The effect of electron detachment on the structure and properties of the chlorine-acetonitrile anionic complex

The results of the theoretical study of ground state potential energy surfaces for the chlorine-acetonitrile anion and its photodetachment product are presented. The shallow potential surfaces allow for the nondefinitive position of the chlorine within the complex. The dissociation energy of the neutral complex, estimated through the thermodynamic cycle, indicates significant structural changes due to the photodetachment process. The excess negative charge is localized mostly on the chlorine atom, and the electron detachment proceeds as an electron is removed from chlorine. The process leads to drastic changes in the electrostatic interactions within the complex. The first electronic excited state corresponds to the excess electron transfer from chlorine to acetonitrile fragment. This state is a precursor of the observed charge-transfer-to-solvent state.     

Covalent chemistry and conformational dynamics of topologically chiral amide-based molecular knots

The readily available in gram quantities tris(allyloxy)knot of the amide-type 5 (knotane) can be completely and partially deprotected with nBu(3)SnH in the presence of a palladium catalyst resulting in hydroxyknotanes 7-9. These, in turn, react with diethylchlorophosphate giving rise to knotanes equipped with between one and three phosphoryl groups. Sulfonylation of bis(allyloxy)monohydroxyknotane 8 with p-toluenesulfonyl chloride and, following removal of one or two allyl groups from the intermediate monosulfonate 13, give rise to sulfonyloxy-allyloxy-hydroxy- and sulfonyloxy-dihydroxy-knotanes 15 and 14, respectively. This provides a convenient method for the preparation of knotanes with any substitution pattern. All new knotanes have been isolated in preparative amounts and as highly pure substances with an exception of allyloxy-dihydroxyknotane 9. This compound could only be obtained as a mixture with the corresponding monohydroxy-derivative 8. The structures of all synthesized compounds were established by means of FAB and MALDI TOF mass spectrometry, (1)H and (31)P NMR spectroscopy. The triphosphorylated knotane 10 exhibits high solubility in alcohols, allowing its complete enantiomeric resolution with a commercially available chiral HPLC column. (1)H,(1)H DQF-COSY correlation spectroscopy along with H/D exchange experiments and ab initio calculations provided the first detailed (1)H NMR signal assignments of knotanes in [D(6)]DMSO solution. The combination of variable temperature (1)H and (31)P NMR spectroscopy and molecular modeling has been applied to study the conformational behavior of the new knotanes in different solvents. It has been shown that in DMSO solution at room temperature knotanes exist in a relatively rigid nonsymmetrical conformation similar to that found in the solid state while faster conformational exchange leading to the average D(3) symmetrical structure was detected in a number of other solvents.     

Theoretical study on the structure and property relationship of the cationic conjugated polyelectrolytes

A theoretical study using density functional theory was performed to understand the structure/property relationship of the cationic conjugated polyelectrolytes, poly[9,9-bis-(6′-N,N,N-trimethylammonium) hexyl] fluorene-alt-4,7-(2,1,3-benzothiadiazole)] (PFBT-X, where X = Br). The torsion angle between the fluorene and benzothiadiazole units in the PFBT monomer was found to substantially affect the structural and electronic properties of the cationic PFBT monomer. The changes of geometrical parameter, HOMO and LUMO energy levels, and band gap, as well as the absorption maximum are discussed in terms of the torsion in the PFBT monomer structure. For comparison, its neutral analogue, the monomer of poly(9,9-di-n-octylfluorene-alt-benzothiadiazole) (F8BT) was also studied. The length of conjugation backbone was also examined.     

Non-Watson-Crick base pairing in RNA. quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family

Large RNA molecules exhibit an astonishing variability of base-pairing patterns, while many of the RNA base-pairing families have no counterparts in DNA. The cis Watson-Crick/sugar edge (cis WC/SE) RNA base pairing is investigated by ab initio quantum chemical calculations. A detailed structural and energetic characterization of all 13 crystallographically detected members of this family is provided by means of B3LYP/6-31G and RIMP2/aug-cc-pVDZ calculations. Further, a prediction is made for the remaining 3 cis WC/SE base pairs which are yet to be seen in the experiments. The interaction energy calculations point at the key role of the 2'-OH group in stabilizing the sugar-base contact and predict all 16 cis WC/SE base-pairing patterns to be nearly isoenergetic. The perfect correlation of the main geometrical parameters in the gas-phase optimized and X-ray structures shows that the principle of isosteric substitutions in RNA is rooted from the intrinsic structural similarity of the isolated base pairs. The present quantum chemical calculations for the first time analyze base pairs involving the ribose 2'-OH group and unambiguously correlate the structural information known from experiments with the energetics of interactions. The calculations further show that the relative importance and absolute value of the dispersion energy in the cis WC/SE base pairs are enhanced compared to the standard base pairs. This may by an important factor contributing to the strength of such interactions when RNA folds in its polar environment. The calculations further demonstrate that the Cornell et al. force field commonly used in molecular modeling and simulations provides satisfactory performance for this type of RNA interactions.     

