4-dimethylaminoacetophenone (4-DMAAP) have been carried out to probe the mechanism of photoinduced intramolecular charge transfer (ICT). In polar acetonitrile, where dual fluorescence appears, both 4-DMABA and 4-DMAAP exhibit a TA band at about 510 nm and 490 nm, which correspond to the absorption spectra of the twisted ICT (TICT) state, with spectral characteristics that correspond to the radical anion absorptions of benzaldehyde or acetophenone. The decay time of the TICT-state absorption corresponds to that of the ICT fluorescence, indicating that the fluorescent ICT state is the TICT states.

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

    SciTech Connect

    Peterson, J.D.

    1991-12-01

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

  15. P450-catalyzed intramolecular sp(3) C-H amination with arylsulfonyl azide substrates.

    PubMed

    Singh, Ritesh; Bordeaux, Melanie; Fasan, Rudi

    2014-01-06

    The direct amination of aliphatic C-H bonds represents a most valuable transformation in organic chemistry. While a number of transition metal-based catalysts have been developed and investigated for this purpose, the possibility to execute this transformation with biological catalysts has remained largely unexplored. Here, we report that cytochrome P450 enzymes can serve as efficient catalysts for mediating intramolecular benzylic C-H amination reactions in a variety of arylsulfonyl azide compouds. Under optimized conditions, the P450 catalysts were found to support up to 390 total turnovers leading to the formation of the desired sultam products with excellent regioselectivity. In addition, the chiral environment provided by the enzyme active site allowed for the reaction to proceed in a stereo- and enantioselective manner. The C-H amination activity, substrate profile, and enantio/stereoselectivity of these catalysts could be modulated by utilizing enzyme variants with engineered active sites.

  16. Intramolecular triplet energy transfer in anthracene-based platinum acetylide oligomers.

    PubMed

    Li, Yongjun; Köse, Muhammet E; Schanze, Kirk S

    2013-08-01

    Platinum acetylide oligomers that contain an anthracene moiety have been synthesized and subjected to photophysical characterization. Spectroscopic measurement and DFT calculations reveal that both the singlet and triplet energy levels of the anthracene segment are lower than those of the platinum acetylide segment. Thus, the platinum acetylide segment acts as a sensitizer to populate the triplet state of the anthrancene segment via intramolecular triplet-triplet energy transfer. The objective of this work is to understand the mechanisms of energy-transfer dynamics in these systems. Fluorescence quenching and the dominant triplet absorption that arises from the anthracene segment in the transient absorption spectrum of Pt4An give clear evidence that energy transfer adopts an indirect mechanism, which begins with singlet-triplet energy transfer from the anthracene segment to the platinum acetylide segment followed by triplet-triplet energy transfer to the anthracene segment.

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

    NASA Astrophysics Data System (ADS)

    Schacht, J.; Zugenmaier, P.; Buivydas, M.; Komitov, L.; Stebler, B.; Lagerwall, S. T.; Gouda, F.; Horii, F.

    2000-04-01

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

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

    PubMed

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

    2005-05-05

    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.

  19. 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.

  20. The role of intramolecular hydrogen bonds in nucleophilic addition reactions of ketenaminals

    NASA Astrophysics Data System (ADS)

    Isaev, A. N.

    2012-08-01

    Quantum-chemical calculations of the geometries and electronic structures of molecules of ketenaminals 3-(diaminomethylene)-2,4-pentanedione and dimethyl-2-(diaminomethylene)-malonate and calculations of the structures of intermediates in the reaction of the nucleophilic addition of the ketenaminals to the acetonitrile molecule are performed by B3LYP/6-31+G** method. Two possible scenarios of the process are shown, depending on the mutual orientation of reacting molecules. The nucleophilic addition proceeds in two stages. It is found that the rate-limiting stage of the process is the transfer of the proton of the intramolecular hydrogen bond in a ketenaminal molecule. The experimentally observed faster reaction of pyrimidine formation for the 3-(diaminomethylene)-2,4-pentanedione molecule relative to that for dimethyl-2-(diaminomethylene)-malonate is explained by the hydrogen bond being stronger and the barrier of proton transfer from the aminogroup to the ketogroup oxygen falling upon nucleophilic attack in the former molecule.

  1. 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.

  2. 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.

  3. Effect of Off-Diagonal Exciton-Phonon Coupling on Intramolecular Singlet Fission.

    PubMed

    Huang, Zhongkai; Fujihashi, Yuta; Zhao, Yang

    2017-07-20

    Intramolecular singlet fission (iSF) materials provide remarkable advantages in terms of tunable electronic structures, and quantum chemistry studies have indicated strong electronic coupling modulation by high frequency phonon modes. In this work, we formulate a microscopic model of iSF with simultaneous diagonal and off-diagonal coupling to high-frequency modes. A nonperturbative treatment, the Dirac-Frenkel time-dependent variational approach is adopted using the multiple Davydov trial states. It is shown that both diagonal and off-diagonal coupling can aid efficient singlet fission if excitonic coupling is weak, and fission is only facilitated by diagonal coupling if excitonic coupling is strong. In the presence of off-diagonal coupling, it is found that high frequency modes create additional fission channels for rapid iSF. Results presented here may help provide guiding principles for design of efficient singlet fission materials by directly tuning singlet-triplet interstate coupling.

  4. Intramolecular C-N bond activation and ring-expansion reactions of N-heterocyclic carbenes.

    PubMed

    Hemberger, Patrick; Bodi, Andras; Berthel, Johannes H J; Radius, Udo

    2015-01-19

    Intramolecular ring-expansion reactions (RER) of the N-heterocyclic carbene 1,3-dimethylimidazolin-2-ylidene were observed upon vacuum ultraviolet (VUV) photoexcitation. Similarly to RERs reported in the solvent phase, for the reaction of NHCs with main-group-element hydrides, hydrogen transfer to the NHC carbon atom is the crucial initial step. In an ionization-mediated protonation, 1,3-dimethylimidazolin-2-ylidene forms an imidazolium ion, which is the rate-limiting step on the pathway to two six-membered ring products, namely, methylpyrimidinium and -pyrazinium ions. To unravel the reaction path, we have used imaging photoelectron photoion coincidence spectroscopy with VUV synchrotron radiation, as well as high-level composite method calculations. Similarities and differences between the mechanism in the gas phase and in the condensed phase are discussed.

  5. Rh-catalyzed isomerization and intramolecular redox reaction of alkynyl ethers affording dihydropyrans and ketoolefins.

    PubMed

    Shikanai, Daisuke; Murase, Hirohiko; Hata, Takeshi; Urabe, Hirokazu

    2009-03-11

    When arylmethyl 4-(sulfonyl)-3-butynyl ether and a catalytic amount of Rh(2)(tfa)(4) (tfa = CF(3)CO(2)-) were heated in toluene, 2-aryl-3-(sulfonyl)-5,6-dihydro-2H-pyran was produced in good yield. Ring closure proceeded in a highly regioselective manner, and no isomeric five-membered product was detected. Alternatively, 2-(5-sulfonyl-4-pentynyl)tetrahydrofuran lacking a benzyl substituent afforded a different product, 9-sulfonyl-1-hydroxy-8-nonen-4-one, upon reaction with the same rhodium catalyst at reflux in wet toluene. Both reactions most likely involve cleavage of the C-H bond alpha to ether in the substrate and subsequent intramolecular transfer of the hydrogen atom to sulfonylacetylene, which is supported by experiments using deuterium-labeled starting materials.

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

    NASA Astrophysics Data System (ADS)

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

    2010-06-01

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

  7. Gold(I)-Catalyzed Intramolecular Hydroamination of Unactivated Terminal and Internal Alkenes with 2-Pyridones.

    PubMed

    Timmerman, Jacob C; Laulhé, Sébastien; Widenhoefer, Ross A

    2017-03-17

    The cationic gold phosphine complex [(P1)Au(NCMe)](+)SbF6(-) [P1 = P(t-Bu)2o-biphenyl; 2] catalyzes the intramolecular hydroamination of 6-alkenyl-2-pyridones to form 1,6-carboannulated 2-pyridones in high yield. The hydroamination of 6-(γ-alkenyl)-2-pyridones was effective for monosubstituted and 1,1- and 1,2-disubstituted aliphatic alkenes, and the method was likewise effective for the hydroamination of 6-(δ-alkenyl)-2-pyridones. Spectroscopic analysis of mixtures of 6-(3-butenyl)-2-pyridone, (P1)AuCl, and AgSbF6 established the N-bound 2-hydroxypyridine complex [(P1)Au(NC6H3-2-OH-6-CH2CH2CH═CH2)](+) SbF6(-) as the catalyst resting state.

  8. 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

  9. Structural and functional studies of Streptococcus pneumoniae neuraminidase B: An intramolecular trans-sialidase.

    PubMed

    Gut, Heinz; King, Samantha J; Walsh, Martin A

    2008-10-15

    The human pathogen Streptococcus pneumoniae expresses neuraminidase proteins that cleave sialic acids from complex carbohydrates. The pneumococcus genome encodes up to three neuraminidase proteins that have been shown to be important virulence factors. Here, we report the first structure of a neuraminidase from S. pneumoniae: the crystal structure of NanB in complex with its reaction product 2,7-anhydro-Neu5Ac. Our structural data, together with biochemical analysis, establish NanB as an intramolecular trans-sialidase with strict specificity towards alpha2-3 linked sialic acid substrates. In addition, we show that NanB differs in its substrate specificity from the other pneumococcal neuraminidase NanA.

  10. Dehydrogenation induced inhibition of intramolecular charge transfer in substituted pyrazoline analogues.

    PubMed

    Kundu, Pronab; Banerjee, Dipanwita; Maiti, Gourhari; Chattopadhyay, Nitin

    2017-05-17

    The detailed photophysics of (E)-1,5-diphenyl-3-styryl-4,5-dihydro-1H-pyrazole (DSDP) and (E)-1,5-diphenyl-3-styryl-1H-pyrazole (DSP) has been investigated and compared to demonstrate the drastic modification of the photophysics upon dehydrogenation of the pyrazoline ring. While DSDP gives dual absorption and dual emission bands corresponding to the locally excited (LE) and the intramolecular charge transfer (ICT) species, DSP yields single absorption and emission bands for the locally excited species only. Comparative steady state and time resolved fluorometric studies reveal that aromatization of the pyrazoline ring inhibits the formation of the ICT species. Quantum chemical calculations corroborate and rationalize the inhibition of the ICT process upon aromatization through depiction of the differential electronic distributions in the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the two fluorophores.

  11. Effect of temperature, energy gap, and distortion of potential surfaces on photoinduced intramolecular electron transfer

    SciTech Connect

    Islampour, R.; Alden, R.G.; Wu, G.Y.C.; Lin, S.H. )

    1993-07-01

    We report the quantitative examination of the effect of distortion of potential energy surfaces and the temperature effect on photoinduced intramolecular electron transfer (PIET) as a function of electronic energy gap. The results demonstrate the importance of distorted oscillators in determining the dependence of the rate of PIET on the energy gap. This phenomenon may in some cases lead to misinterpretations of experimental data, when undistorted oscillators are assumed to be involved in the PIET process. The condition for observing the linear (rather than parabolic) dependence of the ET rate will be determined using the multimode model. The inclusion of multivibrational modes in the nuclear factors results in energy gap behavior, which is markedly different from the single mode case. Finally, a comparison between PIET and internal conversion is discussed. 25 refs., 5 figs., 3 tabs.

  12. Intramolecular Formal anti-Carbopalladation/Heck Reaction: Facile Domino Access to Carbo- and Heterooligocyclic Dienes.

    PubMed

    Pawliczek, Martin; Milde, Bastian; Jones, Peter G; Werz, Daniel B

    2015-08-24

    An intramolecular domino process consisting of a formal anti-carbopalladation followed by Heck reaction is realized. Complex oligo(hetero)cyclic scaffolds are efficiently obtained in one synthetic step from easily obtainable enyne precursors. In contrast to common syn-carbopalladation reactions of alkyne units, the carbopalladation employed here is designed to afford an anti-arrangement of the two new substituents across the emerging double bond. A prerequisite is that the residues next to the alkyne should lack any β-hydrogen atoms. The method paves the way to tri- and tetrasubstituted double-bond systems that have not been accessible by conventional Pd catalysis. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Differentiating subtle variation of weak intramolecular hydrogen bond in vicinal diols by linear infrared spectroscopy.

    PubMed

    Ma, Xiaoyan; Wang, Jianping

    2009-05-28

    Linear IR spectra show "free" and intramolecular hydrogen-bonded (IHB) -OH groups in vicinal diols as two separate O-H stretching absorption bands. Here we present a case study of four linear vicinal diols with different alkyl groups: 1,2-ethylene glycol, 1,2-propanediol, 2,3-butanediol, and 1,2-butanediol. By carefully removing contributions from anharmonic vibrational coupling and local structural effect, "pure" IHB-resulted frequency separation and peak enhancement are obtained and found to exhibit a linear relationship between them. The results suggest that the IHB formation energy in the diols is structurally dependent, and 1,2-propanediol has the smallest vibrational contribution to the IHB energy among the four diols examined.

  14. Experimental evaluation of the electron{endash}intramolecular-vibration coupling constants of tetramethyltetrathiafulvalene

    SciTech Connect

    Meneghetti, M.; Toffoletti, A.; Pasimeni, L.

    1996-12-01

    The relevant electron-intramolecular vibrations coupling constants of tetramethyltetrathiafulvalene (TMTTF) have been experimentally obtained. The determination was possible studying the optical properties of dimers of TMTTF{sup +} in polymethyl-methacrylate films on the basis of a Holstein-Hubbard dimer model. Electron paramagnetic resonance measurements of the singlet-triplet energy gap of the dimers made possible the calculation of the coupling constants without the need for absolute values of the optical spectra and the knowledge of structural parameters. The values of the coupling constants show differences with previously reported values for TMTTF or related molecules like TTF and bis-ethylenedithio-TTF (BEDT-TTF). {copyright} {ital 1996 The American Physical Society.}

  15. Synthesis, intramolecular migrations and enzymic hydrolysis of partially pivaloylated methyl alpha-D-mannopyranosides.

    PubMed

    Tomić, Srdanka; Petrović, Vesna; Matanović, Maja

    2003-03-14

    A series of methyl O-pivaloyl-alpha-D-mannopyranosides was synthesized using pivaloyl chloride in pyridine. The 3,6-di-O-pivaloyl derivative 6 undergoes intramolecular transesterification in neutral conditions (buffer, pH 7.2) to give its 2,6-di-O-pivaloyl analogue 5. The course of this migration was followed using 14C-labelled 6. As opposed to 6 compound 5 was shown to be a good substrate for esterases present in rabbit serum. Thus, regioselective enzymic hydrolysis led to the preferential cleavage of the 2-OPiv group to yield a mixture of 2- and 6-O-monopivalates in a ratio of 1:2.6.

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

    PubMed

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

    2014-11-07

    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.

  17. Insights from Bacterial Subtilases into the Mechanisms of Intramolecular Chaperone-Mediated Activation of Furin

    PubMed Central

    Shinde, Ujwal; Thomas, Gary

    2015-01-01

    Prokaryotic subtilisins and eukaryotic proprotein convertases (PCs) are two homologous protease subfamilies that belong to the larger ubiquitous super-family called subtilases. Members of the subtilase super-family are produced as zymogens wherein their propeptide domains function as dedicated intramolecular chaperones (IMCs) that facilitate correct folding and regulate precise activation of their cognate catalytic domains. The molecular and cellular determinants that modulate IMC-dependent folding and activation of PCs are poorly understood. In this chapter we review what we have learned from the folding and activation of prokaryotic subtilisin, discuss how this has molded our understanding of furin maturation, and foray into the concept of pH sensors, which may represent a paradigm that PCs (and possibly other IMC-dependent eukaryotic proteins) follow for regulating their biological functions using the pH gradient in the secretory pathway. PMID:21805238

  18. 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

    2013-12-02

    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.

  19. 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.

  20. Intramolecular Friedel-Crafts Acylation Reaction Promoted by 1,1,1,3,3,3-Hexafluoro-2-propanol.

    PubMed

    Motiwala, Hashim F; Vekariya, Rakesh H; Aubé, Jeffrey

    2015-11-06

    Simple dissolution of an arylalkyl acid chloride in 1,1,1,3,3,3-hexafluoro-2-propanol promotes an intramolecular Friedel-Crafts acylation without additional catalysts or reagents. This reaction is operationally trivial in both execution and product isolation (only requiring concentration followed by purification) and accommodates a broad range of substrates. Preliminary studies that bear upon potential reaction mechanisms are reported.

  1. 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.

  2. 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.

