Low-lying Conformers Research Articles

Structures and spectra of iodide–water clusters I−(H2O)n=1–6: An ab initio study

To investigate the structures of I−(H2O)n=1–6, extensive ab initio calculations have been carried out. Owing to very flexible potential surfaces of the system (in particular for n=5 and 6), the lowest energy structures are characterized from various possible low-lying energy conformers. In contrast to some previously reported structures, we find a new lowest energy structure (followed by a few low-lying energy conformers) for n=5 and four nearly isoenergetic conformers for n=6. These conformers have surface and near-surface structures with the coordination number of 4. The present results provide the information of possible structures in recent profuse experiments of infrared spectra of I−(H2O)n=1–6 and charge transfer from the excited iodide ion to water molecules. Our predicted ionization potentials and OH stretching frequencies are in good agreement with the experimental data available, while only the cases of the OH frequencies for n=4 and the ionization potential for n=5 need consideration of conformational change by the temperature effect.

Conformational Preferences of Neurotransmitters: Ephedrine and Its Diastereoisomer, Pseudoephedrine

The conformational preferences of the diastereomeric neurotransmitters (1R2S) ephedrine and (1S2S) pseudoephedrine have been studied in the gas phase, under free jet-expansion conditions, using ultraviolet spectroscopy (both R2PI and LIF) and infrared ion-dip and hole-burning spectroscopy in combination with ab initio calculation. This has led to the identification and assignment of two conformers in ephedrine and four in pseudoephedrine. Assignments have been made by comparing their experimental infrared and LIF spectra with ab initio vibrational frequencies and ultraviolet rotational band contours. The relative stabilities of the conformers are controlled by a delicate balance between intramolecular hydrogen bonding and dispersive interactions between the methyl groups of the side chain, both with each other and with the aromatic ring. The relative conformational stabilities calculated for ephedrine do not agree with the experimental results; two of its low-lying conformers were detected, but a third, lying at an intermediate energy, was not. The possibility of its collisional relaxation into the global minimum during the supersonic expansion was not supported by the ab initio calculations, which predict a substantial barrier along the minimum energy pathway. It is possible that the combination of a relatively weak transition moment and a lack of facile pathways for relaxation from higher lying structures into the “missing” conformer may play a role.

Structures, vibrational frequencies, and infrared spectra of the hexa-hydrated benzene clusters

The water hexamer is known to have a number of isoenergetic structures. The first experimental identification of the O–H stretching vibrational spectra of the water hexamer was done in the presence of benzene. It was followed by the identification of the pure water hexamer structure by vibration-rotational tunneling (VRT) spectroscopy. Although both experiments seem to have located only the Cage structure, the structure of the benzene–water hexamer complex is not clearly known, and the effect of benzene in the water hexamer is unclear. In particular, it is not obvious how the energy difference between nearly isoenergetic water hexamer conformers changes in the presence of benzene. Thus, we have compared the benzene complexes with four low-lying isoenergetic water hexamers, Ring, Book, Cage, and Prism structures, using ab initio calculations. We also investigated the effects of the presence of benzene on the structures, harmonic vibrational frequencies, and infrared (IR) intensities for the four low-lying energy conformers. There is little change in the structure of the water hexamer upon its interaction with the benzene molecule. Hence the deformation energies are very small. The dominant contribution to the benzene–water cluster interaction mainly comes from the π–H interactions between benzene and a single water molecule. As a result of this π–H interaction, O–Hπ bond length increases and the corresponding stretching vibrational frequencies are redshifted. The IR spectral features of both (H2O)6 and benzene–(H2O)6 are quite similar. From both the energetics and the comparison of calculated and experimental spectra of the benzene–(H2O)6, the water structure in these complexes is found to have the Cage form. In particular, among the four different Cage structures, only one conformer matches the experimental O–H vibrational frequencies.

