Showing papers on "Intramolecular force published in 1998"

Structure of the amide i band of peptides measured by femtosecond nonlinear-infrared spectroscopy

Abstract: Femtosecond infrared (IR) pump probe and dynamic hole burning experiments were used to examine the ultrafast response of the modes in the 1600−1700 cm-1 region (the so-called amide I modes) of N-methylacetamide (NMA) and three small globular peptides, apamin, scyllatoxin, and bovine pancreatic trypsin inhibitor (BPTI). A value of 16 cm-1 was found for the anharmonicity of the amide I vibration. Vibrational relaxation of the amide I modes of all investigated peptides occurs in ca. 1.2 ps. An even faster value of 450 fs is obtained for NMA, a model for the peptide unit. The vibrational relaxation is dominated by intramolecular energy redistribution (IVR) and reflects an intrinsic property of the peptide group in any environment. Dynamic hole burning experiments with a narrow band pump pulse which selectively excites only a subset of the amide I eigenstates reveal that energy migration between different amide I states is slow compared with vibrational relaxation. Two-dimensional pump−probe (2D-IR) spectra th...

Strong dimerization of ureidopyrimidones via quadruple hydrogen bonding

Abstract: 6-Methyl-2-butylureidopyrimidone dimerizes via four hydrogen bonds in the solid state as well as in CHCl3 solution via a donor−donor−acceptor−acceptor (DDAA) array of hydrogen bonding sites in the 4[1H]-pyrimidinone tautomer. An intramolecular hydrogen bond from the pyrimidine NH group to the urea oxygen atom preorganizes the molecules for dimerization. The dimerization constant of the dimer in CHCl3 exceeds 106 M-1. In CHCl3 containing DMSO, the dimer is in equilibrium with the monomeric 6[1H]-pyrimidinone tautomer. In 6-phenyl-2-butylureidopyrimidone, the 4[1H]-pyrimidinone tautomer coexists with the pyrimidin-4-ol form, which dimerizes with similar high dimerization constants via four hydrogen bonds in a DADA array. The latter tautomer predominates in derivatives with electronegative 6-substituents, like 6-nitrophenyl- and 6-trifluoromethyl-2-butylureidopyrimidone. Due to its simple preparation and high dimerization constant, the ureidopyrimidone functionality is a useful building block for supramolecu...

Force-mediated kinetics of single P-selectin/ligand complexes observed by atomic force microscopy

Abstract: Leukocytes roll along the endothelium of postcapillary venules in response to inflammatory signals. Rolling under the hydrodynamic drag forces of blood flow is mediated by the interaction between selectins and their ligands across the leukocyte and endothelial cell surfaces. Here we present force-spectroscopy experiments on single complexes of P-selectin and P-selectin glycoprotein ligand-1 by atomic force microscopy to determine the intrinsic molecular properties of this dynamic adhesion process. By modeling intermolecular and intramolecular forces as well as the adhesion probability in atomic force microscopy experiments we gain information on rupture forces, elasticity, and kinetics of the P-selectin/P-selectin glycoprotein ligand-1 interaction. The complexes are able to withstand forces up to 165 pN and show a chain-like elasticity with a molecular spring constant of 5.3 pN nm−1 and a persistence length of 0.35 nm. The dissociation constant (off-rate) varies over three orders of magnitude from 0.02 s−1 under zero force up to 15 s−1 under external applied forces. Rupture force and lifetime of the complexes are not constant, but directly depend on the applied force per unit time, which is a product of the intrinsic molecular elasticity and the external pulling velocity. The high strength of binding combined with force-dependent rate constants and high molecular elasticity are tailored to support physiological leukocyte rolling.

