On the encapsulation of hydrocarbon components of natural gas within molecular baskets in water. The role of C-H···π interactions and the host's conformational dynamics in the process of encapsulation.

We examined the encapsulation of CH4, C2H6, C3H8 and iso-C4H10 in water, using four molecular baskets [1]-[4]. The baskets were shown to bind to hydrocarbon gases by forming favourable C-H···π contacts and, concurrently, adjusting the size of their cup-shaped platform.

Computational analysis of the potential energy surfaces of glycerol in the gas and aqueous phases: effects of level of theory, basis set, and solvation on strongly intramolecularly hydrogen-bonded systems.

The 126 possible conformations of 1,2,3-propanetriol (glycerol) have been studied by ab initio molecular orbital and density functional theory calculations in the gas and aqueous phases at multiple levels of theory and basis sets. The partial potential energy surface for glycerol as well as an analysis of the conformational properties and hydrogen-bonding trends in both phases have been obtained. In the gas phase at the G2(MP2) and CBS-QB3 levels of theory, the important, low-energy conformers are structures 100 and 95. In the aqueous phase at the SM5.42/HF/6-31G* level of theory, the lowest energy conformers are structures 95 and 46. Boltzmann distributions have been determined from these high-level calculations, and good agreement is observed when these distributions are compared to the available experimental data. These calculations indicate that the enthalpic and entropic contributions to the Gibbs free energy are important for an accurate determination of the conformational and energetic preferences of glycerol. Different levels of theory and basis sets were used in order to understand the effects of nonbonded interactions (i.e., intramolecular hydrogen bonding). The efficiency of basis set and level of theory in dealing with the issue of intramolecular hydrogen bonding and reproducing the correct energetic and geometrical trends is discussed, especially with relevance to practical computational methods for larger polyhydroxylated compounds, such as oligosaccharides.

Conformational studies of methyl 3-O-methyl-alpha-D-arabinofuranoside: an approach for studying the conformation of furanose rings.

A computational method for probing furanose conformation has been developed using a methylated monosaccharide derivative 1. First, a large library of conformers was generated by a systematic pseudo Monte Carlo search followed by optimization with the AMBER molecular mechanics force field. A subset of these conformers was then subjected to ab initio and density functional theory calculations in both the gas and aqueous phases. These calculations indicate that entropic contributions to the Gibbs free energy are important determinants of the Boltzmann distribution for the conformational preferences of 1 in the gas phase. The results obtained at each level of theory are discussed and compared with the experimentally determined conformer distribution from NMR studies in aqueous solution. In addition, the ability of each level of theory to reproduce the experimentally measured 1H-1H coupling constants in 1 is discussed. Empirical Karplus equations and density functional theory methods were used to determine average 3J(H1,H2), 3J(H2,H3), and 3J(H3,H4) for each level of theory. On the basis of this comparison, consideration of solvation with the MN-GSM model provided good agreement with the experimental data.

A laser flash photolysis and quantum chemical study of the fluorinated derivatives of singlet phenylnitrene.

Laser flash photolysis (LFP, Nd:YAG laser, 35 ps, 266 nm, 10 mJ or KrF excimer laser, 10 ns, 249 nm, 50 mJ) of 2-fluoro, 4-fluoro, 3,5-difluoro, 2,6-difluoro, and 2,3,4,5,6-pentafluorophenyl azides produces the corresponding singlet nitrenes. The singlet nitrenes were detected by transient absorption spectroscopy, and their spectra are characterized by sharp absorption bands with maxima in the range of 300-365 nm. The kinetics of their decay were analyzed as a function of temperature to yield observed decay rate constants, k(OBS). The observed rate constant in inert solvents is the sum of k(R) + k(ISC) where k(R) is the absolute rate constant of rearrangement of singlet nitrene to an azirine and k(ISC) is the absolute rate constant of nitrene intersystem crossing (ISC). Values of k(R) and k(ISC) were deduced after assuming that k(ISC) is independent of temperature. Barriers to cyclization of 4-fluoro-, 3,5-difluoro-, 2-fluoro-, 2,6-difluoro-, and 2,3,4,5,6-pentafluorophenylnitrene in inert solvents are 5.3 +/- 0.3, 5.5 +/- 0.3, 6.7 +/- 0.3, 8.0 +/- 1.5, and 8.8 +/- 0.4 kcal/mol, respectively. The barrier to cyclization of parent singlet phenylnitrene is 5.6 +/- 0.3 kcal/mol. All of these values are in good quantitative agreement with CASPT2 calculations of the relative barrier heights for the conversion of fluoro-substituted singlet aryl nitrenes to benzazirines (Karney, W. L. and Borden, W. T. J. Am. Chem. Soc. 1997, 119, 3347). A single ortho-fluorine substituent exerts a small but significant bystander effect on remote cyclization that is not steric in origin. The influence of two ortho-fluorine substituents on the cyclization is pronounced. In the case of the singlet 2-fluorophenylnitrene system, evidence is presented that the benzazirine is an intermediate and that the corresponding singlet nitrene and benzazirine interconvert. Ab initio calculations at different levels of theory on a series of benzazirines, their isomeric ketenimines, and the transition states converting the benzazirines to ketenimines were performed. The computational results are in good qualitative and quantitative agreement with the experimental findings.

M2 delta-to-oxalate pi* conjugation in oxalate-bridged complexes containing M-M quadruple bonds.

The electronic structures of oxalate-bridged, quadruply-bonded dimolybdenum and ditungsten compounds have been investigated by a variety of computational methods employing density function theory (gradient corrected and time-dependent) which reveal the consequences of strong mixing of M2 delta and oxalate pi orbitals within extended chains and cyclic structures.

The interplay of theory and experiment in the study of phenylnitrene.

The intra- and intermolecular chemistry of phenylnitrene (PhN), its singlet-triplet energy separation, and its electronic spectra are interpreted with the aid of ab initio molecular orbital theory. The key to understanding singlet PhN is the recognition that this species has an open-shell electronic structure, in contrast to the related species, phenylcarbene, which has a closed-shell electronic structure. The thermodynamics of nitrenes, benzazirines, dehydroazepines, aminyl radicals, and their hydrocarbon analogues are also discussed.

The fragmentation pathways of protonated glycine: a computational study.

Numerous studies have demonstrated that protonated aliphatic amino acids, [H2NCHRCO2H + H]+, fragment in the gas phase to form iminium ions, H2N=CHR+. Unfortunately none of these studies have probed the structure of the neutral(s) lost as well as the mechanism of fragmentation. Three main mechanisms have been previously proposed: (1) loss of the combined elements of H2O and CO; (2) loss of dihydroxycarbene (HO)2C: and (3) loss of formic acid, HC(=O)OH. Herein, ab initio and density functional theory calculations have been used to calculate the key reactants, transition states, and products of these and several other competing reaction channels in the fragmentation of protonated glycine. The loss of the combined elements of H2O and CO is thermodynamically and kinetically favored over the alternative formic acid or (HO)2C fragmentation processes.

The response of electrons to structural changes.

The properties of a molecule are determined by the distribution of its electrons. This distribution can be described by the charge density, which is readily obtained from the wave functions derived by ab initio molecular orbital calculations. The charge density may be analyzed in a number of different fashions to give information about the effects of substituents, structural changes, and electronic excitation on the properties of molecules; one common procedure makes use of projection density or charge difference plots. Charge density also may be partitioned among atoms, and by numerical integration over appropriate volume elements one may obtain atomic charges, dipoles, kinetic energies, and other properties of the atoms in a molecule. Many chemical phenomena have been analyzed in terms of charge densities.