A Generalized Unpaired Electron Spin Density Equation and Organic Hyperconjugation Mechanism

A large class of stereochemcial and related interactions in organic chemistry are repulsive and others are attractive, but the relative orientation of two methyl groups and the amount of energy required to twist one relative to the other (the hindered rotation energy barriers), or the alignment of such a group with respect to a conjugated ring to which it is attached (widely attributed to a mechanism called “hyperconjugation”) are estimated to be small in compared with the total energy of the molecule. We used theories of both isotropic and anisotropic proton hyperfine interactions in the π‐electron systems developed in the early sixties. They are approximated by the magnetic dipole nteractions between each proton and an electron spin magnetization that is distributed in 2s and 2p Slater atomic orbitals center on carbon atoms. We have extended these theories to the non‐planar olefinic cation radicals, which are very important in biochemistry as well as in petroleum catalysis. A three dimensional electron spin density equation has been developed in this paper to handle some Jahn‐Teller vibronic molecules. The new electron spin density equation related the observed proton hyperfine splittings to the non‐planar structures of the open‐chain alkene cation radicals generated by radiolysis and various chemical oxidation methods. The spin densities and the conformational calculations based on valence bond theory and symmetry principles are compared with some more elaborated molecular orbital calculations in the literature. The localized valence bond approaches are better in accord with our experimental results. The anomalous line‐width effect of the four methyl groups observed in the 2,3‐dimethyl‐2‐butene cation radicals also confirmed the positive sign of the electron‐proton hyperfine constant of hyper‐conjugation mechanism. A methyl substituent attached to a conjugated molecule often behaves as if it formed part of the region of conjugation; the charge appears to flow from the methyl group into the π electron system and it may also give rise to an appreciable dipole moment. Methylation also gives rise to an appreciable dipole moment, and the resultant red shift of electronic absorption bands is of some importance in the design of dye molecules.     

Isosteres of peptides: boron analogs as dipolar forms of α‐amino acids – a theoretical study

Modification of peptides to produce peptidomimetics is of great interest, with the aim of designing potent, selective, and metabolically stable analogs having certain conformational properties. Organoboranes have been reported in the literature with a wide range of therapeutic applications. One of the therapeutically important class of molecules is amine‐carboxyboranes derived from amino acids by replacement of the Cα atom of an amino acid/peptide by boron. The conformational preferences of these peptides, with respect to backbone ω, ?, and ψ torsion angles, have been investigated by theoretical calculations. The amide bond in these molecules has the same geometry in the ground and transition states as the natural peptides. However, the boron isosteres of glycine and alanine peptides are less structured than their natural derivatives, but are distinguished by structures with a positive value for the ? angle, which is normally disfavored for natural peptides. This property could be used to build peptides with a geometry not usually seen in natural peptides. Copyright © 2007 John Wiley & Sons, Ltd.     

Conformations of fold part in isotactic polypropylene lamella with diamond lattice model

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Identifying potential binding modes and explaining partitioning behavior using flexible alignments and multidimensional scaling

A method is described for the rapid and automatic analysis of flexible molecular alignments using multidimensional scaling and a normalized scoring scheme. A projection scheme was devised to separate orientational and conformational effects. It is shown that the approach can be utilized for the identification of common binding orientations or to the study of differences in partioning behavior. It is suggested that the method can be employed as a novel approach exploring molecular similarity as a dynamic property, so that it includes aspects of motion (by way of mutual orientations), conformations and molecular properties.     

Synthesis and X-ray crystal structures of six [TeL4][MF6] salts, where L is ethylene- or trimethylene-thiourea, and M is Si, Ge or Sn. Five Te(II) complexes with a novel type of structure linked together by unusual N–HF hydrogen bonds

The complexes [Te(etu)₄][SiF₆] (1), [Te(etu)₄][SiF₆] · H₂O (2), [Te(trtu)₄][SiF₆] (3), [Te(etu)₄][GeF₆] · H₂O (4), [Te(trtu)₄][GeF₆] (5) and [Te(etu)₄][SnF₆] (6) (etu = ethylenethiourea, trtu = trimethylenethiourea) have been prepared and their crystal structures determined by X-ray crystallographic methods. The crystals of 1, 3 and 5 are tetragonal; space groups P4cc (No. 103) with Z = 4 for 1, P4nc (No. 104) with Z = 2 for 3, and I4 (No. 79) with Z = 2 for 5. The crystals of 2, 4 and 6 are orthorhombic, space group Pccn (No. 56) with Z = 8 for 2 and 4 and Z = 4 for 6; those of 2 and 4 being isomorphous. The cations contain square planar or slightly distorted square planar TeS₄ coordination groups. In 1, 3 and 5 the Te atoms are located on fourfold rotation axes; the cations have fourfold rotational symmetry and the four thiourea ligands extend to the same side of the TeS₄ plane. These are the first examples of [TeL₄]²⁺ conformers of this type. In 2 and 4 the Te atoms lie on general positions; the cations are distorted versions of those in 1, and also in these the four ligands extend to the same side of the TeS₄ plane. In 6 the Te atoms are located on twofold rotation axes, the conformation of the cations corresponds to the point group C₂ with two neighbouring ligands extending to one side of the coordination plane and the remaining two to the opposite side. In 1–5 each of the four ligands forms a N–HF bond to the same F atom in the counter ion. The crystals of 1–5 are red, and those of 6 are yellow. The red colour is attributed to interactions of Te and S lone electron pairs caused by ligand TeS₄/TeSC tilt angles markedly different from 90°.     

