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Showing papers on "Intramolecular force published in 2003"


Journal ArticleDOI
TL;DR: The Rehybridization of the Acceptor (RICT) and Planarization ofThe Molecule (PICT) III is presented, with a comparison of the effects on yield and radiationless deactivation processes.
Abstract: 6. Rehybridization of the Acceptor (RICT) 3908 7. Planarization of the Molecule (PICT) 3909 III. Fluorescence Spectroscopy 3909 A. Solvent Effects and the Model Compounds 3909 1. Solvent Effects on the Spectra 3909 2. Steric Effects and Model Compounds 3911 3. Bandwidths 3913 4. Isoemissive Points 3914 B. Dipole Moments 3915 C. Radiative Rates and Transition Moments 3916 1. Quantum Yields and Radiationless Deactivation Processes 3916

2,924 citations



Journal ArticleDOI
TL;DR: These results provide the foundation of a unified enamine catalysis mechanism of proline-catalyzed inter- and intramolecular aldol reactions, and are supported by B3LYP/6-31G* calculations.
Abstract: Contrary to the widely accepted mechanism of the Hajos−Parrish−Eder−Sauer−Wiechert reaction, we have obtained evidence for the involvement of only one proline molecule in the transition states of both inter- and intramolecular aldol reactions. Our conclusions are based on kinetic measurements and the absence of nonlinear and dilution effects on the asymmetric catalysis, and are supported by B3LYP/6-31G* calculations. Complementary to recent theoretical studies, our results provide the foundation of a unified enamine catalysis mechanism of proline-catalyzed inter- and intramolecular aldol reactions.

421 citations


Journal ArticleDOI
15 Feb 2003-Proteins
TL;DR: For both solutes, the distribution from the QM/MM simulation shows greater similarity with the distribution in high‐resolution protein structures than is the case for any of the MM simulations.
Abstract: We compare the conformational distributions of Ace-Ala-Nme and Ace-Gly-Nme sampled in long simulations with several molecular mechanics (MM) force fields and with a fast combined quantum mechanics/molecular mechanics (QM/MM) force field, in which the solute's intramolecular energy and forces are calculated with the self-consistent charge density functional tight binding method (SCCDFTB), and the solvent is represented by either one of the well-known SPC and TIP3P models. All MM force fields give two main states for Ace-Ala-Nme, beta and alpha separated by free energy barriers, but the ratio in which these are sampled varies by a factor of 30, from a high in favor of beta of 6 to a low of 1/5. The frequency of transitions between states is particularly low with the amber and charmm force fields, for which the distributions are noticeably narrower, and the energy barriers between states higher. The lower of the two barriers lies between alpha and beta at values of psi near 0 for all MM simulations except for charmm22. The results of the QM/MM simulations vary less with the choice of MM force field; the ratio beta/alpha varies between 1.5 and 2.2, the easy pass lies at psi near 0, and transitions between states are more frequent than for amber and charmm, but less frequent than for cedar. For Ace-Gly-Nme, all force fields locate a diffuse stable region around phi = pi and psi = pi, whereas the amber force field gives two additional densely sampled states near phi = +/-100 degrees and psi = 0, which are also found with the QM/MM force field. For both solutes, the distribution from the QM/MM simulation shows greater similarity with the distribution in high-resolution protein structures than is the case for any of the MM simulations.

266 citations



Journal ArticleDOI
Wenke Zhang1, Xi Zhang1
TL;DR: In this paper, the effect of side groups and tacticity of polymers on single-chain elasticity is discussed. And the relation between the force pattern and the adsorptive conformation and strength is discussed, and the effects of inter-and intra-and inter-molecular suprastructure on polymers are discussed.