Local Softness and Hardness Based Reactivity Descriptors for Predicting Intra- and Intermolecular Reactivity Sequences: Carbonyl Compounds

Abstract: The DFT-based reactivity descriptors “local softness” and “local hardness” are used as reactivity indices to predict the reactivity sequences (both intramolecular and intermolecular) of carbonyl compounds toward nucleophilic attack on them. The finite difference approximation is used to calculate local softness, whereas local hardness is approximated by −Vel/2N, where Vel is the electronic part of the molecular electrostatic potential. Both aldehydes and ketones, aliphatic and aromatic, have been selected as systems. Critical cases, e.g., C6H5CHCHCHO, CH3CHCHCHO, and CH2CHCHO, where a CC double bond is in conjugation with the CO group, are also considered. Two new reactivity descriptors are proposed, “relative electrophilicity” (sk+/sk-) and “relative nucleophilicity” (sk-/sk+), which will help to locate the preferable reactive sites. Our results show that local hardness can be used as a guiding parameter when constructing intermolecular reactivity sequences.

Alternating Donor/Acceptor Repeat Units in Polythiophenes. Intramolecular Charge Transfer for Reducing Band Gaps in Fully Substituted Conjugated Polymers

Abstract: This paper describes a method to limit the band gap widening that occurs in fully substituted conjugated polymers. This is done by constructing step growth [AB] polymers where the A-units are electron rich and the B-units are electron deficient. The thiophene-based polymers were prepared by modified Stille polymerizations using Pd(0)/CuI catalyst systems in which aryldibromides were coupled with aryldistannanes. The donor units were N,N‘-(bis-tert-butoxycarbonyl)-3,4-diaminothiophene, N,N‘-(bis-tert-butoxycarbonyl)-N,N‘-(dimethyl)-3,4-diaminothiophene, 3,4-diaminothiophene, or 3,4-dialkoxythiophenes while the acceptor units were 3,4-dinitrothiophene, 3,4-(N-n-butylimido)thiophene, or 3,4-diketone-containing thiophenes. The optical spectra showed λmax values ranging from 400 to 676 nm (solution) and 400−768 (film) for these fully substituted polythiophenes, consistent with significant decreases in the band gaps. Intramolecular charge transfer character between the consecutive units explained the lowering o...

Self-Complementarity Achieved through Quadruple Hydrogen Bonding

Abstract: Highly stable dimers are formed in solution and in the solid state by a class of readily synthesized, self-complementary building blocks for supramolecular chemistry, which associate through a donor-acceptor-donor-acceptor array of four hydrogen-bonding sites. An additional intramolecular hydrogen bond in the compound whose crystal structure is shown on the right preorganizes the molecule for dimerization.

Palladium-Catalyzed Inter- and Intramolecular α-Arylation of Amides. Application of Intramolecular Amide Arylation to the Synthesis of Oxindoles

Abstract: 2A palladium-catalyzed α-arylation of amides is reported. Intermolecular arylation of N,N-dimethylamides and lactams occurs using aryl halides, silylamide base, and a palladium catalyst. Intramolecular arylation of N-(2-halophenyl)amides occurs using alkoxide base and a palladium catalyst. The palladium catalyst was formed in situ from Pd(dba)2 (dba = trans,trans-dibenzylidene acetone) and BINAP (2,2‘-bis(diphenylphosphino)-1,1‘-binaphthalene). Although the intermolecular arylation of amides is less general than that reported previously for ketones, unfunctionalized and electron-rich aryl halides gave α-arylamides in 48−75% yield and N-methyl-α-phenylpyrrolidinone in 49% yield. These reactions provided the highest yields yet reported for regioselective amide arylations. Intramolecular amide arylation of 2-bromoanilides gave oxindoles in 52−82% yield. Mono- and disubstituted acetanilides gave 1,3-di- and 1,3,3-trisubstituted oxindoles. The use of dioxane, rather than THF, solvent was important for some of ...

