Petko M. Ivanov

Mg@C72 MNDO/d evaluation of the isomeric composition.

Temperature development of the relative stabilities of isomers of Mg@C72 (which has not yet been isolated) is computed using the recently introduced MNDO/d method. Four isomers originally considered for the Ca@C72 case are treated: one isolated-pentagon-rule (IPR) structure, two structures with a pair of adjacent pentagons, and one cage with a heptagon. The IPR structure comes as the lowest in MNDO/d potential energy, being rather closely followed by the two structures with a pentagon-pentagon pair. On the other hand, the structure with a heptagon is located too high in potential energy to be of any experimental significance. The entropy contributions are evaluated by the MNDO/d-based partition functions so that the relative concentrations can be treated accordingly. The computations suggest that if Mg@C72 is isolated, it should be a mixture of either two or three isomers. The prediction depends on temperature prehistory. If preparation takes place at temperatures of approximately 1000 K, two isomers should be produced. If temperatures are increased to approximately 2000 K, there will already be three isomers with significant relative concentrations. The study supplies a further interesting example of the profound role of enthalpy-entropy interplay in stabilities of isomeric fullerenic structures.

Conformations of some large-ring cyclodextrins derived from conformational search with molecular dynamics simulations and principal component analysis.

Principal component analysis (PCA) was applied for postprocessing of trajectories from conformational search, based on 50.0 ns molecular dynamics (MD) simulations, with the purpose to elucidate the conformations of some large-ring cyclodextrins (LR-CDs), CDn (n = 24, 25, 26, 27, 28, 29). The dominant PCA modes for concerted motions of the macroring atoms were monitored in a lower-dimension subspace. The first 10 lowest indexed modes describe more than 90% of the total atomic motions in all cases, with about 85% (CD27, CD29) to more than 90% (CD24, CD25) contribution coming from the six highest-eigenvalue principal components. Representative average geometries of the cyclodextrin macrorings were also obtained for the whole simulation and for the five 10.0 ns time intervals of the simulation. Two conformations for CD26, the largest LR-CD for which X-ray data is available, are characterized by possessing, respectively, one and two helical turns. Resemblance to computed representative conformations of CD26 in water was found for CD27 and CD28, with the similarity being better expressed for the former case. Only CD24, among the two smaller size LR-CDs, displays resemblance during short simulation intervals to one of the conformations of CD26. The formation of small loops of six to seven glucose units is a favorable deformation mode of the macrorings. Besides, once a small loop of six to seven glucoses is formed, the next natural mode for deformation of the macromolecule is toward the creation of a short helix that further enhances the stability of the structure. The average geometry of CD29 has no likeness at all to the conformations of CD26. Thus, the difference of three glucose units between CD26 and CD29 already influences significantly the shape of the most probable conformation.

Conformational energy analysis of substituted diphenylethanes

Abstract The geometry and energy of the stable conformations of the isomeric forms of 1,2-halogeno-1,2-diphenylethanes have been obtained by means of empirical energy functions. A minimization of the conformational energy with respect to the torsion angles and the valence angles around the asymmetrically substituted carbon atoms has been carried out. The evaluated populations of the stable conformations showed good agreement with available experimental data. CNDO/2 calculations on the low-energy conformations of the isomeric forms of 1,2-difluoro-, 1,2-fluorochloro-, and 1,2-dichlorodiphenylethane have been carried out. These yielded improved estimates of the dipole moments for the dichloro isomers.

CONFLEX/MM3 search/minimization study of the conformations of the macrolide antibiotic tylosin

The conformations of the 16-membered macrolide antibiotic tylosin were studied with the MM3 force field. The CONFLEX conformational search procedure was used for finding low-energy conformations. The computed data are indicative for the existence of several conformations in equilibrium. The intramolecular hydrogen bonds play an important role for the preferred geometry of the macroring and the conformations of the side chains. The present results provide further insight into the most probable conformations of tylosin and compliment an earlier analysis based on NMR techniques.

The torsional energy profile of 1,2-diphenylethane: an ab initio study

Abstract Ab initio molecular orbital calculations were carried out for the antiperiplanar (ap), the synclinal (sc), phenyl/phenyl eclipsed (syn barrier), and phenyl/H eclipsed (ap/sc barrier) conformations of 1,2-diphenylethane, and the energy ordering of conformations thus obtained was compared with the torsional energy profile estimated with the MM2 and MM3 molecular mechanics force fields. The basis set effect on the results was studied at the restricted Hartree–Fock (RHF) self-consistent field (SCF) level of theory, and the electron correlation energies were corrected by the second-order (MP2) Moller–Plesset perturbation treatment using the 6-31G* basis set. The performance of a DFT model (Becke-style three-parameter hybrid method using the correlation functional of Lee, Yang and Parr, B3LYP) was also tested to assess relative energies of the conformations using two basis sets, 6-31G* and 6-311G**. The RHF and B3LYP results are qualitatively the same, while the MP2 calculations produced significant differences in the geometries and reversed the order of preference for the antiperiplanar and the synclinal conformations.