238 citations


Journal Article
TL;DR: This study has demonstrated that telomestatin interacts preferentially with intramolecular versus intermolecular G-quadruplex structures and also has a 70-fold selectivity for intramolescular G -quadru Plex structures over duplex DNA, and induces anaphase bridges in sea urchin embryos, whereas TMPyP4 did not have this effect.
Abstract: Demonstration of the existence of G-quadruplex structures in telomeres of Stylonychia macronuclei and in the promoter of c-myc in human cells has validated these secondary DNA structures as potential targets for drug design. The next important issue is the selectivity of G-quadruplex-interactive agents for the different types of G-quadruplex structures. In this study, we have taken an important step in associating specific biological effects of these drugs with selective interaction with either intermolecular or intramolecular G-quadruplex structures formed in telomeres. Telomestatin is a natural product isolated from Streptomyces anulatus 3533-SV4 and has been shown to be a very potent telomerase inhibitor through its G-quadruplex interaction. We have demonstrated that telomestatin interacts preferentially with intramolecular versus intermolecular G-quadruplex structures and also has a 70-fold selectivity for intramolecular G-quadruplex structures over duplex DNA. Telomestatin is able to stabilize G-quadruplex structures that are formed from duplex human telomeric DNA as well as from single-stranded DNA. Importantly, telomestatin stabilizes these G-quadruplex structures in the absence of monovalent cations, which is a unique characteristic among G-quadruplex-interactive compounds. At noncytotoxic concentrations, telomestatin suppresses the proliferation of telomerase-positive cells within several weeks. In contrast, TMPyP4, a compound that preferentially facilitates the formation of intermolecular G-quadruplex structures, suppresses the proliferation of alternative lengthening of telomeres (ALT)-positive cells as well as telomerase-positive cells. We have also demonstrated that TMPyP4 induces anaphase bridges in sea urchin embryos, whereas telomestatin did not have this effect, leading us to conclude that the selectivity of telomestatin for intramolecular G-quadruplex structures and TMPyP4 for intermolecular G-quadruplex structures is important in mediating different biological effects: stabilization of intramolecular G-quadruplex structures produces telomerase inhibition and accelerated telomere shortening, whereas facilitation of the formation of intermolecular G-quadruplex structures induces the formation of anaphase bridges.

201 citations


Journal ArticleDOI
TL;DR: A novel palladium migration/arylation methodology for the synthesis of complex fused polycycles has been developed, in which one or more sequential Pd-catalyzed intramolecular migration processes involving C-H activation are employed.
Abstract: A novel palladium migration/arylation methodology for the synthesis of complex fused polycycles has been developed, in which one or more sequential Pd-catalyzed intramolecular migration processes involving C-H activation are employed. The chemistry works best with electron-rich aromatics, which is in agreement with the idea that these palladium-catalyzed C-H activation reactions parallel electrophilic aromatic substitution.

179 citations


Journal ArticleDOI
TL;DR: It is demonstrated that intramolecular association or folding prevails over intermolecular interaction or self-assembling in the concentration region from 1 microM to 0.1 M, and folded polymeric nanostructures have absorption and fluorescence properties that are distinct from those of unfolded polymers or free monomers.
Abstract: Model foldable polymers with sequences of rigid hydrophobic chromophores and flexible hydrophilic tetra(ethylene glycol) were synthesized and used as a paradigm for studying molecular-folding and self-assembly phenomena. Our results demonstrate that intramolecular association or folding prevails over intermolecular interaction or self-assembling in the concentration region from 1 microM to 0.1 M. Importantly, folded polymeric nanostructures have absorption and fluorescence properties that are distinct from those of unfolded polymers or free monomers. We hypothesize that the origins of folding and self-assembly come from interactions between molecular units, and that the key parameter that regulates the on-and-off of such interactions is the distance R separating the two molecular units. Each molecular unit produces a characteristic force field, and when another molecular unit enters this field, the probability that the two units will interact increases significantly. A preliminary estimate of the radius of such a force field for the perylene tetracarboxylic diimide chromophore is about 90-120 A. As a result, phenomena associated with folding or self-assembly of molecular species are observed when these conditions are met in solution.

