Showing papers on "Intramolecular force published in 1999"
TL;DR: In this paper, electrical transport measurements on single-wall carbon nanotubes (SWNTs) with intramolecular junctions are reported, showing that a metal-semiconductor junction behaves like a rectifying diode with nonlinear transport characteristics that are strongly asymmetric with respect to bias polarity.
Abstract: The ultimate device miniaturization would be to use individual molecules as functional devices. Single-wall carbon nanotubes (SWNTs) are promising candidates for achieving this: depending on their diameter and chirality, they are either one-dimensional metals or semiconductors1,2. Single-electron transistors employing metallic nanotubes3,4 and field-effect transistors employing semiconducting nanotubes5 have been demonstrated. Intramolecular devices have also been proposed which should display a range of other device functions6,7,8,9,10,11. For example, by introducing a pentagon and a heptagon into the hexagonal carbon lattice, two tube segments with different atomic and electronic structures can be seamlessly fused together to create intramolecular metal–metal, metal–semiconductor, or semiconductor–semiconductor junctions. Here we report electrical transport measurements on SWNTs with intramolecular junctions. We find that a metal–semiconductor junction behaves like a rectifying diode with nonlinear transport characteristics that are strongly asymmetric with respect to bias polarity. In the case of a metal–metal junction, the conductance appears to be strongly suppressed and it displays a power-law dependence on temperatures and applied voltage, consistent with tunnelling between the ends of two Luttinger liquids. Our results emphasize the need to consider screening and electron interactions when designing and modelling molecular devices. Realization of carbon-based molecular electronics will require future efforts in the controlled production of these intramolecular nanotube junctions.
1,485 citations
TL;DR: In this paper, a range of compounds in which TTF is covalently linked to an electron acceptor moiety by a variety of linking units, sometimes giving rise to an intramolecular charge transfer (ICT) interaction is reviewed.
Abstract: Although tetrathiafulvalene (TTF) and its derivatives have been extensively studied for more than 25 years as π-electron donors in intermolecular charge-transfer materials, the intriguing potential of TTF as a donor in an intramolecular sense has only recently been developed. Many versatile, functionalized TTF building blocks are now readily available, and this article will review a range of compounds in which TTF is covalently linked to an electron acceptor moiety by a variety of linking units, sometimes giving rise to an intramolecular charge-transfer (ICT) interaction, which is most frequently manifested in the optical and electrochemical properties. In this context, acceptor subunits include: tetracyano-p-quinodimethane, quinones, electron-deficient aryl groups, pyridinium and bipyridinium units, fullerenes, phthalocyanines, and mesomerically conjugated carbonyl, thiocarbonyl, ester, and related groups. This work paves the way for more systematic and detailed studies of TTF–spacer–A molecules (where A is an acceptor) in which there is increased control of the structural, electronic, optical, and magnetic properties arising from ICT interactions in the ground state, or in the excited state.
323 citations
TL;DR: Fluorescence quenching has been used to study the cooperative conformational transition in a series of oligo(phenylene ethynylene)s having tri(ethylene glycol) monomethyl ether side chains as discussed by the authors.
Abstract: Fluorescence quenching has been used to study the cooperative conformational transition in a series of oligo(phenylene ethynylene)s having tri(ethylene glycol) monomethyl ether side chains. In nonpolar solvents such as chloroform, the intensity of fluorescence emission from the backbone chromophore increases smoothly as the chain lengthens from the dimer through the octadecamer. In polar solvents such as acetonitrile, on the other hand, chains having more than eight units exhibit fluorescence quenching concomitant with the growth of an intramolecular excimer-like band. This observation is consistent with π-stacking of aromatic rings for chains that are long enough to fold back on themselves, driven by solvophobic interactions. Titration experiments in which the solvent composition was gradually changed from pure acetonitrile to pure chloroform showed sigmoidal curves characteristic of a cooperative transition. These data were analyzed using a two-state approximation and a model in which the free energy di...
312 citations
TL;DR: In this article, the conceptual van der Waals cut-off criterion was removed for establishing the presence of weak intermolecular and intramolecular interactions, and was replaced by a distance/angle criterion determined by the empirical approach outlined here.
