Showing papers on "Intramolecular force published in 1986"
TL;DR: The aim of this chapter is to present recent developments in the vibrational spectroscopy of peptides, polypeptides, and proteins.
Abstract: Publisher Summary The vibrational spectrum of a molecule is determined by its three-dimensional structure and its vibrational force field. An analysis of this (usually infrared (IR) and Raman) spectrum can therefore provide information on the structure and on intramolecular and intermolecular interactions. The more probing the analysis, the more detailed is the information that can be obtained. Detailed analyses of the vibrational spectra of macromolecules, however, have provided a deeper understanding of structure and interactions in these systems. An important advance in this direction for proteins came with the determination of the normal modes of vibration of the peptide group in N-methylacetamide, and the characterization of several specific amide vibrations in polypeptide systems. Extensive use has been made of spectra-structure correlations based on some of these amide modes, including attempts to determine secondary structure composition in proteins. Polypeptide molecules exhibit many more vibrational frequencies than the amide modes. Over the years, some normal-mode calculations have provided greater insight into the spectra of particular molecules. However, these have often been based on approximate structures or have employed limited force fields. These force fields can now serve as a basis for detailed analyses of spectral and structural questions in other polypeptide molecules. The aim of this chapter is to present these recent developments in the vibrational spectroscopy of peptides, polypeptides, and proteins.
2,640 citations
TL;DR: A series of molecules with the general structure A/sub 1/-Sp-A/sub 2/ have been synthesized and the rates of intramolecular electron transfer were measured as mentioned in this paper.
Abstract: A series of molecules with the general structure A/sub 1/-Sp-A/sub 2/ have been synthesized. Pulse radiolysis was used to convert them into negative ions, and the rates of intramolecular electron transfer were measured. In the first series studied Sp is the androstane skeleton with the acceptors attached to the 3- and 16-positions. The series consisted of eight molecules with A/sub 2/ = 4-biphenyl and eight different A/sub 1/ groups differing in electron affinity by 2.4 eV. The electron transfer rates differ by more than 3 orders of magnitude throughout the series and depend in a very nonlinear fashion on the free energy of the reaction. The second series of molecules was designed to study the effect of the spacer which was varied from the steroid to decalins (eight compounds) and cyclohexanes (four compounds). No comprehensive distance dependence exists. Instead, the rates are strongly influenced by the donor-acceptor attachment geometry which influences the electronic coupling. For the type of spacers studied it was found that the electron transfer rates are slowed down by 1 order of magnitude for each 2.0 bonds for a constant reorganization energy.
500 citations
TL;DR: In this paper, the authors used reaction surface Hamiltonians to model the H atom transfer in malonaldehyde. But they used 3N-6 internal coordinates instead of 3N Cartesian coordinates.
Abstract: Intramolecular H atom transfer in malonaldehyde is described using a reaction surface Hamiltonian. This model utilizes two large amplitude, reaction‐coordinate‐like degrees of freedom—i.e., a surface in the 3N–6 dimensional configuration space of an N atom system—with the remaining 3N–8 degrees of freedom being local harmonic motion away from this 2D surface. The two reaction surface degrees of freedom are chosen to be the two OH bond lengths, i.e., the bond being broken and the bond being formed. The present methodology is developed using 3N–6 internal coordinates, in contrast to our earlier reaction surface model [J. Chem. Phys. 81, 3942 (1984)] that utilized the 3N Cartesian coordinates. From our calculations we conclude that the bare barrier (i.e., with no zero point vibrational corrections) for the H atom transfer is between 6 and 7 kcal/mol.
248 citations
TL;DR: In this article, the authors considered the case that the motion of the system is on a single potential energy surface and the case where this motion occurred on two surfaces was considered elsewhere.
