Nonbonded interactions in membrane active cyclic biopolymers. II. Ion binding by valinomycin

A possible mode for the capture of a cation by the carrier molecule valinomycin has been simulated. The intramolecular nonbonded energy and the binding energy for a centrally located potassium ion at different stages in the capture process have been evaluated using a method proposed earlier. Contrary to intuitive expectations the open conformation of valinomycin is also found to have a strong affinity for K⁺. There appears to be a rather high potential barrier between the open and closed symmetric conformations.     

Nonbonded interactions. 1. Anisotropic hydrogen-hydrogen interactions

The hydrogen-hydrogen nonbonded potential which may be derived from the calculated interactions between hydrogen molecules has been obtained. The best three-parameter Buckingham function gave an RMS error of 0.18 kcal/mol in fitting Price and Stone's ab initio data for 130 pairs of hydrogen molecules, which may be compared with an RMS error of 0.74 kcal/mol using the parameters in the MM2 force field. Burton's basis set is also considered. A better fit to these data requires that the angular relationship between the bonds be included. The data for hydrogen as well as experimental data for chlorine show that these atoms appear “larger” normal to the bond axis than along the axis, and this is probably also the case for other atoms. When simple angular terms are added it is possible to fit the Price and Stone data set with an RMS error of less than 0.06 kcal/mol. The preferred function was: V = [a₀ + a₁(sin θ₁ + sin θ₂)⁴ + a₂r]e^?3r ? [c₀ + c₁(1 + sinθ₁sinθ₂)]/r⁵. Deficiencies in the current ab initio data are discussed.     

Nonbonded, attractive cation-pi interactions in azide-mediated asymmetric ring expansion reactions

The influence of attractive, nonbonded interactions on the reactions of 1,2- and 1,3-hydroxyalkyl azides with ketones has been investigated through experimental and computational means. A series of 1,3-hydroxyalkyl azides bearing electronically tuned aromatic groups at the 2 position were prepared and reacted along with several derivatives designed to conformationally restrict the rotational orientation of the aromatic substituent. These studies showed that a cation-pi interaction between an aryl moiety and an N2(+) leaving group plays a role in determining the stereoselectivity of these reactions. A series of ab initio calculations supported this hypothesis. A computational and experimental analysis suggested a primarily steric model for the analogous reactions of substituted 2-azido-1-ethanol analogues.     

Energy-resolved collision-induced dissociation cross sections of 2:1 bis-oxazoline copper complexes. Nonbonded interactions and nonlinear effects

Absolute ligand binding energies are determined for the 2:1 complexes of bis-oxazoline ligands and Cu(I) in the gas phase by the fitting of energy-resolved collision-induced dissociation cross sections. The complexes were chosen for their occurrence in asymmetric catalysis for which the phenomenon of nonlinear effects is explained by differences in stability for homochiral and heterochiral complexes. Pseudo-enantiomeric ligands are used so that mass spectrometric measurements can be employed. The measurements find that the sterically similar, but electronically different, isopropyl versus phenyl substituents lead to a different stability ordering of the homo- versus heterochiral complexes, which then leads to the prediction of nonlinear effects in asymmetric catalysis by the complexes with isopropyl-substituted ligands. The origin of the difference in stability order is found in noncovalent interactions between the phenyl groups on the ligands, which are poorly described by DFT calculations.     

Polymerization of cyclic iminoethers. III. Effect of ring substituents

2-Substituted oxazolines with substituents in the 4 or 5 positions essentially cannot be polymerized. This is probably due to steric hindrance.     

Nonbonded interactions and the barrier heights to internal rotation of the methyl group: Part I. Cis- and trans-substituted propenes

Strain energies and barrier heights for rotation of the methyl group in several cis- and trans-substituted propenes have been calculated by means of the Wiberg method. The calculations reveal that the lowering of the barriers in cis-substituted propenes, as compared with the values in trans-compounds and in propene itself, can be ascribed to steric factors. The proximity of the barriers in trans-propenes and in the parent molecule is also considered to be due to nonbonded interactions.     

Polymerization of phosphorus containing cyclic monomers: Synthesis of polymers related to biopolymers

The mechanism of polymerization is discussed, in which cyclic esters of phosphoric acid, and related compounds are converted into linear macromolecules, modelling nucleic and teichoic acid backbones. Structures like deoxyribose polyphosphate and glycerol polyphosphate were prepared from the corresponding cyclic compounds. These polymerizations involve heterolytic breaking of the P-O bond in the cyclic monomer and proceed by ionic mechanism. Both 5- and 6-membered monomers have been polymerized. The thermodynamic parameters of the ring-chain interconversion were determined; the 5-membered rings polymerization is driven by the exothermicity of the ring-opening, whereas polymerization of several 6-membered rings is endothermic and allowed because of the positive change of entropy. Anionic polymerization, and particularly the pseudo(coordinate)anionic polymerization provides, in contrast to the cationic process, high-molecular-weight polymers with more uniform structure. Anionic polymerization proceeds mostly (at the applied conditions) on the macroion – -pairs. The elementary reactions consist of the nucleophilic attack of the paired macroanions on the phosphorus atom in the cyclic monomer molecule. Rate constants of the elementary reactions for the model monomers will be presented. Stereochemistry of the propagation steps is shown to be governed by the statistical ring-opening, leading to the three kinds of polymer units (head-to-tail and two symmetrical units). Apart from the ring-opening, the polyaddition of diepoxides to phosphorous and phosphoric acids is described. Finally, a few examples of preparation of models of biopolymers are given, namely poly(deoxyribose phosphate) and poly(glycerol phosphate).     