Intramolecular Nonbonded S···O Interaction Recognized in (Acylimino)thiadiazoline Derivatives as Angiotensin II Receptor Antagonists and Related Compounds

Abstract: The intramolecular nonbonded 1,5-type S···O interactions are recognized in the crystalline structures of the (acylimino)thiadiazoline derivatives (1−3) as angiotensin II receptor antagonists. The relative stability of the nonbonded 1,5-type S···O interaction was investigated using the X-ray crystallographic analyses and the ab initio MO calculations (HF/3-21G*, 6-31G*, and 6-311+G**) of the simplified model compounds (6, 7, and 9). The concept of mimic-fused bicyclic heterocycles consisting of fairly stable nonbonded S···O interaction seems to be an efficient approach toward the design and development of various drugs.

Structure and Thermodynamics of Self-Assembled Monolayers on Gold Nanocrystallites

Abstract: Equilibrium structures and thermodynamic properties of dodecanethiol self-assembled monolayers on small (Au140) and larger (Au1289) gold nanocrystallites were investigated with the use of molecular dynamics simulations Compact passivating monolayers are formed on the (111) and (100) facets of the nanocrystallites, with adsorption site geometries differing from those found on extended flat Au(111) and Au(100) surfaces, as well as with higher packing densities At lower temperatures the passivating molecules organize into preferentially oriented molecular bundles with the molecules in the bundles aligned approximately parallel to each other Thermal disordering starts at T ≳200 K, initiating at the boundaries of the bundles and involving generation of intramolecular conformational (gauche) defects which occur first at bonds near the chains' outer terminus and propagate inward toward the underlying gold nanocrystalline surface as the temperature is increased The disordering process culminates in melting of

Local Treatment of Electron Correlation in Molecular Clusters: Structures and Stabilities of (H2O)n, n = 2−4

Abstract: The structures and stabilities of small water clusters are studied by local electron correlation methods. It is demonstrated that the local treatment eliminates basis set superposition errors (BSSEs) to a large extent and thus allows BSSE-free geometry optimizations. Results for various basis sets are presented which show that the interaction energies and structural parameters obtained by local second-order Moller−Plesset perturbation theory (LMP2) without counterpoise correction are in close agreement with counterpoise-corrected conventional MP2 results. Furthermore, a partitioning of the LMP2 energies of (H2O)n, n = 2−4, into different excitation classes is reported, which underlines the importance of ionic contributions as well as intramolecular correlation for hydrogen-bonded clusters. The results of this analysis are compared with previous data obtained by symmetry-adapted perturbation theory (SAPT).

Bifurcated Hydrogen Bonds: Three-Centered Interactions

Abstract: The nature of bifurcated or three-centered hydrogen bonds (HB) has been investigated. Different families of compounds were chosen: monomers with intramolecular three-centered HB, dimers with a HB donor (HBD) and a molecule with two HB acceptor (HBA) groups, and trimers with one HBD and two HBAs. All the systems were optimized at the B3LYP/6-31G* level, and, in the case of the complexes, the interaction energies were evaluated and corrected with the basis set superposition error (BSSE). The electronic nature of these three-centered HBs was analyzed by means of the atoms in molecules (AIM) approach. The present study indicates the existence of bifurcated bond paths in the AIM analysis with electron densities that can be classified as follows: (i) compounds with symmetric three-centered HBs presenting two symmetric bond critical points with equal values of electron density; (ii) compounds with asymmetric three-centered HBs presenting two bond critical points with different values of electron density; (iii)...

1,1-Diamino-2,2-dinitroethylene: a Novel Energetic Material with Infinite Layers in Two Dimensions

Abstract: The title compound (C2H4N4O4) is a novel and interesting high explosive with high performance and low sensitivity. Single-crystal X-ray diffraction studies of the compound show that the molecules in the crystal structure have bond lengths and bond angles as expected for this type of push–pull ethylene. There are two intramolecular hydrogen bonds present between the nitro-O atoms and the amino-H atoms. The geometry of the molecule indicates that there is extensive π conjugation present. The molecular packing is built up by infinite two-dimensional wave-shaped layers, with extensive intermolecular hydrogen bonding within the layers and ordinary van der Waals inter­actions between the layers. The crystal packing explains some of the physico–chemical properties of the compound such as the absence of a melting point, its low solubility and its low sensitivity to friction and impact compared with the common high explosive RDX (1,3,5-triaza-1,3,5-trinitrocyclohexane).

