Ternary β-Cyclodextrin Complexes as Models of Allosteric Effects

Two guests reacting with cyclodextrins (CDs) may form ternary complexes, in addition to the common competition of 1:1 complexes. One of the guests can really be included into the cavity of the CD, while the second guest molecule is either inserted close to the first one or attached to the outer surface of the supramolecule by H-bonding. There is a further possibility when the included guest bears a substituent outside the cavity and the second guest can interact with it. The properties of the ternary species formed are highly influenced by the solely (or primarily) included guest. The changes are attributed to the altered properties of the hydrophilic domain of the CD. The phenomena can be proved by NMR data obtained for some binary systems of -CD inclusion complexes and acetic acid and by the stability constants of the ternary complexes formed. Allosteric effects as well as coenzyme/apoenzyme/substrate interactions could be well modelled by these types of CD complexes.     

Enthalpies of Dilution of Aqueous Solutions of NaOH, KOH, and CsOH at 300, 325, and 350°C

Dilution enthalpies, measured using isothermal flow calorimetry, are reported for aqueous solutions of KOH and CsOH at 300°C and 11.0 MPa, 325°C and 14.8 MPa, and for aqueous solutions of NaOH, KOH, and CsOH at 350°C and 17.6 MPa. Previously collected dilution enthalpies for aqueous solutions of NaOH at 300°C and 9.3 MPa and at 325°C and 12.4 MPa were included when fitting the Pitzer parameters. The concentration range of the hydroxide solutions was 0.5–0.02 molal. Parameters for the Pitzer excess Gibbs ion-interaction equation were determined from the fits of the experimental heat data. Equilibrium constants, enthalpy changes, entropy changes, and heat capacity changes for alkali metal ion association with hydroxide ion were estimated from the heat data. For all systems, the enthalpy changes and entropy changes were positive and had accelerating increases with temperature. The resulting equilibrium constants show significant, but smaller, increases with temperature.     

The molecular structure and conformation of trichloronitromethane as determined by gas-phase electron diffraction and theoretical calculations

The molecular structure of trichloronitromethane has been studied in the gas phase using electron diffraction data. The molecules are found to undergo low barrier rotation about the CN bond with a planar CNO₂ moiety in agreement with HF/MP2/B3LYP/6-311G(d,p) calculations. The experimental data are consistent with a dynamic model using a potential function for the torsion of V = (V₆/2)(1 − cos 6τ). The major geometrical parameters (r_g and ) for the eclipsed form, obtained from least squares analysis of the data are as follows: r(NO₃) = r(NO₄) = 1.213(2) Å, r(CN) = 1.592(6) Å, r(CCl)_av = 1.749(1) Å, Cl₅CN/Cl₆CN = 109. 6°/106.3°(2), O₃NC/O₄NC = 117. 6°/114.1°(4), τCl₅C₁N₂O₃ = 0.0°, and V₆ = 0.20(25) kcal/mol.     

Infrared and Raman spectra, conformational stability, ab initio calculations of structure, and vibrational assignment of 2-hexyne

The infrared spectra (3500–50 cm⁻¹) of the gas and solid and the Raman spectra (3500–50 cm⁻¹) of the liquid and solid have been recorded for 2-hexyne, CH₃–CC–CH₂CH₂CH₃. Variable temperature studies of the infrared spectrum (3500–400 cm⁻¹) of 2-hexyne dissolved in liquid krypton have also been recorded. Utilizing four anti/gauche conformer pairs, the anti(trans) conformer is found to be the lower energy form with an enthalpy difference of 74±8 cm⁻¹ (0.88±0.10 kJ/mol) determined from krypton solutions over the temperature range −105 to −150 °C. At room temperature it is estimated that there is 42% of the anti conformer present. Equilibrium geometries and energies of the two conformers have been determined by ab initio (HF and MP2) and hybrid DFT (B3LYP) methods using a number of basis sets. Only the HF and DFT methods predict the anti conformer as the more stable form as found experimentally. A vibrational assignment is proposed based on the force constants, relative intensities, depolarization ratios from the ab initio and DFT calculations and on rotational band contours obtained using the calculated equilibrium geometries. From calculated energies it is shown that the CH₃ group exhibits almost completely free rotation which is in agreement with the observation of sub-band structure for the degenerate methyl vibrations from which values of the Coriolis coupling constants, ζ, have been determined. The results are compared to similar properties of some corresponding molecules.     