Abstract: Intramolecular charge transfer are considered for the case that the motion of the system is on a single potential energy surface. The case where this motion occurred on two surfaces was considered elsewhere. The former is shown to be much preferable for studies of solvent dynamics. Several aspects of the relation between ‘‘constant charge’’ dielectric relaxation time of the polar solvent and the experimental decay time of emission from the polar excited state of the solute are discussed for hydrogen‐bonded systems.
183 citations
TL;DR: The field of intramolecular reactions is a mature area in which the merging of concepts from both physical organic chemistry and polymer chemistry leads to a unified treatment of cyclization rates and equilibria in terms of a few simple generalizations and theories as discussed by the authors.
Abstract: Publisher Summary This chapter focuses that the field of intramolecular reactions is a mature area in which the merging of concepts from both physical organic chemistry and polymer chemistry leads to a unified treatment of cyclization rates and equilibria in terms of a few simple generalizations and theories. It is concerned with reaction rates, equilibria, and mechanisms of cyclization reactions of chain molecules. It discusses that parallel to the search for synthetic methods to make rings of all sizes, kinetic studies have appeared with the aim of providing insight into physical aspects of ring closure. A significant portion of the evidence available on the kinetics of intramolecular reactions falls in the domain of neighboring group participation. The term is sufficiently wide to encompass “all intramolecular reactions and all reactions that involve nonelectrostatic through-space interactions between groups in the same molecule.” However, the most common types of neighboring group participation involve nucleophilic participation either with or without anchimeric assistance and intramolecular acid and base catalysis. The chapter explores that intramolecular catalysis phenomena have attracted much attention, both from the experimental and theoretical points of view, not only on account of their inherent mechanistic interest, but also because they are believed to model the extraordinary efficiency of enzyme catalysis.
179 citations
TL;DR: In this article, six tetraquaternary salts have been synthesized, which contain two 4,4'-bipyridinium units which are connected by either one or two rigid bridges.
143 citations
TL;DR: MetMetallocenophanes as discussed by the authors are metallocenes in which the cyclopentadienyl ligands are linked intramolecularly through CmHn or Cm HnX (X = heteroatom) chains.
Abstract: Metallocenophanes are metallocenes in which the cyclopentadienyl ligands are linked intramolecularly through CmHn or CmHnX (X = heteroatom) chains. Two main classes of metallocenophanes are known: in [m]metallocenophanes the ligands of one metallocene are connected by a bridge (or by several bridges); in [m.n]metallocenophanes two (or more) metallocenes are brought together into one molecule by bridging groups. This article briefly describes the first class (mononuclear complexes) and then concentrates on the second (binuclear complexes). The [1.1]metallocenophanes, which are produced by linking two metallocene moieties through two C1, bridges, are of particular interest and are characterized by a variety of unusual and useful properties: they are very flexible conformationally; hydride abstraction from the CH2 bridges produces carbenium ions that are greatly stabilized by the adjacent metallocene moieties; deprotonation of one of the CH2 bridges is surprisingly easy and leads to the unusual situation that an intramolecular CHċC hydrogen bond stabilizes a carbanion; protonation of both metallocene moieties causes the liberation of one mole of hydrogen per mole of [1.1]metallocenophane, thereby allowing the use of these compounds as catalysts for the formation of hydrogen in acidic aqueous solutions.
136 citations
132 citations
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129 citations
TL;DR: In this paper, it was found that the cis isomer reacts slower than the trans although the distance between acceptors is shorter for the cis-isomer than that of the trans.
