Showing papers on "Intramolecular force published in 1983"
TL;DR: In this article, a modification of the central-force model for liquid water is proposed; a spectroscopic potential is adapted to describe the intramolecular interactions, and liquid shifts of internal vibrational frequencies obtained from MD simulations are in good agreement with available spectroscopy data.
442 citations
TL;DR: In this paper, the average survival time was shown to have a non-Kramers dependence on diffusivity, of the type found in the binding kinetics in heme proteins.
Abstract: Intramolecular reactions inside macromolecules (e.g., binding of ligands to iron inside heme proteins) may often be coupled to slow random fluctuations in the reaction center geometry. This motion is ‘‘perpendicular’’ to the reaction coordinate. It can be described as bounded diffusion in the presence of a binding potential field and an intramolecular rate constant which depends on the perpendicular degree of freedom. The diffusion equation is solved under the appropriate reflective boundary conditions. The transient decay of the total population is multiexponential (power law) for small diffusivity, changing to monoexponential kinetics for large diffusivity. For large times or large diffusivity, direct integration is very tedious, but an eigenvalue expansion converges rapidly. It also allows the calculation of the ‘‘average survival time’’ (an extension of the ‘‘first passage time’’) a natural candidate for replacing the reciprocal rate constant in multiexponential kinetics. An example is given for electron transfer between two loosely bound sites in a macromolecule. The average survival time shows a non‐Kramers dependence on diffusivity, of the type found in the binding kinetics in heme proteins.
322 citations
310 citations
TL;DR: In this paper, the authors measured forces between molecularly smooth mica surfaces immersed in tetrachloromethane, benzene, and 2,2,4-trimethylpentane, and compared the results with measurements on cyclohexane, octamethylcyclotetrasiloxane and n-octane.
Abstract: Forces between molecularly smooth mica surfaces immersed in tetrachloromethane, benzene, and 2,2,4‐trimethylpentane have been measured. In tetrachloromethane and benzene the force law is an oscillatory function of the separation between the mica surfaces, with a periodicity equal to the mean molecular diameter and a measurable range of appoximately ten periods, or about 5 nm. Beyond this separation, the oscillations merge into a purely attractive ‘‘tail’’. In 2,2,4‐trimethylpentane the force law shows only short‐range oscillatory behavior, below 2 nm; at larger separations the force is everywhere attractive. The results are compared with measurements on cyclohexane, octamethylcyclotetrasiloxane and n‐octane, including some repeat measurements. When the distance scale is normalized by the mean periodicity of the force curve for each liquid, the results for the four fairly rigid molecules benzene, tetrachloromethane, cyclohexane, and octamethylcyclotetrasiloxane are very similar; minor differences possibly being due to varying trace amounts of water in the liquids. In the above systems the force laws are oscillatory functions of the surface separation, with a periodicity roughly equal to the molecular diameter and a measurable range of about ten periods. The peak‐to‐peak amplitude shows an essentially exponential decay. By contrast, the existence of free intramolecular rotation in the two flexible molecules 2,2,4‐trimethylpentane and n‐octane is sufficient to reduce the range of the solvation forces to 2 nm or less. The results indicate that the amount of liquid structuring for inert liquids depends mainly on the internal rigidity of the molecules, while the effect of molecular shape, size, and temeperature is of secondary importance.
204 citations
TL;DR: In this paper, a procedure of constructing heterocycles using palladium catalyzed intramolecular addition of amino or hydroxyl group to an acetylene bond is described.