  3. FeCl3-Catalyzed Intramolecular Michael Reaction of Styrenes for the Synthesis of Highly Substituted Indenes.

    PubMed

    Dethe, Dattatraya H; Murhade, Ganesh M; Ghosh, Sourav

    2015-08-21

    An intramolecular FeCl3-catalyzed Michael addition reaction of styrene, a poor nucleophile, onto α,β-unsaturated ketones was developed for the synthesis of highly substituted indene derivatives. The method was further applied to the total synthesis of the sesquiterpene natural products (±)-jungianol and 1-epi-jungianol.

  4. Catalyst-free intramolecular oxidative cyclization of N-allylbenzamides: a new route to 2,5-substituted oxazoles.

    PubMed

    Zhou, Wei; Xie, Chen; Han, Jianlin; Pan, Yi

    2012-09-21

    A catalyst-free intramolecular oxidative cyclization reaction of N-allylbenzamides has been developed to prepare 2,5-disubstituted oxazoles with good yields. This reaction gives an efficient synthetic strategy to form an oxazole nucleus directly from easily accessible substrates under temperate conditions.

  5. Enantiospecific bromonium ion generation and intramolecular capture: a model system for asymmetric bromonium ion-induced polyene cyclisations.

    PubMed

    Braddock, D Christopher; Marklew, Jared S; Thomas, Alexander J F

    2011-08-28

    Scalemic bromonium ions generated enantiospecifically by the action of catalytic triflic acid on scalemic regioisomeric bromohydrin derivatives are trapped intramolecularly, enantiospecifically and regioselectively to give bicyclic brominated carbocycles in excellent yield and high enantiomeric excess. This enantiospecific pathway is not significantly perturbed by the addition of a trisubstituted alkene.

  6. Electronic and nuclear factors in intramolecular charge and excitation transfer processes. [Annual report], October 1992--September 1993

    SciTech Connect

    Piotrowiak, P.

    1993-12-31

    A qualitative discussion is given of initial work on the following topics: intramolecular triplet excitation transfer bands, donor-- bridge--acceptor systems with a tethered ion, and depolarization of transient microwave conductivity. A number of special compounds were synthesized, such as spiranes, 2,6-diamino-dihydroanthracene precursor, and para-amino-nitro-biphenyl and -terphenyl.

  7. Highly activated Michael acceptor by an intramolecular hydrogen bond as a fluorescence turn-on probe for cyanide.

    PubMed

    Park, Seokan; Kim, Hae-Jo

    2010-12-28

    An activated Michael acceptor type of probe by an intramolecular hydrogen bond has shown a selective fluorescence turn-on response to cyanide through a conjugated addition of the nucleophilic anion to the enone probe with a 1300-fold increase in its fluorescence intensity.

  8. Intramolecular catalytic Friedel-Crafts reactions with allenyl cations for the synthesis of quinolines and their analogues.

    PubMed

    Ishikawa, Teruhiko; Manabe, Shinobu; Aikawa, Toshiaki; Kudo, Takayuki; Saito, Seiki

    2004-07-08

    [reaction: see text] This paper describes a novel method to synthesize a quinoline backbone by incorporating allenyl cations into a catalytic intramolecular Friedel-Crafts reaction. The initial products were isomerized and aromatized upon treatment with acid and base, respectively, to give quinolines. The basic concept also proved to be promising for 1-benzazepine, 1-benzazocine, or isoquinoline synthesis.

  9. 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

  10. Ruthenium-catalyzed intramolecular selective halogenation of O-methylbenzohydroximoyl halides: a new route to halogenated aromatic nitriles.

    PubMed

    Chinnagolla, Ravi Kiran; Pimparkar, Sandeep; Jeganmohan, Masilamani

    2013-04-18

    The intramolecular halogenation of O-methylbenzohydroximoyl halides in the presence of a Ru catalyst and the ligand diphenylacetylene afforded halo substituted aromatic nitriles in a highly regioselective manner. Further, substituted nitriles were converted into substituted tetrazole derivatives in the presence of NaN3 and I2.

  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. Intramolecular Paternò-Büchi reaction of atropisomeric α-oxoamides in solution and in the solid-state.

    PubMed

    Raghunathan, Ramya; Kumarasamy, Elango; Iyer, Akila; Ugrinov, Angel; Sivaguru, J

    2013-10-07

    Atropisomeric α-oxoamides were synthesized and employed for intramolecular Paternò-Büchi reaction leading to very high enantio- and diastereoselectivity in the bicyclic oxetane photoproduct. A reversal of product selectivity was observed in solution and in the solid-state.

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

    SciTech Connect

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

    2009-07-21

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

  14. Analytical method for simultaneous determination of bulk and intramolecular (13) C-isotope compositions of acetic acid.

    PubMed

    Nimmanwudipong, Tarin; Gilbert, Alexis; Yamada, Keita; Yoshida, Naohiro

    2015-12-30

    Headspace solid-phase microextraction (HS-SPME) combined with gas chromatography/pyrolysis-gas chromatography/combustion-isotope ratio mass spectrometry (GC/Py-GC/C-IRMS) was developed for the simultaneous determination of the intramolecular and molecular carbon-isotopic composition (δ(13) C value) of acetic acid. The δ(13) C values of carboxyl and methyl carbon were standardized using calibration curves constructed from the regression between the measured δ(13) C values and the δ(13) C values of working standards determined in a previous study. We applied this developed HS-SPME-GC/Py-GC/C-IRMS technique to commercial vinegars. In one injection analysis, the bulk and intramolecular δ(13) C values of pure acetic acid standards can be obtained. The repeatability (1σ) of the bulk δ(13) C values is within ±0.4‰, and that of the δ(13) Ccarboxyl and δ(13) Cmethyl values is within ±0.6‰. The intramolecular δ(13) C values of acetic acid in vinegars exhibit a similar pattern. The average Δδ value (δ(13) CCOOH - δ(13) CCH3 ) is 4.3 ± 2.0‰. The approach presented herein for the molecular and intramolecular δ(13) C determination of acetic acid avoids switching between configuration systems and thereby reduces systematic errors. It is expected to be useful for examining isotope fractionation associated with processes related to organic acid (bio)transformations. Copyright © 2015 John Wiley & Sons, Ltd.

  15. 1H, 15N and 13C assignments of an intramolecular Lmo2-LIM2/Ldb1-LID complex.

    PubMed

    Wilkinson-White, Lorna E; Dastmalchi, Siavoush; Kwan, Ann H; Ryan, Daniel P; Mackay, Joel P; Matthews, Jacqueline M

    2010-10-01

    Lmo2 is a LIM-only protein involved in hematopoiesis and the development of T-cell acute lymphoblastic leukaemia. Here we report backbone and side chain NMR assignments for an engineered intramolecular complex of the C-terminal LIM domain from Lmo2 tethered to the LIM interaction domain (LID) from LIM domain binding protein 1 (Ldb1).

  16. 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.

  17. When an Intramolecular Disulfide Bridge Governs the Interaction of DUOX2 with Its Partner DUOXA2

    PubMed Central

    Carré, Aurore; Louzada, Ruy A.N.; Fortunato, Rodrigo S.; Ameziane-El-Hassani, Rabii; Morand, Stanislas; Ogryzko, Vasily; de Carvalho, Denise Pires; Grasberger, Helmut; Leto, Thomas L.

    2015-01-01

    Abstract Aims: The dual oxidase 2 (DUOX2) protein belongs to the NADPH oxidase (NOX) family. As H2O2 generator, it plays a key role in both thyroid hormone biosynthesis and innate immunity. DUOX2 forms with its maturation factor, DUOX activator 2 (DUOXA2), a stable complex at the cell surface that is crucial for the H2O2-generating activity, but the nature of their interaction is unknown. The contribution of some cysteine residues located in the N-terminal ectodomain of DUOX2 in a surface protein–protein interaction is suggested. We have investigated the involvement of different cysteine residues in the formation of covalent bonds that could be of critical importance for the function of the complex. Results: We report the identification and the characterization of an intramolecular disulfide bond between cys-124 of the N-terminal ectodomain and cys-1162 of an extracellular loop of DUOX2, which has important functional implications in both export and activity of DUOX2. This intramolecular bridge provides structural support for the formation of interdisulfide bridges between the N-terminal domain of DUOX2 and the two extracellular loops of its partner, DUOXA2. Innovation: Both stability and function of the maturation factor, DUOXA2, are dependent on the oxidative folding of DUOX2, indicating that DUOX2 displays a chaperone-like function with respect to its partner. Conclusions: The oxidative folding of DUOX2 that takes place in the endoplasmic reticulum (ER) appears to be a key event in the trafficking of the DUOX2/DUOXA2 complex as it promotes an appropriate conformation of the N-terminal region, which is propitious to subsequent covalent interactions with the maturation factor, DUOXA2. Antioxid. Redox Signal. 23, 724–733. PMID:25761904

  18. Intermolecular and intramolecular quencher based quantum dot nanoprobes for multiplexed detection of endonuclease activity and inhibition.

    PubMed

    Huang, Yong; Zhao, Shulin; Shi, Ming; Chen, Jia; Chen, Zhen-Feng; Liang, Hong

    2011-12-01

    DNA cleavage by endonucleases plays an important role in many biological events such as DNA replication, recombination, and repair and is used as a powerful tool in medicinal chemistry. However, conventional methods for assaying endonuclease activity and inhibition by gel electrophoresis and chromatography techniques are time-consuming, laborious, not sensitive, or costly. Herein, we combine the high specificity of DNA cleavage reactions with the benefits of quantum dots (QDs) and ultrahigh quenching abilities of inter- and intramolecular quenchers to develop highly sensitive and specific nanoprobes for multiplexed detection of endonucleases. The nanoprobe was prepared by conjugating two sets of DNA substrates carrying quenchers onto the surface of aminated QDs through direct assembly and DNA hybridization. With this new design, the background fluorescence was significantly suppressed by introducing inter- and intramolecular quenchers. When these nanoprobes are exposed to the targeted endonucleases, specific DNA cleavages occur and pieces of DNA fragments are released from the QD surface along with the quenchers, resulting in fluorescence recovery. The endonuclease activity was quantified by monitoring the change in the fluorescence intensity. The detection was accomplished with a single excitation light. Multiplexed detection was demonstrated by simultaneously assaying EcoRI and BamHI (as model analytes) using two different emissions of QDs. The limits of detection were 4.0 × 10(-4) U/mL for EcoRI and 8.0 × 10(-4) U/mL for BamHI, which were at least 100 times more sensitive than traditional gel electrophoresis and chromatography assays. Moreover, the potential application of the proposed method for screening endonuclease inhibitors has also been demonstrated. The assay protocol presented here proved to be simple, sensitive, effective, and easy to carry out.

  19. Strong intramolecular calcium-π interactions with aryl substituents--requirements and limitations.

    PubMed

    Loh, Claas; Seupel, Susanne; Koch, Alexander; Görls, Helmar; Krieck, Sven; Westerhausen, Matthias

    2014-10-14

    The amidines Dipp-N=C(tBu)-N(H)-Qu (1a) (Dipp = 2,6-diisopropylphenyl, Qu = 8-quinolyl) and Dipp-N=C(tBu)-N(H)-Py (1b) (Py = 2-pyridyl) are deprotonated with KN(SiMe3)2, yielding potassium N-(2,6-diisopropylphenyl)-N'-(8-quinolyl)pivalamidinate (2a) and potassium N-(2,6-diisopropylphenyl)-N'-(2-pyridyl)pivalamidinate (2b). Metalation of 1a with [(thf)2Ca{N(SiMe3)2}2] in tetrahydrofuran (thf) leads to the formation of ether-free calcium bis[N-(2,6-diisopropylphenyl)-N'-(8-quinolyl)pivalamidinate] (3a) with a strong intramolecular calcium-π interaction with one Dipp group. Furthermore, agostic bonds to one tert-butyl substituent complete the coordination sphere of the metal center and stabilize this bonding situation. The metathesis reaction of 2b with [(thf)4CaI2] yields the thf adduct of calcium bis[N-(2,6-diisopropylphenyl)-N'-(2-pyridyl)pivalamidinate] (3b). In addition to the bonds between calcium and the hard Lewis bases (oxygen of thf, nitrogen atoms of the pyridylamido moieties), anagostic Ca-H bonds to the tert-butyl substituents complete the coordination sphere. The intramolecular calcium-π interaction with an aryl group as observed in 3a requires steric shielding of the alkaline earth metal center, safely excluding the formation of a complex with more than one thf ligand.

  20. Metal-support effects on intramolecular selectivity during acetophenone hydrogenation over Pt catalysts

    SciTech Connect

    Lin, S.D.; Sanders, D.K.; Vannice, M.A. )

    1994-05-01

    The choice of support to disperse a metal can have a significant effect in certain reactions, and one of the best examples of metal-support interactions (MSI) is the hydrogenation of C[double bond]O bonds over noble metals such as Pt. It was first shown that the turnover frequency (TOF) for CH[sub 4] formation on Pt from CO and H[sub 2] could be increased by two orders of magnitude using TiO[sub 2] as a support. This reaction is structure insensitive and the TOF is independent of crystallite size. The explanation the authors have preferred for this behavior is the creation of special sites at the metal-support interface which interact with the oxygen end of the molecule to enhance the reactivity of the C[double bond]O bond towards hydrogen. As further support of this concept, the hydrogenation of acetone to isopropanol also showed marked enhancements in TOF (ca. 500-fold) over Pt/TiO[sub 2] catalysts, and the intramolecular selectivity during crotonaldehyde hydrogenation was altered by favoring hydrogenation of the carbonyl bond compared to the C[double bond]C double bond to increase the crotyl alcohol/butyraldehyde product ratio. The next step in examining the influence of MSI on intramolecular selectivity was a comparison of the rates of hydrogenation of a carbonyl bond vs an aromatic ring, and acetophenone (C[sub 6]H[sub 5]COCH[sub 3]) represents one of the simplest molecules containing these two types of bond systems which also has a high enough vapor pressure to allow a vapor-phase reaction to be utilized. These results are reported here. 34 refs., 1 fig., 2 tabs.

  1. Spectral investigation of the intramolecular charge-transfer in some aminotriazole Schiff bases

    NASA Astrophysics Data System (ADS)

    Issa, Y. M.; Hassib, H. B.; Abdelaal, H. E.; Kenawi, I. M.

    2011-09-01

    3-Amino-1,2,4-triazole Schiff bases were reported to contain intramolecular charge-transfer. The enhancing and depressing effects were remarkable as the substituent was changed from electron-donating to electron-withdrawing groups. The path of the resonating delocalization was reversed in the case of the p-NO 2 group. To validate these results we effectively used Weinhold et al's natural bond orbital analysis to assess the UV and FT-IR spectrophotometric monitoring of the change reflected in this phenomenon when the substituent in the benzene ring is altered. The NBO analysis was simulated by ab inito computations at the HF/6-31G(d) level of theory, in order to properly detect any possible presence of a hydrogen bond association. The changes occurring in electron occupancies of double-centered bonds, antibonding orbitals and in lone-pair orbitals appraised the results, as did the s and p character listings of the two-centered bonds and the simultaneous changes occurring in the geometric parameters of the molecules in question. Contrary to its normal preference, in these molecules the nitrogen used sp 2 hybrid orbitals for its interaction, housing its electron lone-pair in the third p hybrid orbital. Furthermore, NBO analysis reflected the presence of a very soft intramolecular hydrogen association (C-H⋯π), labelled by UV and FT-IR assignments, between the benzene and triazole rings in all Schiff bases but p-N(Me) 2. The n-π* stabilization energy decreased in the order: p-OH > p-OCH 3 > p-Cl > p-CH 3 > H > p-NO 2 > o-OH. The relation between the band position and Hammett substitution constant is interpreted in relation to the molecular structure.

  2. Spectral investigation of the intramolecular charge-transfer in some aminotriazole Schiff bases.

    PubMed

    Issa, Y M; Hassib, H B; Abdelaal, H E; Kenawi, I M

    2011-09-01

    3-Amino-1,2,4-triazole Schiff bases were reported to contain intramolecular charge-transfer. The enhancing and depressing effects were remarkable as the substituent was changed from electron-donating to electron-withdrawing groups. The path of the resonating delocalization was reversed in the case of the p-NO2 group. To validate these results we effectively used Weinhold et al's natural bond orbital analysis to assess the UV and FT-IR spectrophotometric monitoring of the change reflected in this phenomenon when the substituent in the benzene ring is altered. The NBO analysis was simulated by ab inito computations at the HF/6-31G(d) level of theory, in order to properly detect any possible presence of a hydrogen bond association. The changes occurring in electron occupancies of double-centered bonds, antibonding orbitals and in lone-pair orbitals appraised the results, as did the s and p character listings of the two-centered bonds and the simultaneous changes occurring in the geometric parameters of the molecules in question. Contrary to its normal preference, in these molecules the nitrogen used sp2 hybrid orbitals for its interaction, housing its electron lone-pair in the third p hybrid orbital. Furthermore, NBO analysis reflected the presence of a very soft intramolecular hydrogen association (C-H⋯π), labelled by UV and FT-IR assignments, between the benzene and triazole rings in all Schiff bases but p-N(Me)2. The n-π* stabilization energy decreased in the order: p-OH>p-OCH3>p-Cl>p-CH3>H>p-NO2>o-OH. The relation between the band position and Hammett substitution constant is interpreted in relation to the molecular structure. Copyright © 2011 Elsevier B.V. All rights reserved.