178 citations


Journal ArticleDOI
TL;DR: Spectral behavior with annealing indicates that the Argon matrix-isolation infrared spectra of 1-methoxy-2-(dimethylamino)ethane exhibit a band that is assigned to the most stable conformer, trans-gauche-(trans| gauche'), with an intramolecular C-H...O hydrogen bond.
Abstract: Experimental evidence for intramolecular blue-shifting C-H...O hydrogen bonding is presented. Argon matrix-isolation infrared spectra of 1-methoxy-2-(dimethylamino)ethane exhibit a band at 3016.5 cm-1. Spectral behavior with annealing indicates that this band is assigned to the most stable conformer, trans-gauche-(trans|gauche'), with an intramolecular C-H...O hydrogen bond. Density functional calculations show that this band arises from the stretching vibration of the C-H bond participating in the formation of the C-H...O hydrogen bond. The C-H bond is shortened by 0.004 A, and the C-H stretching band is blue-shifted by at least 35 cm-1 on the formation of the hydrogen bond. The (C)H...O distance is calculated as 2.38 A, which is shorter than the corresponding van der Waals separation by 0.3 A.

177 citations


Journal ArticleDOI
TL;DR: Regioselective cyclizations, where R(3) = H, can be achieved in high yield under CuI/1,10-phenanthroline-catalyzed conditions, whereas palladium catalysis results in the formation of regioisomeric products.

Journal ArticleDOI
TL;DR: The effect of charge delocalization on charge recombination dynamics of a catechol−TiO2 nanoparticle charge transfer (CT) complex and an intramolecular CT complex, [Ti(cat)3]2- were compared in this paper.
Abstract: Ultrafast electron-transfer dynamics of a catechol−TiO2 nanoparticle charge transfer (CT) complex and an intramolecular CT complex, [Ti(cat)3]2- were compared. Both complexes show similar CT bands, suggesting similar donor (catechol) and acceptor(Ti) orbitals are involved in CT transition. However, the electron is localized on one Ti center in the [Ti(cat)3] complex, but can delocalize into other Ti centers in TiO2 nanoparticles. The effect of charge delocalization on charge recombination dynamics was examined by comparing these complexes. In both cases, 400 nm excitation of the CT bands led to instantaneous promotion of an electron from a catechol ligand to a Ti(IV) center(s). In the molecular complex, the back electron-transfer dynamics from the Ti center to catechol ligand was observed on a 200 fs time scale. In the adsorbate-to-nanoparticle complex, back ET was much more complex, consisting of a 0.4 ps fast component and multiple slower components. The fast component was attributed to electrons trappe...

Journal ArticleDOI
TL;DR: Intramolecular hydrogen transfer in five model amide and peptide radicals and cation-radicals was investigated by combined B3LYP-MP2 calculations and predicted k(H migration)/k(H loss) branching ratios that increase with the ring size of the cyclic transition state for the migration.
Abstract: Intramolecular hydrogen transfer in five model amide and peptide radicals and cation-radicals was investigated by combined B3LYP-MP2 calculations. Hypervalent ammonium radicals produced by electron capture in protonated peptides undergo competitive elimination of ammonia, H-atom loss, and H-atom migration to neighboring amide carbonyls. The calculated transition state energies for H-atom migration are slightly but uniformly lower than those for H-atom loss. Transition state theory calculations with inclusion of quantum tunneling effects predict k(H migration)/k(H loss) branching ratios that increase with the ring size of the cyclic transition state for the migration. Intramolecular hydrogen-atom migration in amide and peptide radicals can be described by the proton-coupled electron transfer mechanism. The migrating hydrogen atom shows a negligible spin density and substantial positive charge that are typical of a proton migration. Electron transfer occurs through a pi-orbital system and proceeds in the same (clockwise) or opposite (counterclockwise) direction as the proton motion, depending on the electronic properties of the chain connecting the ammonium group and the amide bond.

Journal ArticleDOI
TL;DR: The use of an in situ generated Ni(0) catalyst associated with 2,2'-bipyridine or N,N'-bis(2,6-diisopropylphenyl)dihydroimidazol-2-ylidene (SIPr) as a ligand and NaO-t-Bu as the base for the intramolecular coupling of aryl chlorides with amines is described.