Abstract: Novel procedures of constructing heterocycles are described which employ palladium catalyzed intramolecular addition of amino or hydroxyl group to an acetylene bond as a key reaction. Pyrroles and furans are prepared from l-amino-3-alkyn-2-ols and 3-alkyne-l,2-diols, respectively. Successive addition of two hydroxyl groups to one acetylene bond gives various types of acetals. Insect pheromones containing intramolecular acetal linkage are produced by applying this reaction. INTRODUCTION Ilydration of unactivated acetylenes to form ketones has found considerable synthetic use (Ref. 1). Terminal acetylenes almost invariably yield methyl ketones. Regioselective hydration of internal acetylenes stems from anchimeric assistance (Ref. 2,3) and intramolecular reaction of hydroxyl group to acetylene bond plays a key role to synthesize prostacyclin (Ref. 3,4). The above described reactions are usually catalyzed by mercuric salts. Intramolecular addition of protic group such as amino and hydroxyl to carbon carbon triple bond seems to be promising to construct venous kinds of heterocycles. Studies on the subject utilizing palladium catalyst are described in this paper. INTRAMOLECULAR ADDITION OF HYDROXYL OR AMINO GROUP TO ACETYLENES Palladium(II) species have been found to be effective to the intramolecular addition of hydroxyl across acetylenes. Regioslelctivity of the reactions is illustrated by the cases of 3-, 4-, and 5-alkyn-l-ols. Reactions are carried out in anhydrous ether utilizing PdCl2(PhCN)., as catalyst (condition A) or in aqueous acetonitrile utilizing PdC12 as catalyst (condition B). Under condition A, 3-decyn-l-ol cyclizes in 5-Endo-Dig manner giving dihydrofuran 2 as a predominant product. Reaction under condition B gives exclusively hydroxy ketone 3 which is the hydrolyzed product of 2. CH3(CH2)5CECCH2CH2OH CH (CH ) 4[) + CH3(CH2)5(CH2)3OH 3 25 0 0 I A: PdC12(PhCN)2 (0.01—0.03 equiv.) 30% anhydrous Et2O, r.t., 5-10 h B: PdCl2 (0.01—0.05 equiv.) aqueous CH3CN, ref lux 30 mm. 5-Undecen-l-ol cyclizes in 6-Exo-Dig manner and gives dihydropyran 5 and its hydrolyzed hydroxy ketone 6.
198 citations
169 citations
TL;DR: Results have been interpreted to indicate that most of the hemeproteins investigated catalyze N-demethylation reactions viaalpha-carbon hydrogen atom abstraction, while the reactions catalyzed by cytochrome P-450 and chloroperoxidase proceed via alpha-carbon deprotonation.
156 citations
154 citations
TL;DR: In this article, the presence or absence of intramolecular vibrational relaxation (or more precisely state mixing) from an excited C-H stretch in 23 representative molecules varying in size from methane to nonbornene.
Abstract: Infrared fluorescence measurements have been used to determine the presence or absence of intramolecular vibrational relaxation (or more precisely state mixing) from an excited C–H stretch in 23 representative molecules varying in size from methane to nonbornene. Included are aliphatic hydrocarbons, aromatic molecules, ethers, and ketones, including cyclic molecules. The rate of resonance fluorescence, calculated relative to a nonrelaxing molecule, was used as the criterion of relaxation. Small rates imply state mixing and hence in the large molecule limit, relaxation. The primary correlation with the presence of mixing is with state density; about ten states per wave number (cm−1) are needed to insure mixing. The spread in threshold densities reflects variations in anharmonicity. For some molecules true relaxed (non C–H stretch) fluorescence is observed. These experiments were done in a molecular beam, using a pulsed optical parametric oscillator for excitation and a circular variable filter for spectral...
141 citations
138 citations
TL;DR: In this article, photoelectron spectroscopy has proven an informative and valuable extension to other methods, since orbital interactions are involved in most intramolecular effects of this kind.
Abstract: Classical structural formulas often convey the impression only those relationships between the atoms are of importance which hold a molecule together as symbolized by the chemical bonds. However, many interactions between atoms or groups of atoms are not adequately denoted in this manner. Nevertheless, their existence can have important consequences for ground state energies (cis-difluoroethylene is more stable than trans-difluoroethylene), conformations (the syn form of methyl vinyl ether is more stable than the anti form), reactivities (an endo cyclopropane ring in 7-anti-norbornyl derivatives accelerates solvolysis by a factor of 1014), UV spectra (“superposition” of the π-systems of acridine and purine-bonded through a four-membered chain-results in hypochromism), CD spectra (the inherently symmetrical but dissymmetrically perturbed chromophore of 2-deuterionorbornadiene allows the observation of three transitions in the near UV), and ESR spectra (the long-range coupling with H-4 in the bridgehead bicyclo[2.1.1]hex-1-yl radical equals 22.5 G). Since orbital interactions are involved in most intramolecular effects of this kind, photoelectron spectroscopy has proven an informative and valuable extension to other methods.
TL;DR: In this paper, the formation of polymers between different proteins by reacting them with transglutaminase was studied and it was shown that the different proteins were polymerized through formation of intermolecular crosslinks.
