A study on the anisole-water complex by molecular beam-electronic spectroscopy and molecular mechanics calculations

An experimental and theoretical study is made on the anisole-water complex. It is the first van der Waals complex studied by high resolution electronic spectroscopy in which the water is seen acting as an acid. Vibronically and rotationally resolved electronic spectroscopy experiments and molecular mechanics calculations are used to elucidate the structure of the complex in the ground and first electronic excited state. Some internal dynamics in the system is revealed by high resolution spectroscopy.     

A density-functional study on pi-aromatic interaction: benzene dimer and naphthalene dimer

The long-range correction (LC) scheme of density-functional theory (DFT) was applied to the calculation of the pi-aromatic interaction of the benzene dimer and naphthalene dimer. In previous calculations, it was confirmed that the LC scheme [Iikura et al., J. Chem. Phys. 115, 3540 (2001)] gives very accurate potential- energy surfaces (PESs) of small van der Waals (vdW) complexes by combining with the Anderson-Langreth-Lundqvist (ALL) vdW correlation functional [Andersson et al., Phys. Rev. Lett. 76, 102 (1996)] (LC-DFT + ALL). In this study, LC-DFT+ALL method was examined by calculating a wide range of PES of the benzene dimer including parallel, T-shaped, and parallel-displaced configurations. As a result, we succeeded in reproducing very accurate PES within the energy deviance of less than 1 kcalmol in comparison with the results of high-level ab initio molecular-orbital methods at all reference points on the PES. It was also found that LC-DFT + ALL gave accurate results independent of exchange-correlation functional used, in contrast with the strong functional dependencies of conventional pure functionals. This indicates that both exchange repulsion and van der Waals attractive interactions should be correctly incorporated in conventional pure functionals in order to calculate accurate pi-aromatic interactions. We also found that LC-DFT + ALL method has a low basis-set dependency in the calculations of pi-aromatic interactions. The present scheme was also successfully applied to the pi,[ellipsis (horizontal)],pi stacking interactions of naphthalene dimer. This may suggest that LC-DFT + ALL method would be a powerful tool in the calculations of large molecules such as biomolecules.     

Spectra of the dications of benzene,naphthalene and azulene

Spectra of the dications of benzene, naphthalene and azulene produced by double photoionisation of the parent compounds are presented. All the electron distributions show evidence of inner-valence Auger processes, which enhance population of low energy states of the dications. It is confirmed that the ground state of the benzene dication is a triplet, contrary to a recent theoretical prediction. The double ionisation energies of the three title molecules are determined as 24.65 ± 0.03, 21.28 ± 0.03 and 20.2 ± 0.2 eV, respectively.     

Orientation of guest benzene molecules in Hofmann-type and related clathrates by molecular mechanics calculation

Molecular mechanics calculations were carried out to interpret the observed orientational angle of the benzene molecule enclathrated in the Hofmann-type M(NH₃)₂Ni(CN)₄·2 C₆H₆ (M = Mn, Ni, Cu, and Cd), Hofmann-en-type Cd(en)Ni(CN)₄·2 C₆H₆ (en = NH₂CH₂CH₂NH₂), and Hofmannmea-type(2) Cd(mea)Ni(CN)₄·2 C₆H₆ (mea = NH₂CH₂CH₂OH) clathrates using the van der Waals potential functions in Molecular Mechanics Version 2. The angle is most influenced by the guest-to-guest contact in the interlayer space between the two-dimensionalcatena-[metal(II) tetra--cyanonickelate(II)] networks for the Hofmann-type series. The discrepancy between the calculated and the observed angles in each crystal structure was at largest 3.5°; the structures of Cd(NH₃)₂Ni(CN)₄·2 C₆H₆ and Cd(en)Ni(CN)₄·2 C₆H₆ have been revised using new data collected by counter-methods.     

A molecular mechanics study of alkyl peroxides

Studies have been carried out on alkyl peroxides with MM3 that have led to a parameter set that allows the calculation of geometries, energies, vibrational frequencies, and heats of formation for alkyl hydroperoxides (R? O? O? H) and dialkyl peroxides (R₁? O? O? R₂). The results obtained are in agreement with the available experimental and theoretical data. A similar, although less good, parameter set has been developed for MM2. © 1993 John Wiley & Sons, Inc.     

Formation of naphthalene, indene, and benzene from cyclopentadiene pyrolysis: a DFT study

Four new reaction pathways for polycyclic aromatic hydrocarbon growth from cyclopentadiene pyrolysis are proposed and investigated using the B3LYP/6-31G(d,p) level of theory. These pathways allow for the production of indene, naphthalene, and benzene through intramolecular addition, C-H beta-scission, and C-C beta-scission reaction mechanisms, respectively. Results show that the intramolecular addition channel is favored at low temperatures, and the C-H beta-scission channel and the newly identified C-C beta-scission pathway become significant when the temperature increases. These results are in qualitative agreement with the experimental results previously obtained by this research group indicating that the main product at low temperature is indene, while benzene and naphthalene production dominate at the high-temperature end.     

Calculated molecular structures and electronic spectra of the geometric isomers of a model carotenoid molecule, 6,11-dimethylhexadecaheptaene

The molecular structures and the electronic spectra of the geometric isomers of a model carotenoid polyene, 6,11-dimethylhexadecaheptaene, were calculated. It was concluded that solvent effects and conformational isomerization must be taken into account in order to satisfactorily explain the observed spectra. Molecular structures were calculated using molecular mechanics (MM2), and electronic spectra using the VESCF-MO-CI method including all singly-excited configurations. A method based on the calculated and observed spectra of simple linear polyenes was devised to estimate the solvent effects.     