Organolanthanide-catalyzed intra- and intermolecular tandem C-N and C-C bond-forming processes of aminodialkenes, aminodialkynes, aminoalkeneynes, and aminoalkynes. New regiospecific approaches to pyrrolizidine, indolizidine, pyrrole, and pyrazine skeletons

Abstract: This contribution describes catalytic tandem C−N and C−C bond-forming reactions involving the intramolecular hydroamination/bicyclization and intermolecular hydroamination/cyclization of olefins and alkynes using the organolanthanide complexes Cp‘2LnCH(SiMe3)2 and Me2SiCp‘‘2LnCH(SiMe3)2 (Cp‘ = η5-Me5C5; Cp‘‘ = η5-Me4C5; Ln = lanthanide) as precatalysts. In the case of the intramolecular processes, substrates of the structures RC⋮C(CH2)aNH(CH2)bC⋮CR, RC⋮C(CH2)cNH(CH2)dCHCH2, and H2CCH−(CH2)eNH(CH2)fCHCH2 are regiospecifically bicyclized to the corresponding pyrrolizidine and indolizidine skeletons, with turnover frequencies ranging from 2 to 777 h-1 at 21 °C and isolated product yields ranging from 85 to 93%. In the case of e = 3 and f = 1 mediated by Cp‘2Sm−, the kinetic rate law is zero-order in substrate concentration and first-order in lanthanide concentration. In the case of R = Ph, c = 3, and d = 1, the Cp‘2Ln-catalyzed turnover frequencies fall precipitously with decreasing Ln+3 ionic radius. In the...

Theory of d10−d10 Closed-Shell Attraction. III. Rings

Abstract: We study the dependence of the intramolecular MI−MI interaction on electron correlation effects in eight-membered rings of type [M2(PH2CH2PH2)2]2+, [M2(NHCHNH)2], [M2(SCHS)2] (M = Au, Ag, Cu), [Au2...

Bacteriorhodopsin's Intramolecular Proton-Release Pathway Consists of a Hydrogen-Bonded Network†

Abstract: In its proton-pumping photocycle, bacteriorhodopsin releases a proton to the extracellular surface at pH 7 in the transition from intermediate L to intermediate M. The proton-release group, named XH, was assigned in low-temperature FT-IR studies to a single residue, E204 [Brown, L. S., Sasaki, J., Kandori, H., Maeda, A., Needleman, R. , and Lanyi, J. K. (1995) J. Biol. Chem. 270, 27122-27126]. The time-resolved room-temperature step-scan FT-IR photocycle studies on wild-type and E204Q-, and E204D-mutated bacteriorhodopsin, which we present here, show in contrast that the FT-IR data give no evidence for deprotonation of E204 in the L-to-M transition. Therefore, it is unlikely that E204 represents XH. On the other hand, IR continuum absorbance changes indicate intramolecular proton transfer via an H-bonded network to the surface of the protein. It appears that this H-bonded network is spanned between the Schiff base and the protein surface. The network consists at least partly of internally bound water molecules and is stabilized by E204 and R82. Other not yet identified groups may also contribute. At pH 5, the intramolecular proton transfer to the surface of the protein seems not to be disturbed. The proton seems to be buffered at the surface and later in the photocycle released into the bulk during BR recovery. Intramolecular proton transfer via a complex H-bonded network is proposed to be a general feature of proton transfer in proteins.

Intramolecular charge transfer in dual fluorescent 4-(dialkylamino)benzonitriles.