Abstract: Guinea pig liver transglutaminase has been found to catalyze the formation of inter- and intramolecular e-(γ-glutamyl)lysyl crosslinks in proteins. In this paper we study the formation of polymers between different proteins by reacting them with transglutaminase. Analysis of reaction products between acetylated αs1 -casein and several proteins (αs1 -, k-casein, β-lactoglobulin, soybean 11S and 7S globulin) by sodium dodecyl sulfate polyacrylamide gel electrophoresis and high-performance liquid chromatography indicated that the different proteins were polymerized through the formation of intermolecular crosslinks. This reaction may represent a procedure to improve the properties of food proteins.
TL;DR: The fluorescence decay times for intramolecular electron transfer of the S 1,np state of 6-(4-methylphenyl) amino-2-naphthalenesulfon-N,N-dimethylamide (TNSDMA) correlate well with the constant charge dielectric relaxation times [τ 1 v = (e 00 /e s ) τ 1 ] in linear alcohols as discussed by the authors.
TL;DR: Etude de polymere atactique isotactique et syndiotactique as discussed by the authors, a.k.a., polymer atactiques isotactiques, isometry.
Abstract: Etude de polymere atactique isotactique et syndiotactique. Comparaison avec le spectre en solution
TL;DR: In this article, an anharmonic HC bond coupled to a chain of harmonically coupled carbon atoms is modeled and the HC stretch is initially excited to various vibrational states and the flow of energy from the HC bond is observed.
Abstract: Intramolecular energy transfer in hydrocarbons is modeled with an anharmonic HC bond coupled to a chain of harmonically coupled carbon atoms. The HC stretch is initially excited to various vibrational states and the flow of energy from the HC bond is observed. It is found that, at sufficiently high excitation, vibrational energy flow is irreversible and occurs on a time scale of roughly 100 fs, independent of chain length. This corresponds very well to experimentally observed spectral bandwidths. By analyzing the motion in a set of natural dynamical modes, it is shown that this energy transfer is due to sequential nonlinear resonances in the chain. Analytic modeling of the mode–mode couplings then provides a simple approximate description of the energy transfer process.
TL;DR: Experimental measurements of disulfide bond stability at various stages of protein folding are considered in terms of the effective concentrations of the thiol groups relative to each other, so that intramolecular interactions within the interior of a protein are much more stable, and provide greater stability to the folded conformation, than those on the surface or in a flexible segment.
Abstract: Experimental measurements of disulfide bond stability at various stages of protein folding are considered in terms of the effective concentrations of the thiol groups relative to each other; values of up to 107M are observed, so that intramolecular interactions within the interior of a protein are much more stable, and provide greater stability to the folded conformation, than those on the surface or in a flexible segment. Intramolecular interactions can have substantially lower free energies than intermolecular, for solely entropic reasons; this implies that polar interactions, such as hydrogen bonds and salt bridges, can provide net stabilization to a folded conformation, in spite of the unfolded protein having intermolecular interactions with the solvent. These considerations can account for the lower free energy and enthalpy of the folded state and are useful for considering protein flexibility.
TL;DR: In this paper, the signal multiplets and magnitudes of isotope effects are used to assign the spectra of carbohydrates as shown for both..cap alpha..- and..beta..-forms of the 6-linked and 4-linked disaccharides.
Abstract: /sup 13/C NMR measurements have been made in dimethylsulfoxide-d/sub 6/ solutions of some carbohydrates (methyl ..cap alpha..-D-gluco- and galactopyranosides, melibiose, maltose, and ..beta..-cyclodextrin) in which exchangeable protons have been partially deuterated. Signals from single carbon atoms are observed as a series of multiplets (singlets to octets) with intensity ratios that vary quantitatively with OH:OD ratios. Partial deuteration of exchangeable protons in molecules permits direct observation of the different isotopomers measured under conditions of slow exchange and the resonance line separations can be analyzed in terms of the two-bond (..beta..) and three-bond (..gamma..) istope effects that contribute to the deuterium-induced secondary isotope shift. Magnitudes of ..beta.. and ..gamma.. effects are found to vary with configuration of carbon atoms, and substitution and hydrogen bonding of hydroxyl groups. Signal multiplets and magnitudes of isotope effects are used to assign the spectra of carbohydrates as shown for both ..cap alpha..- and ..beta..-forms of the ..cap alpha..1-..-->..6-linked (melibiose) and ..cap alpha..1..-->..4-linked (maltose) reducing disaccharides. The method also confirms the presence and direction of intramolecular hydrogen bonding in ..cap alpha..1..-->..4 glucosides (i.e., C2'-O2'...H-O-C3) by observation of an isotope effect on C2' transmitted through a hydrogen bond. Measurements by NMR spectroscopy of secondary isotope multiplets of partiallymore » labeled entities (SIMPLE NMR) have widespread application for signal assignment and for studying isotope effects in molecules. 5 figures, 4 tables.« less
TL;DR: In this article, the structure of N,N-dimethylformamide (DMF) was determined at 25 °C by means of X-ray diffraction using a θ-θ type Xray diffractometer, and the least squares analysis of the reduced intensities results that a DMF molecule has a practically planar skeletal structure in the liquid state.
