Search

Inspired by the helical structure as well as the conductivity of DNA and substituted polyphenylacetylenes, a new kind of substituted polyacetylene is introduced. More specifically, polycytosineacetylene ((RC CH) n , R = cytosine) with a trans-polyacetylene backbone is investigated theoretically. The neutral and cationic geometries are optimized as single helical chains with n = 20. It is found that when an electron is removed the polymer stretches from 19.80 A to 28.41 A. The polyacetylene backbone in the optimized cationic polymer exhibits the formation of a soliton. It is predicted that a doped polycytosineacetylene would have good conductivity, and would also behave as a nanomechanical spring and as a piezoelectric material.

We propose a general definition of the radius of an atom in terms of its ionization energy. A relationship between these two fundamental properties is derived from the radial distribution function and the exponential decay of the electron density. Strong correlations with well-known atomic radii lead us to conclude that we have found a universally valid definition of the atomic radius, defined exclusively in terms of an intrinsic property, the ionization energy of an atom, which is equally available from experiments and theoretical computations.

Triply hydrogen-bonded complexes of the form AAA-DDD are shown to have the strongest interaction when the complex is substituted with electron withdrawing groups on the donor molecule (DDD) and electron donating groups on the acceptor molecule (AAA). In particular, the largest effects are observed when the withdrawing groups act through resonance. This serves to flatten the entire system resulting in more linear, and consequently stronger, hydrogen bonds. Furthermore, the present calculations show that the binding energy correlates with the electron density at the bond critical points and inversely with the hydrogen bond lengths.

We report a study of the inclusion complex of p-chlorophenol inside α-cyclodextrin (α-CD) by the theory of atoms in molecules (AIM). We use a quantitative comparison of some AIM properties of isolated p-chlorophenol (PCP) and the inclusion complex (PCP-CD) and we characterize some weak interactions within the host–guest complex. Furthermore, we compare the electrophilic aromatic substitution on the p-chlorophenol in the isolated state and inside α-CD. The analysis of the bond critical points of PCP shows that there is no trend in the effect on the AIM properties of PCP due to inclusion in the α-CD.

A type of cage critical point (CCP) that has remained so far only a ‘mathematical possibility’ is reported for the first time. A CCP enclosed by two ring surfaces is found in a single ring in each of three derivatives of 1,12-difluorobenzo[c]phenanthrene. The two fluorine nuclei are linked by a bond path which results in the closure of a seven-membered ring in the ‘bay’ region. The crowding of the fluorine atoms forces an α-helical (staircase) twisting of the molecule causing the ring surface to split into two giving rise to a CCP. The Poincare–Hopf relationship is satisfied in each case.

We report a detailed characterization of the valence shell charge concentration (VSCC) of fluorine in methyl fluoride through the atoms in molecules theory. A comparison between the VSCCs of fluorine and neighboring elements (N, O, P, S, Cl) in the periodic table is also presented. The fluorine VSCC is shown to be tetrahedral and the most compact with the highest values of ρ and −∇ 2 ρ . Our results calculated at several post Hartree–Fock levels of theory using a large basis set show a remarkable insensitivity to the level of theory.

The performance of the DFT functionals B3LYP, B3PW91 and PBE1PBE in conjunction with selected basis sets for the prediction of 15N and 13C nuclear shieldings for small nitrogen-containing molecules is assessed. For molecules containing only singly bonded nitrogen and carbon atoms, the PBE1PBE/6-311+G(2df,p) level of theory is shown to provide reliable 15N and 13C nuclear shieldings. For the triply bonded nitrogen-containing molecules N2, CH3CN and HCN, all three levels of theory are much less satisfactory.

The gas phase and solution electron affinities and ionization potentials of uracil, thymine and a series of 5-halouracils ( 5XU, X=F, Cl, Br ) are investigated with B3LYP. Halogen substitution has a smaller effect on the IP than the EA of U . The EAs are calculated to increase according to T U 5FU 5ClU 5BrU . The calculated barriers for the dissociation of the resulting 5XU anions to X − plus uracil-centered radicals decrease along the series 5FU − > 5ClU − > 5BrU − . The calculated trends are consistent with suggestions that 5XUs enhance the sensitivity of deoxyribonucleic acid, DNA (ribonucleic acid, RNA) to ionizing radiation and that 5BrU leads to the greatest enhancement.

Density-functional theory (B3LYP functional) is used to investigate the ionization potentials and electron affinities of the DNA and RNA nucleotide bases. For the first time, anions lying lower in energy than the neutral species have been calculated for both thymine and uracil (i.e., positive adiabatic electron affinities). Additionally, the calculations show that anion formation leads to significant geometrical changes to the nucleobases. This is a very important finding as previous calculations have indicated that the anions are very similar in geometry to the neutral species and reported negative valence adiabatic electron affinities.

The molecular quadrupole moments of benzene and naphthalene are calculated using a range of ab initio and density functional methods, with basis sets as large as aug-CC-PVTZ for benzene and CC-PVTZ for naphthalene. The quadrupole moments calculated using Hartree-Fock wavefunctions are lower than the experimentally determined values, and all DFT values are higher than the experimental values. The use of the hybrid B3P86 and B3PW91 functionals, with a large basis set, produce quadrupole moments which are within experimental error for these two small aromatic molecules.