Abstract: The intramolecular charge transfer (ICT) reaction from the locally excited state (LE) to the charge transfer state (CT) in the singlet excited state is investigated for the dual fluorescent 4-(dial...

Potential models for simulations of the solvated proton in water

Abstract: Analytical potential models are designed for simulations of water with excess protons. The potentials describe both intramolecular and intermolecular interactions, and allow dissociation and formation of the species (H2O)nH+. The potentials are parametrized in the form of interactions between H+ and O2− ions, with additional three-body (H–O–H) interaction terms and self-consistent treatment of the polarizability of the oxygen ions. The screening of electrostatic interactions caused by the overlap of the electron clouds in the real molecules is modeled by functions modifying the electric field at short distances. The model was derived by fitting to the potential surface of the H5O2+ ion and other species, as obtained from ab initio MP2 calculations employing an extensive basis set. Emphasis was put on modeling the potential-energy surface for the proton-transfer reaction. Potential-surface profiles, geometry-optimized structures and formation energies of H5O2+, protonated water clusters [H+(H2O)n, n=2–4] a...

Conformational Behavior of α-Alanine. Matrix-Isolation Infrared and Theoretical DFT and ab Initio Study

Abstract: Two conformers of the nonionized α-alanine and its isotopomer N,N,O-d3-alanine have been observed in low-temperature Ar matrixes Their infrared spectra have been analyzed and assigned using DFT/B3LYP/aug-cc-pVDZ and MP2/aug-cc-pVDZ geometry and frequency theoretical calculations Two different intramolecular H-bonds, bifurcated NH2···OC and N···H−O, were found in the observed α-alanine conformers, I and IIa We found that the DFT/B3LYP/aug-cc-pVDZ method yields vibrational frequencies of the α-alanine conformers in excellent agreement with the experimental data

Olefin Metathesis of a Ruthenium Carbene Complex by Electrospray Ionization in the Gas Phase

Abstract: Surprisingly similar reactions in the gas phase and in solution [Eq. (a)]: The ion 1 obtained by electrospray ionization behaves in the gas phase analogously to the corresponding complex [RuCl2 (=CHPh)(PCy3 )2 ] in solution. Measured relative rates for ring-opening metathesis are interpreted under the assumption of an intramolecular π complex, which leads to an estimation of the equilibrium constant for π complexation.

Catalytic Asymmetric Synthesis of Quaternary Carbon Centers. Exploratory Studies of Intramolecular Heck Reactions of (Z)-α,β-Unsaturated Anilides and Mechanistic Investigations of Asymmetric Heck Reactions Proceeding via Neutral Intermediates

Abstract: Intramolecular Heck reactions of seven (Z)-α,β-unsaturated 2-iodoanilides catalyzed by Pd−BINAP were surveyed using two reaction conditions: (1) silver-promoted cyclizations in the presence of 2 equiv of Ag3PO4 and (2) base-promoted cyclizations in the presence of 4 equiv of 1,2,2,6,6-pentamethylpiperidine (PMP). A comparison of these results with the outcome of the corresponding intramolecular Heck reactions of the E stereoisomers leads to the following conclusions: (1) (E)- and (Z)-α,β-unsaturated 2-iodoanilides give opposite enantiomers of the Heck product when Ag3PO4 is the HI acceptor (cationic pathway); the absolute configuration of the product is independent of alkene geometry when the HI acceptor is PMP (neutral pathway). (2) When the 2-substituent is Me or prim-alkyl, stereoinduction is optimal in PMP-promoted insertions of Z substrates which occur with ee's as high as 97%. (3) When the 2-substituent is large, stereoinduction is optimal in insertions of E substrates carried out in the presence ...