The conformational structures of defect-containing chains in the crystalline regions of isotactic polypropylene

Calculations were performed to assign defect-resonance patterns observed in solid-state 13C NMR spectra obtained from the crystalline regions of isotactic polypropylene. The spectral features of interest are associated with stereo, regio, and comonomer-type defects, which can typically be found in metallocene-synthesized polymers. The calculations were carried out as follows: a model of the crystalline region of defect-free isotactic polypropylene was constructed from available X-ray data corresponding to the α-lattice. A series of irregularities including ethylene comonomer, stereo-mrrm, regio 2,1-erythro, and butylene-comonomer defects were introduced one at a time at various positions in a specific stem occupying a central position in the model crystallite. Low-lying conformations were then obtained from simulated annealing calculations that were initiated from these structures. Finally, quantum mechanical calculations were performed on the representative segments of the defect-containing chains excised from the annealed crystallites and the calculated chemical shifts were compared to the observed resonances. The results of the calculations were used as a basis for interpreting the NMR intensities of defect-related resonances in terms of the partitioning of defects and to help establish the conformational structures of the defect-containing stems.

Comparative ab initio study of the structures, energetics and spectra of X−⋅(H2O)n=1–4 [X=F, Cl, Br, I] clusters

X − ⋅(H 2 O) n=1–4 [X=F, Cl, Br, I] have been studied using high level ab initio calculations. This extensive work compares the structures of the different halide water clusters and has found that the predicted minimum energy geometries for different cluster are accompanied by several other structures close to these global minima. Hence the most highly populated structures can change depending on temperature due to the entropy effect. As the potential surfaces are flat, the wide-ranging zero point vibrational effects are important at 0 K, and not only a number of low-lying energy conformers but also large amplitude motions can be important in determining structures, energies, and spectra at finite temperatures. The binding energies, ionization potentials, charge-transfer-to-solvent (CTTS) energies, and the O–H stretching frequencies are reported, and compared with the experimental data available. A distinctive difference between F−⋅(H2O)n and X−⋅(H2O)n (X=Cl, Br, I) is noted, as the former tends to favor internal structures with negligible hydrogen bonding between water molecules, while the latter favors surface structures with significant hydrogen bonding between water molecules. These characteristics are well featured in their O–H spectra of the clusters. However, the spectra are forced to be very sensitive to the temperature, which explains some differences between different spectra. In case of F−⋅(H2O)n, a significant charge transfer is noted in the S0 ground state, which results in much less significant charge transfer in the S1 excited state compared with other hydrated halide clusters which show near full charge transfers in the S1 excited states. Finally, the nature of the stabilization interactions operative in these clusters has been explained in terms of many-body interaction energies.

Theoretical Conformational Analysis of Thiacrown Macrocycles

A gas phase conformational analysis was performed on four sulfur-containing macrocycles (9-thiacrown-3, 12-thiacrown-4, 15-thiacrown-5, and 18-thiacrown-6) using a combination of empirical and ab initio methods. Candidates for low-lying conformers were initially generated from high-temperature molecular dynamics simulations. A more computationally manageable subset of conformations was selected for further study based on their relative energies at successively higher levels of ab initio theory. The highest level of theory included second-order perturbation theory with the aug-cc-pVDZ basis set. The lowest conformation of 9-thiacrown-3 was found to have an exodentate C2 structure with an electronic energy that is 4 kcal/mol below the C3 crystal structure. For 12-thiacrown-4, the lowest energy structure possesses D4 structure in both the gas and crystal phase. In the case of 15-thiacrown-5 the lowest energy conformer possesses an oblong, partially exodentate, gas phase structure with C2 symmetry. The crystal structure has C1 symmetry and lies 3 kcal/mol higher in energy. 18-Thiacrown-6 has an exodentate C2 symmetry, which is estimated with a large uncertainty to be 1 kcal/mol below the folded C2 structure of the crystal. Zero-point vibrational effects shift relative energies by up to 0.3 kcal/mol across an energy span of 5−7 kcal/mol, but the effect on close-lying conformers is less.

