Showing papers on "Intramolecular force published in 2006"

Proton abstraction mechanism for the palladium-catalyzed intramolecular arylation.

Abstract: Under the usual conditions, the Pd-catalyzed arylation does not involve an electrophilic aromatic substitution reaction. On the basis of DFT calculations, we propose a mechanism for the Pd-catalyzed arylation that involves a proton abstraction by a carbonate or related ligand and that provides a satisfactory explanation for the experimental data.

Catalytic direct arylation with aryl chlorides, bromides, and iodides: intramolecular studies leading to new intermolecular reactions.

Abstract: A catalyst for the intramolecular direct arylation of a broad range of simple and heterocyclic arenes with aryl iodides, bromides, and chlorides has been developed. These reactions occur in excellent yield and are highly selective. Studies with aryl iodides substrates revealed that catalyst poisoning occurs due to the accumulation of iodide in the reaction media. This can be overcome by the addition of silver salts which also permits these reactions to occur at lower temperature. The utility of the methodology is illustrated by a rapid synthesis of a carbazole natural product and by the synthesis of sterically encumbered tetra-ortho-substituted biaryls via ring-opening reactions of the direct arylation products. Mechanistic investigations have provided insight into the catalyst's mode of action and show the presence of a kinetically significant C-H bond cleavage in palladium-catalyzed direct arylation of simple arenes. Knowledge garnered from these studies has led to the development of new intermolecular arylation reactions with previously inaccessible arenes, opening the door for the development of other new direct arylation processes.

Structural conformation and vibrational spectroscopic studies of 2,6-bis(p-N,N-dimethyl benzylidene)cyclohexanone using density functional theory

Abstract: NIR-FT Raman and FT-IR spectra of the crystallized 2,6-bis (p-N,N-dimethyl benzylidene)cyclohexanone (C24H28N2O) have been recorded in the region 3200–500 and 4000–400 cm−1, respectively. The spectral interpretation has been done following full structure optimization and vibrational wavenumber calculations based on the density functional theory (DFT) using the standard B3LYP/6-31G* basis set. The predicted vibrational spectra are in excellent agreement with the experiment, permitting an unambiguous assignment for the unusual downshifting of νCO caused by expanded conjugation effects in the dienone system. The optimized geometry clearly demonstrates the ‘half-chair’ conformation of the central nonheterocyclic ring. The ring CH stretching vibrational modes involving aromatic hydrogen atoms participating in steric interaction have been observed with low intensities. There are valid structural and spectral bases for the enhancement of its bioactivity due to full charge transfer reaction by the substitution of the electron-donating 4-dimethylamino group into the aryl rings. The existence of intramolecular, CH…O, improper, blue-shifted hydrogen bond was investigated by means of the natural bonding orbitals (NBO) analysis. There are also slight dissimilarities in the bond lengths and endocyclic bond angles of both phenyl rings due to the effect of the heavy substitution. The characteristic ring modes have also been assigned in detail. Copyright © 2006 John Wiley & Sons, Ltd.

Highly Active Au(I) Catalyst for the Intramolecular exo-Hydrofunctionalization of Allenes with Carbon, Nitrogen, and Oxygen Nucleophiles

Abstract: Reaction of benzyl (2,2-diphenyl-4,5-hexadienyl)carbamate (4) with a catalytic 1:1 mixture of Au[P(t-Bu)2(o-biphenyl)]Cl (2) and AgOTf (5 mol %) in dioxane at 25 °C for 45 min led to isolation of benzyl 4,4-diphenyl-2-vinylpyrrolidine-1-carboxylate (5) in 95% yield. The Au(I)-catalyzed intramolecular hydroamination of N-allenyl carbamates tolerated substitution at the alkyl and allenyl carbon atoms and was effective for the formation of piperidine derivatives. γ-Hydroxy and δ-hydroxy allenes also underwent Au-catalyzed intramolecular hydroalkoxylation within minutes at room temperature to form the corresponding oxygen heterocycles in good yield with high exo-selectivity. 2-Allenyl indoles underwent Au-catalyzed intramolecular hydroarylation within minutes at room temperature to form 4-vinyl tetrahydrocarbazoles in good yield. Au-catalyzed cyclization of N-allenyl carbamates, allenyl alcohols, and 2-allenyl indoles that possessed an axially chiral allenyl moiety occurred with transfer of chirality from the...