Abstract: The extensive occurrence of C–H···Cl hydrogen bonds has been established through a systematic statistical analysis of the Cambridge Crystallographic Database; chloride anions are shown to be better hydrogen-bond accepor systems than neutral chloride-containing molecules, and a similar situation pertains for the other halides. As a result of this study, we propose that the conceptual van der Waals cut-off criterion be dropped for establishing the presence of weak intermolecular and intramolecular interactions, and be replaced by a distance/angle criterion determined by the empirical approach outlined here.
294 citations
TL;DR: In this article, the turnover-limiting step in these catalytic cycles is proposed to be intramolecular insertion into the Ln−N bond of the proximal allenic CC linkage, followed by rapid protonolytic cleavage of the resulting ln−C bond.
Abstract: The total syntheses of the pyrrolidine alkaloid (+)-197B (1) and pyrrolizidine alkaloid (+)-xenovenine (2) are described. The strategy involves enantioselective syntheses of the aminoallene, (5S,8S)-5-amino-trideca-8,9-diene (3), and the aminoallene-alkene, (5S)-5-amino-pentadeca-1,8,9-triene (4), which then undergo regio- and stereoselective cyclohydroamination catalyzed by the organolanthanide precatalysts Cp‘2LnCH(TMS)2 and Me2SiCp‘ ‘(tBuN)LnN(TMS)2 (Cp‘ = η5-Me5C5; Cp‘ ‘ = η5-Me4C5; Ln = lanthanide; TMS = Me3Si). These reactive organolanthanide complexes efficiently mediate highly diastereoselective intramolecular hydroamination/cyclization (IHC) reactions under mild conditions. The turnover-limiting step in these catalytic cycles is proposed to be intramolecular insertion into the Ln−N bond of the proximal allenic CC linkage, followed by rapid protonolytic cleavage of the resulting Ln−C bond. The rate and selectivity of the insertion process is highly sensitive to the steric demands of the substrate.
243 citations
TL;DR: Menger et al. as discussed by the authors introduced the term near attack conformation (NAC) to define the required conformation for juxtaposed reactants to enter a transition state (TS).
Abstract: reactions, rate enhancements of 108 M have been observed (Table 1).2 Intramolecular reactions where severe ground state strain is relieved upon formation of the transition state are known to be as large as 1016 M.3 Kirby4 has compiled a compendium of intramolecular reactions and has pointed out the relationship of rate to exothermicity. The importance of ground state conformations and the lack of translational entropy in intramolecular and enzymatic reactions have drawn attention from Menger5 and ourselves, while Jencks and Page6 have offered an explanation based on entropic driving forces stemming from the freezing out of motions and the dampening of vibrational frequencies in the transition state. Houk,7 in a scholarly study, has provided a correlation between rate constants for certain lactonization reactions and transition state stabilization. We provide here an account of our recent computational results8-10 dealing with the driving forces for enzymatic and intramolecular reactions. We introduce8 the term near attack conformation (NAC) to define the required conformation for juxtaposed reactants to enter a transition state (TS). The greater the mole fraction of reactant conformations that are present as NACs, the greater the rate constant. Rate constants for bond making and breaking in enzymatic reactions depend on, (i) the fraction of E‚S present as NACs, (ii) the change in solvation of reactant species within the NAC, as compared to water, and (iii) electrostatic forces11 which can stabilize the TS. The latter may include hydrogen bonds and metal ligation. Covalency in metal ligation and hydrogen bonding (low barrier hydrogen bonding12) most probably are introduced in the ground state. These features are best appreciated when ground state conformations and TS structures can be examined separately.
241 citations
TL;DR: In this paper, an extensive analysis of trans-hydrogen bond 2hJNN and 1hJHN scalar couplings, the covalent 1HJN couplings and the imino proton chemical shifts is presented for Hoogsteen−Watson−Crick T•A−T and C+•G−C triplets of an intramolecular DNA triplex.
Abstract: An extensive analysis of trans-hydrogen bond 2hJNN and 1hJHN scalar couplings, the covalent 1JHN couplings, and the imino proton chemical shifts is presented for Hoogsteen−Watson−Crick T•A−T and C+•G−C triplets of an intramolecular DNA triplex. The 2hJNN coupling constants for the Watson−Crick base pairs have values ranging from 6 to 8 Hz, while the Hoogsteen base paired thymines and protonated cytidines have values of approximately 7 and 10 Hz, respectively. Distinct decreases of 2hJNN are observed at the triplex strand ends. Trans-hydrogen bond J correlations (1hJHN) between the donor 1H nucleus and the acceptor 15N nucleus are observed for this triplex by a novel, simple quantitative J-correlation experiment. These one-bond 1hJHN couplings range between 1 and 3 Hz. A strong correlation is found between the chemical shift of the imino proton and the size of 2hJNN, with stronger J couplings corresponding to downfield chemical shifts. A similar, but inverse correlation is found between the proton chemical...