Potential anticonvulsants. III. The condensation of isatin with cyclic ketones

Isatin has been condensed with a series of cyclic ketones to give 3-substituted-3-hydroxyoxindoles as potential anticonvulsant agents.     

Bond length alternation in cyclic polyenes. III. Alternant molecular orbital method

The bond length alternation problem in cyclic polyene models as described by the Pariser–Parr–Pople Hamiltonian and an empirical quasiharmonic π-core potential is investigated using the one-parameter alternant molecular orbital (AMO) method. It is shown that in contrast to the unrestricted Hartree–Fock (UHF) results, which lead to symmetric equidistant structures, the one-parameter AMO results yield bond length alternating structures similar to those obtained with the restricted HF approach. The correlation energy recovered by the AMO method is examined for the symmetric polyenes in the whole range of coupling constants for both the Pariser–Parr–Pople and Hubbard Hamiltonians and compared with exact full configuration interaction (FCI) results. For the first member of the cyclic polyene series we also compared the FCI and AMO correlation energies for different nuclear framework distortions. This comparison indicates that in contrast to the UHF results the fraction of the correlation energy recovered by the AMO approach is very uniform over the range of nuclear distortions considered. The AMO results thus strongly indicate the dimerization in the polyenic chains.     

Lattice dynamics with second-neighbor interactions. III. Green's matrix

The theory of pth-order singular differential equations is adaptable to the study of the system of recurrence relations occurring in the problem of a one-dimensional chain with pth-neighbor interactions. By using Green's formula, a mapping is defined between the space V_n of eigenvectors to the dynamical matrix and the symplectic space V_2p of boundary conditions for the recurrence equations. The properties of the resolvent are obtained from an analysis of the solutions of a system of inhomogeneous equations and Green's matrix is constructed for the case of standard Sturm–Liouvilletype boundary conditions. The Weyl surface is discussed and its properties used for the construction of square summable sequences which in turn can be employed in expansion formulas. The generalization of Weyl's m-function in the second-order case (p = 1) becomes for p ≥ 2 a p × p matrix M (λ), where λ is a complex parameter. The imaginary part Im { M (λ)} is related to the spectral properties and serves as basis for the discussion of different concepts of spectral density for the normal modes of lattice dynamical problems. An important practical result is the equation M = ?ΨΦ_a valid in the limit point case, generalizing the corresponding second-order formula.     

Effects of electrostatic and hydrophobic interactions on the chromatographic behavior of biopolymers in HPLC columns

The effect of electrostatic and hydrophobic interactions on the chromatographic behavior of biopolymers with the use of chemically bonded silica-based HPLC columns and aqueous buffered mobile phases containing neutral salts in a wide range of concentration is discussed. Two columns packed with stationary phases appositely designed for biopolymer HPLC in size exclusion and anion exchange mode, respectively, are examined. Experimental data are evaluated by plotting the measured isocratic elution volumes of several standard proteins of different isoelectric point against the salt concentration in the mobile phase. Depending on the concentration and nature of salt, both columns exhibit different domains where either sieving effect or electrostatic or hydrophobic interactions are predominant. At sufficiently low salt concentrations electrostatic interactions are predominant leading to either increasing or decreasing elution volumes depending on the sign of the charges on the stationary phase and the protein, respectively. On the other hand, at high salt concentrations of a salt with sufficiently high molal surface tension increment proteins may be retained by hydrophobic interactions.     

Cyclic acylimines and cyclic carbinolamides III. Piperidone and isoindolone

6-Phenyl-2,3,4,5-tetrahydro-3,3,5,5-tetramethyl-2-pyridone ( 6 ), 1-phenyl-3-isoindolone, and their methanol ( 5 ) and butanol ( 19 ) addition products, as well as 6-methoxy-3,3,5,5-tetramethyl-2-piperidone ( 4 ) and 1-methoxy-3-isoindolinone ( 11 ) were prepared and their chemical properties studied. The cyclic acylimines and their methanol addition products were found to react with weak nucleophiles (amides, alcohols), active methylene compounds (acetone, dimedone) or dienes (1,2,3,4-tetramethyl and 2,3-dimethylbutadiene) to give addition products.