Multiple polypeptide forms observed in two-dimensional gels of Methylococcus capsulatus (Bath) polypeptides are generated during the separation procedure

We have examined two-dimensional electrophoresis (2-DE) gel maps of polypeptides from the Gram-negative bacterium Methylococcus capsulatus (Bath) and found the same widespread trains of spots as often reported in 2-DE gels of polypeptides of other Gram-negative bacteria. Some of the trains of polypeptides, both from the outer membrane and soluble protein fraction, were shown to be generated during the separation procedure of 2-DE, and not by covalent post-translational modifications. The trains were found to be regenerated when rerunning individual polypeptide spots. The polypeptides analysed giving this type of trains were all found to be classified as stable polypeptides according to the instability index of Guruprasad et al. (Protein Eng. 1990, 4, 155-161). The phenomenon most likely reflects conformational equilibria of polypeptides arising from the experimental conditions used, and is a clear drawback of the standard 2-DE procedure, making the gel picture unnecessarily complex to analyse.     

Conformational studies of basic poly (α-amino acid)s in reversed micelles

The conformation of various basic poly (-amino acid)s was investigated by CD measurements in aqueous solutions containing bis (2-ethylhexyl)sodium sulfosuccinate (AOT) as well as in the AOT reversed micelles. The addition of AOT into an aqueous solution of poly(L-lysine) induces the conformational transition from coil to ordered structure, followed by aggregation. On the other hand, poly(L-lysine) assumes-structure in the reversed micelles at low w_ovalue (w_o=[H₂O]/[AOT]). Similarly to poly(L-lysine), poly(L-ornithine) takes an ordered structure in the aqueous solution containing AOT and-structure in the reversed micelles. In this case, however, these ordered structures are not so stable, compared with that of poly(L-lysine). Poly(L-arginine) undergoes the conformational transition from coil to helix by addition of AOT into the aqueous solution. Further addition of AOT allows transformation into-structure. Copoly(L-lysyl-L-leucine) with 63% leucine residue was shown to take a stable helical conformation even in pure water. In the reversed micelles, however, this ordered structure is significantly changed probably because the hydrophobic interaction among the leucyl residues is lowered in the reversed micelles.     

Conformational flexibility of 1,4-dihydroazine carbonyl derivatives

Summary The molecular geometry of 4-oxo derivatives of 1,4-dihydropyridine, 1,4-dihydropyrimidine, 1,4-dihydropyridazine, and 1,4-dihydro-1,3,5-triazine has been calculated by the semi-empirical quantum-chemical AM1 method. It could be shown that the dihydrocycle in these compounds is not conformationally rigid. Changing the angle between the endocyclic double bond planes ±15° causes less than 1 kcal/mol increase of energy.

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Konformative Flexibilität von 1,4-Dihydroazin-carbonyl-Derivaten (Kurze Mitt.)

Zusammenfassung Die molekulare Geometrie von 4-Oxo-Derivaten von 1,4-Dihydropyridin, 1,4-Dihydropyrimidin, 1,4-Dihydropyridazin und 1,4-Dihydro-1,3,5-triazin wurde mittels der semiempirischen quantenchemischen AM1-Methode berechnet. Es konnte gezeigt werden, daß der zweifach hydrierte Ring in diesen Verbindungen nicht starr ist. Eine Änderung des Winkels zwischen den Ebenen der endocyclischen Doppelbindungen um ±15° bewirkt eine Energieerhöhung von weniger als 1 kcal/mol.