Journal ArticleDOI
TL;DR: The stereocontrolled total synthesis of (-)-ephedradine A has been accomplished and features an asymmetric C-H insertion reaction, an intramolecular ester-amide exchange reaction, and a Sharpless asymmetric aminohydroxylation reaction.
Abstract: The stereocontrolled total synthesis of (−)-ephedradine A has been accomplished. The synthesis features an asymmetric C−H insertion reaction, an intramolecular ester−amide exchange reaction, and a Sharpless asymmetric aminohydroxylation reaction. Construction of the complex macrocyclic ring was performed by Ns-strategy and an intramolecular aza-Wittig reaction.

Journal ArticleDOI
TL;DR: In this article, a dipole-in-a-sphere model is used to estimate the solvation stabilization energies of peridinin a variety of solvents.
Abstract: We present theoretical confirmation of an intramolecular charge-transfer (CT) state in peridinin in agreement with experimental results of Frank and co-workers (J. Phys. Chem. B 1999, 103, 8751 and J. Phys. Chem. B 2000, 104, 4569). Quantum chemical calculations using time-dependent density functional theory under the Tamm−Dancoff approximation were made on two structures: fully optimized peridinin and a molecule from the crystal structure of peridinin−chlorophyll−protein. The CT state appears as the third and second excited singlet state, respectively, for the two structures. A dipole-in-a-sphere model is used to estimate the solvation stabilization energies of each state in a variety of solvents. The energy of the CT state is shown to decrease dramatically in solvents of increasing polarity while the energy of the dark S1 (Ag--like) state remains comparatively constant.


Journal ArticleDOI
TL;DR: Chiral non-racemic complexes [ML{N(SiMe2H)2}(thf)] were found to be effective catalysts for the intramolecular hydroamination of aminoalkenes, but new amino/phenoxide ligand designs without reducible functional groups led to long-lived and enantioselective catalysts as mentioned in this paper.

Journal ArticleDOI
TL;DR: A unique system is demonstrated, in which ESIPT incorporates an appreciably large energy barrier fine-tuned by the skeletal reorganization, which makes 1a-d systems ideal models for probing the reaction potential energy surface.
Abstract: The excited-state intramolecular proton transfer (ESIPT) reaction in five-membered N−H···N hydrogen-bonding systems has been explored through design and syntheses of a series of 5-(2-pyridyl) 1-H-pyrazoles 1a−d. The ESIPT mechanism was confirmed through spectroscopy, relaxation dynamics, and corresponding methylated analogues. The results demonstrate for the first time a unique system among ESIPT molecules, in which ESIPT incorporates an appreciably large energy barrier fine-tuned by the skeletal reorganization. This makes 1a−d systems ideal models for probing the reaction potential energy surface.

Journal ArticleDOI
TL;DR: Intramolecular addition of a boron-cyano bond across a carbon-carbon triple bond was achieved using palladium and nickel catalysts, which served as new precursors for the synthesis of highly substituted alpha,beta-unsaturated nitriles via transition-metal-catalyzed transformations.
Abstract: Intramolecular addition of a boron−cyano bond across a carbon−carbon triple bond was achieved using palladium and nickel catalysts. Cyano(diisopropylamino)boryl homopropargyl ethers underwent regio- and stereoselective 5-exo cyclization, forming five-membered cyclic boryl ethers in high yields. The cyanoboration products thus obtained served as new precursors for the synthesis of highly substituted α,β-unsaturated nitriles via transition-metal-catalyzed transformations.


Journal ArticleDOI
TL;DR: A homologous series of bis-silicon-bridged stilbenes has been synthesized on the basis of a new intramolecular reductive cyclization of bis(o-silyl)-diphenylacetylenes with excess lithium naphthalenide.
Abstract: A homologous series of bis-silicon-bridged stilbenes has been synthesized on the basis of a new intramolecular reductive cyclization of bis(o-silyl)-diphenylacetylene. Thus, the reaction of bis(o-silyl)-diphenylacetylenes with excess lithium naphthalenide undergoes the two-electron reduction at the acetylene moiety to produce a dianion intermediate, which further undergoes a double cyclization in a 5-exo mode to produce the bis-silicon-bridged stilbenes. This methodology can also be applied to the synthesis of tetrakis-silicon-bridged bis(styryl)benzenes. The silicon-bridged pi-conjugated systems thus prepared show intense fluorescence in the visible region. Comparison of a bis-silicon-bridged stilbene with its carbon analogue demonstrates the substantial effects of the silicon-bridges on the electronic structures and thus on the fluorescence properties.