Structures, energetics, and spectra of fluoride–water clusters F−(H2O)n, n=1–6: Ab initio study

F − (H 2 O) n (n=1–6) clusters have been studied using ab initio calculations. This is an extensive work to search for various low-lying energy conformers, for example, including 13 conformers for n=6. Our predicted enthalpies and free energies are in good agreement with experimental values. For n=4 and 6, both internal and surface structures are almost isoenergetic at 0 K, while internal structures are favored with increasing temperature due to the entropic effect. For n=5, the internal structure is favored at both 0 and 298 K under 1 atm. These are contrasted to the favored surface structures in other small aqua–halide complexes. The ionization potential, charge-transferto-solvent (CTTS) energy, and O–H stretching vibrational spectra are reported to facilitate future experimental work. Many-body interaction potential analyses are presented to help improve the potential functions used in molecular simulations. The higher order many-body interaction energies are found to be important to compare the energetics of the various conformers and compare the stability of the internal over the surface state.

Ab initio study of water hexamer anions

The wet electron - an electron interacting with a small cluster of water molecules - is a simple yet fundamental system for understanding the behavior of electrons in complex molecular systems. A comprehensive post Hartree-Fock ab initio study is performed on the wet electron in various water hexamer clusters including the low-lying energy conformers of the neutral species. The predicted geometries, total energies, photoemission ionization energies, electronic structure and orbital character of the excess electron in ground and excited states are discussed. To understand the behavior of the excess electron in the clusters, the s-orbital-like character of the HOMOs and the p-orbital-like character of the LUMOs are investigated.

Multiconformational composite molecular potential fields in the analysis of drug action. I. Methodology and first evaluation using 5-HT and histamine action as examples.

The quality of molecular electrostatic maps generated by non-quantum mechanical methods has been improved using extended electron distributions. Further simplification has been achieved by distilling these maps down to their energy extrema. A new means of defining surface interaction has been added and the resulting composite map has been plotted for a limited number of low-lying conformers of a series of agonists and antagonists of the H2 and H3 receptors and 5-HT1A and 5-HT1D receptors. The results from the cross-comparison of these maps indicate their ability to distinguish the specific receptor. Interesting consequences of the method are that structural overlay is irrelevant, that several conformations may contribute to the overall binding pattern and that lesser pharmacological activities may be deduced from the results.

Theoretical Studies of Dihydroxybuckminsterfullerene, C60(OH)2

The relative energies of various conformers of 1,2- and 1,4-C{sub 60}(OH){sub 2} have been calculated at the MNDO AM-1 semiempirical molecular orbital level based on geometries obtained at this level. There are three low-lying conformers of 1,2-C{sub 60}(OH){sub 2} and six low-lying conformers of 1,4-C{sub 60}(OH){sub 2}. The conformers of 1,2-C{sub 60}(OH){sub 2} all are lower in energy as compared to the energy of the most stable conformer of 1,4-C{sub 60}(OH){sub 2}. The energies were recalculated at the nonlocal density functional theory (NLDFT) level with a polarized double-{zeta} basis set. The relative energies at this ab initio level are similar to the values obtained at the MNDO/AM-1 level. The energy difference between the lowest energy conformers of 1,2-C{sub 60}(OH){sub 2} and 1,4-C{sub 60}-(OH){sub 2} is 6.6 kcal/mol at the NLDFT level. An analysis of various conformations of ethylene glycol is also presented at the DFT and semiempirical molecular orbital levels as an aid to understanding the behavior of the dihydroxyfullerene derivatives. 34 refs., 6 figs., 3 tabs.

What is the global minimum energy structure of the water hexamer? The importance of nonadditive interactions

The global minimum energy structures of the water hexamer predicted by widely used analytic water potentials are very different from each other, while the cyclic hexamer does not appear to be a low-lying energy structure. However, high levels of ab initio calculation predict that a number of low-lying energy conformers including the cyclic conformer are almost all isoenergetic due to the balance of two-body and nonadditive interactions. For modeling of water potentials, we suggest that the binding energy of the dimer be between −5.0 and −4.7 kcal (mol dimer)−1, while the three-body corrections be taken into account to a large extent.