  3. Identification and characterization of intramolecular γ-halo interaction in d(0) complexes: a theoretical approach.

    PubMed

    Debnath, Tanay; Ash, Tamalika; Sarkar, Subhendu; Das, Abhijit K

    2017-07-01

    A mechanistic investigation to detect intramolecular M⋯X-C type interactions in d(0) neutral and cationic complexes was carried out through a benchmark study employing different density functional methods. As γ-halogen is involved in M⋯X-C type interactions, it is denoted as a γ-halo interaction and the respective conformers are designated as halo-conformers. By analyzing the geometrical parameters of halo-conformers, it was observed that, irrespective of the nature of the metal and the halogen, the Cγ-X bond distance increases compared to the usual C-X bond, which brings the M and X centers close enough to generate a weak interaction. Generation of the M⋯X-C interaction was confirmed by performing NBO, AIM and Wiberg bond index analyses, from which the persistence of γ-halo interaction was seen to be prominent. Moreover, for each neutral and cationic complex, the values of Wiberg bond order are in good agreement with the AIM results. The effect of the metal center, as well as γ-halogen substitution, on γ-halo interaction was also studied in the present work. To justify the practical subsistence of the halo-conformers, we checked the stability of the conformers with respect to their β-conformers by comparing the zero-point-corrected electronic energies. Therefore, the entire study was designed in such a way that it can provide evidence in support of intramolecular M⋯X-C interactions, where, instead of the C-H bond, the Cγ-X bond will interact with the central transition metal.

  4. Evidence for intramolecularly folded i-DNA structures in biologically relevant CCC-repeat sequences.

    PubMed Central

    Manzini, G; Yathindra, N; Xodo, L E

    1994-01-01

    The structural behaviour of repetitive cytosine DNA is examined in the oligodeoxynucleotide sequences of (CCCTAA)3CCCT (HTC4), GC(TCCC)3TCCT(TCCC)3 (KRC6) and the methylated (CCCT)3TCCT(CCCT)3C (KRM6) by circular dichroism (CD), gel electrophoresis (PAGE), and ultra violet (UV) absorbance studies. All the three sequences exhibit a pH-induced cooperative structural transition as monitored by CD. An intense positive CD band around 285 nm develops on lowering the pH from 8 to slightly acidic condition, indicative of the formation of base pairs between protonated cytosines. The oligomers are found to melt in a fully reversible and cooperative fashion, with a melting temperature (Tm) of around 50 degrees C at pH 5.5. The melting temperatures are independent from DNA concentration, indicative of an intramolecular process involved in the structural formation. PAGE experiments performed with 32P-labeled samples as well as with normal staining procedures show a predominantly single band migration for all the three oligomers suggestive of a unimolecular structure. From pH titrations the number of protons required for generating the structures formed by HTC4, KRC6 and KRM6 results to be around six. These findings strongly suggest that all the three sequences adopt an intramolecular i-motif structure. The demonstration of i-motif structure for KRC6, a critical functional stretch of the c-ki-ras promoter proto-oncogene, besides the human telomeric sequence HTC4, may be suggestive of larger significance in the functioning of DNA. Images PMID:7984411

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

    PubMed

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

    2015-04-21

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

  6. Oxidative turnover increases the rate constant and extent of intramolecular electron transfer in the multicopper enzymes, ascorbate oxidase and laccase.

    PubMed

    Tollin, G; Meyer, T E; Cusanovich, M A; Curir, P; Marchesini, A

    1993-12-07

    Using laser flash photolysis of lumiflavin/EDTA solutions containing ascorbate oxidase, we find that the rate constant for intramolecular electron transfer varies from one enzyme preparation to another and is generally a more sensitive measure of the state of the active site than are steady-state assays. Thus, type I copper is initially reduced in a second-order reaction followed by first-order reoxidation by the type II-III trinuclear copper center. The observed rate constant for this intramolecular process in presumably native enzyme is 160 s-1 at pH 7, whereas an enzyme preparation which had less than 20% activity had a rate constant of 2.6 s-1. Other samples of relatively active enzyme showed biphasic intramolecular kinetics intermediate between the above values. The inactive enzyme sample could be reactivated by dialysis against ascorbate or by treatment with ferricyanide, resulting in a corresponding increase in the intramolecular rate constant for type I copper reoxidation to a value comparable to that of native enzyme. Using this same methodology, we have determined that the type I copper in Japanese lacquer tree laccase is reoxidized by the type II-III trinuclear copper center in a first-order (intramolecular) process with rate constants of 1 s-1 at pH 7.0 and 4.9 s-1 at pH 6.0, values which are approximately two orders of magnitude smaller than for ascorbate oxidase. The intramolecular rate constant and enzyme activity for laccase also increased, but only by a factor of 2-6, when the enzyme was treated with ascorbate or ferricyanide, respectively. We further found that intramolecular electron transfer in laccase was completely inhibited by fluoride ion, in contrast to ascorbate oxidase which is unaffected by this ion. These differences in behavior for these two very similar enzymes are rather remarkable, when it is considered that the distance between copper atoms is constrained by the location of the protein-derived copper ligands in the three

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

    SciTech Connect

    Gonthier, Jérôme F.; Corminboeuf, Clémence

    2014-04-21

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

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

    PubMed

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

    2014-01-01

    The structures of hydrazinium dinitramide (HDN) in the gas phase and in aqueous solution have been studied at different levels of theory by using quantum chemistry. The intramolecular hydrogen-bond interactions in HDN were studied by employing the quantum theory of atoms in molecules (QTAIM), as well as those in ammonium dinitramide (ADN), hydrazinium nitroformate (HNF), and ammonium nitroformate (ANF) for comparison. The results showed that HDN possessed the strongest hydrogen bonds, with the largest hydrogen-bond energy (-47.95 kJ mol(-1)) and the largest total hydrogen-bond energy (-60.29 kJ mol(-1)). In addition, the charge transfer between the cation and the anion, the binding energy, the energy difference between the frontier orbitals, and the second-order perturbation energy of HDN were all the largest among the investigated compounds. These strongest intramolecular interactions accounted for the highest decomposition temperature of HDN among all four compounds. The IR spectra in the gas phase and in aqueous solution were very different and showed the significant influence of the solvent. The UV spectrum showed the strongest absorption at about 253 nm. An orbital-interaction diagram demonstrated that the transition of electrons mainly happened inside the anion of HDN. The detonation velocity (D=8.34 km s(-1)) and detonation pressure (P=30.18 GPa) of HDN were both higher than those of ADN (D=7.55 km s(-1) and P=24.83 GPa). The composite explosive HDN/CL-20 with the weight ratio wCL-20 /wHDN =0.388:0.612 showed the best performance (D=9.36 km s(-1) , P=39.82 GPa), which was close to that of CL-20 (D=9.73 km s(-1), P=45.19 GPa) and slightly better than that of the composite explosive ADN/CL-20 (wCL-20 /wADN =0.298:0.702, D=9.34 km s(-1), P=39.63 GPa). Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Interaction of molybdocene dichloride with cysteine-containing peptides: coordination, regioselective hydrolysis, and intramolecular aminolysis.

    PubMed

    Erxleben, Andrea

    2005-02-21

    Reactions of the organometallic compound molybdocene dichloride (Cp2MoCl2, Cp = eta5-cyclopentadienyl) with the cysteine-containing peptides L-cysteinylglycine (Cys-Gly), N-acetyl-L-cysteine (AcCys), glycyl-L-cysteine (Gly-Cys), glycyl-L-cysteinylglycine (Gly-Cys-Gly), and gamma-L-glutamyl-L-cysteinylglycine (glutathione, GSH) have been studied in aqueous solution in the pH range 2-9. The dipeptides Cys-Gly and Gly-Cys and the acetylated amino acid AcCys form 1:1 and 2:1 complexes of composition [Cp2Mo(peptide-S)(OH(2))]n+/- and [Cp2Mo(peptide-S)2]n+/- as well as the chelates [Cp2Mo(AcCys-S,O)], [Cp2Mo(Gly-Cys-S,O)]+, and [Cp2Mo(Cys-Gly-S,N)] with the Cp2Mo2+ unit binding to the deprotonated thiolate group and the free amino or carboxylate group of the cysteine residue. Upon treatment of Gly-Cys-Gly and the naturally occurring tripeptide GSH with Cp2MoCl2 at elevated temperature, release of free glycine was observed. The Cp2Mo2+ entity coordinates to the thiolate group of GSH and mediates regioselective hydrolysis of the Cys-Gly peptide bond by intramolecular metal hydroxide activation. Cp2Mo2+-promoted hydrolysis of GSH was followed at pD 7.4 and 5.2 and 40 and 60 degrees C. By contrast, the Cys-Gly bond in [Cp2Mo(Gly-Cys-Gly-S,N)] is cleaved by intramolecular aminolysis at pD > or = 7.4 and 60 degrees C leading to glycine and the Cp2Mo2+ complex of the 2,5-diketopiperazine derivative cyclo-(Gly-Cys). Chelating coordination of the Cp2Mo2+ moiety to the thiolate group and to the deprotonated amide nitrogen of the tripeptide changes the configuration of the peptide bond from (preferred) trans to cis, thus enabling nucleophilic attack of the primary amino group at the Cys-Gly bond. The reaction product [Cp2Mo{cyclo-(Gly-Cys)}] x 2H2O has been characterized by X-ray crystallography.

  10. Effect of nucleotides and actin on the intramolecular cross-linking of myosin subfragment-1.

    PubMed

    Blotnick, E; Muhlrad, A

    1994-06-07

    The heavy chain of myosin subfragment-1 (S1) is cleaved by limited trypsinolysis into three fragments, 27, 50, and 20 kDa--aligned in this order from the N-terminus. The tertiary structure of the molecule is essentially not affected by trypsinolysis. The spatial relations between the various regions of the molecule and the nucleotide- and actin-induced intramolecular movements were studied by cross-linking tryptic S1 with N-(ethoxycarbonyl)-2-ethoxy-1,2-dihydroquinoline (EEDQ), 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide (EDC), phenylenediglyoxal (PDG), and glutaraldehyde. The formation of cross-linked products was monitored by SDS-PAGE, using the fluorescent probes 9-anthronitrile and N-(iodoacetyl)-N'-(5-sulfo-1-naphthyl)ethylenediamine (IAEDANS), which specifically label the 27- and 20-kDa fragments, respectively. The reaction with the cross-linkers leads to the formation of 50-kDa/20-kDa, 27-kDa/20-kDa, 27-kDa/50-kDa, and 20-kDa/light chain cross-linked products. Of these, the most intensive was the formation of the 50-kDa/20-kDa products, which appeared as a doublet on the SDS-PAGE with all the cross-linkers. This indicates that the interface between the two fragments is rather extended. The presence of MgATP or MgADP promoted the formation of the 20-kDa/50-kDa cross-linked products, especially with the lower electrophoretic mobility band, when EEDQ was used as a cross-linker. With PDG as a cross-linker, MgATP also affected the cross-link formation between the 20-kDa fragment and the light chains whereas it had no influence on the formation of other products. On the other hand, the effect of actin on the cross-linking with the various cross-linkers was quite extensive, and it was manifested in the reduction of cross-link formation between the various S1 domains. It is concluded that both nucleotides and actin induce intramolecular movements in S1 and that the nucleotide-induced movements are more restricted than those induced by actin, which extend to larger

  11. Recent experimental advances on excited-state intramolecular proton coupled electron transfer reaction.

    PubMed

    Hsieh, Cheng-Chih; Jiang, Chang-Ming; Chou, Pi-Tai

    2010-10-19

    Proton-coupled electron transfer reactions form the basis of many important chemical processes including much of the energy conversion that occurs within living cells. However, much of the physical chemistry that underlies these reaction mechanisms remains poorly understood. In this Account, we report on recent progress in the understanding of excited-state intramolecular proton-coupled electron transfer (PCET) reactions. The strategic design and synthesis of various types of PCET molecules, along with steady-state and femtosecond time-resolved spectroscopy, have uncovered the mechanisms of several excited-state PCET reactions in solution. These experimental advancements correlate well with current theoretical models, in which the proton has quantum motion with a high probability of tunneling. In addition, the rate of proton transfer is commonly incorporated within the rate of rearrangement of solvent molecules. As a result, the reaction activation free energy is essentially governed by the solvent reorganization because the charge redistribution is considered based on a solvent polarity-induced barrier instead of the height of the proton migration barrier. In accord with this theoretical basis, we can rationalize the observation that the proton transfer for many excited-state PCET systems occurs during the solvent relaxation time scale of 1-10 ps: the highly exergonic reaction takes place before the system reaches its equilibrium polarization. Also, we have used various derivatives of proton transfer molecules, especially those of 3-hydroxyflavone to clearly demonstrate how researchers can tune the dynamics of excited-state PCET through changes in the magnitude or direction of the dipole vector within the reaction. Subsequently, using 2-(2'-hydroxyphenyl)benzoxazole as the parent model, we then report on methods for the development of an ideal system for probing PCET reaction. Because future biomedical applications of such systems will likely occur in aqueous

  12. 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

  13. 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

  14. Folding domains and intramolecular ionic interactions of lysine residues in glyceraldehyde 3-phosphate dehydrogenase.

    PubMed Central

    Lambert, J M; Perham, R N

    1977-01-01

    1. Treatment with methyl acetimidate was used to probe the topography of several tetrameric glyceraldehyde 3-phosphate dehydrogenases, in particular the holoenzymes from rabbit muscle and Bacillus stearothermophilus. During the course of the reaction with the rabbit muscle enzyme, the number of amino groups fell rapidly from the starting value of 27 per subunit to a value of approx. five per subunit. This number could be lowered further to values between one and two per subunit by a second treatment with methyl acetimidate. The enzyme remained tetrameric throughout and retained 50% of its initial catalytic activity at the end of the experiment. 2. Use of methyl [1-14C]acetimidate and small-scale methods of protein chemistry showed that only one amino group per subunit, that of lysine-306, was completely unavailable for reaction with imido ester in the native enzyme. This results is consistent with the structure of the highly homologous glyceraldehyde 3-phosphate dehydrogenase of lobster muscle deduced from X-ray-crystallographic analysis, since lysine-306 can be seen to form an intrachain ion-pair with aspartic acid-241 in the hydrophobic environment of a subunit-subunit interface. 3. Several other amino groups in the rabbit muscle enzyme that reacted only slowly with the reagent were also identified chemically. These were found to be located entirely in the C-terminal half of the polypeptides chain, which comprises a folding domain associated with catalytic activity and subunit contact in the three-dimensional structure. Slow reaction of these 'surface' amino groups with methyl acetimidate is attributed to intramolecular ionic interactions of the amino groups with neighbouring side-chain carboxyl groups, a conclusion that is compatible with the reported three-dimensional structure and with the dependence of the reaction of ionic stength. 4. Very similar results were obtained with the enzymes from B. stearothermophilus and from ox muscle and ox liver, supporting

  15. Revising Estimates of the Methane Production Pathway in Peatland Porewater Using Intramolecular Isotopic Analyses of Acetate

    NASA Astrophysics Data System (ADS)

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

    2007-12-01

    Stable isotopic measurements of methane and carbon dioxide are routinely applied to environmental samples to assess the relative importance of methane production by either aceticlastic or hydrogenotrophic methanogenesis. Such estimates rely upon assumptions about isotopic fractionation during methane production and oxidation. Rigorous isotope-based pathway estimates require knowledge of the carbon isotopic composition of both carbon dioxide and acetate. In practice, technical barriers have limited measurements of the isotopic composition of whole acetate in natural samples. Yet, the estimate of whole acetate isotopic values, even when available, may not represent accurately the composition of the methyl carbon, which is, in fact, the precursor to methane. It is exceedingly rare to find carbon isotopic measurements of acetate-methyl in the literature, and, to our knowledge, the d13C of the acetate-methyl precursor to methane has never before been reported from peatland porewater samples. Extremely 13C-depleted methane, -70 permil VPDB, and 13C-enriched carbon dioxide from acidic northern peat bogs are typically interpreted as signatures of hydrogenotrophic methanogenesis. The hypothesized dominance of methane production from hydrogen in acidic bogs contrasts with the vast majority of freshwater wetlands in which aceticlastic methanogenesis dominates. Using a new technique for the online analysis of the intramolecular carbon isotopic composition of acetate in natural samples, we find the acetate-methyl in peat porewaters can be significantly depleted relative to bulk organic matter. In porewater profiles from both winter and summer, acetate is as much as 15 permil depleted relative to bulk carbon. We hypothesize that acetate- methyl isotopic depletion results from conditions that favor autotrophic acetogenesis and subsequent acetate consumption by aceticlastic methanogens. Porewater depth profiles during winter and summer illustrate depth- dependent increases in the

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

    PubMed

    Foloppe, Nicolas; Chen, I-Jen

    2016-05-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  18. 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

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

    NASA Astrophysics Data System (ADS)

    Roohi, Hossein; Mohtamedifar, Nafiseh; Hejazi, Fahemeh

    2014-11-01

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

  20. 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.