A structural investigation of the N-B interaction in an o-(N,N-dialkylaminomethyl)arylboronate system

Abstract: o-(Pyrrolidinylmethyl)phenylboronic acid (4) and its complexes with bifunctional substrates such as catechol, alpha-hydroxyisobutyric acid, and hydrobenzoin have been studied in detail by X-ray crystallography, (11)B NMR, and computational analysis. The N-B interactions in analogous boronic acids and esters have been extensively cited in molecular recognition and chemosensing literature. The focal point of this study was to determine the factors that are pertinent to the formation of an intramolecular N-B dative bond. Our structural study predicts that the formation of an N-B dative bond, and/or solvent insertion to afford a tetrahedral boronate anion, depends on the solvent and the complexing substrate present. Specifically, from (11)B NMR studies, complexation of 4 with electron-withdrawing and/or vicinally bifunctionalized substrates promotes both the formation of N-B dative bonds and the solvation of sp(2) boron to a tetrahedral sp(3) boronate. In the solid state, the presence of an N-B dative bond in the complex of 4 and catechol (7) depends on the solvent from which it crystallizes. From chloroform, an N-B bond was observed, whereas from methanol, a methoxylated boronate was formed, where the methoxy group is hydrogen-bonded with the neighboring tertiary ammonium ion. The structural optimization of compounds 4 and 7 using density functional theory in a simulated water continuum also predicts that complexation of 4 and catechol promotes either the formation of an N-B bond or solvolysis if 1 equiv of water is present. The conclusion from this study will help in the design of future chemosensing technologies based on o-(N,N-dialkylaminomethyl)arylboronate scaffolds that are targeting physiologically important substances such as saccharides, alpha-hydroxycarboxylates, and catecholamines.

Asymmetric Synthesis of Hydrobenzofuranones via Desymmetrization of Cyclohexadienones Using the Intramolecular Stetter Reaction

Abstract: Dearomatization of phenols followed by oxidation affords cyclohexadienyloxyacetaldehydes, which produce hydrobenzofuranones via asymmetric intramolecular Stetter reaction in good to excellent yield. Quaternary as well as up to three contiguous stereocenters may be formed in good to excellent enantioselectivities and high diastereoselectivities.

End-to-end distance distributions and intrachain diffusion constants in unfolded polypeptide chains indicate intramolecular hydrogen bond formation

Abstract: Characterization of the unfolded state is essential for the understanding of the protein folding reaction. We performed time-resolved FRET measurements to gain information on the dimensions and the internal dynamics of unfolded polypeptide chains. Using an approach based on global analysis of data obtained from two different donor–acceptor pairs allowed for the determination of distance distribution functions and diffusion constants between the chromophores. Results on a polypeptide chain consisting of 16 Gly-Ser repeats between the FRET chromophores reveal an increase in the average end-to-end distance from 18.9 to 39.2 A between 0 and 8 M GdmCl. The increase in chain dimensions is accompanied by an increase in the end-to-end diffusion constant from (3.6 ± 1.0) × 10−7 cm2 s−1 in water to (14.8 ± 2.5) × 10−7 cm2 s−1 in 8 M GdmCl. This finding suggests that intrachain interactions in water exist even in very flexible chains lacking hydrophobic groups, which indicates intramolecular hydrogen bond formation. The interactions are broken upon denaturant binding, which leads to increased chain flexibility and longer average end-to-end distances. This finding implies that rapid collapse of polypeptide chains during refolding of denaturant-unfolded proteins is an intrinsic property of polypeptide chains and can, at least in part, be ascribed to nonspecific intramolecular hydrogen bonding. Despite decreased intrachain diffusion constants, the conformational search is accelerated in the collapsed state because of shorter diffusion distances. The measured distance distribution functions and diffusion constants in combination with Szabo–Schulten–Schulten theory were able to reproduce experimentally determined rate constants for end-to-end loop formation.