     

Cis- and trans-3-hexene: infrared spectrum in liquid argon solution, ab initio calculations of equilibrium geometry, normal coordinate analysis, and vibrational assignments

The infrared spectra of cis-3-hexene and trans-3-hexene dissolved in liquid argon have been obtained at temperatures from 93 to 120 K. The absorptions were observed with a low-temperature cell and a Fourier transform infrared spectrophotometer. Ab initio molecular orbital calculations were performed to obtain the equilibrium geometry, vibrational frequencies, force fields, and infrared intensities. The calculations were done at the Hartree-Fock level using 6-31G basis set. The Cartesian force fields from ab initio calculations have been converted to the force field in symmetry coordinates. The scale factors of ab initio calculated force fields were determined. Normal coordinate calculations were performed using a scaled quantum mechanical (SQM) force field. Vibrational normal modes calculated for the lowest energy rotamers of cis- and trans-3-hexene have been assigned to infrared absorption bands observed in liquid argon solution. The assignments were based on calculated frequencies and potential energy distributions. The equilibrium geometries of the two lowest energy rotamers (symmetry C₂ and C_s) of cis-3-hexene and of the three lowest energy rotamers (symmetry C_i, C₂, and C₁) of trans-3-hexene were calculated. Variable temperature studies of the infrared spectrum of cis- and trans-3-hexenes dissolved in liquid argon were done to obtain the ΔH of conversion between the rotamers C₂ and C_s of cis-3-hexene and between the rotamers C_i, C₂, and C₁ of trans-3-hexene.     

A proposal for the molecular basis of μ and δ opiate receptor differentiation based on modeling of two types of cyclic enkephalins and a narcotic alkaloid

Summary The molecular basis underlying the divergent receptor selectivity of two cyclic opioid peptides Tyr-c[N -d-Orn²-Gly-Phe-Leu-] (c-ORN) and [d-Pen², l-Cys⁵]-enkephalinamide (c-PEN) was investigated using a molecular modeling approach. Ring closure and conformational searching procedures were used to determine low-energy cyclic backbone conformers. Following reinsertion of amino acid side chains, the narcotic alkaloid 7-[(1R)-1-methyl-1-hydroxy-3-phenylpropyl]-6,14-endoethenotetrahydro oripavine (PEO) was used as a flexible template for bimolecular superpositions with each of the determined peptide ring conformers using the coplanarity and cocentricity of the phenolic rings as the minimum constraint. A vector space of PEO, accounting for all possible orientations for the C₂₁-aromatic ring of PEO served as a geometrical locus for the aromatic ring of the Phe⁴ residue in the opioid peptides. Although a vast number of polypeptide conformations satisfied the criteria of the opiate pharmacophore, they could be grouped into three classes differing in magnitude and sign of the torsional angle values of the tyrosyl side chain. Only class III conformers for both c-ORN and c-PEN, having tyramine dihedral angles ₁ =–150° ± 30° and ₂=–155° ± 20°, had significant structural and conformational properties that were mutually compatible while respecting the PEO vector space. Comparison of these properties in the context of the divergent receptor selectivity of the studied opioid peptides suggests that the increased distortion of the peptide backbone in the closure region of c-PEN together with the pendant ,-dimethyl group, combine to generate a steric volume which is absent in c-ORN and that may be incompatible with a restrictive topography of the receptor. The nature and stereo-chemistry of substituents adjacent to the closure region of the peptides could also modulate receptor selection by interacting with a charged () or neutral () subsite.     

Structure-activity relationship of Ca2+ channel blockers: A study using conformational analysis and chemometric methods

Summary A structure-activity relationship study has been done on 8 compounds with the activity known as Ca²⁺ channel blockers. Conformational analysis was carried out using a molecular mechanics method. The 3D-QSAR approach was used and the most polar functional groups present in all the molecules were considered. Eight interatomic distances are necessary to define the relative spatial disposition of these relevant molecular fragments. The structure-activity relationship between interatomic distances and biological activity was performed using statistic and chemometric methods. In particular, with Principal Component Analysis, it was possible to reduce the number of interatomic distances: only six of the eight distances are sufficient to describe the system in a useful way. A classification method was iteratively used to select the most probable conformations linked to the biological activity and to build a model able to classify conformations according to their biological behaviour. Cluster analysis on the active selected conformations subsequently allowed the identification of two different geometrical patterns for the active compounds. Finally the validity of the model was verified by correctly predicting the activity of other molecules not used in the construction of the model but possessing known activity.