235 citations
TL;DR: In this article, the effects of photoinduced intramolecular charge transfer on the electronic and molecular properties of a series of differently twisted 4-N,N-dimethylamino-4'-cyanobiphenyls are investigated by steady-state and time-resolved fluorescence.
Abstract: This photophysical study addresses the general question of how electron transfer in bichromophoric molecules influences the conformational relaxation, which can be toward either more or less π-conjugation. The effects of photoinduced intramolecular charge transfer on the electronic and molecular properties of a series of differently twisted 4-N,N-dimethylamino-4‘-cyanobiphenyls are investigated by steady-state and time-resolved fluorescence. The dipole moments, radiative rates, and torsional relaxations in the excited state are analyzed by comparison with the absorption spectra and interannular twist angle (φ)-dependent CNDO/S calculations. Independent of the twist angle φ and solvent polarity, the first excited singlet state of these donor−acceptor (D−A) biphenyls (I−III) is an emissive intramolecular 1CT state of the 1La-type transferring charge from the dimethylaminobenzene (D) to the cyanobenzene (A) subunit. Similar to the planar restricted D−A fluorene I, the flexible D−A biphenyl II shows only a we...
223 citations
TL;DR: In this paper, the NO bond activation at a corrugated Ru(0001) surface was investigated using density functional theory, and it was found that the favorable barriers at the step edges result from the attractive chemisorption potential energies of the noninteracting reaction products, atomic N and O, and from a minimal degree of intramolecular repulsion mediated through the substrate.
Abstract: The NO bond activation at a corrugated Ru(0001) surface is investigated using density functional theory. Monatomic steps in the Ru surface are found to offer completely new reaction pathways with highly reduced energy barriers compared to reaction at a flat surface. The calculated energy barriers are found to be dominated by final state effects. The favorable barriers at the step edges result from the attractive chemisorption potential energies of the noninteracting reaction products, atomic N and O, and from a minimal degree of intramolecular repulsion mediated through the substrate.
169 citations
TL;DR: In this article, the existence of these species is presumably due to interactions between the free electron pairs on the nitrogen atoms and the carbene carbon atom or the silicon atom, and the properties of these molecules are compared with the results of quantum chemical calculations.
Abstract: The isolation and characterization of thermally stable diaminocarbenes and diaminosilylenes has reawakened interest in the low-coordinated compounds of group-14 elements. The existence of these species is presumably due to interactions between the free electron pairs on the nitrogen atoms and the carbene carbon atom or the silicon atom. The present review is mainly concerned with the heavier analogues R2Ge:, R2Sn:, and R2Pb:, systems without intramolecular donor stabilization that owe their existence principally to steric shielding by the voluminous alkyl or aryl groups R. Dimerizations of these electron-sextet molecules give rise to the double-bond systems of the digermenes, distannenes, and diplumbenes; the latter species have for a long time been considered as being incapable of existence. The properties of these molecules are compared with the results of quantum chemical calculations. A separate section is devoted to the isomers of Si4R6, which include novel tetrasilacyclobutenes and the diene analogues, the tetrasilabuta-1,3-dienes.
166 citations
TL;DR: Characterization of chemical exchange as a function of Ca2+ concentration has enabled the extraction of unique information on the rapidly exchanging and weakly populated (<10 %) (Ca2+)1 state that is otherwise inaccessible to direct study due to strongly cooperativeCa2+ binding.
TL;DR: The effect of methoxy substitution on the phenolic-hydrogen bond dissociation enthalpy has been established by a photoacoustic calorimetric method and by means of density functional theory (DFT) calculations as discussed by the authors.