  1. Tandem synthesis of pyrroloacridones via [3 + 2] alkyne annulation/ring-opening with concomitant intramolecular aldol condensation.

    PubMed

    Verma, Akhilesh K; Kotla, Siva K Reddy; Aggarwal, Trapti; Kumar, Sonu; Nimesh, Hemlata; Tiwari, Rakesh K

    2013-06-07

    An efficient cascade strategy for the direct synthesis of pyrrolo[3,2,1-de]acridones 4a-v, 5a-h from iodo-pyranoquinolines 2a-i by the palladium-catalyzed regioselective [3 + 2] alkyne annulation/ring-opening followed by intramolecular aldol condensation under microwave irradiation is described. The chemistry involves the in situ formation of pyrroloquinolines Y, via palladium-catalyzed selective [3 + 2] annulation of iodopyranoquinolines and internal akynes with ring-opening and successive intramolecular cross-aldol condensation. Both the symmetrical and unsymmetrical internal alkynes were reacted smoothly to provide the desired pyrroloacridones in good yields. This methodology provides the facile conversion of easily accessble iodopyranoquinoline into highly functionalized biologically important pyrroloacridones in a single process.

  2. Theoretical and experimental study on the intramolecular charge transfer excited state of the new highly fluorescent terpyridine compound

    NASA Astrophysics Data System (ADS)

    Song, Peng; Sun, Shi-Guo; Liu, Jian-Yong; Xu, Yong-Qian; Han, Ke-Li; Peng, Xiao-Jun

    2009-10-01

    Experimental and theoretical methods have been used to investigate the relaxation dynamics and photophysical properties of the donor-acceptor compound 4'-(4-N,N-diphenylaminophenyl)-2,2':6',2″-terpyridine (DPAPT), a compound which is found to exhibit efficient intramolecular charge transfer emission in polar solvents with relatively large Stokes shifts and strong solvatochromism. The difference between the ground and excited state dipole moments (Δ μ) is estimated to be 13.7 D on the basis of Lippert-Mataga models. To gain insight into the relaxation dynamics of DPAPT in the excited state, the potential energy curves for conformational relaxation are calculated. From the frontier molecular orbital (MO) pictures at the geometry of the twisted ICT excited state, the intramolecular charger transfer mainly takes place from HOMO (triphenylamine) to LUMO (terpyridine) in this donor-acceptor system.

  3. Complete σ* intramolecular aromatic hydroxylation mechanism through O2 activation by a Schiff base macrocyclic dicopper(I) complex.

    PubMed

    Poater, Albert; Solà, Miquel

    2013-01-01

    In this work we analyze the whole molecular mechanism for intramolecular aromatic hydroxylation through O2 activation by a Schiff hexaazamacrocyclic dicopper(I) complex, [Cu(I) 2(bsH2m)](2+). Assisted by DFT calculations, we unravel the reaction pathway for the overall intramolecular aromatic hydroxylation, i.e., from the initial O2 reaction with the dicopper(I) species to first form a Cu(I)Cu(II)-superoxo species, the subsequent reaction with the second Cu(I) center to form a μ-η(2):η(2)-peroxo-Cu(II) 2 intermediate, the concerted peroxide O-O bond cleavage and C-O bond formation, followed finally by a proton transfer to an alpha aromatic carbon that immediately yields the product [Cu(II) 2(bsH2m-O)(μ-OH)](2+).

  4. Intramolecular Nitrone Cycloaddition of α-(Trifluoromethyl)styrenes. Role of the CF3 Group in the Regioselectivity.

    PubMed

    Rabasa-Alcañiz, Fernando; Asensio, Amparo; Sánchez-Roselló, María; Escolano, Marcos; Del Pozo, Carlos; Fustero, Santos

    2017-03-03

    The intramolecular 1,3-dipolar cycloaddition of ortho-substituted 1,1,1-trifluoromethylstyrene-derived nitrones is described. Tricyclic fused isoxazolidines were obtained as major or exclusive products, in contrast to the case for nonfluorinated substrates, which rendered the bridged derivatives. This change in the regioselectivity was attributed to the electronic and, particularly, steric requirements of the trifluoromethyl group in comparison to the methyl group. It is worth mentioning that trifluoromethylstyrenes have been employed for the first time as dipolarophiles in a 1,3-dipolar intramolecular cycloaddition reaction, leading to the corresponding isoxazolidines bearing a quaternary trifluoromethyl moiety. Finally, the synthetic utility of the developed methodology has been illustrated with the synthesis of a family of bicyclic fluorinated 1,3-amino alcohols.

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  8. Theoretical study of the substituent effect on the intramolecular hydrogen bonds in di(4-hydroxycoumarin) derivatives

    NASA Astrophysics Data System (ADS)

    Mihaylov, Tzvetan; Georgieva, Ivelina; Bauer, Günther; Kostova, Irena; Manolov, Ilia; Trendafilova, Natasha

    Geometry optimization of ortho-, meta-, and para-pyridyl-substituted di(4-hydroxycoumarin) [di(4-HC)] was performed with the density functional theory (DFT) [B3LYP/6-31G(d)] method. Two asymmetrical intramolecular O bond H?O hydrogen bonds (HBs) stabilized the structures. The calculated single HB energies varied from -62.56 to -47.53 kJ mol-1 and pointed to a relative strong hydrogen bond in the systems studied. The 2- and 6-pyridyl substituents produced the largest geometrical changes in di(4-hydroxycoumarin) fragment. The highest total HB energy was found for 2-pyridyl-substituted and the lowest one for 6-pyridyl-substituted di(4-hydroxycoumarin). The HB energy variations were confirmed with rotational barrier method calculations. Both steric and electrostatic factors were found to be responsible for the HB asymmetry in the compounds studied. According to the molecular electrostatic potential (MEP) calculations the most preferred reactive site for electrophilic attack of pyridyl-substituted di(4-hydroxycoumarin)s are the pyridine nitrogen and the carbonyl oxygens, followed by the hydroxyl oxygens.

  9. Intramolecular condensation reactions of {alpha},{omega}-bis(triethoxysilyl)alkanes. Formation of cyclic disilsesquioxanes

    SciTech Connect

    Loy, D.A.; Carpenter, J.P.; Myers, S.A.; Assink, R.A.; Small, J.H.; Greaves, J.; Shea, K.J.

    1996-09-04

    In this paper, we used mass spectrometry and {sup 29}Si NMR spectroscopy to discover that the length of the alkylene-bridging groups had a pronounced effect on the competition between cyclization and polymerization of {alpha},{omega}-bis(triethoxysilyl)alkanes and on the formation of polymeric gels. While the intramolecular reaction clearly slows gelation, the cyclic disilsesquioxanes are still tetrafunctional monomers theoretically capable of forming polymeric gels. If the ring structures, which bear a striking resemblence to carbohydrates, are preserved through the polymerization, the resulting poly(cyclic disilsesquioxane) gels may have structural similarities to branched or cross-linked carbohydrates, such as cellulose or chitosan. Under base-catalyzed sol-gel polymerization conditions, 3 and 4 (six- and seven-membered cyclic disilsesquioxanes, respectively) quickly reacted to give gels with significant ring opening as determined from the {sup 29}Si chemical shifts in solid-state (CP MAS) NMR spectra. However, gels prepared under acidic conditions reveal some or all of the cyclic disilsesquioxane functionality was preserved in the polymers. 13 refs., 1 fig.

  10. Amplified excited state intramolecular proton transfer fluorescence of butterfly-shaped bis-2,6-dibenzothiazolylphenol

    NASA Astrophysics Data System (ADS)

    Zhang, Xuan; Ma, Wei-Wei

    2017-06-01

    A butterfly-shaped benzothiazole derivative, bis-2,6-dibenzothiazolylphenol (2), was synthesized via 4-methylene bridging two 2,6-dibenzothiazolylphenol (1) molecules, and the excited-state intramolecular proton transfer (ESIPT) fluorescence of 1 and 2 were comparably investigated by steady-state spectroscopic experiments with the aid of theoretical simulations for structure and energy. It was found that 2 showed similar ESIPT emissions to those of 1 in solution and solid states, but the ESIPT fluorescence quantum yield was substantially amplified in the case of the more ‘integrated’ 2. In both tetrahydrofuran (THF) and CHCl3 solvents, ESIPT occurred and orange emissions at 580-590 nm from keto tautomers were observed, where the absolute fluorescence quantum yield was measured to be 0.28 and 0.41 for 1, as well as 0.41 and 0.59 for 2, respectively. In the solid state, 2 showed an ESIPT emission at 570 nm with an absolute fluorescence quantum yield of 0.38, which is substantially shorter and larger than the corresponding values of 1 (592 nm and 0.26) respectively. Furthermore, both 2 and 1 showed strongly blue-shifted green emissions around 520 nm from the deprotonated anion species in N,N-dimethyl formamide (DMF). A similar blue-shifted green emission was also found with the addition of fluoride in the THF solution of 2 or 1, suggesting that the competitive deprotonation makes the ESIPT impossible.

  11. An FT-IR study on intramolecular hydrogen-bonding in ethylene glycol derivatives

    NASA Astrophysics Data System (ADS)

    Singelenberg, F. A. J.; van der Maas, J. H.; Kroon-Batenburg, L. M. J.

    1991-05-01

    The OH-streching region of a number of mono-alkyl ethers of (poly) ethylene glycols in dilute CCl 4 solution has been investigated by FT-IR. Non-H-bonded conformers are observed in addition to intramolecularly H-bonded ones. Different H-bonds can be distinguished when more than one ether-oxygen is present. The frequency of the non-bonded conformer is identical for all compounds and the same holds for the 5-R conformer. Furthermore the relative intensities of these peaks are identical in all spectra. The OH-frequency of the 8-R and 11-R conformers depends on the length and the type of the chain substituted at O(3) and O(4), respectively. MM2 calculations have been carried out for some of the compounds. The stability of the conformers proves to be in the order 11-R&>;5-R&>;;8-R&>; non-H-bonded. Interatomic distances and angles indicate that the H-bonds in the 8-R and 11-R conformers are bifurcated and "trifurcated", respectively.

  12. Understanding optoelectronic properties of cyano-terminated oligothiophenes in the context of intramolecular charge transfer.

    PubMed

    González, Sandra Rodríguez; Orduna, Jesús; Alicante, Raquel; Villacampa, Belén; McGee, Kari A; Pina, João; de Melo, J Seixas; Schwaderer, Kathryn M; Johnson, Jared C; Blackorbay, Brady A; Hansmeier, Jacob J; Bolton, Victoria F; Helland, Tyler J; Edlund, Brett A; Pappenfus, Ted M; Navarrete, Juan T López; Casado, Juan

    2011-09-15

    In this paper we have prepared a new series of oligothiophenes capped with hexyl groups and a variety of strong acceptors, mainly cyanovinyl moieties. An exhaustive analysis of the absorption, photophysical, electrochemical, solid state, nonlinear optical and vibrational properties has been presented guided by theoretical calculations. The investigation is centered on the efficiency of the intramolecular charge transfer (i.e., chain length and acceptor dependence) and its impact on all the relevant electronic, structural, optical, and vibrational properties. The most significant features imparted by the acceptors through the π-conjugated oligothiophene path are (i) intense visible electronic absorptions, (ii) tuned fluorescence wavelength emissions, (iii) solid state π-stacking, (iv) ambipolar redox behavior, (v) S(1) ⇝ S(0) internal conversion as being the major route for the deactivation of the excited state, and (vi) large electronic and vibrational contributions to their nonlinear optical response (hyperpolarizability). The analysis establishes connections between the different properties of the materials and structure-function relationships useful in organic electronics.

  13. Glutathione-coordinated [2Fe-2S] cluster is stabilized by intramolecular salt bridges.

    PubMed

    Li, Jingwei; Pearson, Stephen A; Fenk, Kevin D; Cowan, J A

    2015-12-01

    Halide salts of alkali and alkaline earth metals were used to probe the contributions of intramolecular salt bridge formation on the stability of glutathione-coordinated [2Fe-2S] cluster toward hydrolysis. The effect of ionic strength on cluster stability was quantitatively investigated by application of Debye-Hückel theory to the rates of hydrolysis. Results from this study demonstrate that ionic strength influences the stability of the cluster, with the rate of cluster degradation depending on the charge density, hydrated ionic radius, and hydration energy. The identity of the salt ions was also observed to be correlated with the binding affinity toward the cluster. Based on the modified Debye-Hückel equation and counterion screening effect, these results suggest that interactions between glutathione molecules in the [2Fe-2S](GS)4 cluster is via salt bridges, in agreement with our previous results where modifications of glutathione carboxylates and amines prevented solution aggregation and cluster formation. These results not only provide a rationale for the stability of such clusters under physiological conditions, but also suggest that the formation of glutathione-complexed [2Fe-2S] cluster from a glutathione tetramer may be facilitated by salt bridge interactions between glutathione molecules prior to cluster assembly, in a manner consistent with Nature's equivalent of dynamic combinatorial chemistry.

  14. An Intramolecular CAr-H•••O=C Hydrogen Bond and the Configuration of Rotenoids.

    PubMed

    Ren, Yulin; Gallucci, Judith C; Kinghorn, A Douglas

    2017-04-20

    Over the past half a century, the structure and configuration of the rotenoids, a group of natural products showing multiple promising bioactivities, have been established by interpretation of their NMR and electronic circular dichroism spectra and confirmed by analysis of single-crystal X-ray diffraction data. The chemical shift of the H-6' (1)H NMR resonance has been found to be an indicator of either a cis or trans C/D ring system. In the present study, four structures representing the central rings of a cis-, a trans-, a dehydro-, and an oxadehydro-rotenoid have been plotted using the Mercury program based on X-ray crystal structures reported previously, with the conformations of the C/D ring system, the local bond lengths or interatomic distances, hydrogen bond angles, and the H-6' chemical shift of these compounds presented. It is shown for the first time that a trans-fused C/D ring system of rotenoids is preferred for the formation of a potential intramolecular C6'-H6'•••O=C4 H-bond, and that such H-bonding results in the (1)H NMR resonance for H-6' being shifted downfield. Georg Thieme Verlag KG Stuttgart · New York.

  15. Ultrafast intramolecular charge transfer of formyl perylene observed using femtosecond transient absorption spectroscopy.

    PubMed

    Mohammed, Omar F

    2010-11-04

    The excited-state photophysics of formylperylene (FPe) have been investigated in a series of nonpolar, polar aprotic, and polar protic solvents. A variety of experimental and theoretical methods were employed including femtosecond transient absorption (fs-TA) spectroscopy with 130 fs temporal resolution. We report that the ultrafast intramolecular charge transfer from the perylene unit to the formyl (CHO) group can be facilitated drastically by hydrogen-bonding interactions between the carbonyl group oxygen of FPe and hydrogen-donating solvents in the electronically excited state. The excited-state absorption of FPe in methanol (MeOH) is close to the reported perylene radical cation produced by bimolecular quenching by an electron acceptor. This is a strong indication for a substantial charge transfer in the S(1) state in protic solvents. The larger increase of the dipole moment change in the protic solvents than that in aprotic ones strongly supports this observation. Relaxation mechanisms including vibrational cooling and solvation coupled to the charge-transfer state are also discussed.

  16. High resolution photoelectron spectroscopy and femtosecond intramolecular dynamics of H2CCO + and D2CCO +

    NASA Astrophysics Data System (ADS)

    Niu, Baohua; Bai, Ying; Shirley, David A.