Journal ArticleDOI
TL;DR: The dichotomy between ketone alpha-arylation and carbonyl-addition in the reactions of omega-(2-haloanilino) alkanones has been rationalized by the intermediacy of unprecedented four-membered azapalladacycles, from which X-ray data and chemical behavior are reported.
Abstract: An exploration of the scope and limitations of Pd(0)-catalyzed intramolecular coupling reactions of amino-tethered aryl halides and ketones has been conducted. Two different and competitive reactio...

Journal ArticleDOI
TL;DR: In this article, the structure and thermodynamics of the hydrated electron were probed with resonance Raman spectroscopy of isotopic mixtures of H2O and D2O.
Abstract: The structure and thermodynamics of the hydrated electron are probed with resonance Raman spectroscopy of isotopic mixtures of H2O and D2O. The strongly enhanced intramolecular bends of e-(H2O) and e-(D2O) produce single downshifted bands, whereas the e-(HOD) bend consists of two components: one slightly upshifted from the 1446 cm-1 bulk frequency to 1457 cm-1 and the other strongly downshifted to ∼1396 cm-1. This 60 cm-1 split and the 200 (120) cm-1 downshifts of the OH (OD) stretch frequencies relative to bulk water reveal that the water molecules that are Franck−Condon coupled to the electron are in an asymmetric environment, with one proton forming a strong hydrogen bond to the electron. The downshifted bend and librational frequencies also indicate significantly weakened torsional restoring forces on the water molecules of e-(aq), which suggests that the outlying proton is a poor hydrogen bond donor to the surrounding solvent. A 1.6-fold thermodynamic preference of the electron for H2O is observed b...

Journal ArticleDOI
TL;DR: The results clearly demonstrate that the molecular engineering criteria for metal-containing nonlinear optical chromophores can differ dramatically from those for purely organic compounds.
Abstract: We have used several techniques, including hyper-Rayleigh scattering and Stark spectroscopy, to investigate the effects of polyene chain length on the optical properties of complexes containing ruthenium(II) electron donor groups and pyridinium electron acceptors. In marked contrast with all other known donor-acceptor polyenes, conjugation extension beyond a single double bond in the dipolar complexes studied leads to blue-shifting of the intramolecular charge-transfer absorptions. Furthermore, the static first hyperpolarizabilities beta0 become maximized with trans-1,3-butadienyl linkages and then decrease in complexes with three CH=CH bonds. Our results clearly demonstrate that the molecular engineering criteria for metal-containing nonlinear optical chromophores can differ dramatically from those for purely organic compounds.

Journal ArticleDOI
TL;DR: In this paper, an empirical force field is used in molecular simulations for two Noxide species, N,N,N-trimethylamineN-oxide (TMAO) and N-methylmorpholine-Noxide (NMMO).
Abstract: Aliphatic N-oxides as cosolvents with water play an important role in stabilizing and destabilizing the structure of biopolymers such as cellulose and proteins. To allow for detailed microscopic investigations, an empirical force field to be used in molecular simulations is developed for two N-oxide species, N,N,N-trimethylamineN-oxide (TMAO) and N-methylmorpholine-N-oxide (NMMO). The intra- and intermolecular force field is parametrized mainly on the basis of quantum-chemical calculations and is tested against available experimental spectroscopic, crystallographic, and liquid state data. Special emphasis is put on the identification of transferable potential terms in order to guide future parametrization of other species. By construction, the force field is compatible with widely used potential functions for proteins and carbohydrates. With the resulting parameter set, molecular dynamics simulations are carried out on binary mixtures of water and N-oxides, revealing structural features and the influence of intramolecular N-oxide flexibility. Limitations and possible extensions of the presented models are also discussed.