Abstract: The structure of N,N-dimethylformamide (DMF) was determined at 25 °C by means of X-ray diffraction using a θ-θ type X-ray diffractometer. The least-squares analysis of the reduced intensities results that a DMF molecule has a practically planar skeletal structure in the liquid state. Intramolecular structural parameters within a DMF molecule were determined as follows: C=O; 1.24 A, N–C(CHO); 1.35 A, and N–C(CH3); 1.45 A. The bond lengths are not appreciably different from those found in the gas phase, except for the C=O length, which is slightly longer by 0.04 A in the liquid state than in the gaseous one. The radial distribution curve of DMF shows that the intermolecular arrangement of DMF molecules is practically fully disordered and no evidence has been found for the cluster formation of DMF molecules in the liquid state. The experimental result for the weak intermolecular interactions between DMF molecules is supported by ab initio MO-SCF calculations.
TL;DR: Cross polarization/magic angle sample spinning (CP/MAS)/sup 13/C NMR spectra were obtained at various contact times on five solid organic compounds containing carbon atoms far from intramolecular protons or containing very few hydrogen atoms as discussed by the authors.
Abstract: Cross polarization/magic angle sample spinning (CP/MAS)/sup 13/C NMR spectra were obtained at various contact times on five solid organic compounds containing carbon atoms far from intramolecular protons or containing very few hydrogen atoms. Carbon atoms four or more bonds fromthe nearest intramolecular proton cannot be fully polarized before T/sub 1p/(H) effects begin to dominate the proton magnetization. Rapid molecular motion aggrevates the problem because of motional attenuation of the dipolar interaction. Computer-fitted T/sub CH/ and T/sub 1p/(H) parameters are consistent with these experimental results. The simple theories of cross polarization account for incomplete polarization in these cases. In 1,2:4,5-benzenetetracarboxylic dianhydride, C/sub 10/H/sub 2/O/sub 6/, the relative aromatic and carbonyl signal intensities are only 5% from the ideal values on the basis of atomic ratios, but absolute intensities can be seriously reduced. In general, CP/MAS NMR provides a convenient and useful quantitative method for studying diamagnetic, organic solids of low molecular weight that is competitive to other physical methods even for molecules of low or remote protonation.
TL;DR: In this paper, the authors used X-ray spectroscopy to confirm the 1,3-double bridging examles of polylithium compounds, such as 1,4-dilithiobiphenyl and 1,5-dimitriu-1,3cis,cis-butadiene.
Abstract: The dimerization energies of lithium compounds, 2LiX-(LiX)9, are quite large and depend principally on the electronegativity of X. Intramoleular association, the equivalent of dimerization, is comparably favorable energetically. Thus, many polylithium compounds, including many synthetically useful "dianions", are found by molecular orbital calculations to prefer structures in which the lithium atoms bridge symmetrically. An example is o,o'-dilithiobiphenyl, whose predicted structure has now been confirmed by X-ray spectroscopy. Dilithiated species based on propene (CH9CHCHLi9), propane (LiCH9CH9CH9Li), acetaldehyde (Li CHCHO), acetone (LiCH2COH Li ahd Li CHCOCH), ahd mies (e.g., HCOLi9) are amog 1,3-double bridging examles. Besies o,o -dilithiobiphenyl, 1,4-double lithium bridging is exhibited by 1,4-dilithiobutane, 1,4-dilithio-2-cis-butene, and 1,4-dilithio-1,3-cis,cis-butadiene. While electrostatic interactions provide the simplest explanation for these structures, multi center covalent bonding also is important in determining geometrical details and energetic differences.
TL;DR: In this paper, the atomic distances within a formamide molecule and the intermolecular N···O distance between the hydrogen-bonded molecules are determined by the X-ray diffraction experiment.