    1993-08-01

    High resolution helium Iα (584 Å) photoelectron spectra of H2CCO and D2CCO are reported. The present spectra of the ground states of ketene cations show more vibrational fine structure than previously reported. The adiabatic ionization energies (AIEs) of the cations' first, second, and fifth excited states are determined unambiguously. The doubletlike fine structures present in the first excited states of ketene cations imply the excitation of a ``soft'' mode that was not observed before. It was assigned to the ν5 mode, which is characterized by the CH2 (CD2) group out-of-plane wagging motion. The complexity of the photoelectron spectra obtained for the ionic first excited states is attributed to the possible dissociation and predissociation of this state. Strong isotope effects are observed in the vibronic (vibrational) couplings in most of the ionic states. Vibrational autocorrelation functions are calculated from the high-resolution photoelectron spectra for four of the six ionic states observed. The dynamics of the ground states of the cations are characterized by a wave packet oscillating with small amplitude around the minimum of the upper potential energy surfaces (PES). The decay dynamics of the ionic first and fifth excited states of ketene are characterized by ultrafast intramolecular processes such as dissociation and predissociation.

  17. Suppression of human immunodeficiency virus type 1 activity in vitro by oligonucleotides which form intramolecular tetrads.

    PubMed

    Rando, R F; Ojwang, J; Elbaggari, A; Reyes, G R; Tinder, R; McGrath, M S; Hogan, M E

    1995-01-27

    An oligonucleotide (I100-15) composed of only deoxyguanosine and thymidine was able to inhibit human immunodeficiency virus type-1 (HIV-1) in culture assay systems. I100-15 did not block virus entry into cells but did reduce viral-specific transcripts. As assessed by NMR and polyacrylamide gel methods, I100-15 appears to form a structure in which two stacked guanosine tetrads are connected by three two-base long loops. Structure/activity experiments indicated that formation of intramolecular guanosine tetrads was necessary to achieve maximum antiviral activity. The single deoxyguanosine nucleotide present in each loop was found to be extremely important for the overall antiviral activity. The toxicity of I100-15 was determined to be well above the 50% effective dose (ED50) in culture which yielded a high therapeutic index (> 100). The addition of a cholesterol moiety to the 3' terminus of I100-15 (I100-23) reduced the ED50 value to less than 50 nM (from 0.12 microM for I100-15) and increased the duration of viral suppression to greater than 21 days (versus 7-10 days for I100-15) after removal of the drug from infected cell cultures. The favorable therapeutic index of such molecules coupled with the prolonged suppression of HIV-1, suggest that such compounds further warrant investigation as potential therapeutic agents.

  18. Theoretical investigation of intramolecular vibrational energy redistribution in highly excited HFCO

    NASA Astrophysics Data System (ADS)

    Pasin, Gauthier; Gatti, Fabien; Iung, Christophe; Meyer, Hans-Dieter

    2006-05-01

    The present paper is devoted to the simulations of the intramolecular vibrational energy redistribution (IVR) in HFCO initiated by an excitation of the out-of-plane bending vibration [nν6=2,4,6,…,18,20]. Using a full six-dimensional ab initio potential energy, the multiconfiguration time-dependent Hartree (MCTDH) method was exploited to propagate the corresponding six-dimensional wave packets. This study emphasizes the stability of highly excited states of the out-of-plane bending mode which exist even above the dissociation threshold. More strikingly, the structure of the IVR during the first step of the dynamics is very stable for initial excitations ranging from 2ν6 to 20ν6. This latter result is consistent with the analysis of the eigenstates obtained, up to 10ν6, with the aid of the Davidson algorithm in a foregoing paper [Iung and Ribeiro, J. Chem. Phys. 121, 174105 (2005)]. The present study can be considered as complementary to this previous investigation. This paper also shows how MCTDH can be used to predict the dynamical behavior of a strongly excited system and to determine the energies of the corresponding highly excited states.

  19. 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.

  20. 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

  1. Intramolecular cycloaddition reactions of furo[3,4-b]indoles for alkaloid synthesis.

    PubMed

    Padwa, Albert; Zou, Yan; Cheng, Bo; Li, Hao; Downer-Riley, Nadale; Straub, Christopher S

    2014-04-04

    Model studies dealing with the Cu(II)- or Rh(II)-catalyzed carbenoid cyclization/cycloaddition cascade of several α-diazo indolo amido esters have been carried out as an approach to the alkaloid scandine. The Cu(II)-catalyzed reaction of an α-diazo indolo diester that contains a tethered oxa-pentenyl side chain was found to give rise to a reactive benzo[c]furan which undergoes a subsequent [4 + 2]-cycloaddition across the tethered π-bond. The reaction proceeds by the initial generation of a copper carbenoid intermediate which cyclizes onto the adjacent carbonyl group to give a reactive benzo[c]furan which in certain cases can be isolated. Disappointingly, the analogous reaction with the related amido indolo ester failed to take place, even when the tethered π-bond contained an electron-withdrawing carbomethoxy group. It would seem that the geometric requirements for the intramolecular cycloaddition of the furo[3,4-b]indole system with the tethered π-bond imposes distinct restrictions upon the bond angles of the reacting centers to prevent the cycloaddition reaction from occurring. However, the incorporation of another carbonyl group on the nitrogen atom of the tethered alkenyl diazo amido indolo ester seemingly provides better orbital overlap between the reacting π-systems and allows the desired cycloaddition reaction to occur.

  2. 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.

  3. 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

  4. 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.

  5. Excited-state intramolecular proton transfer and photoswitching in hydroxyphenyl-imidazopyridine derivatives: A theoretical study

    NASA Astrophysics Data System (ADS)

    Omidyan, Reza; Iravani, Maryam

    2016-11-01

    The MP2/CC2 and CASSCF theoretical approaches have been employed to determine the excited state proton transfer and photophysical nature of the four organic compounds, having the main frame of hydroxyphenyl-imidzaopyridine (HPIP). The nitrogen insertion effect, in addition to amine (-NH2) substitution has been investigated extensively by following the transition energies and deactivation pathways of resulted HPIP derivatives. It has been predicted that the excited state intramolecular proton transfer with or without small barrier is the most important feature of these compounds. Also, for all of the considered HPIP derivatives, a conical intersection (CI) between ground and the S1 excited state has been predicted. The strong non-adiabatic coupling in the CI (S1/S0), drives the system back to the ground state in which the proton may either return to the phenoxy unit and thus close the photocycle, or the system can continue the twisting motion that results in formation of a γ-photochromic species. This latter species can be responsible for photochromism of HPIP derivative systems.

  6. Synthesis and chemoselective intramolecular crosslinking of a HER2-binding affibody.

    PubMed

    Ekblad, Torun; Tolmachev, Vladimir; Orlova, Anna; Lendel, Christofer; Abrahmsén, Lars; Karlström, Amelie Eriksson

    2009-01-01

    The human epidermal growth factor receptor HER2 has emerged as an important target for molecular imaging of breast cancer. This article presents the design and synthesis of a HER2-targeting affibody molecule with improved stability and tumor targeting capacity, and with potential use as an imaging agent. The 58 aa three-helix bundle protein was assembled using solid-phase peptide synthesis, and a chemoselective ligation strategy was used to establish an intramolecular thioether bond between the side chain thiol group of a cysteine residue, positioned in the loop between helices I and II, and a chloroacetyl group on the side chain amino group of the C-terminal lysine residue. The tethered protein offered an increased thermal stability, with a melting temperature of 64 degrees C, compared to 54 degrees C for the linear control. The ligation did not have a major influence on the HER2 binding affinity, which was 320 and 380 pM for the crosslinked and linear molecules, respectively. Biodistribution studies were performed both in normal and tumor-bearing mice to evaluate the impact of the crosslinking on the in vivo behavior and on the tumor targeting performance. The distribution pattern was characterized by a low uptake in all organs except kidney, and rapid clearance from blood and normal tissue. Crosslinking of the protein resulted in a significantly increased tumor accumulation, rendering the tethered HER2-binding affibody molecule a valuable lead in the development of superior HER2 imaging agents.

  7. Dependency of the regio- and stereoselectivity of intramolecular, ring-closing glycosylations upon the ring size

    PubMed Central

    Claude, Patrick; Lehmann, Christian

    2011-01-01

    Summary Phenyl 3,4,6-tri-O-benzyl-2-O-(3-carboxypropionyl)-1-thio-β-D-galactopyranoside (1) was condensed via its pentafluorophenyl ester 2 with 5-aminopentyl (4a), 4-aminobutyl (4b), 3-aminopropyl (4c) and 2-aminoethyl 4,6-O-benzylidene-β-D-glucopyranoside (4d), prepared from the corresponding N-Cbz protected glucosides 3a–d, to give the corresponding 2-[3-(alkylcarbamoyl)propionyl] tethered saccharides 5a–d. Intramolecular, ring closing glycosylation of the saccharides with NIS and TMSOTf afforded the tethered β(1→3) linked disaccharides 6a–c, the α(1→3) linked disaccharides 7a–d and the α(1→2) linked disaccharide 8d in ratios depending upon the ring size formed during glycosylation. No β(1→2) linked disaccharides were formed. Molecular modeling of saccharides 6–8 revealed that a strong aromatic stacking interaction between the aromatic parts of the benzyl and benzylidene protecting groups in the galactosyl and glucosyl moieties was mainly responsible for the observed regioselectivity and anomeric selectivity of the ring-closing glycosylation step. PMID:22238538

  8. A super intramolecular self-enhanced electrochemiluminescence immunosensor based on polymer chains grafted on palladium nanocages

    NASA Astrophysics Data System (ADS)

    Wang, Haijun; He, Ying; Chai, Yaqin; Yuan, Ruo

    2014-08-01

    An intramolecular self-enhanced electrochemiluminescent derivative is prepared by grafting polystyrene (PS)-based polymer chains with pendant Ru(ii) luminophore from poly(ethylenimine) (PEI) on the surface of palladium nanocages (PdNCs). In this way, the Ru(ii) luminophore and its co-reactive group (amine groups in PEI) exist in the same polymer molecule, which shortens the electronic transmission distance between them and enhances the luminous stability. Meanwhile, through atom transfer radical polymerization (ATRP), the loading amount of Ru(ii) luminophore is greatly increased. Therefore, the obtained electrochemiluminescent derivative (PdNC-PEI-PSRu) has high luminous efficiency and stability. Furthermore, due to their special nanostructures of porous walls and hollow interiors, PdNCs have great advantages in high specific surface areas and good electrocatalytic ability, which make them act as an excellent immobilized platform for PEI and detection antibody. Based on the sandwiched immunoreactions, a sensitive ``signal on'' electrochemiluminescence immunosensor is constructed for the detection of carbohydrate antigen 15-3 (CA 15-3). As a result, a wide linear range from 0.01 U mL-1 to 120 U mL-1 is acquired with a relatively low detection limit of 0.003 U mL-1.

  9. 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.

  10. Ultrafast excited state dynamics of fucoxanthin: excitation energy dependent intramolecular charge transfer dynamics.

    PubMed

    Kosumi, Daisuke; Kusumoto, Toshiyuki; Fujii, Ritsuko; Sugisaki, Mitsuru; Iinuma, Yoshiro; Oka, Naohiro; Takaesu, Yuki; Taira, Tomonori; Iha, Masahiko; Frank, Harry A; Hashimoto, Hideki

    2011-06-14

    Carotenoids containing a carbonyl group in conjugation with their polyene backbone are naturally-occurring pigments in marine organisms and are essential to the photosynthetic light-harvesting function in aquatic algae. These carotenoids exhibit spectral characteristics attributed to an intramolecular charge transfer (ICT) state that arise in polar solvents due to the presence of the carbonyl group. Here, we report the spectroscopic properties of the carbonyl carotenoid fucoxanthin in polar (methanol) and nonpolar (cyclohexane) solvents studied by steady-state absorption and femtosecond pump-probe measurements. Transient absorption associated with the optically forbidden S(1) (2(1)A) state and/or the ICT state were observed following one-photon excitation to the optically allowed S(2) (1(1)B) state in methanol. The transient absorption measurements carried out in methanol showed that the ratio of the ICT-to-S(1) state formation increased with decreasing excitation energy. We also showed that the ICT character was clearly visible in the steady-state absorption in methanol based on a Franck-Condon analysis. The results suggest that two spectroscopic forms of fucoxanthin, blue and red, exist in the polar environment. This journal is © the Owner Societies 2011

  11. Solution conformation of peptides by the intramolecular nuclear Overhauser effect experiment. Study of valinomycin-K+.

    PubMed Central

    Krishna, N R; Agresti, D G; Glickson, J D; Walter, R

    1978-01-01

    This study demonstrates how the intramolecular nuclear Overhauser effect (NOE) experiment can be employed quantitatively to select from a set of possible conformations for a peptide or a protein the particular conformation (or a group of conformations) most consistent with the data. This procedure is demonstrated on a model depsipeptide system--valinomycin K+ in CDCl3--for which the solution conformation has been inferred by other methods. The NOE enhancements are very sensitive to the conformations assumed by this antibiotic. It is shown that the set of conformations, collectively labeled as A2 (including the X-ray crystallographic structure) gives a very good description of the NOE enhancements. The structure proposed by Bystrov et al. (1977. Eur. J. Biochem. 78:63) for the uncomplexed valinomycin in nonpolar solvents is also consistent with the experimental data on the potassium complex. Using statistical hypothesis testing involving the Hamilton R-factor ratio criterion, all the other models have been rejected as inconsistent with the experimental data. A general formalism is presented for describing the NOE effects in isotropically reorienting molecules. The formalism is not restricted to the extreme narrowing limit of the rotational correlation times and hence applies to both small and large molecules. Some of the factors that can influence the NOE measurements, viz. anisotropic rotational diffusion, conformational averaging, and nuclear spin diffusion, have been considered in this study. PMID:737287

  12. 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.

  13. AibA/AibB Induces an Intramolecular Decarboxylation in Isovalerate Biosynthesis by Myxococcus xanthus.

    PubMed

    Bock, Tobias; Luxenburger, Eva; Hoffmann, Judith; Schütza, Vlad; Feiler, Christian; Müller, Rolf; Blankenfeldt, Wulf

    2017-08-07

    Isovaleryl coenzyme A (IV-CoA) is an important precursor for iso-fatty acids and lipids. It acts in the development of myxobacteria, which can produce this compound from acetyl-CoA through alternative IV-CoA biosynthesis (aib). A central reaction of aib is catalyzed by AibA/AibB, which acts as a cofactor-free decarboxylase despite belonging to the family of CoA-transferases. We developed an efficient expression system for AibA/AibB that allowed the determination of high-resolution crystal structures in complex with different ligands. Through mutational studies, we show that an active-site cysteine previously proposed to be involved in decarboxylation is not required for activity. Instead, AibA/AibB seems to induce an intramolecular decarboxylation by binding its substrate in a hydrophobic cavity and forcing it into a bent conformation. Our study opens opportunities for synthetic biology studies, since AibA/AibB may be suitable for the production of isobutene, a precursor of biofuels and chemicals. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Vibrational overtone spectroscopy and intramolecular dynamics of C-H stretches in pyrrole

    NASA Astrophysics Data System (ADS)

    Portnov, Alexander; Epshtein, Michael; Rosenwaks, Salman; Bar, Ilana

    2013-05-01

    Room-temperature photoacoustic spectra and jet-cooled action spectra of the regions of the first and second C-H stretch overtones of pyrrole were measured with the goal of gaining new insight on the vibrational patterns and the intramolecular energy flow out of the initially excited vibrational states. The rotational cooling of the action spectra helped in observing hitherto unresolved features, assisting determination of the existing multiple bands and their positions in each region. These bands were analyzed by building vibrational Hamiltonian matrices related to a simplified joint local-mode/normal-mode (LM/NM) model, accounting for two types of C-H stretches and their Fermi resonances with the CCH deformation modes. The diagonalization of the LM/NM vibrational Hamiltonians and the fitting of the eigenvalues to the band positions revealed model parameters, enabling assignment of the observed bands. The time dependences of the survival probabilities of the C-H stretches in the region of the first and second overtones, deduced from the vibrational Hamiltonian, show quantum beats due to the couplings to the deformations and decays driven by weaker interactions to the bath states. The C-H stretches, although somewhat lower in energy, show stronger coupling than the N-H stretches.

