Molecular orbital studies of dinitrogen tetroxide and related molecules

Hartree-Fock LCAO MO calculations for N₂O₄ have been performed in a basis of symmetry orbitals formed from a minimal Slater basis set. Effects of rounding and truncation errors were minimized by the use of the symmetry basis, which also allowed the order or tilling of molecular orbitals to be specified independently of orbital energies. Convergence difficulties were overcome by combined use of the conjugate gradients method and Roothaan's iterative procedure; the method of steepest descents was less effective than either of these. Multicentre ‘non-NDDO’ two-electron integrals were evaluated by the gaussian expansion technique. The wavefunction obtained for the lowest state is NN antibonding, largely as a result of the filling of the 6b_1u antibonding sigma orbital in preference to the 6a_g bonding sigma orbital. There is only a small amount of NN pi-bonding. A bond energy analysis shows that the lowest state is markedly stabilized by NNO three-centre interactions.     

Conformational analysis of aromatic molecules

The mechanical model used in conformation calculations is discussed. A method is developed for strained aromatic systems with possible out-of-plane deformations. An approximate analysis is presented to reveal criteria for planarity.     

Conformational studies on substituted purines

CNDO/2 calculations are performed on 9-methyl-8-phenyl-6-thiopurine in order to determine the molecular equilibrium conformation. The two methyl hydrogens are found to be staggered to the ortho hydrogen on the phenyl ring, and the dihedral angle between the phenyl group and the purine system was found to be equal to 30°, in good agreement with experimental data. The results are discussed in relation to other conformational analyses performed with the CNDO/2 method.     

Conformational studies on (+)-anatoxin-a and derivatives

Summary Anatoxin-a (AnTX) is a highly potent agonist acting at the nicotinic acetylcholine receptor (nAChR) and represents a valuable tool in the study of this receptor. Molecular mechanics, semi-empirical and ab initio molecular orbital energy minimization procedures were conducted to investigate the conformation of AnTX. For each minimization procedure, the s-trans enone isomer of protonated AnTX was the energetically favoured conformer due to intramolecular electrostatic interactions. Our studies are discussed in the light of previous experimental observations and conformational studies, in addition to their importance in the development of future pharmacophore models for nAChR agonist binding.     

Conformational elasticity theory of chain molecules

This paper develops a conformational elasticity theory of chain molecules, which is based on three key points: (i) the molecular model is the rotational isomeric state (RIS) model; (ii) the conformational distribution function of a chain molecule is described by a function of two variables, the end-to-end distance of a chain conformation and the energy of the conformation; (iii) the rule of changes in the chain conformational states during deformation is that a number of chain conformations would vanish. The ideal deformation behavior calculated by the theory shows that the change in chain conformations is physically able to make the upward curvature of the stress-strain curve at the large-scale deformation of natural rubber. With the theory, different deformation behaviors between polymers with different chemical structures can be described, the energy term of the stress in the deformations can be predicted, and for natural rubber the fraction of the energy term is around 13%, coinciding with the experi     

Probing molecular shape. 1. Conformational studies of 5-hydroxyhexahydropyrimidine and related compounds

Understanding the factors that determine molecular shape enables scientists to begin to understand and tailor molecular properties and reactivity. Many biomolecules and bioactive compounds contain aliphatic heterocyclic rings whose conformations play a major role in their biological activity. The interplay of a number of factors, both steric and electronic, is examined for 5-hydroxyhexahydropyrimidine (1) and related compounds with use of spectroscopy and molecular modeling.     

Calixcrowns and related molecules

The synthesis of 1,2- and 1,3-calix[4]-bis-crowns, double calix[4]arenes and double calixcrowns have been shown to depend on the reaction conditions (nature of the base, structure of the ditosylates, and the stoichiometry of the reactants). The 1,3-alternate conformation of the 1,3-calix[4]-bis-crowns was shown to be favourable to the selective complexation of cesium cation. The observed Na⁺/Cs⁺ selectivity was exploited in separation processes using them as carriers in transport through supported liquid membranes (SLMs). The best Na⁺/Cs⁺ selectivity (1/45 000) was observed for the naphthyl derivative 7. Calix(aza) crowns and 1,3-calix[4]-bis-(aza)-crowns were also produced through the preliminary formation of the Schiff base-calixarenes, which were further hydrogenated. The syntheses consisted of the 1,3-selective alkylation of calixarenes followed by cyclization into a 1,3-bridged calixarene or by the direct 1,3-capping of the calixarene with appropriate ditosylates. Soft metal complexation by these ligands is also presented.This paper is dedicated to the commemorative issue on the 50th anniversary of calixarenes.     

Conformational studies of haloperidol

The high field¹H,¹⁹F, and¹³C NMR spectra of haloperidol (HP) in CDCl₃ solution were recorded and analyzed with the aid of both homonuclear (H, H-COSY, H, H-COSYLR) and heteronuclear (H,C-COSY) chemical shift correlation experiments. Through space interactions between (1) the piperidine ring and the chlorinated phenyl ring and (2) the fluorinated phenyl ring and a methylene group were identified using phase sensitive Nuclear Overhauser and Exchange Spectroscopy (NOESY). The NOESY results are consistent with a planar structure rather than a folded version of haloperidol.     