Abstract: The molecular and liquid structures of formamide have been studied by means of X-ray diffraction. Relative stabilities of aggregates of formamide molecules have been calculated by using the ab initio LCGO-MO-SCF procedure and minimal basis sets. The atomic distances within a formamide molecule and the intermolecular N···O distance between the hydrogen–bonded molecules are determined by the X-ray diffraction experiment as follows: C=O: 1.24(1) A, C–N: 1.33(1) A, N···O (intramolecular): 2.25(2) A, and N···O (intermolecular): 3.05(5) A. The intermolecular (Remark: Graphics omitted.) bond angle (Θ) is about 120°. It is concluded from the X-ray diffraction experiment that liquid formamide mainly consists of the chain-like hydrogen–bonded structure of formamide molecules by combining through –NH2···O=CH– interactions. The conclusion is supported by the ab initio calculations. Formation of ring-dimers in the liquid formamide has not been confirmed by the X-ray diffraction study, although a possibility of the for...
TL;DR: In this paper, the time-dependent processes occurring in polyatomic molecules during and after intense infrared irradiation, for example in infrared photochemistry, are discussed in terms of underlying structures in the absorption spectra.
Abstract: The time-dependent processes occurring in polyatomic molecules during and after intense infrared irradiation, for example in infrared photochemistry, are discussed in terms of underlying structures in the absorption spectra. Origins of homogeneous and inhomogeneous spectral structures are identified in high-resolution spectra of small molecules (CF3H and CF3CCH). Temperature-dependent bandshapes of large polyatomic molecules, (CF3)3CH and (CF3)3C—CCH are evaluated in terms of the most relevant parameters of the vibrational structures, using a new method. The bandshape parameters can be interpreted in terms of intramolecular vibrational processes on the picosecond and subpicosecond time-scales. Characteristic differences in the dynamic coupling behaviour of the acetylenic CH stretching and the saturated CH stretching vibrations are identified in the fundamental and the overtone spectra.
TL;DR: In this article, the relationship between molecular structure and intramolecular hydrogen bonding in polyfunctional oxonium ions in terms of enthalpy (..delta..H/sub HB//sup 0/) and entropy of the internal bond; the thermal stability of the bond as reflected by the bond opening temperature T, the bond weakening factor, and the entropy of cyclization per single C-C, C-O, or C-N bond incorporated into the ring.
Abstract: Observations are reported of the relationship between molecular structure and intramolecular hydrogen bonding in polyfunctional oxonium ions in terms of enthalpy (..delta..H/sub HB//sup 0/) and entropy (..delta..S/sub HB/) of the internal bond; the thermal stability of the bond as reflected by the bond opening temperature T, the bond weakening factor ..delta..H/sub BWF/, and the entropy of cyclization per single C-C, C-O, or C-N bond incorporated into the ring ..delta..S/sub HB/n/. In the smallest compounds the cyclic structure may only amount to a stabilized cis conformation, while in the largest compounds the hydrogen bond approaches its full intermolecular strength. Combined with previous results, the present data show that intramolecular bonding is prevalent in complex organic ions. 1 figure, 2 tables.
TL;DR: In this paper, the identification of solid-state defects on calcined H-ZSM-5 powder is discussed in terms of positive holes on oxygen atoms between the tetrahedral structure of silica-alumina.
TL;DR: In this paper, an attempt was made to improve the tendency of Allinger's latest empirical force field MM2 to underestimate barrier heights of rotation about C-C single bonds, and the modified force field correctly reproduced chair-chair interconversion barrier of all-cis-l, 2,3,4,5,6-hexamethylcyclohexane (calc. 16.7, obsd. 17.426 A.
TL;DR: The kinetics and mechanism of the reaction in the photo-excited state of 7-hydroxycoumarin and its derivative have been studied in aqueous solutions by means of measuring the fluorescence spectra and fluorescence lifetime as mentioned in this paper.
Abstract: The kinetics and mechanism of the reaction in the photo-excited state of 7-hydroxycoumarin and its derivative have been studied in aqueous solutions by means of measuring the fluorescence spectra and the fluorescence lifetime. The four fluorescence bands have been identified as emissions from the neutral, anionic, tautomeric, and cationic forms of 7-hydroxycoumarins. The quantitative analysis was performed by using the rate equation which included the term for the direct conversion of the excited neutral molecule to its tautomer in addition to the usual reaction term of dissociation. The rate constants of the tautomerization and dissociation were discussed in detail, and it was revealed that the tautomerization in aqueous solutions was mainly caused by the transfer of a proton between two active sites in the molecule. Such an intramolecular proton-transfer of the coumarins, found first in this paper, is considered to be promoted by water molecules with a hydrogen bond surrounding the excited molecule.