  15. On prediction of OH stretching frequencies in intramolecularly hydrogen bonded systems

    NASA Astrophysics Data System (ADS)

    Hansen, Poul Erik; Spanget-Larsen, Jens

    2012-06-01

    OH stretching frequencies are investigated for a series of non-tautomerizing systems with intramolecular hydrogen bonds. Effective OH stretching wavenumbers are predicted by the application of empirical correlation procedures based on the results of B3LYP/6-31G(d) theoretical calculations in the harmonic and PT2 anharmonic approximations, as well as on experimental NMR parameters, i.e., proton chemical shifts (δH) and two-bond deuterium isotope effects on 13C chemical shifts (2ΔCOD). The procedures are applied in a discussion of the spectra of 2,6-dihydroxy-4-methylbenzaldehyde and 8-hydroxyquinoline N-oxide. The spectrum of the former displays a broad, composite band between 3500 and 2500 cm-1 which can be assigned to overlapping monomer and dimer contributions. In the latter case, the results support a reassignment of the OH stretching band of 8-hydroxyquinoline N-oxide; the reassignment is supported by correlation with the IR spectra of a series of substituted derivatives.

  16. Phosphorylation and Intramolecular Stabilization of the Ligand Binding Domain in the Nuclear Receptor Steroidogenic Factor 1

    PubMed Central

    Desclozeaux, Marion; Krylova, Irina N.; Horn, Florence; Fletterick, Robert J.; Ingraham, Holly A.

    2002-01-01

    Steroidogenic factor 1 (SF-1) is an orphan nuclear receptor with no known ligand. We showed previously that phosphorylation at serine 203 located N′-terminal to the ligand binding domain (LBD) enhanced cofactor recruitment, analogous to the ligand-mediated recruitment in ligand-dependent receptors. In this study, results of biochemical analyses and an LBD helix assembly assay suggest that the SF-1 LBD adopts an active conformation, with helices 1 and 12 packed against the predicted alpha-helical bundle, in the apparent absence of ligand. Fine mapping of the previously defined proximal activation function in SF-1 showed that the activation function mapped fully to helix 1 of the LBD. Limited proteolyses demonstrate that phosphorylation of S203 in the hinge region mimics the stabilizing effects of ligand on the LBD. Moreover, similar effects were observed in an SF-1/thyroid hormone LBD chimera receptor, illustrating that the S203 phosphorylation effects are transferable to a heterologous ligand-dependent receptor. Our collective data suggest that the hinge together with helix 1 is an individualized specific motif, which is tightly associated with its cognate LBD. For SF-1, we find that this intramolecular association and hence receptor activity are further enhanced by mitogen-activated protein kinase phosphorylation, thus mimicking many of the ligand-induced changes observed for ligand-dependent receptors. PMID:12242296

  17. A ratiometric fluorescent probe for alkaline phosphatase via regulation of excited-state intramolecular proton transfer.

    PubMed

    Fan, Chunlei; Luo, Shengxu; Qi, Haiping

    2016-03-01

    A ratiometric fluorescent probe 2-(benzimidazol-2-yl)phenyl phosphoric acid (1) for alkaline phosphatase (ALP) is designed and synthesized. The method employs the modulation of the excited-state intramolecular proton transfer (ESIPT) process of 2-(2'-hydroxyphenyl)benzimidazole (HPBI) through the hydroxyl group protection/deprotection reaction. Upon phosphorylated with POCl3 , HPBI shows only an emission peak at 363 nm due to the blockage of ESIPT. However, once selective enzymatic hydrolysis with alkaline phosphatase (ALP) in Tris-HCl buffer occurs, the probe 1 is returned to HPBI and the ESIPT process is switched on, which results in a decrease in the emission band at 363 nm and an increase in a new fluorescence peak around 430 nm. The fluorescence intensity ratio at 430 and 360 nm (I430/I360) increases linearly with the activity of ALP up to 0.050 U/mL and the detection limit is 0.0013 U/mL. The proposed probe shows excellent specificity toward ALP.

  18. The energy of the intramolecular hydrogen bond in chloro-substituted N-methyl-salicylidene imines

    NASA Astrophysics Data System (ADS)

    Koll, A.; Karpfen, A.; Wolschann, P.

    2007-11-01

    The energetic effects of the conformational rearrangement of eight Schiff bases, differently chloro-substituted, are discussed on the basis of the results of B3LYP/6-31+G(d,p) calculations. The proton transfer tautomers as well as "open"-non-hydrogen-bonded forms were considered. It was found, that the hydrogen-bonded forms have the lowest energy, but the second most stable were the proton transfer states with an O…H sbnd N intramolecular hydrogen bond. The proton transfer in Schiff bases dominates in comparison to other conformational rearrangements. This is important for the understanding of thermochromic and photochromic properties of these molecules. By using a thermodynamic cycle, the steric effects connected with chelate ring formation are estimated to be up to 5 kcal/mol, much higher than in related Mannich bases (˜1 kcal/mol) which do not form resonance assisted hydrogen bonds. Accounting these effects the "real" value of the energy of hydrogen bond formation was estimated to be 15 kcal/mol which increases with growing number of chlorine atoms up to 16.5 kcal/mol for 4,5,6-trichloro substitution.

  19. Dynamics and intramolecular ligand binding of DtxR studied by MD simulations and NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Yi, Myunggi; Bhattacharya, Nilakshee; Zhou, Huan-Xiang

    2005-11-01

    Diphtheria toxin repressor (DtxR) regulates the expression of the diphtheria toxin gene through intramolecular ligand binding (Wylie et al., Biochemistry 2005, 44:40-51). Protein dynamics is essential to the binding process of the Pro-rich (Pr) ligand to the C-terminal SH3 domain. We present MD and NMR results on the dynamics and ligand interactions of a Pr-SH3 construct of DtxR. NMR relaxation data (T1, T2, and NOE) showed that the Pr ligand is very flexible, suggesting that it undergoes binding/unbinding transitions. A 50-ns MD trajectory of the protein was used to calculate T1, T2, and NOE, reproducing the NMR results for the SH3 domain but not for the Pr segment. During the MD simulation, the ligand stayed bound to the SH3 domain; thus the simulation represented the bound state. The NMR data for the Pr-segment could be explained by assuming that they represented the average behavior of a fast binding/unbinding exchange. Though unbinding was not observed in the MD simulation, the simulation did show large fluctuations of a loop which forms part of the wall of the binding pocket. The fluctuations led to opening up of the binding pocket, thus weakening the interaction with the Pr segment and perhaps ultimately leading to ligand unbinding.

  20. Using Thz Spectroscopy to Probe Intramolecular Electron Transfer and Solvent Dynamics

    NASA Astrophysics Data System (ADS)

    Schmuttenmaer, Charles

    2002-03-01

    We have measured the electromagnetic radiation emitted during intramolecular electron transfer using a method does not rely on secondary processes.^1 The motion of the electrons themselves generates the measured signal (as understood by Maxwell's equations). If the electron transfer occurs on a timescale of 0.1 to 10 picoseconds, the emitted radiation will fall in the THz or far-infrared region of the spectrum (1 THz = 33.33 wavenumbers). We photoexcite a sample of partially oriented molecules and measure the emitted waveform. The polarity of the emitted field determines the direction of charge transfer unambiguously, and the shape of the field encodes the dynamics of the charge transfer -- a slower transfer rate produces a broader temporal pulse. Solvent repolarization dynamics also contribute to the measured response, and will be discussed. Future work will extend this method to systems that are difficult to study by traditional means. 1. M. C. Beard, G. M. Turner, and C. A. Schmuttenmaer, J. Phys. Chem. A, In Press (2001).

  1. 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.

  2. 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.

  3. Evidence for the intramolecular pleating model of fibrillin microfibril organisation from single particle image analysis.

    PubMed

    Lu, Yinhui; Holmes, David F; Baldock, Clair

    2005-05-27

    Fibrillin microfibrils endow mammalian connective tissues with elasticity and are fundamental for the deposition of elastin. The microfibrils are 57nm periodic supramolecular protein polymers with a mass of 2.4MDa per repeat. The detailed structure and organisation of most matrix assemblies is poorly understood due to their large size and complexity and it has proved a major challenge to define their structural organisation. Therefore, we have used low dose electron microscopy and single particle image analysis to study the structure of fibrillin microfibrils. Three novel features were detected: a globular feature that bridges the "arm" region, a double band of density crossing the microfibril and stain penetrating holes present in the interbead region, possibly produced by the removal of microfibril associated proteins in the purification procedure. Fine filaments of approximately 2.4nm diameter are resolved in the interbead region, which correspond to the reported diameter of the fibrillin molecule. Comparison of the stain exclusion pattern of microfibrils with the theoretical stain exclusion pattern of fibrillin packing models indicates that the intramolecular pleating model, where each fibrillin molecule is pleated within one microfibril period allowing extensibility by unpleating, has the best fit to the data.

  4. 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.

  5. Identifying tips for intramolecular NC-AFM imaging via in situ fingerprinting

    PubMed Central

    Sang, Hongqian; Jarvis, Samuel P.; Zhou, Zhichao; Sharp, Peter; Moriarty, Philip; Wang, Jianbo; Wang, Yu; Kantorovich, Lev

    2014-01-01

    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. PMID:25327642

  6. An intramolecular signaling element that modulates dynamin function in vitro and in vivo.

    PubMed

    Chappie, Joshua S; Acharya, Sharmistha; Liu, Ya-Wen; Leonard, Marilyn; Pucadyil, Thomas J; Schmid, Sandra L

    2009-08-01

    Dynamin exhibits a high basal rate of GTP hydrolysis that is enhanced by self-assembly on a lipid template. Dynamin's GTPase effector domain (GED) is required for this stimulation, though its mechanism of action is poorly understood. Recent structural work has suggested that GED may physically dock with the GTPase domain to exert its stimulatory effects. To examine how these interactions activate dynamin, we engineered a minimal GTPase-GED fusion protein (GG) that reconstitutes dynamin's basal GTPase activity and utilized it to define the structural framework that mediates GED's association with the GTPase domain. Chemical cross-linking of GG and mutagenesis of full-length dynamin establishes that the GTPase-GED interface is comprised of the N- and C-terminal helices of the GTPase domain and the C-terminus of GED. We further show that this interface is essential for structural stability in full-length dynamin. Finally, we identify mutations in this interface that disrupt assembly-stimulated GTP hydrolysis and dynamin-catalyzed membrane fission in vitro and impair the late stages of clathrin-mediated endocytosis in vivo. These data suggest that the components of the GTPase-GED interface act as an intramolecular signaling module, which we term the bundle signaling element, that can modulate dynamin function in vitro and in vivo.

  7. An Intramolecular Signaling Element that Modulates Dynamin Function In Vitro and In Vivo

    PubMed Central

    Chappie, Joshua S.; Acharya, Sharmistha; Liu, Ya-Wen; Leonard, Marilyn; Pucadyil, Thomas J.

    2009-01-01

    Dynamin exhibits a high basal rate of GTP hydrolysis that is enhanced by self-assembly on a lipid template. Dynamin's GTPase effector domain (GED) is required for this stimulation, though its mechanism of action is poorly understood. Recent structural work has suggested that GED may physically dock with the GTPase domain to exert its stimulatory effects. To examine how these interactions activate dynamin, we engineered a minimal GTPase-GED fusion protein (GG) that reconstitutes dynamin's basal GTPase activity and utilized it to define the structural framework that mediates GED's association with the GTPase domain. Chemical cross-linking of GG and mutagenesis of full-length dynamin establishes that the GTPase-GED interface is comprised of the N- and C-terminal helices of the GTPase domain and the C-terminus of GED. We further show that this interface is essential for structural stability in full-length dynamin. Finally, we identify mutations in this interface that disrupt assembly-stimulated GTP hydrolysis and dynamin-catalyzed membrane fission in vitro and impair the late stages of clathrin-mediated endocytosis in vivo. These data suggest that the components of the GTPase-GED interface act as an intramolecular signaling module, which we term the bundle signaling element, that can modulate dynamin function in vitro and in vivo. PMID:19515832

  8. 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.

  9. Donor-acceptor substituted phenylethynyltriphenylenes – excited state intramolecular charge transfer, solvatochromic absorption and fluorescence emission

    PubMed Central

    Nandy, Ritesh

    2010-01-01

    Summary Several 2-(phenylethynyl)triphenylene derivatives bearing electron donor and acceptor substituents on the phenyl rings have been synthesized. The absorption and fluorescence emission properties of these molecules have been studied in solvents of different polarity. For a given derivative, solvent polarity had minimal effect on the absorption maxima. However, for a given solvent the absorption maxima red shifted with increasing conjugation of the substituent. The fluorescence emission of these derivatives was very sensitive to solvent polarity. In the presence of strongly electron withdrawing (–CN) and strongly electron donating (–NMe2) substituents large Stokes shifts (up to 130 nm, 7828 cm−1) were observed in DMSO. In the presence of carbonyl substituents (–COMe and –COPh), the largest Stokes shift (140 nm, 8163 cm−1) was observed in ethanol. Linear correlation was observed for the Stokes shifts in a Lippert–Mataga plot. Linear correlation of Stokes shift was also observed with E T(30) scale for protic and aprotic solvents but with different slopes. These results indicate that the fluorescence emission arises from excited state intramolecular charge transfer in these molecules where the triphenylene chromophore acts either as a donor or as an acceptor depending upon the nature of the substituent on the phenyl ring. HOMO–LUMO energy gaps have been estimated from the electrochemical and spectral data for these derivatives. The HOMO and LUMO surfaces were obtained from DFT calculations. PMID:21085512

  10. Metal ion-directed dynamic splicing of DNA through global conformational change by intramolecular complexation.

    PubMed

    Ihara, Toshihiro; Ohura, Hiroyuki; Shirahama, Chisato; Furuzono, Tomohiro; Shimada, Hiroshi; Matsuura, Hirotaka; Kitamura, Yusuke

    2015-04-07

    Chemically engineered DNAs—in which global conformation can be modulated in response to specific stimuli—could be allosteric functional DNAs themselves or work as a modulator of the functional nucleic acids such as DNAzymes and aptamers. Here, we show that two terpyridines built in the DNA backbone form a stable intramolecular 1:2 complex, [M(terpy)2](2+), with divalent transition metal ions. Upon complexation, the DNA conjugates adopt a Ω-shape structure, in which two distal sequences located outside the terpyridines connect with each other to form a continuous segment with a specific structure or sequence. Such a DNA structure is globally controlled by local metal complexation events that can be rationally designed based on general coordination chemistry. This method is regarded as metal ion-directed dynamic sequence edition or DNA splicing. DNAzymes with peroxidase-like activity can thus be regulated by several transition metal ions through sequence edition techniques based on the Ω-motif.

  11. 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.

  12. Intramolecular allosteric communication in dopamine D2 receptor revealed by evolutionary amino acid covariation.

    PubMed

    Sung, Yun-Min; Wilkins, Angela D; Rodriguez, Gustavo J; Wensel, Theodore G; Lichtarge, Olivier

    2016-03-29

    The structural basis of allosteric signaling in G protein-coupled receptors (GPCRs) is important in guiding design of therapeutics and understanding phenotypic consequences of genetic variation. The Evolutionary Trace (ET) algorithm previously proved effective in redesigning receptors to mimic the ligand specificities of functionally distinct homologs. We now expand ET to consider mutual information, with validation in GPCR structure and dopamine D2 receptor (D2R) function. The new algorithm, called ET-MIp, identifies evolutionarily relevant patterns of amino acid covariations. The improved predictions of structural proximity and D2R mutagenesis demonstrate that ET-MIp predicts functional interactions between residue pairs, particularly potency and efficacy of activation by dopamine. Remarkably, although most of the residue pairs chosen for mutagenesis are neither in the binding pocket nor in contact with each other, many exhibited functional interactions, implying at-a-distance coupling. The functional interaction between the coupled pairs correlated best with the evolutionary coupling potential derived from dopamine receptor sequences rather than with broader sets of GPCR sequences. These data suggest that the allosteric communication responsible for dopamine responses is resolved by ET-MIp and best discerned within a short evolutionary distance. Most double mutants restored dopamine response to wild-type levels, also suggesting that tight regulation of the response to dopamine drove the coevolution and intramolecular communications between coupled residues. Our approach provides a general tool to identify evolutionary covariation patterns in small sets of close sequence homologs and to translate them into functional linkages between residues.

  13. Intramolecular excited-state proton transfer in 3-hydroxyflavone. Hydrogen-bonding solvent perturbations

    SciTech Connect

    McMorrow, D.; Kasha, M.