Abstract: The effect of methoxy substitution on the phenolic-hydrogen bond dissociation enthalpy has been established by a photoacoustic calorimetric method and by means of density functional theory (DFT) calculations. Experimentally, the relative BDE(O−H) in kcal mol-1 with respect to phenol are found to be as follows: 2-methoxyphenol (−4.0), 4-methoxyphenol (−4.9), 2,6-dimethoxyphenol (−10.6), 2,4-dimethoxyphenol (−9.0), 2,4,6-trimethoxyphenol (−13.6), and ubiquinol-0 (−12.0). The intramolecular hydrogen-bond enthalpy in o-methoxy-substituted phenol is −4.3 kcal mol-1; the intramolecularly hydrogen-bonded molecule forms an additional hydrogen bond with HBA solvents. The low BDE(O−H) for ubiquinol-0 of 78.5 kcal mol-1 and the protective intramolecular hydrogen bond make it a good antioxidant.
TL;DR: In this article, a series of bithiophene derivatives bearing an intramolecular monosilanylene (ILN) bridge between the β and β positions were synthesized, and their properties were investigated.
TL;DR: The GCN4 leucine zipper is a peptide homodimer that has been the subject of a number of experimental and theoretical investigations into the determinants of affinity and specificity and this model system is utilized to investigate electrostatic effects in protein binding using continuum calculations.
Abstract: The GCN4 leucine zipper is a peptide homodimer that has been the subject of a number of experimental and theoretical investigations into the determinants of affinity and specificity. Here, we utilize this model system to investigate electrostatic effects in protein binding using continuum calculations. A particularly novel feature of the computations made here is that they provide an interaction-by-interaction breakdown of the electrostatic contributions to the free energy of docking that includes changes in the interaction of each functional group with solvent and changes in interactions between all pairs of functional groups on binding. The results show that (1) electrostatic effects disfavor binding by roughly 15 kcal/mol due to desolvation effects that are incompletely compensated in the bound state, (2) while no groups strongly stabilize binding, the groups that are most destabilizing are charged and polar side chains at the interface that have been implicated in determining binding specificity, and (3) attractive intramolecular interactions (e.g., backbone hydrogen bonds) that are enhanced on binding due to reduced solvent screening in the bound state contribute significantly to affinity and are likely to be a general effect in other complexes. A comparison is made between the results obtained in an electrostatic analysis carried out calculationally and simulated results corresponding to idealized data from a scanning mutagenesis experiment. It is shown that scanning experiments provide incomplete information on interactions and, if overinterpreted, tend to overestimate the energetic effect of individual side chains that make attractive interactions. Finally, a comparison is made between the results available from a continuum electrostatic model and from a simpler surface-area dependent solvation model. In this case, although the simpler model neglects certain interactions, on average it performs rather well.
TL;DR: In this article, a nonphotochemical methodology was proposed for enantioselective synthesis of a helical skeleton employing the Ni(cod) 2 /(S)-(−)-MOP catalytic system.
TL;DR: The sequential cycloaddition method was used for a formal synthesis of the pyrrolophenanthridone alkaloid hippadine and represents a new route to this rare heterocyclic ring system.
Abstract: The intramolecular Diels-Alder reaction of 2-substituted aminofurans (IMDAF) results in the formation of various indolines and tetrahydroquinolines. The isolation of these ring systems from the IMDAF reaction can be rationalized in terms of an initial [4 + 2]-cycloaddition that first produces an oxa-bridged cycloadduct, which was not detected since it readily underwent nitrogen-assisted ring opening. Proton exchange followed by an eventual dehydration provides the aromatic product. In certain cases, the intermediate cyclohexadienol can be isolated and independently converted to the final product in high yield. The starting 2-aminofurans were readily prepared from furanyl acyl azide by a Curtius rearrangement in the presence of an alcohol. Alkylation of the resulting N-alkyl carbamate with an alkenyl bromide allows for the synthesis of a wide variety of cycloaddition precursors. The scope of the IMDAF reaction was evaluated by using mono- and disubstituted alkenes, electron rich and electron deficient olefins, and acetylenic tethers. Cyclic 2-amidofurans were also synthesized using a related intramolecular Diels-Alder reaction of 2-amido-substituted oxazoles which contain a tethered alkyne. This transformation represents a new route to this rare heterocyclic ring system. The sequential cycloaddition method was used for a formal synthesis of the pyrrolophenanthridone alkaloid hippadine.
TL;DR: In this article, the reaction rate is zero-order in [aminoallene] and first order in [catalyst] over 3 or more half-lives, implying turnover-limiting allene insertion into the Ln−N bond followed by rapid protonolysis of the resulting ln−C bond.
