Reactions of 3-nitro-2-trihalomethyl-2H-chromenes with S-and N-nucleophiles. Synthesis and stereochemistry of 2,3,4-trisubstituted chromanes

The reactions of 3-nitro-2-trifluoromethyl-and 3-nitro-2-trichloromethyl-2H-chromenes with thiols and aromatic amines proceed via the nucleophilic addition type to the activated double bond to form 2,3,4-trisubstituted chromanes in high yields. The stereoisomeric compositions and structures of the diastereomers were determined by ¹H, ¹⁹F NMR and 2D NOESY spectroscopies and X-ray diffraction analysis. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 309–321, February, 2006.     

Tautomeric and conformational isomerism of natural hydroxyanthraquinones

Natural 1,5-di-, 1,4,5-tri-, and 1,4,5,8-tetrahydroxyanthraquinones and their anions and metal complexes were shown to be equilibrium mixtures of tautomers and conformers using quantum-chemical and correlation analysis of elecronic absorption spectra. Solvent effects, ionization, complexation, and the introduction and substitution of substituents were accompanied by shifts of tautomeric and conformational equilibria that determine the color of the compounds. __________ Translated from Khimiya Prirodnykh Soedinenii, No. 3, pp. 224–229, May–June, 2006.     

Utilising Saturated Hydrocarbon Isosteres of para Benzene in the Design of Twist-Bend Nematic Liquid Crystals

The nematic twist-bend (N_TB) liquid crystal phase possesses a local helical structure with a pitch length of a few nanometres and is the first example of spontaneous symmetry breaking in a fluid system. All known examples of the N_TB phase occur in materials whose constituent mesogenic units are aromatic hydrocarbons. It is not clear if this is due to synthetic convenience or a bona fide structural requirement for a material to exhibit this phase of matter. In this work we demonstrate that materials consisting largely of saturated hydrocarbons can also give rise to this mesophase.     

Predictive Abilities of Scaled Quantum Mechanical Molecular Force Fields: Application to 1,3-Butadiene

The positions of some IR bands of the s-trans-1,3-butadiene-h ₆ and -1,1,2-d ₃ isotopomers in the gas phase have been measured using a Brucker IFS 120 HR spectrometer with a resolution of 2 cm^–1. The structural parameters of the s-trans- and s-gauche-1,3-butadiene conformers were optimized completely at the MP2/6-31G* theoretical level and their MP2/6-31G*//MP2/6-31G* quantum mechanical force fields (QMFFs) were calculated. Using only the experimental vibrational frequencies of s-trans-1,3-butadiene-h ₆ the QMFF of the s-trans conformer was corrected by Pulay's scaling method (eight scale factors were involved). The scaled QMFF was used to calculate the mean vibrational amplitudes and the Coriolis coupling constants of s-trans-1,3-butadiene-h ₆ and the vibrational frequencies of 12 of its deuterated isotopomers. The set of scale factors obtained for correction of the s-trans QMFF was transferred to the QMFF of the s-gauche conformer. Its theoretical vibrational spectrum and those of some deuterated and C¹³ isotopomers were calculated. The ability of this scaling approach (transferring of scale factors) to predict the vibrational frequencies of rotational conformers and their isotopomers, as well as other molecular characteristics, and to permit detection of perturbations of the experimental bands are discussed.     

Assessing the reliability of density functional methods in the conformational study of polypeptides: the treatment of intraresidue nonbonding interactions

The role of intraresidue interactions in determining the conformational behavior of polypeptides is analyzed by means of density functional and post-Hartree-Fock computations on the alanine dipeptide analog and other model compounds. Our computations show that the accuracy of current density functionals is sufficient for H-bond, electrostatic, inductive, and short-range repulsive interactions, whereas medium-range attractions between electron-rich atoms and/or bonds are underestimated. This leads, in turn, to an underestimation of the stability of helical structures w.r.t. extended or folded conformers involving H-bonds. Those results could pave the route for devising local ad hoc corrections able to significantly improve structural and dynamic predictions for polypeptides issuing from DFT computations.     

Ab initio study of the structure of enolic and ketonic forms of β-diketones with the general formula R″COCH2COR′ (R′ and R″ = H, CH3, CF3)

Geometric parameters, values of force constants and vibration frequencies for different geometric configurations of enolic and ketonic forms of molecules of β-diketones, R″COCH₂COR′ (R″ and/or R′ are H, CH₃, CF₃) have been computed by the ab initio method MO LCAO SCF using wide bases of Cartesian Gaussians. The enolic form of the considered molecules is most energetically favorable. Values of isomerization energy, the height of internal rotation barriers, and energies of the intramolecular hydrogen bond were obtained for it. The stabilization of the enolic form was shown to be caused by the presence of the intramolecular hydrogen bond in the chelate ring. The effect of a substituent on the computed values of molecular parameters was examined. The comparison with the available experimental data testifies to a sufficiently high reliability of the data obtained.     

Conformational analysis of a farnesyltransferase peptide inhibitor, CVIM

The conformational states of the peptide Cys-Val-Ile-Met (or CVIM) were computed and characterized. CVIM inhibits farnesylation of the Ras oncogene product, p21^ras, at the cysteine residue of the C-terminal segment. CVIM is active in an extended conformation. A similar peptide (KTKCVFM) appears to bind the enzyme in the Type I bend conformation. In the present study, the conformations of CVIM were computed in an aqueous environment with the peptide in the zwitterionic state. Solvation free energy based on solvent accessible surface area and a distance dependent dielectric were used in the calculations. Final conformations of multiple independent Monte Carlo simulated annealing (MCSA) conformational searches were used as starting points for Metropolis Monte Carlo (MMC) runs. Conformations saved at intervals during MMC runs were analyzed. Conformers were separated by interactive clustering in dihedral angle coordinates. The four lowest energy conformers corresponding to a Type I bend, extended, AB-bend, and BA-bend were within 0.3 kcal/mol of each other, and dominant in terms of population. The Type I bend and extended conformers were supported by the binding studies. The extended conformer was the most populated. In the AB-bend conformer, `A' indicates the -helix conformation of Val, and `B' indicates the -strand conformation of Ile. The AB- and BA-bend conformations differed from the extended conformation in the value of Val and Ile , respectively, and from the Type I bend conformation in the value of Ile and Val , respectively. The four lowest energy conformers were characterized in terms of energy, density of low energy conformations (or entropy), structure, side chain rotamer fraction population, and interatomic distances.     

Vibrational and electronic spectra of benzophenone in different phase states: Ab initio calculations and experiment

An ab initio method has been used to perform quantum mechanical calculations of the formation energy of different conformers of benzophenone: planar molecule, twisted molecule, planar molecule dimer, twisted molecule dimer; electronic and vibrational spectra of these conformers were also obtained. An assessment of the medium (solvent) influence on the optimal geometry, dipole moment and stability of different forms of benzophenone was performed in the self-consistent reaction field approximation. It is shown that the twisted conformer is more stable than the planar one (the difference of free energies is 32 kJ/mol for free molecules) and it becomes even more stable with the increase in solvent polarity. The calculated electronic and vibrational spectra agree well with the experimental data and properly reflect the complication of the vibrational spectrum when passing from the gaseous phase to the condensed state of benzophenone. The difference between spectral properties of the two dimer forms allows their identification from the spectra and qualitative explanation of the observed peculiarities of phosphorescence of the amorphous phase of benzophenone by the stabilization of different conformers.