Conformational analysis of 2-oxo-1,2,3,4,-tetrahydropyridine and its alkyl- and phenyl-substituted derivatives

The molecular geometries and inversion barriers of the rings in 2-oxo-1,2,3,4-tetrahydropyridine and its alkyl-substituted (Me, Et, Prⁱ, or Bu^t) and phenyl-substituted derivatives were calculated by the molecular mechanics method. The introduction of substituents has no substantial effect on the equilibrium conformation of the heterocycle (a distorted sofa). For 4-alkyl- and 3-alkyl-substituted derivatives (except for 4-Me and 4-Et derivatives), an axial orientation of the alkyl group is more favorable. The phenyl substituents have equatorial and axial orientations at postions 4 and 3, respectively. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1584–1586, September, 1997.     

Parameterization of OPLS-AA force field for the conformational analysis of macrocyclic polyketides

The parameters for the OPLS-AA potential energy function have been extended to include some functional groups that are present in macrocyclic polyketides. Existing OPLS-AA torsional parameters for alkanes, alcohols, ethers, hemiacetals, esters, and ketoamides were improved based on MP2/aug-cc-pVTZ and MP2/aug-cc-pVDZ calculations. Nonbonded parameters for the sp(3) carbon and oxygen atoms were refined using Monte Carlo simulations of bulk liquids. The resulting force field predicts conformer energies and torsional barriers of alkanes, alcohols, ethers, and hemiacetals with an overall RMS deviation of 0.40 kcal/mol as compared to reference data. Densities of 19 bulk liquids are predicted with an average error of 1.1%, and heats of vaporization are reproduced within 2.4% of experimental values. The force field was used to perform conformational analysis of smaller analogs of the macrocyclic polyketide drug FK506. Structures that adopted low-energy conformations similar to that of bound FK506 were identified. The results show that a linker of four ketide units constitutes the shortest effector domain that allows binding of the ketide drugs to FKBP proteins. It is proposed that the exact chemical makeup of the effector domain has little influence on the conformational preference of tetraketides.     

Toward separation of nuclear spin isomers with coherent light.

We propose an approach for separating nuclear spin isomers with coherent light and illustrate it by numerical calculations using fulvene as a model system. The scheme employs the equivalence of torsion and interchange of equivalent H-atoms in a class of molecules of which fulvene is a simple example. The exchange symmetry couples with the rotational symmetry to produce a spatial distinction between the two photo-excited nuclear spin isomers, and wavepacket interferometry is applied to separate the species.     

Conformational statistics of polymer chain terminally attached to wall (Ⅲ)——NRW model loop chain

When the two end groups of a linear polymer chain are absorbed on a solid surface,the polymer chain forms the "loop" conformation.Investigation has been made on the conformational statistics of a model loop chain by the normal landom walk (NRW) on a lattice confined in the half-infinite space.Based on the conformational distribution function of the NRW model tail chain,it is easy to deduce an analytical formula expressing the conforma-tional number of the model loop chain.It was found that the ratio of the conformational number of the model loop chain to that of the free chain varies with the power function N-2/3 when the chain length N→∞ The same result was obtained by means of the recursion equation.The ratio of the mean square end-to-end distance h2 for the model loop chain to its mean square bond length I2 is 2N/3 Compared with the free chain with the same length N,the mean square end-to-end distance of the model loop chain contracts to a certain extent.The basic relationships deduced were support     

Molecular structure of (diethyldithiocarbomoyl)diphenylthiophosphinate

X-Ray study of (diethyldithiocarbomoyl)diphenylthiophosphinate was carried out. AZ-conformation of the diethyldithiocarbomoyl ligand, which results in a short nonvalent intramolecular P...S contact (3.315 Å), is realized in the molecule. Steric hindrances in the molecule increase the P-S-C bond angle to 106.39°.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1978–1980, October, 1995.The work was financially supported by the International Science Foundation (Gram RH1 000).     

Approaching supramolecular functionality

Functional molecules require a high degree of complexity which is difficult to achieve by covalent synthesis. This article discusses supramolecular approaches to the creation of larger architectures through noncovalent bonds, self-assembly, and template strategies. It highlights selected examples for the structural and conformational control of function and attempts to identify difficulties and challenges which may arise in future.     

Lattice models of peptide aggregation: evaluation of conformational search algorithms

We present a series of conformational search calculations on the aggregation of short peptide fragments that form fibrils similar to those seen in many protein mis-folding diseases. The proteins were represented by a face-centered cubic lattice model with the conformational energies calculated using the Miyazawa-Jernigan potential. The searches were performed using algorithms based on the Metropolis Monte Carlo method, including simulated annealing and replica exchange. We also present the results of searches using the tabu search method, an algorithm that has been used for many optimization problems, but has rarely been used in protein conformational searches. The replica exchange algorithm consistently found more stable structures then the other algorithms, and was particularly effective for the octamers and larger systems.     

Equilibrium conformations of polymer chains Part II. Conformons in networks

With regard to the ideal network it is shown that the concept ofN non-interacting polymer chains can be transformed in a problem of non interacting excitations (called conformons) for rubber elasticity. Modelling the interaction on permanent crosslinks as a scattering problem and taking the finite chain length into account, an interpretation of the second Mooney coefficient can be given. There is some evidence that the junctions move by constrained self diffusion.Dedicated to Prof. Dr. W. Ruland on the occasion of his 60th birthday.     

Molar excess heat capacities and volumes for mixtures of alkanoates with cyclohexane at 25°C

Molar excess volumes V ^E at 25°C have been determined by vibrating-tube densimetry, as a function of mole fraction x for different series of an alkanoate (H _2m+1 C _m COOC _n H _2n+1 )+cyclohexane. Three types of alkanoates were investigated, i.e., methanoates (m=0, with n=3 and 4), ethanoates (m=1, with n=2, 3, and 4) and propanoates (m=2, with n=1, 2, and 3). In addition, a Picker flow calorimeter was used to obtain molar excess heat capacities C _p ^E at constant pressure at the same temperature. V ^E is positive for all systems and rather symmetric, with V ^E (x=0.5) amounting to almost identical values in a series of mixtures containing an alkanoate isomer of same formula (say C₄H₈O₂, C₅H₁₀O₂, or C₆H₁₂O₂). The composition dependence of C _p ^E is rather unusual in that two more or less marked minima are observed for most of the mixtures, especially when the alkanoate is a methanoate or an ethanoate. These results are discussed in terms of possible changes in conformation of both the ester and cyclohexane.