    1984-01-01

    The phenomenon of excited-state proton transfer in 3-hydroxyflavone is shown to depend sensitively on traces of H-bonding impurities in hydrocarbon solvents. In extremely dry and highly purified hydrocarbon solvents, a unique tautomer yellow-green fluorescence (region I) is observed from 298 to 77 K, independent of solvent temperature and viscosity, in contradiction to the results of previous research. With traces of water present, three regions of fluorescence of 3-hydroxyflavone of 3-hydoxyflavone (2.0 x 10/sup -5/ M in methylcyclohexane (MCH)) can be observed, the tautomer yellow-green fluorescence (maximum at 523 nm) (region I), another green fluorescence (maximum at 497 nm) (region II) attributed to the solute anion, and a blue-violet fluorescence (maximum at 400 nm) (region III) attributed to the normal electromer of 3-hydroflavone. Excitation spectroscopy confirms the presence of a series of ground-state solvates which are correlated with the diverse luminescence behavior observed with water, alcohol, and ether both as trace impurities and as pure solvents. Potential energy curves for the various molecular species studied, and for various solvation modes, are used to reinterpret laser kinetic studies previously published. In particular the reported biexponential normal molecule fluorescence (III) decay, and tautomer fluorescence (I) rise time, are shown to represent a slow solvent-reorganization step from the polysolvated 3-hydroxyflavone and an ultrarapid intrinsic portion-transfer step for the intramolecularly H-bonded 3-hydroxyflavone.

  14. 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

  15. 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

  16. Thermochromic Magnetic Ionic Liquids from Cationic Nickel(II) Complexes Exhibiting Intramolecular Coordination Equilibrium.

    PubMed

    Lan, Xue; Mochida, Tomoyuki; Funasako, Yusuke; Takahashi, Kazuyuki; Sakurai, Takahiro; Ohta, Hitoshi

    2017-01-18

    Among the various thermochromic materials, liquid thermochromic materials are comparatively rare. To produce functional thermochromic liquids, we have designed ionic liquids based on cationic nickel complexes with ether side chains, [Ni(acac)(Me2 NC2 H4 NR(1) R(2) )]Tf2 N ([1]Tf2 N: R(1) =C3 H6 OEt, R(2) =Me; [2]Tf2 N: R(1) =C3 H6 OMe, R(2) =Me; [3]Tf2 N: R(1) =R(2) =C3 H6 OMe), where acac=acetylacetonate and Tf2 N=(F3 CSO2 )2 N(-) . The side chains (R(1) , R(2) ) can moderately coordinate to the metal center, enabling temperature-dependent coordination equilibria in the liquid state. [1]Tf2 N is a liquid at room temperature. [2]Tf2 N is obtained as a solid (Tm =352.7 K) but remains liquid at room temperature after melting. [3]Tf2 N is a solid with a high melting point (Tm =422.3 K). These salts display thermochromism in the liquid state, appearing red at high temperatures and orange, light-blue, or bluish-green at lower temperatures, and exhibiting concomitant changes in their magnetic properties. This phenomenon is based on temperature-dependent equilibrium between a square-planar diamagnetic species and a paramagnetic species with intramolecular ether coordination.

  17. Impact of inter- and intramolecular interactions on the physical stability of indomethacin dispersed in acetylated saccharides.

    PubMed

    Kaminska, E; Adrjanowicz, K; Tarnacka, M; Kolodziejczyk, K; Dulski, M; Mapesa, E U; Zakowiecki, D; Hawelek, L; Kaczmarczyk-Sedlak, I; Kaminski, K

    2014-08-04

    Differential scanning calorimetry (DSC), broadband dielectric (BDS), and Fourier transform infrared (FTIR) spectroscopies as well as theoretical computations were applied to investigate inter- and intramolecular interactions between the active pharmaceutical ingredient (API) indomethacin (IMC) and a series of acetylated saccharides. It was found that solid dispersions formed by modified glucose and IMC are the least physically stable of all studied samples. Dielectric measurements showed that this finding is related to neither the global nor local mobility, as the two were fairly similar. On the other hand, combined studies with the use of density functional theory (DFT) and FTIR methods indicated that, in contrast to acetylated glucose, modified disaccharides (maltose and sucrose) interact strongly with indomethacin. As a result, internal H-bonds between IMC molecules become very weak or are eventually broken. Simultaneously, strong H-bonds between the matrix and API are formed. This observation was used to explain the physical stability of the investigated solid dispersions. Finally, solubility measurements revealed that the solubility of IMC can be enhanced by the use of acetylated carbohydrates, although the observed improvement is marginal due to strong interactions.

  18. Two-photon circular dichroism of an axially dissymmetric diphosphine ligand with strong intramolecular charge transfer.

    PubMed

    Díaz, Carlos; Echevarria, Lorenzo; Rizzo, Antonio; Hernández, Florencio E

    2014-02-06

    In this article we report on the study of the polarization dependent two-photon absorption (TPA) of (S)-(+)-(1,1'-binaphthalene-2,2'-diyl)bis(diphenylphosphine) (S-BINAP) in solution, and the theoretical-experimental analysis of its two-photon circular dichroism (TPCD) spectrum. The comparative examination of the following two correlation functionals, using the 6-31G* basis set, showed that the Coulomb attenuated method variant of the Becke's three-parameter exchange and the Lee-Yang-Parr (CAM-B3LYP) is more reliable than B3LYP in molecules such as S-BINAP, a heteroaromatic diphosphine chiral ligand with strong intramolecular charge transfer. To access the theoretical TPCD spectra, we employed time dependent density functional theory (TD-DFT) at the mentioned level of theory and over the first 40 electronic excited states including solvent effects by means of the polarizable continuum model (PCM). The extended calculation on twice as many electronic excited states in vacuo proved to be crucial for the correct assignment of the experimental bands. TPA measurements were performed in the femtosecond regime and over a broad spectral range using the double L-scan technique.

  19. 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.

  20. A manganese catalyst for highly reactive yet chemoselective intramolecular C(sp3)-H amination

    NASA Astrophysics Data System (ADS)

    Paradine, Shauna M.; Griffin, Jennifer R.; Zhao, Jinpeng; Petronico, Aaron L.; Miller, Shannon M.; Christina White, M.

    2015-12-01

    C-H bond oxidation reactions underscore the existing paradigm wherein high reactivity and high selectivity are inversely correlated. The development of catalysts capable of oxidizing strong aliphatic C(sp3)-H bonds while displaying chemoselectivity (that is, tolerance of more oxidizable functionality) remains an unsolved problem. Here, we describe a catalyst, manganese tert-butylphthalocyanine [Mn(tBuPc)], that is an outlier to the reactivity-selectivity paradigm. It is unique in its capacity to functionalize all types of C(sp3)-H bond intramolecularly, while displaying excellent chemoselectivity in the presence of π functionality. Mechanistic studies indicate that [Mn(tBuPc)] transfers bound nitrenes to C(sp3)-H bonds via a pathway that lies between concerted C-H insertion, observed with reactive noble metals such as rhodium, and stepwise radical C-H abstraction/rebound, as observed with chemoselective base metals such as iron. Rather than achieving a blending of effects, [Mn(tBuPc)] aminates even 1° aliphatic and propargylic C-H bonds, demonstrating reactivity and selectivity unusual for previously known catalysts.

  1. Highly Efficient Intramolecular Electrochemiluminescence Energy Transfer for Ultrasensitive Bioanalysis of Aflatoxin M1.

    PubMed

    Liu, Jia-Li; Zhao, Min; Zhuo, Ying; Chai, Ya-Qin; Yuan, Ruo

    2017-02-03

    The intermolecular electrochemiluminescence resonance energy transfer (ECL-RET) between luminol and Ru(bpy)3(2+) was studied extensively to achieve the sensitive bioanalysis owing to the perfect spectral overlap of the donor and acceptor, but it still suffers from the challenging issue of low energy-transfer efficiency. The intramolecular ECL-RET towards the novel ECL compound containing the donor of luminol and the acceptor of Ru(bpy)2 (mcpbpy)(2+) (Lum-Ru) was designed and investigated. With the high-efficient ECL-RET in one molecule, the highly intense ECL signal of Lum-Ru was obtained owing to the short path of energy transmission and less energy loss between luminol and Ru(bpy)2 (mcpbpy)(2+) . Lum-Ru was further applied to construct a signal-off electrochemiluminescence (ECL) aptasensor for ultrasensitive detection of a harsh carcinogen of Aflatoxin M1 (AFM1). This sensing platform also provides a significant boost for the trace detection of other biomolecules in clinical analysis.

  2. Ab initio study on an excited-state intramolecular proton-transfer reaction in ionic liquid.

    PubMed

    Hayaki, Seigo; Kimura, Yoshifumi; Sato, Hirofumi

    2013-06-06

    An excited-state intramolecular proton transfer (ESIPT) reaction of 4'-N,N-dimethylamino-3-hydroxyflavone in room temperature ionic liquid is theoretically investigated using RISM-SCF-SEDD, which is a hybrid method of molecular liquid theory and ab initio molecular orbital theory. The photo-excitation and proton-transfer processes are computed by considering the solvent fluctuation. The calculated absorption and emission energy are in good agreement with the experiments. The changes in the dipole moment indicate that the drastic solvation relaxation is accompanied by the excitation and an ESIPT process, which is consistent with the remarkable dynamic Stokes shift observed in the experiments. We calculated the nonequilibrium free-energy contour as a function of the proton coordinate and the solvation coordinate. We conclude that although immediately after the excitation the barrier height of the ESIPT process is relatively small, the barrier becomes larger as the solvation relaxation to the excited normal state proceeds. The solvation relaxation process is also investigated on the basis of microscopic solvation structure obtained by RISM calculations.

  3. 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.

  4. 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.

  5. Intramolecular Cooperativity in the Reaction of Diacyl Phosphates with Serine ß-Lactamases

    PubMed Central

    Majumdar, Sudipta; Pratt, R.F.

    2010-01-01

    Asymmetric diaroyl phosphates (ArCOOPO2−OCOAr′, where Ar = Ph, Ar′ = 4-biphenyl, 2-benzothiophenyl and 2-benzofuranyl), have been prepared, evaluated as serine (classes A, C, D) β-lactamase inhibitors, and compared with respect to the latter with their symmetric “parents”, where Ar = Ar′. The asymmetric compounds, in general, were found to react with the β-lactamases in two modes, corresponding to different orientations with respect to the active site, whereby either of the two aroyl groups may acylate the enzyme to form two different inert acyl-enzymes, E-COAr and E-COAr′. In all cases, the asymmetric compounds, in one orientation, react more rapidly with the enzymes tested than one symmetrical “parent” but not both. From comparisons of activation free energy differences, it was found that the changes in free energy on changing from one aryl group to another, in either the acyl group or the leaving group, were not additive, i.e. that the effect of changing one aroyl group to another depended on the leaving group and vice versa. Thus, intramolecular cooperativity between the aroyl groups must exist, arising either from direct interaction between them or from protein-mediated interaction, or from a combination of both. Such cooperativity brings fresh opportunities and challenges to the search for novel ß-lactamase inhibitors. PMID:19678666

  6. The role of intramolecular nonbonded interaction and angle sampling in single-step free energy perturbation

    NASA Astrophysics Data System (ADS)

    Chiang, Ying-Chih; Pang, Yui Tik; Wang, Yi

    2016-12-01

    Single-step free energy perturbation (sFEP) has often been proposed as an efficient tool for a quick free energy scan due to its straightforward protocol and the ability to recycle an existing molecular dynamics trajectory for free energy calculations. Although sFEP is expected to fail when the sampling of a system is inefficient, it is often expected to hold for an alchemical transformation between ligands with a moderate difference in their sizes, e.g., transforming a benzene into an ethylbenzene. Yet, exceptions were observed in calculations for anisole and methylaniline, which have similar physical sizes as ethylbenzene. In this study, we show that such exceptions arise from the sampling inefficiency on an unexpected rigid degree of freedom, namely, the bond angle θ. The distributions of θ differ dramatically between two end states of a sFEP calculation, i.e., the conformation of the ligand changes significantly during the alchemical transformation process. Our investigation also reveals the interrelation between the ligand conformation and the intramolecular nonbonded interactions. This knowledge suggests a best combination of the ghost ligand potential and the dual topology setting, which improves the accuracy in a single reference sFEP calculation by bringing down its error from around 5kBT to kBT.

  7. Molecular dynamics simulations of small DNA plasmids: effects of sequence and supercoiling on intramolecular motions.

    PubMed

    Tan, R K; Sprous, D; Harvey, S C

    1996-08-01

    Small (600 base pair) DNA plasmids were modeled with a simplified representation (3DNA) and the intramolecular motions were studied using molecular mechanics and molecular dynamics techniques. The model is detailed enough to incorporate sequence effects. At the same time, it is simple enough to allow long molecular dynamics simulations. The simulations revealed that large-scale slithering occurs in a homogeneous sequence. In a heterogeneous sequence, containing numerous small intrinsic curves, the centers of the curves are preferentially positioned at the tips of loops. With more curves than loop tips (two in unbranched supercoiled DNA), the heterogeneous sequence plasmid slithers short distances to reposition other curves into the loop tips. However, the DNA is immobilized most of the time, with the loop tips positioned over a few favored curve centers. Branching or looping also appears in the heterogeneous sequence as a new method of repositioning the loop tips. Instead of a smooth progression of increasing writhing with increasing linking difference, theoretical studies have predicted that there is a threshold between unwrithed and writhed DNA at a linking difference between one and two. This has previously been observed in simulations of static structures and is demonstrated here for dynamic homogeneous closed DNA. Such an abrupt transition is not found in the heterogeneous sequence in both the static and dynamic cases.

  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. Optimized measurements of separations and angles between intra-molecular fluorescent markers

    PubMed Central

    Mortensen, Kim I.; Sung, Jongmin; Flyvbjerg, Henrik; Spudich, James A.

    2015-01-01

    We demonstrate a novel, yet simple tool for the study of structure and function of biomolecules by extending two-colour co-localization microscopy to fluorescent molecules with fixed orientations and in intra-molecular proximity. From each colour-separated microscope image in a time-lapse movie and using only simple means, we simultaneously determine both the relative (x,y)-separation of the fluorophores and their individual orientations in space with accuracy and precision. The positions and orientations of two domains of the same molecule are thus time-resolved. Using short double-stranded DNA molecules internally labelled with two fixed fluorophores, we demonstrate the accuracy and precision of our method using the known structure of double-stranded DNA as a benchmark, resolve 10-base-pair differences in fluorophore separations, and determine the unique 3D orientation of each DNA molecule, thereby establishing short, double-labelled DNA molecules as probes of 3D orientation of anything to which one can attach them firmly. PMID:26509412

  10. 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.

  11. 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.

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

    DOE PAGES

    Seipp, Charles A.; Williams, Neil J.; Bryantsev, Vyacheslav S.; ...

    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.

  13. 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.

  14. Stereoselective synthesis of 3-substituted tetrahydropyrazinoisoquinolines via intramolecular cyclization of enantiomerically enriched dihydro-2H-pyrazines.

    PubMed

    Reginato, Gianna; Catalani, Maria Pia; Pezzati, Bernardo; Di Fabio, Romano; Bernardelli, Andrea; Curcuruto, Ornella; Moro, Elisa; Pozzan, Alfonso; Mordini, Alessandro

    2015-02-06

    The preparation of 3-substituted tetrahydropyrazinoisoquinolines using the tributyltin hydride mediated intramolecular radical cyclization of suitably protected 2-substituted 3,4-dihydropyrazines is reported. The compounds are obtained as single enantiomers, as the relative configuration of the new generated stereogenic center is driven by the stereochemistry of the 2-substituted carbon in the starting materials, which is in turn derived from naturally occurring amino acids.

  15. Enantioselective synthesis of benzoindolizidine derivatives using chiral phase-transfer catalytic intramolecular domino aza-Michael addition/alkylation.

    PubMed

    Guo, Jiajia; Yu, Shouyun

    2015-01-28

    An efficient and enantioselective strategy to synthesize benzoindolizidines from α,β-unsaturated amino ketones via domino intramolecular aza-Michael addition/alkylation was developed. These reactions were enabled by cinchona alkaloid-derived quaternary ammonium salts as the phase-transfer catalyst. A variety of benzoindolizidines were prepared in good yields (up to 93%) and enantioselectivities (up to 92.8:7.2 er).

  16. The Intramolecular Asymmetric Allylation of Aldehydes via Organo-SOMO Catalysis: A Novel Approach to Ring Construction.

    PubMed

    Pham, Phong V; Ashton, Kate; Macmillan, David W C

    2011-08-01

    The intramolecular asymmetric cyclization of aldehydes has been accomplished using singly occupied molecular orbital (SOMO) catalysis. Selective oxidation of chiral enamines (formed by the condensation of an aldehyde and a secondary amine catalyst) leads to the formation of a 3π-electron radical species. These chiral SOMO-activated radical cations undergo enantioselective cyclization with an array of pendent allylsilanes thus efficiently providing a new approach to the construction of five-, six- and seven-membered carbocycles and heterocycles.