Conformational energy analysis of substituted diphenylethanes: Part X. Conformations of some N-substituted 3-amino-2,3-diphenyl propanols and 4-amino-3,4-diphenyl-2-methyl-2-butanols. Emphasis on non-hydrogen bonded conformations

Abstract The conformational preferences in diastereoisomeric N -substituted 3-amino-2,3-diphenyl propanols and 4-amino-3,4-diphenyl-2-methyl-2-butanols were estimated by means of extensive empirical energy calculations with Momanys (rigid rotor approximation) and Allingers 1977 (full-relaxation calculations) force fields. Complete geometry optimization appears to be quite important in order to obtain results in satisfactory consistency with experimental data. Further improvements in this case are seen along with explicitly accounting for the possibility of intramolecular hydrogen bond formation and a readjustment of the torsional parameters for the four-atom unit C ar C al C al C ar .

Conformational energy analysis of substituted diphenylethanes: Part VI. Calculations of the solvent dependence of the conformational equilibria in stilbene dihalogenides. Intramolecular interactions in the PCILO fr

Abstract As part of a theoretical analysis of the conformational equilibria of stilbene dihalogenides, the free energy at 300 K of each stable conformational isomer of these molecules has been estimated for a solvent of dielectric constant 3.5. Classical empirical potential functions were used. Interaction with the solvent was considered only in terms of a continuous dielectric medium interacting with the local dipoles and quadrupoles of the molecule. Simulation of the experimental conditions (i.e. appropriate values for the dielectric constant of the solvent) yielded better agreement with the available experimental data, which were mainly dipole moments and optical rotation values. The quadrupole energy term has a very small influence on the calculated conformational populations and can be neglected when dibenzyl derivatives are considered. The mechanism of the intramolecular interactions is discussed within the PCILO framework.

Molecular mechanics conformational analysis of tylosin

Abstract The conformations of the 16-membered macrolide antibiotic tylosin were studied with molecular mechanics (AMBER∗ force field) including modelling of the effect of the solvent on the conformational preferences (GB/SA). A Monte Carlo conformational search procedure was used for finding the most probable low-energy conformations. The present study provides complementary data to recently reported analysis of the conformations of tylosin based on NMR techniques. A search for the low-energy conformations of protynolide, a 16-membered lactone containing the same aglycone as tylosin, was also carried out, and the results were compared with the observed conformation in the crystal as well as with the most probable conformations of the macrocyclic ring of tylosin. The dependence of the results on force field was also studied by utilizing the MM3 force field. Some particular conformations were computed with the semiempirical molecular orbital methods AM1 and PM3.

MM2 conformational analysis of diastereoisomers with phenyl groups on neighbouring carbon atoms and intramolecular hydrogen bonding

Abstract The conformations of a set of compounds containing phenyl groups on neighbouring carbon atoms and substituents with the potentiality for formation of an intramolecular hydrogen bond (diols, diamines and amino-alcohols) have been studied with the MM2 force field, enhanced with the addition of electrostatic corrections to the aromatic force field; as proposed by Allinger and Lii (dipole-dipole interactions), and the special MM2 hydrogen bonding parameters for the van der Waals function. The molecular mechanics results are in satisfactory agreement with experimental conformational data (mainly NMR and IR). An average deviation of 1.0 Hz was obtained between 20 observed vicinal proton coupling constants and those estimated with the Haasnoot-Altona equation. Previous indications regarding the electrostatic corrections for modelling phenyl-phenyl interactions and the parameters for the C sp 2 C sp 3 C sp 3 C sp 2 torsional potential are further supported. The molecular mechanics results for the low-energy conformations of six compounds have been supplemented with AM1, PM3 and MM-EHMO estimates of their conformational energies. The results are encouraging for attempting a complete SE-MO conformational analysis of such systems.

Molecular mechanics of diastereoisomers with phenyl groups on neighbouring carbon atoms

Abstract Results are summarized from systematic studies by the molecular mechanics method of the conformations of diastereoisomeric pairs of 1,2-disubstituted-1,2-diphenylethanes. An overall result in both series is the preference for conformations with the minimal number of synclinal interactions around the C(1)C(2) bond. Special attention is devoted to the performance of the MM2 force field with the 1,2-diarylethane system. With the readjustment of the V 1 parameter for the torsional unit C ar C al C al C ar MM2 operates reasonably well in the case of substituents of a moderate size. For the 1,2,3-triphenylpropane system however, where phenyl groups participate in 1,3-parallel interactions, this force field fails completely. A further more substantial revision of the MM2 force field is necessary in order to achieve internal consistency between different energy contributions in such systems.