Donor-substituted 1,1,4,4-tetracyanobutadienes (TCBDS): new chromophores with efficient intramolecular charge-transfer interactions by atom-economic synthesis.

Abstract: A wide variety of monomeric and oligomeric, donor-substituted 1,1,4,4-tetracyanobutadienes (TCBDs) have been synthesized by [2+2] cycloaddition between tetracyanoethylene (TNCE) and donor-substituted alkynes, followed by electrocyclic ring opening of the initially formed cyclobutenes. Reaction yields are often nearly quantitative but can be affected by the electron-donating power and steric demands of the alkyne substituents. The intramolecular charge-transfer (CT) interactions between the donor and TCBD acceptor moieties were comprehensively investigated by X-ray crystallography, electrochemistry, UV-visible spectroscopy, and theoretical calculations. Despite the nonplanarity of the new chromophores, which have a substantial twist between the two dicyanovinyl planes, efficient intramolecular CT interactions are observed, and the crystal structures demonstrate a high quinoid character in strong donor substituents, such as N,N-dimethylanilino (DMA) rings. The maxima of the CT bands shift bathochromically upon reduction of the amount of conjugative coupling between strong donor and acceptor moieties. Each TCBD moiety undergoes two reversible, one-electron reduction steps. Thus, a tri-TCBD derivative with a 1,3,5-trisubstituted benzene core shows six reversible reduction steps within an exceptionally narrow potential range of 1.0 V. The first reduction potential E(red,1) is strongly influenced by the donor substitution: introduction of more donor moieties causes an increasingly twisted TCBD structure, a fact that results in the elevation of the LUMO level and, consequently, a more difficult first reduction. The potentials are also strongly influenced by the nature of the donor residues and the extent of donor-acceptor coupling. A careful comparison of electrochemical data and the correlation with UV-visible spectra made it possible to estimate unknown physical parameters such as the E(red,1) of unsubstituted TCBD (-0.31 V vs Fc+/Fc) as well as the maxima of highly broadened CT bands. Donor-substituted TCBDs are stable molecules and can be sublimed without decomposition. With their high third-order optical nonlinearities, as revealed in preliminary measurements, they should become interesting chromophores for ultra-thin film formation by vapor deposition techniques and have applications in opto-electronic devices.

Investigation of two-photon absorption properties in branched alkene and alkyne chromophores.

Abstract: Novel alkene and alkyne branched structures have been synthesized, and their two-photon absorption (2PA) properties are reported. This series of alkene and alkyne trimer systems tests the mechanistic approach for enhancing the 2PA process which is usually dictated by the pi-bridging, delocalization length, and corresponding charge transfer on the 2PA cross sections. The results suggest that alkene branched systems have higher 2PA cross sections. While steady-state absorption and emission measurements were not successful in predicting the observed trend of 2PA cross sections, time-resolved measurements have explained the trends observed. It was found that, upon photoexcitation, there is an ultrafast charge localization to an intramolecular charge-transfer (ICT) state, followed by the presence of a solvent and conformationally relaxed ICT state in these branched systems.

DNA condensation and cell transfection properties of guanidinium calixarenes: dependence on macrocycle lipophilicity, size, and conformation.