Abstract: Recent experimental work has been directed toward the study of intramolecular electron transfer (ET) rates in radical anions of the type A/sub 1//sup -/-Sp-A/sub 2/A/sub 1/-Sp-A/sub 2//sup -/ where A/sub 1/ and A/sub 2/ are electron acceptors and Sp is a rigid hydrocarbon spacer with no electron affinity of its own. Specifically, for the case of A/sub 1/ = 4-biphenyl, A/sub 2/ = 2-naphtyl, and Sp = 1,4-cyclohexadiyl it was found that the cis isomer reacts slower than the trans although the distance between acceptors is shorter for the cis isomer. With other spacers, such as decalins, it also appears that distance between acceptors is not the only factor in determining the rate. It is most probable that electronic coupling between donor and acceptor is influenced by the sigma-orbitals of the spacer, making it a function of the position as well as the geometry of attachment. While the problem of through-bond coupling has been addressed before here stereoelectronic effects are addressed. To test this hypothesis ab initio calculations for the simplified model are carried out with transequatorial-equatorial, trans-axial-axial, and cis-equatorial-axial geometries. 13 references, 1 figure.
Book•
01 Jan 1986
TL;DR: In this article, the authors classified organometallic intramolecular-coordination compounds into two types, i.e., σ-coordinations compounds and π-coordinator compounds.
Abstract: Organometallic intramolecular-coordination compounds are classified into two types, i.e., σ-coordination compounds and π-coordination compounds. Most studies have been on σ-coordination compounds, however, because the products are five-membered ring compounds that are extremely easily regioselectively synthesized by cyclometalation reactions. Since the 1970s, the author has compiled a great many articles on them and has published many reviews and a monograph, mainly on coordinating atoms such as N, P, As, O, and S and some coordinating groups, as described in the preface and Chap. 1.
TL;DR: The X-ray structural information for both 1 and 2 is consistent with a cyano rather than an isocyano arrangement,1° and this is confirmed by the infrared spectra.
Abstract: 31.30; H, 5.22; N, 36.52. Found: C, 31.34; H, 5.25; N, 36.70. Low-resolution mass spectral analysis showed the expected molecular ion at m / e 345. The infrared spectrum contained a cyano stretching peak at 2180 cm-'. The 31P NMR spectrum consisted of a singlet at -7.8 ppm. Crystals suitable for X-ray analysis were grown by slow evaporation of a solution of 2 in hexane. The structure of 2 is illustrated in Figure 2, and important structural parameters are given in Table I.9 Both compounds, 1 and 2, are stable in contact with the atmosphere and are unaffected when heated to moderate temperatures. The X-ray structural information for both 1 and 2 is consistent with a cyano rather than an isocyano arrangement,1° and this is confirmed by the infrared spectra.\" The triple bonds of the cyano groups in 2 are slightly longer than that in 1, but no evidence could Figure 2. ORTEP representation of the structure of non-gem-trans-tris(dimethy1amino)tricyanocyclotriphosphazene (2).
TL;DR: In this paper, the activation of benzylic sp/sup 3/ hybridized carbon-hydrogen bonds and their catalytic conversion into an indole product using an isocyanide moiety to trap the activated species are discussed.
Abstract: The intramolecular cyclometalation of sp/sup 3/ hybridized carbon-hydrogen bonds in ligand alkyl groups is well documented in transition-metal chemistry. Recent studies have demonstrated the feasibility of intermolecular activation of sp/sup 3/ hybridized carbon-hydrogen bonds in free alkane molecules, which has stimulated a search for the functionalization of the C-H bond in a catalytic fashion. The authors report here the activation of benzylic sp/sup 3/ hybridized C-H bonds and their catalytic conversion into an indole product using an isocyanide moiety to trap the activated species.
TL;DR: In this article, the potential energy of a molecular crystal is expressed as a function of the center of mass positions and the orientations of all molecules, and a detailed description of the different ways in which the potential can be expressed, each way having its own merits, depending on the subsequent calculations in which it has to be used.
Abstract: Publisher Summary This chapter illustrates the dynamics of molecular crystals. The intramolecular vibrations and intermolecular vibrations (usually called lattice vibrations) are discussed. Because the chapter deals with molecules, two types of lattice vibrations can be distinguished; translational and rotational. In order to describe these motions, the potential energy of the crystal is expressed as a function of the center of mass positions and the orientations of all molecules. The chapter provides a detailed description of the different ways in which the potential can be expressed, each way having its own merits, depending on the subsequent calculations in which it has to be used. Later, the chapter briefly discusses the harmonic and quasi-harmonic models that are commonly used to describe the molecular motions— that is, the lattice vibrations, in molecular crystals. A description of perturbation theory around the harmonic model and of the self-consistent phonon method is also presented. The dynamical models for large-amplitude motions are also presented.