  17. FeCl3·6H2O-catalyzed intramolecular allylic amination: synthesis of substituted dihydroquinolines and quinolines.

    PubMed

    Wang, Zhiming; Li, Shen; Yu, Bin; Wu, Haibo; Wang, Yurong; Sun, Xiaoqiang

    2012-10-05

    A facile and efficient method to synthesize 2- or 4-substituted 1,2-dihydroquinolines and quinolines catalyzed by FeCl(3)·6H(2)O (2 mol %) was described. The iron-catalyzed intramolecular allylic amination of 2-aminophenyl-1-en-3-ols proceeded smoothly to afford 13 1,2-dihydroquinoline and 8 quinoline derivatives under mild reaction conditions with good to excellent yields (up to 96%).

  18. Backbone dynamics in an intramolecular prolylpeptide-SH3 complex from the diphtheria toxin repressor, DtxR

    PubMed Central

    Bhattacharya, Nilakshee; Yi, Myunggi; Zhou, Huan-Xiang; Logan, Timothy M.

    2008-01-01

    Summary The diphtheria toxin repressor contains an SH3-like domain that forms an intramolecular complex with a proline-rich (Pr) peptide segment and stabilizes the inactive state of the repressor. Upon activation of DtxR by transition metals, this intramolecular complex must dissociate as the SH3 domain and Pr segment form different interactions in the active repressor. In this study we investigate the dynamics of this intramolecular complex using backbone amide nuclear spin relaxation rates determined using NMR spectroscopy and molecular dynamics trajectories. The SH3 domain in the unbound and bound states showed typical dynamics in that the secondary structures were fairly ordered with high generalized order parameters and low effective correlation times while residues in the loops connecting β-strands exhibited reduced generalized order parameters and required additional motional terms to adequately model the relaxation rates. Residues forming the Pr segment exhibited low order parameters with internal rotational correlation times on the order of 0.6 – 1 ns. Further analysis showed that the SH3 domain was rich in millisecond timescale motions while the Pr segment was rich in motions on the 100s μs timescale. Molecular dynamics simultations indicated structural rearrangements that may contribute to the observed relaxation rates and, together with the observed relaxation rate data, suggested that the Pr segment exhibits a binding ↔ unbinding equilibrium. The results of this study provide new insights into the nature of the intramolecular complex and provide a better understanding of the biological role of the SH3 domain in regulating DtxR activity. PMID:17976643

  19. Mechanistic analysis of intramolecular free radical reactions toward synthesis of 7-azabicyclo[2.2.1]heptane derivatives.

    PubMed

    Soriano, Elena; Marco-Contelles, José

    2009-06-05

    The mechanisms for the formation of conformationally constrained epibatidine analogues by intramolecular free radical processes have been computationally addressed by means of DFT methods. The mechanism and the critical effect of the 7-nitrogen protecting group on the outcome of these radical-mediated cyclizations are discussed. Theoretical findings account for unexpected experimental results and can assist in the selection of proper precursors for a successful cyclization.

  20. Copper-catalyzed tandem azide-alkyne cycloaddition, Ullmann type C-N coupling, and intramolecular direct arylation.

    PubMed

    Pericherla, Kasiviswanadharaju; Jha, Amitabh; Khungar, Bharti; Kumar, Anil

    2013-09-06

    A ligand-free copper-catalyzed tandem azide-alkyne cycloaddition (CuAAC), Ullmann-type C-N coupling, and intramolecular direct arylation has been described. The designed strategy resulted in the synthesis of a novel trazole-fused azaheterocycle framework. The reaction gave good yields (59-77%) of 1,2,3-triazole-fused imidazo[1,2-a]pyridines in a single step.

  1. Synthesis of cis-octahydroindoles via intramolecular 1,3-dipolar cycloaddition of 2-acyl-5-aminooxazolium salts.

    PubMed

    Basch, Corey H; Brinck, Jameson A; Ramos, Joaquin E; Habay, Stephen A; Yap, Glenn P A

    2012-11-16

    A concise method for the diastereoselective synthesis of octahydroindoles is presented. The products contain 2-amido and 7-hydroxyl substituents. A series of 2-acyl-5-aminooxazoles were prepared in one step. Upon methylation of the oxazole nitrogen atom, the substrates underwent rapid intramolecular 1,3-dipolar cycloaddition with a tethered alkene and, after reduction with excess hydride, produced octahydroindoles with excellent diastereoselectivity. The method allows for the installation of α-quaternary stereogenic carbon atoms.

  2. Planarized and Twisted Intramolecular Charge Transfer: A Concept for Fluorophores Showing Two Independent Rotations in Excited State.

    PubMed

    Haberhauer, Gebhard

    2017-07-12

    TICT (twisted intramolecular charge transfer) compounds are characterized by showing a rotation around a single bond in the excited state: starting from an almost planar geometry in the ground state, a twisted system is formed in the electronic excited state. The previously reported PLICT (planarized intramolecular charge transfer) compounds show inverse behavior: starting from a twisted geometry in the electronic ground state, a planarized system is formed in the excited state by rotation around a single bond. Here, a concept for planarized and twisted intramolecular charge transfer (PLATICT) states is presented which amalgamates both (TICT and PLICT) effects. Due to an intramolecular charge transfer, both a twisting around one single bond and a planarization around another one occurs. In sum, the PLATICT system shows two independent rotations around different axes in the excited state. By means of quantum chemical calculations (TD-cam-B3LYP and CC2) and experimental studies, it is demonstrated that N-aryl-substituted 1-aminoindoles are able to form photoinduced PLATICT states. In the fluorescence spectra of N-aryl-substituted 1-aminoindoles with a methoxycarbonyl or a cyano group as substituent in the aryl ring, very large Stokes shifts (ca. 18 000 cm(-1) ; >250 nm) are observed. The two independent rotations in the excited state, the very large Stokes shifts and their easy availability starting from indoline, make them very attractive for use as optical switches and motors in various fields of chemistry. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. 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.

  4. Donor-Acceptor Conjugated Linear Polyenes: A Study of Excited State Intramolecular Charge Transfer, Photoisomerization and Fluorescence Probe Properties.

    PubMed

    Hota, Prasanta Kumar; Singh, Anil Kumar

    2014-07-27

    Numerous studies of donor-acceptor conjugated linear polyenes have been carried out with the goal to understand the exact nature of the excited state electronic structure and dynamics. In this article we discuss our endeavours with regard to the excited state intramolecular charge transfer, photoisomerization and fluorescence probe properties of various donor-acceptor substituted compounds of diphenylpolyene [Ar(CH = CH) n Ar] series and ethenylindoles.

  5. Intramolecular alkylative arylation of oxabicylic alkene: a potential diene approach for the synthesis of estrone and analogous steroid structures.

    PubMed

    Li, Wei-Dong Z; Wei, Kun

    2004-04-15

    Regioselective and stereospecific intramolecular alkylative arylation of unsaturated oxabicyclic diol 6, mediated by Lewis acid or strong protic acid to give the tetracyclic products 7a and 7b, as shown above, represents the first example of an electrophilic (cationic in character) ring-opening-cyclization of oxabicyclic alkene. This constitutes the key cyclization step for a long-standing and potentially useful diene approach for the synthesis of estrone and analogous steroid structures. [structure: see text

  6. Palladium-Catalyzed Tandem Carbene Migratory Insertion and Intramolecular Cyclization: Synthesis of Chromeno[4,3-b]chromene Compounds.

    PubMed

    Shang, Xue Song; Li, Nian Tai; Siyang, Hai Xiao; Liu, Pei Nian

    2015-05-01

    Chromeno[4,3-b]chromene is a ubiquitous structural motif found in various pharmaceuticals and biologically active compounds. A concise palladium-catalyzed reaction of vinyl iodides and salicyl N-tosylhydrazones has been achieved to afford a series of compounds containing the chromeno[4,3-b]chromene scaffold in moderate to high yield. This tandem reaction involves palladium(II) carbene migratory insertion and intramolecular cyclization assisted by an O nucleophile and tolerates various functional groups.

  7. Remote Stereoinductive Intramolecular Nitrile Oxide Cycloaddition: Asymmetric Total Synthesis and Structure Revision of (-)-11β-Hydroxycurvularin.

    PubMed

    Choe, Hyeonjeong; Pham, Thuy Trang; Lee, Joo Yun; Latif, Muhammad; Park, Haeil; Kang, Young Kee; Lee, Jongkook

    2016-03-18

    The first total synthesis and structure revision of (-)-11β-hydroxycurvularin (1b), a macrolide possessing a β-hydroxyketone moiety, were accomplished. The β-hydroxyketone moiety in this natural product was introduced by cleavage of the N-O bond in an isoxazoline ring that was formed diastereoselectively in a 1,5-remote stereocontrolled fashion by employing intramolecular nitrile oxide cycloaddition.

  8. Use of a methoxy substituent in controlling the stereochemistry of intramolecular iron-mediated diene/olefin cyclocoupling.

    PubMed

    Pearson, A J; Dorange, I B

    2001-05-04

    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 postcyclization 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.

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

    PubMed

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

    2012-04-16

    Intramolecular π-π stacking interaction in one kind of phosphorescent cationic iridium complexes has been controlled through fluorination of the pendant phenyl rings on the ancillary ligands. Two blue-green-emitting cationic iridium complexes, [Ir(ppy)(2)(F2phpzpy)]PF(6) (2) and [Ir(ppy)(2)(F5phpzpy)]PF(6) (3), with the pendant phenyl rings on the ancillary ligands substituted with two and five fluorine atoms, respectively, have been synthesized and compared to the parent complex, [Ir(ppy)(2)(phpzpy)]PF(6) (1). Here Hppy is 2-phenylpyridine, F2phpzpy is 2-(1-(3,5-difluorophenyl)-1H-pyrazol-3-yl)pyridine, F5phpzpy is 2-(1-pentafluorophenyl-1H-pyrazol-3-yl)-pyridine, and phpzpy is 2-(1-phenyl-1H-pyrazol-3-yl)pyridine. Single crystal structures reveal that the pendant phenyl rings on the ancillary ligands stack to the phenyl rings of the ppy ligands, with dihedral angles of 21°, 18°, and 5.0° between least-squares planes for complexes 1, 2, and 3, respectively, and centroid-centroid distances of 3.75, 3.65, and 3.52 Å for complexes 1, 2, and 3, respectively, indicating progressively reinforced intramolecular π-π stacking interactions from complexes 1 to 2 and 3. Compared to complex 1, complex 3 with a significantly reinforced intramolecular face-to-face π-π stacking interaction exhibits a significantly enhanced (by 1 order of magnitude) photoluminescent efficiency in solution. Theoretical calculations reveal that in complex 3 it is unfavorable in energy for the pentafluorophenyl ring to swing by a large degree and the intramolecular π-π stacking interaction remains on the lowest triplet state. © 2012 American Chemical Society

  10. 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.

  11. 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

    2014-11-07

    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.

  12. Intramolecular monomer-on-monomer (MoM) Mitsunobu cyclization for the synthesis of benzofused thiadiazepine-dioxides.

    PubMed

    Maity, Pradip K; Kainz, Quirin M; Faisal, Saqib; Rolfe, Alan; Samarakoon, Thiwanka B; Basha, Fatima Z; Reiser, Oliver; Hanson, Paul R

    2011-12-14

    The utilization of a monomer-on-monomer (MoM) intramolecular Mitsunobu cyclization reaction employing norbornenyl-tagged (Nb-tagged) reagents is reported for the synthesis of benzofused thiadiazepine-dioxides. Facile purification was achieved via ring-opening metathesis (ROM) polymerization initiated by one of three metathesis catalyst methods: (i) free metathesis catalyst, (ii) surface-initiated catalyst-armed silica, or (iii) surface-initiated catalyst-armed Co/C magnetic nanoparticles.

  13. Di- and triheteroarylalkanes via self-condensation and intramolecular Friedel-Crafts type reaction of heteroaryl alcohols.

    PubMed

    Dhiman, Seema; Ramasastry, S S V

    2013-12-14

    An efficient synthetic approach to diheteroarylmethanes and 1,3-diheteroarylpropenes has been developed via Yb(III)-catalyzed sequential self-condensation of 2-furfuryl (or 2-thienyl or 3-indolyl) alcohols followed by intramolecular Friedel-Crafts type reaction and elimination of an aldehyde. This method offers a powerful entry and a potential alternative to the traditional synthesis of diheteroarylalkanes, which are precursors to the synthesis of several intriguing heteroaryls and more significantly, to the synthesis of biofuels.

  14. Diverted organic synthesis (DOS): accessing a new, natural product inspired, neurotrophically active scaffold through an intramolecular Pauson-Khand reaction.

    PubMed

    Mehta, Goverdhan; Samineni, Ramesh; Srihari, Pabbaraja; Reddy, R Gajendra; Chakravarty, Sumana

    2012-09-14

    Drawing inspiration from the impressive neurotrophic activity exhibited by the natural product paecilomycine A, we have designed a new natural product-like scaffold employing an intramolecular Pauson-Khand reaction. Several compounds based on the new designer scaffold exhibited promising neurotrophic activity and are worthy of further biological evaluation. Our findings also highlight the importance of a DOS strategy in creating useful therapeutical leads.

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

    SciTech Connect

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

    2015-11-30

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

  16. Palladium-catalyzed C-H activation/intramolecular amination reaction: a new route to 3-aryl/alkylindazoles.

    PubMed

    Inamoto, Kiyofumi; Saito, Tadataka; Katsuno, Mika; Sakamoto, Takao; Hiroya, Kou

    2007-07-19

    A method for the catalytic C-H activation of hydrazone compounds followed by intramolecular amination is described. It requires the use of a catalytic amount of Pd(OAc)2 in the presence of Cu(OAc)2 and AgOCOCF3, which efficiently effects the cyclization to afford variously substituted indazoles. The reactions proceed under relatively mild conditions and thus tolerate a variety of functional groups, including alkoxycarbonyl and cyano groups and halogen atoms.

  17. A novel synthesis of 2-aryl-2H-indazoles via a palladium-catalyzed intramolecular amination reaction.

    PubMed

    Song, J J; Yee, N K

    2000-02-24

    [reaction: see text] A variety of 2-aryl-2H-indazoles were synthesized by the palladium-catalyzed intramolecular amination of the corresponding N-aryl-N(o-bromobenzyl)hydrazines. Of several sets of reaction conditions surveyed, the combination of Pd(OAc)2/dppf/tBuONa gave the best results. This method applies to a wide scope of substrates containing electron-donating and electron-withdrawing substituents.

  18. Pd(0)-catalyzed intramolecular α-arylation of sulfones: domino reactions in the synthesis of functionalized tetrahydroisoquinolines.

    PubMed

    Solé, Daniel; Pérez-Janer, Ferran; Mancuso, Raffaella

    2015-03-16

    A new strategy for the synthesis of tetrahydroisoquinolines based on the Pd(0)-catalyzed intramolecular α-arylation of sulfones is reported. The combination of this Pd-catalyzed reaction with intermolecular Michael and aza-Michael reactions allows the development of two- and three-step domino processes to synthesize diversely functionalized scaffolds from readily available starting materials. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. A facile phenol-driven intramolecular diastereoselective thermal/base-catalyzed dipolar [2+2] annulation reactions: an easy access to complex bioactive natural and unnatural benzopyran congeners.

    PubMed

    Mondal, Mukulesh; Puranik, Vedavati G; Argade, Narshinha P

    2007-03-16

    The complex bioactive natural and unnatural benzopyran congeners have been synthesized using one-/two-step approaches in very good yields from the reactions of two different dihydroxyphthalides, natural resorcyclic acid derivative, and trihydroxybenzophenone with citral and/or farnesal, via the phenol-driven intramolecular diastereoselective thermal/base-catalyzed dipolar [2+2] cycloaddition reactions and three different thermal intramolecular cyclization reactions. The effects of the nature and the position of phenolic groups in the starting materials on the course of these cycloaddition reactions have also been described. Depending upon the absence or presence of intramolecular hydrogen bonding of the phenolic group with the carbonyl moiety in the starting materials, these phenol-driven intramolecular thermal/base-catalyzed dipolar [2+2] cycloaddition reactions either furnished the kinetically controlled products or directly formed the thermodynamically controlled rearranged products, respectively.

  20. Regiospecific and stereoselective syntheses of (+/-) morphine, codeine, and thebaine via a highly stereocontrolled intramolecular 4 + 2 cycloaddition leading to a phenanthrofuran system.

    PubMed

    Stork, Gilbert; Yamashita, Ayako; Adams, Julian; Schulte, Gary R; Chesworth, Richard; Miyazaki, Yoji; Farmer, Jay J

    2009-08-19

    Total syntheses of the morphine alkaloids are described that use a direct stereoselective formation of the phenanthrofuran system via an intramolecular 4 + 2 cycloaddition of a diene tethered to the 4-position of a 7-methoxybenzofuran-3-carboxylic acid ester.