N-Amino Derivatives of Condensed Imidazole Systems

The previously unknown 1-amino- and 3-aminonaphtho[1,2-d]imidazoles, 1-aminonaphtho[2,3-d]imidazole, 1-aminophenanthro[9,10-d]imidazole and the N-amino-N'-methylimidazolium picrates corresponding to them have been obtained by direct amination of a series of condensed imidazoles with O-picrylhydroxylamine. An X-ray structural investigation of 1-amino-3-methylnaphtho[1,2-d]imidazolium picrate showed that, in difference to 1-aminobenzimidazolium salts, a conformation exists in it in which the hydrogen atoms of the N-NH₂ group are directed to the side of the meso carbon atom.     

Molecular and crystal structure of 2-(N-benzyl-N-phenylhydrazinoethylidene)-3-(2H)-benzo[b]-thiophenone

X-ray structural analysis was used to determine the molecular and crystal structure of 2-(N-benzyl-N-phenylhydrazinoethylidene)-3-(2H)-benzo[b]thiophenone. The crystals are monoclinic, the space group isC2/c,a=16.022(6),b=11.202(3),c=22.111(4) Å, =81.08(3)°, and andZ=8. It was shown that the ability of hydrazones of a similar class to exhibit photochromic properties is a function of the steric stresses in the molecules and their confirmation.Institute of Chemical Physics in Chernogolovka, Russian Academy of Sciences, 142432 Chernogolovka. Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 12, pp. 2805–2809, December, 1992.     

Theoretical studies of molecular conformation. Derivation of an additive procedure for the computation of intramolecular interaction energies. Comparison withab initio SCF computations

An additive procedure (SIBFA) is developed for the rapid computation of conformational energy variations in very large molecules. The macromolecule is built out of constitutive molecular fragments and the intramolecular energy is computed as a sum of interaction energies between the fragments. The electrostatic and the polarization components are calculated using multicenter multipole expansions of theab initio SCF electron density of the fragments. The repulsion component is obtained as a sum of bond and lone pair interactions.Tests of the procedure on a series of model compounds containing ether oxygens and pyridine-like nitrogens are reported and compared with the results of correspondingab initio SCF calculations. The resulting methodology is compatible with the simultaneous computation of intermolecular interactions.     

The host-guest chemistry of resorcinarenes

Conformations, acid-base and supramolecular properties of phenolic metacyclophanes obtained from the condensation of resorcinol with aldehydes are discussed, including the mechanisms involved in the formation of these macrocycles. The strong binding of choline-type compounds and the inhibition of acetylcholine hydrolysis with therccc stereoisomers is mechanistically evaluated; arctt isomer shows strong conformational coupling for, e.g., choline binding and simultaneous proton release. The presence of larger alkyl residues at the bottom of therccc macrocycle leads to an additional binding site for small lipophilic substrates, which is independent of the upper complexation center for positively charged substrates. Substitution at the upper rim by carboxylic groups at the 2-position of the phenyl rings yields receptors for, e.g., , -diammonium ions with alternate equatorial and axial arylunits. Positively charged substituents at the upper rim, introduced by aminoalkylation, lead to little change of complexation as a result from their orientation away from the binding center. Aminoacid substituents, for the same reason, do not lead to enantioselective complexation, but allow particularly for strong binding of transition metal ions. Preliminary studies show that resorcinarenes bearing a wide array of positive charges are potent groove binders to ds-DNA without intercalative contributions.This paper is dedicated to the commemorative issue on the 50th anniversary of calixarenes.     

Intramolecular hydrogen bonds and conformations of the 1,4-butanediol molecule

IR and Raman spectra of 1,4-butanediol (BD) versus variations in the medium (CCl₄, CH₃CN), concentration, temperature, and phase state were obtained. The observed changes attest to the conformational variety of BD molecules under the experimental conditions. On the basis of the analysis of the v(OH) region it is concluded that both in the gas phase and in CCl₄ solution conformers of BD with free OH groups coexist with conformers with O-H...O intramolecular hydrogen bonds. The difference in enthalpies, H, for the groups of conformers with and without intramolecular hydrogen bonds was found from the temperature dependence of the v(OH)_free and v(OH)_intra band intensities. The structures and energies for 70 possible spectrally and energetically distinguishable conformers of BD that do not take into account intramolecular hydrogen bonds were calculated by molecular mechanics with account of electron lone pairs of oxygen atoms. Using the experimental values of H and the calculated relative conformer energies,E, the intramolecular hydrogen bond energyE _intra= 3.7 kcal mol^–1 was found.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1572–1577, September, 1993.