Self-Folding Cavitands

Abstract: A novel class of resorcinarene-based cavitands 2a−e that fold into a deep (8 × 10 A dimensions) open-ended cavity by means of intramolecular hydrogen bonds has been synthesized. As follows from the FTIR and 1H NMR spectral data in apolar solvent, a seam of eight intramolecular hydrogen bonds is stitched along the upper rim of the structure 2a−e; the amide CO...H−N interactions bridge adjacent ringsinterannular bindingand are held in place by the seven-membered intraannular hydrogen bonds. The self-folding in 2a−e is reversibly controlled by solvent and temperature. Complexation of self-folding cavitands 2a−e with organic molecules such as (1-substituted) adamantanes, lactams, and cyclohexane derivatives was demonstrated by 1H NMR spectroscopy in CDCl3, benzene-d6 and p-xylene-d10; the binding energy -ΔG° values of 2−4 kcal mol-1 in p-xylene-d10 at 295 K were calculated. The exchange between complexed and free guest species is slow on the NMR time-scale, and it is proposed that hydrogen bonds are responsib...

Intramolecular energy transfer mechanism between ligands in ternary rare earth complexes with aromatic carboxylic acids and 1,10-phenanthroline

Abstract: A series of binary and ternary rare earth (Gd, Eu, Tb) complexes with aromatic acids and 1,10-phenanthroline have been synthesized. The lowest triplet state energies of ligands have been obtained by measuring the phosphorescence spectra of binary gadolinium complexes. By comparing the phosphorescence spectra of binary complexes with those of ternary ones, it is found that there exists another intramolecular energy transfer process from the aromatic acids to 1,10-phenanthroline besides the intramolecular energy transfer process between the aromatic acids and the central rare earth ions. The intramolecular energy transfer efficiencies have been calculated by determining phosphorescence lifetimes of binary and ternary gadolinium complexes. The luminescence properties of corresponding europium and terbium complexes are in agreement with the prediction based on energy transfer mechanism.

N-Functionalized 1-Alkynylamides: New Building Blocks for Transition Metal Mediated Inter- and Intramolecular [2+2+1] Cycloadditions.

Abstract: A conceptually new, stereoselective approach to compounds such as 1 and 2 is expected from the so far unknown class of N-functionalized 1-alkynylamides. Building blocks of the type I and II can be applied to inter- and intramolecular, regio- and stereoselective [Co2(CO)8]-mediated [2+2+1] cycloadditions.

Metal-Induced Self-Assembly of a Pyrene-Tethered Hydroxamate Ligand for the Generation of Multichromophoric Supramolecular Systems. The Pyrene Excimer as Switch for Iron(III)-Driven Intramolecular Fluorescence Quenching

Abstract: We report the first example of intramolecular excimer formation in supramolecular trichromophoric systems resulting from the metal-directed self-assembly of chromophore-labeled ligand molecules. The trichromophoric gallium(III) chelate, (1)3Ga, shows an intense pyrene excimer fluorescence emission in acetonitrile, while the iron(III) analogue, (1)3Fe, exhibits a fluorescence of very low intensity compared to that of the free hydroxamate ligand 1. The trivalent gallium metal cation is demonstrated to play the role of an inert and transparent linker, whereas the ferric center acts additionally as an extra chromophore that quenches the pyrene singlet state. On the basis of low-temperature fluorescence measurements, the mechanism of quenching within (1)3Fe is attributed to a pyrene-to-iron electronic energy transfer process. 1H NMR and electronic absorption spectroscopies show that intramolecular interactions between pyrene chromophores prevail in the ground state, which leads to the formation of preassociate...

Oxidative Intramolecular Phenolic Coupling Reaction Induced by a Hypervalent Iodine(III) Reagent: Leading to Galanthamine-Type Amaryllidaceae Alkaloids

Abstract: By extending our oxidative phenol-coupling reactions using a hypervalent iodine(III) reagent, a versatile synthetic procedure for the galanthamine-type Amaryllidaceae alkaloids was accomplished. The first total synthesis of (±)-sanguinine and the total syntheses of (±)-galanthamine, (±)-narwedine, (±)-lycoramine, and (±)-norgalanthamine were also successfully carried out.