Journal ArticleDOI
TL;DR: The electron transmission and dissociative electron attachment (DEA) spectra of chloroalkyl ethene and ethyne derivatives are reported in this paper, where the virtual orbital energies for the optimised geometries of the neutral states of these molecules and other related π-systems are evaluated.
Abstract: The electron transmission (ET) and dissociative electron attachment (DEA) spectra of chloroalkyl ethene and ethyne derivatives are reported. B3LYP/6-31G* calculations are employed to evaluate the virtual orbital energies for the optimised geometries of the neutral states of these molecules and other related π-systems. The calculated π* MO energies correlate linearly with the energies of electron attachment to the π* LUMO measured in the ET spectra with a correlation coefficient of 0.993. The vertical attachment energies supplied by B3LYP/6-311+G** calculations, where the basis set includes diffuse functions, are often in significant disagreement with experiment, describing the singly occupied MO of the lowest-lying anion state as a diffuse σ* MO rather than a valence π* MO. The relative Cl− anion currents measured in the DEA spectra of the present molecular systems are compared to those previously found in benzene analogues. The Cl− yield reflects the efficiency of intramolecular electron transfer from the π-system (where the extra electron is first trapped) to the remote chlorine atom. Replacement of a carbon atom with a silicon atom in the intermediate saturated alkyl chain causes a notable increase of the Cl− current, ascribed to the lower energy of the empty σ*Si–C MOs and consequent greater ability to promote through-bond coupling between the π* and σ*C–Cl MOs. Comparison between the corresponding benzene, ethene and ethyne derivatives reveals that the Cl− current is also significantly influenced by the nature of the π-functional group, in agreement with the inverse dependence on energy of the lifetime of the temporary π* anion state.

Journal ArticleDOI
TL;DR: The role of solute−solvent hydrogen bonding in modulating the excited-state intramolecular proton transfer (ESIPT) reaction in 3-hydroxyflavone derivatives was discussed in this paper.
Abstract: We address the important, frequently discussed, and still unresolved question of the role of solute−solvent hydrogen bonding in modulating the excited-state intramolecular proton transfer (ESIPT) reaction in 3-hydroxyflavone (3HF) derivatives, which provides a dramatic variation of the relative intensities of normal (N*) and phototautomer (T*) emissive species. We synthesized a new 3HF derivative, 5,6-benzo-4‘-diethylamino-3-hydroxyflavone (BFE), in which the additional benzene ring protects the 4-carbonyl from H-bonding with the protic solvents but allows the intramolecular bond with the 3-hydroxyl group, which is the pathway of ESIPT, to be maintained. The absorption and fluorescence properties of BFE and its parent analogue 4‘-diethylamino-3-hydroxyflavone (FE) were studied in a set of 20 representative solvents. In aprotic media, these dyes in absorption and fluorescence spectra show similar solvatochromism, whereas in protic solvents dramatic differences are observed, which demonstrate that for BFE t...

Journal ArticleDOI
TL;DR: The cyclic triamide of 3'-amino-3-biphenylcarboxlic acid is readily synthesized in a stepwise manner and represents a novel class of anion receptors with a large central cavity that binds more strongly to tetrahedral anions than spherical or planar anions in organic solvents.
Abstract: The cyclic triamide of 3'-amino-3-biphenylcarboxlic acid is readily synthesized in a stepwise manner and represents a novel class of anion receptors with a large central cavity. This macrocycle binds more strongly to tetrahedral anions than spherical or planar anions in organic solvents. The binding stoichiometries for anions with symmetrical charge distribution depend on the solvent polarity, while tetrahedral p-tosylate binds to the macrocycle with 1:1 stoichiometry in all solvents studied. The (1)H NMR chemical shift changes of the protons lining the interior of the macrocycle's central cavity also depend on the geometry of the bound anion. The importance of the convergent array of hydrogen bond donors for anion binding by the macrocycle was confirmed by control studies with an acyclic triamide and a macrocycle with intramolecular hydrogen bonds.