TL;DR: In this paper, high level quantum chemistry calculations have been applied in order to explore the intramolecular proton transfer process in the tautomers of adenine and the presence of hydration water stabilizes th...
Abstract: High level quantum chemistry calculations have been applied in order to explore the intramolecular proton transfer process in the tautomers of adenine. The presence of hydration water stabilizes th...
TL;DR: The structure illustrates how a nucleophilic side chain may attack the scissile peptide bond at the immediate upstream backbone carbonyl and provides an understanding of the structural basis for peptide Bond cleavage via an N --> O or N --> S acyl shift that is used by various groups of intramolecular autoprocessing proteins.
TL;DR: Carbazoloquinones, carbazole, dibenzofuran, and related compounds have been synthesized from the respective noncyclic aromatic compounds with catalytic amounts of palladium and oxygen as the single oxidant as mentioned in this paper.
Abstract: Carbazoloquinones, carbazole, dibenzofuran, and related compounds (see scheme) have been synthesized from the respective noncyclic aromatic compounds with catalytic amounts of palladium and oxygen as the single oxidant. Intermolecular couplings of aromatic systems can also be performed with this catalytic system.
TL;DR: Substituted pyrroles are synthesized from γ,δ-unsaturated ketone O-pentafluorobenzoyloximes by the intramolecular Heck-type amination of the olefinic moiety catalyzed by Pd(PPh3)4.
Abstract: Substituted pyrroles are synthesized from γ,δ-unsaturated ketone O-pentafluorobenzoyloximes by the intramolecular Heck-type amination of the olefinic moiety catalyzed by Pd(PPh3)4
TL;DR: In this paper, a mechanism for nucleophilic vinylpalladation of aromatic aldehydes is proposed, where the aldehyde function is modelled as a binary function.
TL;DR: In this paper, the potential energy profile for intramolecular proton transfer in salicylic acid has been studied by ab initio molecular orbital calculations using the 6-31G** basis set at the restricted Hartree -Fock (RHF) and configuration interaction-single excitation (CIS) levels and also using the semi-empirical method AM1 at the RHF level as well as with single and pair doubles excitation configuration interaction spanning eight frontier orbitals (PECI ) 8).
Abstract: Energetics of the ground and excited state intramolecular proton transfer in salicylic acid have been studied by ab initio molecular orbital calculations using the 6-31G** basis set at the restricted Hartree -Fock (RHF) and configuration interaction-single excitation (CIS) levels and also using the semiempirical method AM1 at the RHF level as well as with single and pair doubles excitation configuration interaction spanning eight frontier orbitals (PECI ) 8). The ab initio potential energy profile for intramolecular proton transfer in the ground state reveals a single minimum corresponding to the primary form. In the first excited singlet state, however, there are two minima corresponding to the primary and tautomeric forms, separated by a barrier of 6 kcal/mol, thus accounting for dual emission in salicylic acid. Electron density changes with electronic excitation and tautomerism indicate no zwitterion formation. Changes in spectral characteristics with change in pH, due to protonation and deprotonation of salicylic acid, are also accounted for, qualitatively. Although the AM1 calculations suggest a substantial barrier for proton transfer in the ground as well as the first excited state of SA, it predicts the transition wavelength in near quantitative accord with the experimental results for salicylic acid and its protonated and deprotonated forms.
TL;DR: A detailed theoretical analysis of the thermodynamics and functional energetics of protein?DNA binding in the EcoRI endonuclease?DNA complex is presented in this article, where the standard free energy of complexation is considered in terms of a thermodynamic cycle of seven distinct steps decomposed into a total of 24 well-defined components.
TL;DR: In this paper, a series of low-valent organoselenium compounds were synthesized, characterized, and examined for nonbonding and non-bonding interactions, and a correlation between Se···N intramolecular distance and 77 Se chemical shift was attempted.
Abstract: A series of novel low-valent organoselenium compounds stabilized by Se···N intramolecular
interactions (such as the one in the figure) were synthesized, characterized, and examined for Se···N nonbonding
interactions. A correlation between Se···N intramolecular distance and 77 Se chemical shift is
attempted.
TL;DR: In this article, three ortho hydroxy Schiff bases 2-(N- methyl- α -iminoethyl)-phenol (I), 2-( N- benzyl- α-imino methyl)-phenols (II) and 3-phenols were synthesized in which the hydrogen atoms in C-C(H)N group were replaced by an alkyl substituent.