Abstract: Calix[n]arenes functionalized with guanidinium groups at the upper rim and alkyl chains at the lower rim bind to DNA, condense it, and in some cases, promote cell transfection depending on their structure and lipophilicity. Atomic force microscopy (AFM) studies indicate that upon DNA binding the hydrophobic association of the lipophilic chains of cone guanidinium calix[4]arenes drives the formation of intramolecular DNA condensates, characterized by DNA loops emerging from a dense core. Furthermore, hexyl and octyl chains confer to these calixarenes cell transfection capabilities. Conversely, larger and conformationally mobile calix[6]- and calix[8]arene methoxy derivatives form intermolecular aggregates characterized by "gorgonlike" structures composed of multiple plectomenes. These adducts, in which interstrand connections are dominated by electrostatic interactions, fail to promote cell transfection. Finally, calix[4]arenes in a 1,3-alternate conformation show an intermediate behavior because they condense DNA, but the process is driven by charge-charge interactions.

The photolysis of ortho-nitrophenols: a new gas phase source of HONO.

Abstract: Formation of nitrous acid (HONO) in the gas phase has been observed for the first time in a flow tube photoreactor upon irradiation (λ = 300–500 nm) of 2-nitrophenol and methyl substituted derivatives using a selective and sensitive instrument (LOPAP) for the detection of HONO. Formation of HONO by heterogeneous NO2 photochemistry has been excluded, since production of NO2 under the experimental conditions is negligible. Variation of the surface to volume ratio and the nitrophenol concentration showed that the photolysis occurred in the gas phase indicating that HONO formation is initiated by intramolecular hydrogen transfer from the phenolic OH group to the nitro group. From the measured linear dependence of the HONO formation rate on the reactant’s concentration and photolysis light intensity, a non-negligible new HONO source is proposed for the urban atmosphere during the day. Unexpectedly high HONO mixing ratios have been observed recently in several field campaigns during the day. It is proposed that the photolysis of aromatic compounds containing the ortho-nitrophenol entity could help to explain, at least in part, this high contribution of HONO to the oxidation capacity of the urban atmosphere.

Gold- and Copper-Catalyzed [4+2] Benzannulations between Enynal or Enynone Units and 2π-Systems

Abstract: Gold-catalyzed formal [4+2] benzannulation between enynal or enynone units, including ortho-alkynyl(oxo)benzenes, and 2π-systems, such as alkynes and carbonyl compounds (enol forms), produces aromatic ketones in good to high yields. By simply changing the catalyst from gold to copper-Bronsted acid system, decarbonylated aromatic compounds can be prepared in the reactions using alkynes as the 2n-system. An efficient synthetic approach to angucyclinone antibiotics, (+)-ochromycinone and (+)-rubiginone B 2 , is developed by applying the present benzannulation to an intramolecular version. The reaction proceeds most probably through the formation of the benzo[c]pyrylium ate complex via the intramolecular nucleophilic addition of the carbonyl oxygen atom to the alkyne part of enynal or enynone units, which is induced by carbophilic gold and copper catalysts.

Synthesis of aryl ketones or ketimines by palladium-catalyzed arene C-H addition to nitriles.

Abstract: The unprecedented palladium-catalyzed C−H addition of arenes to nitriles provides moderate to excellent yields of aryl ketones or the corresponding hindered imines. The addition of a small amount of DMSO increases the yields dramatically. Both intermolecular and intramolecular reactions are successful, although the intramolecular reactions tend to be more sluggish. This novel chemistry is believed to involve palladium-catalyzed C−H activation of the arene by electrophilic aromatic substitution, followed by the unusual carbopalladation of a nitrile. Similar reactions have been successfully developed employing arylboronic acids and nitriles. A concise route to xanthones starting from cheap starting materials has been developed employing this synthetic protocol.