TL;DR: In this paper, a detailed classical trajectory study of the overtone-induced dissociation of hydrogen peroxide HO2H and its isotopic variant HO2D is presented, and the factors affecting intramolecular energy flow, such as nonlinear resonances and the various couplings, are examined in detail.
Abstract: A detailed classical trajectory study of the overtone‐induced dissociation of hydrogen peroxide HO2H and its isotopic variant HO2D is presented. The factors affecting intramolecular energy flow, such as nonlinear resonances and the various couplings, are examined in detail. The dissociation lifetimes are found to be on the order of picoseconds and comparable with statistical lifetimes, although the intramolecular energy redistribution is not complete within the lifetime of the molecules. Lifetime broadening contributes very little to the rather large width of the overtone excitation feature, which we conclude is in the main inhomogeneously broadened by rotational structure instead. The implications of our results are discussed.
TL;DR: An intramolecular disulfide bond is introduced into T4 lysozyme and this molecule is shown to be significantly more stable than the wild-type molecule to irreversible thermal inactivation and to be further enhanced by additional modification with thiol-specific reagents.
Abstract: We have introduced an intramolecular disulfide bond into T4 lysozyme and have shown this molecule to be significantly more stable than the wild-type molecule to irreversible thermal inactivation [Perry, LJ, & Wetzel, R (1984) Science (Washington, DC) 226, 555-557] Wild-type T4 lysozyme contains two free cysteines, at positions 54 and 97, and no disulfide bonds By directed mutagenesis of the cloned T4 lysozyme gene, we replaced Ile-3 with Cys Oxidation in vitro generated an intramolecular disulfide bond; proteolytic mapping showed this bond to connect Cys-3 to Cys-97 While this molecule exhibited substantially more stability against thermal inactivation than wild type, its stability was further enhanced by additional modification with thiol-specific reagents This and other evidence suggest that at basic pH and elevated temperatures Cys-54 is involved in intermolecular thiol/disulfide interchange with the engineered disulfide, leading to inactive oligomers Mutagenic replacement of Cys-54 with Thr or Val in the disulfide-cross-linked variant generated lysozymes exhibiting greatly enhanced stability toward irreversible thermal inactivation
TL;DR: The chapter highlights that the presence of an intramolecular hydrogen bond in an acid considerably modifies the acid–base behavior and rates of proton transfer are different from the diffusion-limited values.
Abstract: Publisher Summary This chapter reviews that acid and base catalysis of a chemical reaction involves the assistance by acid or base of a particular proton-transfer step in the reaction. Many enzyme catalyzed reactions involve proton transfer from an oxygen or nitrogen centre at some stage in the mechanism and often the role of the enzyme is to facilitate a proton transfer by acid or base catalysis. Proton transfer at one site in the substrate assists formation and/or rupture of chemical bonds at another site in the substrate. It discusses that an increasing number of categories of proton transfer of oxygen and nitrogen acids are being discovered that do not fit this simple picture and many of these more complex proton transfers have been proposed as components of multi-step mechanisms. In a sense, the more complex proton transfers are of greater chemical interest than processes controlled by the rate of encounter between reactant molecules. The chapter highlights that the presence of an intramolecular hydrogen bond in an acid considerably modifies the acid–base behavior and rates of proton transfer are different from the diffusion-limited values.
TL;DR: In this paper, the room temperature crystal structures of three hydroxy-flavone derivatives have been solved, and the relationships between molecular conformation and solid-state aggregate patterns of 3-hydroxyflavones and related molecules are discussed in terms of possible ground state solute solute-solvent and solvent-solute solution structures.