Solvent effects on the electronic spectrum of Reichardt's dye

The extreme sensitivity of the absorption spectrum to small changes in the medium polarity has made Reichardt's dyes useful molecular probes in the study of micelle/solution interfaces and phospholipid bilayers. This work reports preliminary results of semiempirical quantum chemical calculations on some conformations of 2,6-diphenyl-(2,4,6-triphenyl-1-pyridinium)-N-phenoxide betaine (Reichardt's betaine, RB), which exhibits negative solvatochromic effects. We have used the AM1 Hamiltonian of Dewar in the geometry optimizations, and the Intermediate Neglect of Differential Overlap method parameterized for spectroscopy (INDO/S). For RB, two low-lying conformations have been found. The small difference in energy between them suggests that both forms may be present in solution, an observation confirmed by calculations on the spectra using the SCRF model: the superposition of the calculated spectra for these two forms matches the experimental spectra very well. For nonpolar solvents, the general pattern consists of variation of Et(30) concurrent with variation of the dielectric constant. We have also carried out calculations for solvents which form specific (e.g., H-bond) binding to the solute, namely methanol and water, using a supermolecule approach. Our results are in excellent agreement with the experiment and present an accurate description of the spectra. © 1994 John Wiley & Sons, Inc.

10]Annulene: The Wealth of Energetically Low-Lying Structural Isomers of the Same (CH)10 Connectivity

Ab initio quantum mechanical methods, as well as molecular mechanics (MM2 and MM3) and semiempirical theoretical methods (AM1), have been used to predict the molecular structures and energetics of the plausible isomers of [10]annulene. Standard double-[zeta] (DZ) and double-[zeta] plus polarization (DZP) basis sets have been used for the ab initio self-consistent-field (SCF) studies. Full geometry optimizations have been carried out by these different methods. The harmonic vibrational frequencies and their infrared intensities are also predicted for all these isomers. The most likely observable isomers are the two structures with C[sub 2] symmetry, one of which could be called naphthalene-like and the other twisted. Isomers with C[sub s] (including a low-lying boat-like structure) and C[sub 1] (including a low-lying azulene-like structure) symmetries are also discussed. The aromatic character for the planar isomers, which are not local minima, has been studied using second-order perturbation theory. A random conformational searching procedure based on the MM3 method was also carried out to avoid losing any possible energetically low-lying conformations. The latter procedure uncovered one low-lying structure that had never been suggested previously. A comparison with the experimental conclusions of Masamune and co-workers is made. 21 refs., 4 tabs.

The importance of conformation in the reactivity of radical cations. Changing configuration at saturated carbon centres

Irradiation of an acetonitrile solution of cis 1-methyl-2-phenylcyclopentane (1bcis); 1,4-dicyanobenzene (2), an electron-accepting photosensitizer; and 2,4,6-collidine (3), a nonnucleophilic base, leads to configurational isomerization of the cyclopentane; the photostationary state lies > 99% in favour of the trans isomer. The mechanism proposed for this reaction involves formation of the radical cation of 1bcis by photoinduced electron transfer to the singlet excited state of 2, deprotonation of the radical cation assisted by the base 3, reduction of the resulting benzylic radical by the radical anion [Formula: see text], and reprotonation of the benzylic anion to give both the cis and the trans isomers of 1b. The photostationary state is controlled by the relative rates of deprotonation of the radical cations of 1bcis and trans; these rates are dependent upon the extent of overlap of the SOMO of the radical cation, which is largely associated with the phenyl ring, and the benzylic carbon–hydrogen bond. Molecular mechanics calculations (MM3 and MMP2) are used to calculate the preferred conformations of the isomers. The required orbital overlap is 31% effective with the global minimum conformation of the cis isomer and essentially ineffective for the low-lying conformations of the trans isomer. This proposed mechanism is supported by Stem–Volmer quenching studies, which indicate that both isomers quench the singlet excited state of 2 at the diffusion-controlled rate, and by deuterium incorporation studies. When irradiation of the cis isomer is carried out in acetonitrile–methanol-O-d as solvent, isomerization is accompanied by deuterium exchange at the benzylic position; the trans isomer is stable under these conditions. Keywords: photosensitized electron transfer, radical cation, deprotonation, configurational isomerization, conformation, molecular mechanics (MM3).