Rhodium-Catalyzed Intramolecular, Anti-Markovnikov Hydroamination. Synthesis of 3-Arylpiperidines

Abstract: The intramolecular anti-Markovnikov hydroamination of 1-(3-aminopropyl)vinylarenes in the presence of a readily available rhodium catalyst to form 3-arylpiperidines is reported. In contrast to intermolecular hydroamination of vinylarenes, which occurred in high yields in the presence of rhodium catalysts containing DPEphos, the intramolecular reaction occurred in high yield in the presence of [Rh(COD)(DPPB)]BF4 as catalyst. Reactants with substituents β to the nitrogen occurred in high yield, and these reactions formed 3,5-disubstituted piperidines with high diastereomeric excess. The regiochemistry of these cyclizations contrasts with the regiochemistry of intramolecular hydroaminations catalyzed by lanthanide complexes, group III metal complexes, and platinum complexes, all of which have been reported to form cyclization products from Markovnikov addition.

A highly efficient preparative method of alpha-ylidene-beta-diketones via Au(III)-catalyzed acyl migration of propargylic esters.

Abstract: A highly efficient synthesis of alpha-alkylidene or benzylidene-beta-diketones from readily available propargylic esters has been developed. The proposed key transformation is a novel intramolecular acyl migration to nucleophilic AuIII-C(sp2) bonds. Noteworthy features of this method are its efficiency and stereoselectivity. The yields of this reaction were mostly close to quantitative, and high to excellent stereoselectivities were observed in the cases of dienyl beta-diketones.

Highly Enantioselective Synthesis of Tetrahydro-β-Carbolines and Tetrahydro-γ-Carbolines Via Pd-Catalyzed Intramolecular Allylic Alkylation

Abstract: A novel Pd-catalyzed intramolecular allylic alkylation of indoles allows THBCs and THGCs to be effectively synthesized in high yields and excellent enantiomeric excesses (ee up to 97%).

A Novel Method for Detecting Intramolecular Coevolution: Adding a Further Dimension to Selective Constraints Analyses

Abstract: Protein evolution depends on intramolecular coevolutionary networks whose complexity is proportional to the underlying functional and structural interactions among sites. Here we present a novel approach that vastly improves the sensitivity of previous methods for detecting coevolution through a weighted comparison of divergence between amino acid sites. The analysis of the HIV-1 Gag protein detected convergent adaptive coevolutionary events responsible for the selective variability emerging between subtypes. Coevolution analysis and functional data for heat-shock proteins, Hsp90 and GroEL, highlight that almost all detected coevolving sites are functionally or structurally important. The results support previous suggestions pinpointing the complex interdomain functional interactions within these proteins and we propose new amino acid sites as important for interdomain functional communication. Three-dimensional information sheds light on the functional and structural constraints governing the coevolution between sites. Our covariation analyses propose two types of coevolving sites in agreement with previous reports: pairs of sites spatially proximal, where compensatory mutations could maintain the local structure stability, and clusters of distant sites located in functional domains, suggesting a functional dependency between them. All sites detected under adaptive evolution in these proteins belong to coevolution groups, further underlining the importance of testing for coevolution in selective constraints analyses.

Influence of Intermolecular Orientation on the Photoinduced Charge Transfer Kinetics in Self-Assembled Aggregates of Donor−Acceptor Arrays

Abstract: The kinetics of photoinduced charge transfer reactions in covalently linked donor−acceptor molecules often undergoes dramatic changes when these molecules self-assemble from a molecular dissolved state into a nanoaggregate. Frequently, the origin of these changes is only partially understood. In this paper, we describe the intermolecular spatial organization of three homologous arrays, consisting of a central perylene bisimide (PERY) acceptor moiety and two oligo(p-phenylene vinylene) (OPV) donor units, in nanoaggregates and identify both face-to-face (H-type) and slipped (J-type) stacking of the OPV and PERY chromophores. For the J-type aggregates, short intermolecular OPV−PERY distances are created that give rise to a charge-transfer absorption band. The proximity of the donor and acceptor groups in the J-type aggregates enables a highly efficient photoinduced charge separation with a rate (kcs > 1012 s-1) that significantly exceeds the rate of the intramolecular charge transfer of the same compounds wh...