The influence of microhydration on the ionization energy thresholds of uracil and thymine

In the present study the ionization energy thresholds (IET's) of uracil and thymine have been calculated (with the B3LYP, PMP2, and P3 levels of theory using the standard 6-31++G(d,p) basis set) with one to three water molecules placed in the first hydration shell. Then (B3LYP) polarizable continuum model (PCM) calculations were performed with one to three waters of the hydration shell included. Calculations show there is a distinct effect of microhydration on uracil and thymine. For uracil, one added water results in a decrease in the IET of about 0.15 eV. The second and third water molecules cause a further decrease by about 0.07 eV each. For thymine, the first water molecule is seen to decrease the IET by about 0.1 eV, while the second and third water molecules cause a further decrease of less than 0.1 eV each. The changes in IET calculated here for thymine with one to three waters of hydration are smaller than the experimental values determined by Kim et al. (Kim, S. K.; Lee, W.; Herschbach, D. R. J. Phys. Chem. 1996, 100, 7933). Preliminary results presented here indicate that the experimental results may involve keto-enol tautomers of thymine. The results of placing the microhydrated structures of uracil and thymine in a PCM cavity was seen to make very little difference in the IET when compared to the IET of ordinary uracil or thymine in a PCM cavity. The implications are that accurate calculations of the IET's of uracil and thymine can be obtained by simply considering long-range solvation effects.     

Tricyclo[2.2.0.0]hexane: a new hypothetical molecule which should have only one inverted carbon atom

HF and MP2 calculations with the 6-31G** and 6-311G** basis sets and those at MP2/cc-pVTZ level were carried out for the hypothetical tricyclo[2.2.0.0^1,3]hexane. The results indicate that the molecule under study should have one carbon atom with highly unusual inverted configuration. The analysis of the vibrational frequencies of this molecule as well as the analysis of its plausible decomposition routes performed at the DFT level indicate that this unique molecule could be a plausible synthetic target.     

Attractive halogen–halogen interactions: F3CCl⋯FH and F3CCl⋯FCH3 dimers

The F₃CCl?FH and F₃CCl?FCH₃ dimers, which feature the halogen–halogen contacts, are investigated at MP2/6–311++G(d,p) and MP2/aug–cc–pVDZ levels of approximation. The binding energies of these complexes are found to be comparable to those of the weak hydrogen bonds. In both complexes the Cl?F are found to be significantly shorter than the sum of the corresponding van der Waals radii. The C–Cl?F contacts are also found to exhibit certain deviation from linearity. However, the energy differences between linear and bent structures are very small and primarily accounted for by electrostatic interactions between remote parts of the dimer. This indicates a high conformational flexibility of the halogen–halogen contacts and may help to explain the diversity of structural features in crystals formed by halogen-containing molecules. In both dimers the halogen–halogen interaction leads to certain shortening of the C–Cl electron accepting bond. This is accompanied by a small increase of the C–Cl stretching frequency. Hence, the two investigated dimers can possibly be classified as the blue-shifting halogen–halogen contacts.     

Monomer basis-set truncation effects in calculations of interaction energies: A model study

Supermolecular interaction energies are analyzed in terms of the symmetry-adapted perturbation theory and operators defining the inaccuracy of the monomer wave functions. The basis set truncation effects are shown to be of first order in the monomer inaccuracy operators. On the contrary, the usual counterpoise correction schemes are of second order in these operators. Recognition of this difference is used to suggest an approach to corrections for basis-set truncation effects. Also earlier claims--that dimer-centered basis sets may lead to interaction energies free of basis-set superposition effects--are shown to be misleading. According to the present study the basis-set truncation contributions, evaluated by means of the symmetry-adapted perturbation theory with monomer-centered basis sets, provide physically and mathematically justified corrections to supermolecular results for interaction energies.