TL;DR: In this article, the carbon-13 resonances of atoms bearing phenolic or enolic hydroxyl groups, that are engaged in intramolecular hydrogen bonds, experience large upfield deuterium isotope effects.
Abstract: The carbon-13 resonances of atoms bearing phenolic or enolic hydroxyl groups, that are engaged in intramolecular hydrogen bonds, experience large (/sup 2/..delta.. may exceed 1 ppm) upfield deuterium isotope effects. The magnitude of the two-bond isotope effect, /sup 2/..delta.., correlates with the hydrogen bond energy as obtained from the hydroxyl proton chemical shift. In the conjugated systems investigated in this work, the isotope effects extend over several (up to six) chemical bonds. The signs and magnitudes of the long-range isotope effects are related to molecular structure.
TL;DR: In this article, photo-induced electron transfer from porphyrins to quinone and methylviologen capping groups has been demonstrated to occur on the picosecond time scale.
TL;DR: In this article, reactions d'halogenures d'acide benzeneseleninique avec des N-[alcene-4-and -5yl] acetamides ou des butene-3yl-4 pyrrolidone-2 and -azetidinone-6 carbapename
Abstract: Reactions d'halogenures d'acide benzeneseleninique avec des N-[alcene-4- et -5yl] acetamides ou des butene-3yl-4 pyrrolidone-2 et -azetidinone-2: synthese de phenylselenomethyl-2 pyrrolidines et phenylseleno-3- et phenylselenomethyl-2 piperidines N-acetylees, de phenylselenomethyl-3 pyrrolizidine et de phenylselenomethyl-3 isopropyl-6 carbapename
TL;DR: In this paper, the relationship between potential energy surfaces and unimolecular reaction dynamics is surveyed, and the specific topics discussed are the accuracy of the classical trajectory technique for treating non-RRKM dynamics, intramolecular vibrational energy redistribution, and sensitivity of experimental measurements to non-RKM behavior.
Abstract: The relationship between potential energy surfaces and unimolecular reaction dynamics is surveyed The specific topics discussed are the accuracy of the classical trajectory technique for treating unimolecular dynamics, intramolecular vibrational energy redistribution, and the sensitivity of experimental measurements to non-RRKM behavior 102 references, 6 figures, 3 tables
TL;DR: The solvent and pH dependence of the absorption and fluorescence of 2-(2′-hydroxyphenyl)benzoxazole was studied in this paper, where four different species were observed in both ground and excited states: the anion, the neutral molecule with intramolecular hydrogen bonding, the monocation and the dication.
TL;DR: In this paper, the collisional energy transfer between excited SO/sub 2/ and Ar has been simulated by classical trajectory calculations and the influences of the intramolecular and intermolecular potentials, of temperature, and of excitation of SO/ sub 2/ on vibrational and rotational energy transfer are demonstrated.
Abstract: The collisional energy transfer between excited SO/sub 2/ and Ar has been simulated by classical trajectory calculations. The influences of the intramolecular and intermolecular potentials, of temperature, and of excitation of SO/sub 2/ on vibrational and rotational energy transfer are demonstrated. Average energies transferred and collisional and transition probabilities are reported.
TL;DR: In this paper, the distance dependence of the rate of photo-induced electron transfer reactions is studied using a quantum mechanical method CNDO/S. The results are in fair agreement with the experimental results.
Abstract: The distance dependence of the rate of photo‐induced electron transfer reactions is studied. A quantum mechanical method CNDO/S is applied to a series of molecules recently investigated by Hush et al. experimentally. The calculations show a large interaction through the saturated bridge which connects the two chromophores. The electronic matrix element HAB decreases a factor 10 in about 4 A. There is also a decrease of the rate due to less exothermicity for the longer molecule. The results are in fair agreement with the experimental results.