Interaction of cyclopentane with benzene,carbon tetrachloride and cyclohexane

Heats of mixing cyclopentane + benzene, + carbon tetrachloride, + cyclohexane at 308.15 K and for cyclohexane + carbon tetrachloride at 298.15 K have been determined in an adiabatic calorimeter. The data have been examined for current theories (McGlashan, Flory and Barker) of solutions and show that McGlashan's theory predicts values for H^E and G^E that are in good agreement with their corresponding experimental values. Interaction energy between the components of these mixtures has also been determined.     

A sequential molecular mechanics/quantum mechanics study of the electronic spectra of amides

We report gas-phase electronic spectra of formamide, N-methyformamide, acetamide, and N-methylacetamide at 300 K calculated using a combination of classical molecular dynamics and time-dependent density functional theory (TDDFT). In comparison to excitation energies computed using the global minima structures, the valence npi* and pi(nb)pi* states show a significant red-shift of 0.1-0.35 eV, while smaller shifts are found for the n3s and pi(nb)3s Rydberg states. In this work, we have identified the physical origin of these shifts arising from variations of the molecular structure. We present simple relationships between key geometrical parameters and spectral shifts. Consequently, electronic spectra can be generated directly from ground-state structures, without additional quantum chemical calculations. The electronic spectrum of formamide in aqueous solution is computed using TDDFT using an explicit solvent model. This provides a quantitative determination of the condensed-phase spectrum. In general, this study shows that temperature effects can change the predicted excitation energies significantly and demonstrates how electronic spectra at elevated temperatures can be computed in a computationally efficient way.     

Ebulliometric study of solutions of certain salts in benzene and carbon tetrachloride

The activity coefficients of the solvent (1n f ₁) have been determined by ebulliometry for solutions of certain salts in benzene and CCl₄. The results, together with data in the literature have been used to calculate the second and third virial coefficients of 1n f ₁ for a number of salt solutions in benzene, CCl₄, and dioxane. It is shown that the positive deviations from ideality in such solutions depend on the nature of the anion, the length of the amine radical, the temperature, and the nature of the solvent.     

A theoretical study of configurational inversion of 1,1′-binaphthyl by molecular mechanics

The molecular mechanics method has been applied to the study of various pathways and transition states for the configurational inversion of 1,1′-binaphthyl. The preferred pathway is found to be one on the anti (“trans”) side involving one point of H?H nonbonded contact in each of two identical transition states, separated by a very shallow minimum. Very satisfactory agreement with available experimental values for the enthalpy of activation is achieved.     

Conformational study of the cembranolide diterpene denticulatolide by molecular mechanics method

The most stable conformation of denticulatolide (1), an ichthyotoxic cembranolide, obtained as a major metabolite of the soft coral, Lobophytum denticulatum, was given by molecular mechanics calculations and it was confirmed by ¹H NMR measurement. The geometry of 14-membered carbocycle of 1 was found to be different from that of derivative (2) especially around the juncture part of γ-lactone. The molecular mechanics calculation successfully reproduced the conformational changes between 1 and 2.     

The radical anions and the electron affinities of perfluorinated benzene,naphthalene and anthracene

Although benzene and naphthalene do not have electron affinities in the conventional sense, perfluorobenzene and perfluoronaphthalene have nonzero electron affinities. Theoretical methods extensively calibrated with experiment for the prediction of electron affinities (EAs) predict the EAs of perfluorobenzene, perfluoronaphthalene and perfluoroanthracene as 0.69, 1.02 and 1.84 eV, respectively. A rough estimate of 2.39 eV is made for the electron affinity of perfluorotetracene. Thus the perfluoro polycyclic aromatic hydrocarbons (PAHs) are predicted to be effective electron acceptors.     

Ice growth from supercooled aqueous solutions of benzene, naphthalene, and phenanthrene

Classical molecular dynamics (MD) were performed to investigate the growth of ice from supercooled aqueous solutions of benzene, naphthalene, or phenanthrene. The main objective of this study is to explore the fate of those aromatic molecules after freezing of the supercooled aqueous solutions, i.e., if these molecules become trapped inside the ice lattice or if they are displaced to the QLL or to the interface with air. Ice growth from supercooled aqueous solutions of benzene, naphthalene, or phenanthrene result in the formation of quasi-liquid layers (QLLs) at the air/ice interface that are thicker than those observed when pure supercooled water freezes. Naphthalene and phenanthrene molecules in the supercooled aqueous solutions are displaced to the air/ice interface during the freezing process at both 270 and 260 K; no incorporation of these aromatics into the ice lattice is observed throughout the freezing process. Similar trends were observed during freezing of supercooled aqueous solutions of benzene at 270 K. In contrast, a fraction of the benzene molecules become trapped inside the ice lattice during the freezing process at 260 K, with the rest of the benzene molecules being displaced to the air/ice interface. These results suggest that the size of the aromatic molecule in the supercooled aqueous solution is an important parameter in determining whether these molecules become trapped inside the ice crystals. Finally, we also report potential of mean force (PMF) calculations aimed at studying the adsorption of gas-phase benzene and phenanthrene on atmospheric air/ice interfaces. Our PMF calculations indicate the presence of deep free energy minima for both benzene and phenanthrene at the air/ice interface, with these molecules adopting a flat orientation at the air/ice interface.     

A molecular-orbital-based molecular mechanics approach to study conjugated systems

The Allinger's MM2 program has been extended to calculate conjugated systems including N, O, and S hetero atoms.