Conformational energy landscapes of liquid crystal molecules

The conformational energy landscape of the prototypical nematic liquid crystal 4-pentyl-4cyanobiphenyl (5CB) is studied using first principles computer modelling. It is found that the most favourable conformation occurs when the two constituent phenyl rings are inclined at an angle of 31 with respect to each other. Also, the orientation of the alkyl chain is found to have an important influence on the ring-ring torsional potential. We fit the energy surface of these coupled torsions to yield an accurate intramolecular potential for use in empirical modelling. To test the strength of the coupling between the alkyl tail and the phenyl rings and the cyano group, we also calculate potentials for the relative orientation of the phenyl rings in biphenyl and cyanobiphenyl (0CB). Our calculations are performed using density functional theory using pseudo-potentials and the generalized gradient approximation to exchange and correlation. The molecular electronic wavefunction is expanded in terms of a plane wave basis set. We compare our results with recent NMR and Gaussian-based quantum chemistry calculations where available.     

Tork: Conformational analysis method for molecules and complexes

A conformational search method for organic molecules and bimolecular complexes is presented. The method, termed Tork, uses normal-mode analysis in bond-angle-torsion coordinates and focuses on a key subset of torsional coordinates to identify natural molecular motions that lead the initial conformation to new energy minima. New conformations are generated via distortion along these modes and their pairwise combinations, followed by energy minimization. For complexes, special treatment is accorded to the six coordinates that specify the position and orientation of one molecule relative to the other. Tests described here show that Tork is highly efficient for cyclic, acyclic, and mixed single molecules, as well as for host-guest complexes.     

Conformational studies on somep-dimethylaminostyryl dyes

PCILO computations have been carried out on the conformations of five p-dimethylaminostyryl dyes derived from quinoline-4 (I), quinoline-2 (II), pyridine-4 (III), pyridine-2 (IV) and benzothiazole (V). The stable conformations of I–IV are found to be nonplanar, while V is almost planar. The results have been explained in terms of various possible steric interactions.     

Molecular modelling studies and the chromatographic behaviour of oxiracetam and some closely related molecules

Summary Modelling studies have been carried out on the cellulose-based chiral stationary phase used to separate the enantiomers of three simple lactams. These studies have helped in understanding differences in the chromatographic behaviour of these molecules.     

Ab initio studies of the structures and force fields of ketenimine and related molecules

Theoretical equilibrium geometries for ketenimine, aminoacetylene and ethynol have been obtained using the MP3/6-31G** ab initio method. Empirical scaling factors have been introduced to estimate the rotational constants A_o, B_o and C_o. In addition the complete harmonic force fields for ketenimine, ketene and diazomethane have been computed, normal coordinate analyses have been performed and the quartic centrifugal distortion constants estimated.     

Topological studies on heteroconjugated molecules

A graph-theoretical analysis of certain -electron properties of alternant molecules with one heteroatom is given. Topological formulas for total -electron energy, -electron charge density, bond order and various polarizabilities are derived. The main results of the paper are summarized in Rules 1-7.     

Conformational analysis of lipid molecules by self-organizing maps

The authors have studied the use of the self-organizing map (SOM) in the analysis of lipid conformations produced by atomic-scale molecular dynamics simulations. First, focusing on the methodological aspects, they have systematically studied how the SOM can be employed in the analysis of lipid conformations in a controlled and reliable fashion. For this purpose, they have used a previously reported 50 ns atomistic molecular dynamics simulation of a 1-palmitoyl-2-linoeayl-sn-glycero-3-phosphatidylcholine (PLPC) lipid bilayer and analyzed separately the conformations of the headgroup and the glycerol regions, as well as the diunsaturated fatty acid chain. They have elucidated the effect of training parameters on the quality of the results, as well as the effect of the size of the SOM. It turns out that the main conformational states of each region in the molecule are easily distinguished together with a variety of other typical structural features. As a second topic, the authors applied the SOM to the PLPC data to demonstrate how it can be used in the analysis that goes beyond the standard methods commonly used to study the structure and dynamics of lipid membranes. Overall, the results suggest that the SOM method provides a relatively simple and robust tool for quickly gaining a qualitative understanding of the most important features of the conformations of the system, without a priori knowledge. It seems plausible that the insight given by the SOM could be applied to a variety of biomolecular systems and the design of coarse-grained models for these systems.     

Conformational ordering of chain molecules in liquid crystals

Deuterium NMR studies have been performed to elucidate orientational characteristics of some ether-type main-chain liquid crystals. Spacers used are of the type -O(CH₂)_nO- with n = 9 and 10. Dimers, homopolymers as well as copolymers in which spacers n = 9 and 10 are arranged in an alternative fashion were investigated. The quadrupolar splitting data obtained from the deuterium-labeled mesogenic core and spacer have been studied within the rotational isomeric state (RIS) approximation. The ordering characteristics thus estimated were found to be consistent with the magnetic susceptibility data obtained by using superconducting quantum interference device (SQUID) for the same polymers.     

Conformational changes of polybutylisocyanate molecules in mixed solvents

Hydrodynamic and electro-optical properties have been investigated for polybutylisocyanate (PBIC) molecules in mixtures of tetrachloromethane and pentaphtorophenol (PFPh). It was shown that variation of PFPh content (up to 20 per cent) leads to a reversible 5-fold change in the equilibrium rigidity of PBIC macromolecules. Coiling of PBIC chains with increasing PFPh concentration in solution arises from the effect of the aromatic component of the solvent on the conjugation in the main chain of the polymer. It was established that the conformational transformations in PBIC chains cannot be likened to the coil—helix transition in synthetics polypeptides.