The structures and relative stabilities of the four different forms of hydroxypyridine and hydroxyquinoline (normal, protonated cation, deprotonated anion and zwitterion) in the gas phase have been calculated at the Moller-Plesset (MP) perturbation and coupled-cluster theory levels with basis sets up to 6–31+ G ∗∗ . The solvation free energies of the reactions were treated with the SMx series of aqueous solvation models by Cramer and Truhlar. By combining the PM3-SM3 model for solvation with the MP 2/6–31+ G ∗∗ level treatment for the gass-phase species, it is found that the free energy changes of the proton transfer reactions can be predicted reasonably well.

The thermally induced decomposition of ethylene, C2H4, to acetylene, C2H2, on the Ni(111) surface has been treated theoretically: potential-energy curves were computed within a modified extended-Huckel framework and reaction rates estimated via a master equation approach. As a preliminary step, adsorbate geometries and binding energies were optimized for one and two molecules of each hydrocarbon species chemisorbed in various sites on rigid bulk cluster models of the Ni substrate. A fragmentation pathway is proposed, eliciting the concerted tunnelling of intermolecular H's from a transient bimolecular complex comprised of two rotated C2H4's, which rationalizes the observed second-order decomposition kinetics.

The internal motion of benzene is studied in the gas phase at 30 and 300 K and in the liquid phase at 300 K by means of a molecular dynamics method based on a hybrid of quantum and molecular mechanical force fields. The fluctuations of bond lengths, bond angles and torsional angles are calculated and compared with available experimental data. A conformational analysis for the planar, boat, chair and twisted structures of benzene is carried out and liquid benzene is found to be effectively a planar hexagon at room temperature.

The interactions between an alkali metal atom (Li, Na, K) and acetylene/vinylidene are investigated by means of gradient corrected (‘PWP’) density functional theory. Particular emphasis is made on the determination of equilibrium geometries, energetics and atomic hyperfine structures of the MHCCH van der Waals addition complexes, and the MHCCH and MCCH2 charge-transfer complexes. The PWP optimized geometries are found to be similar to previous ab initio data, and the generated hyperfine structures are in excellent accord with experimental matrix isolation ESR data recorded at 4 K. In the charge transfer complex formation, the metal atoms are found to donate 0.6–0.8 electron from an excited p orbital to the antibonding CC π∗ orbital of the hydrocarbon fragment. The calculated trend in charge donation matches the order of increasing atomic s → p excitation energies, K < Li < Na. This is the first application of the present method to metal atom hyperfine structures, and the results are promising for future studies.

Density functional theory calculations of isotropic couplings of the atoms B to O are carried out with a variety of functional forms and basis sets. It is shown that the atomic isotropic coupling constants are very dependent on functional form, auxiliary basis set and orbital set. The calculations on the molecular systems NH 2 and H + 3 show less dependence for isotropic couplings and almost independence for anisotropic couplings. It is found that the combination of Perdew and Wang's non-local exchange functional and Perdew's correlation correction functional with a [7s, 6p, 2d]/(5, 2; 5, 2) orbital/auxiliary basis set gives results in semiquantitative agreement with experiment and MRSDCI calculations.

The influence of up to six Ne atoms on the isotropic hyperfine (hf) coupling constants of the hydrogen atoms in CH+4 is investigated using density functional theory. It is found that at very short NeH distances (R = 1.8 A), the hf structure is strongly affected, whereas at the more realistic van der Waals distance (R ≈ 2.5 A), the methane radical experiences a very weak field from the surrounding Ne atoms. At larger distances, the effects of the Ne matrix are negligible. It is furthermore found that at small R, the changes in aiso (H) are strongly dependent on the relative positions of the Ne atoms.

Ab initio SCF MO calculations for the hydrogen-bonded complexes between nitriles and hydrogen fluoride suggest a strong linear relationship between the charge density at the hydrogen-bond critical point and the hydrogen-bond energy. Further investigation of the topological properties of the charge density indicates that the generalization of the bond-length-bond-order relationship of CC bonds due to Bader et al. may be extended to intermolecular hydrogen bonding. Calculations at the 6–31G ** level, including complete geometry optimization, are reported for the complexes, where R  H, Li, F, Cl, HO, LiO, NC, HCC, CH 3 and CH 3 O.

The density difference ΔD(r1), defined as the difference between the exact and the Hartree-Fock radial density functions is reported for the 2 3S and the 2 1S excited states of the helium atom. The density differences in both cases resemble the inverse of the helium ground-state density difference, but are more long-ranged due to the diffuseness of the excited states. The effect of electron correlation on one-electron distributions is also demonstrated by comparison of (r1n) expectation values and several indices of the relative sizes of atoms. Electron correlation leads to a contraction of the Hartree-Fock electron clouds.

The topological properties of the charge density of the hydrogen-bonded complexes between nitrites and hydrogen chloride correlate linearly with theoretical estimates of the hydrogen-bond energy. At the 6-31G** level, the hydrogenbond energies range from a low of 10 kJ mol m NCCN—HC1 to a high of 38 kJ mol in LiCN—HCl. A linear relationship between the charge density at the hydrogen-bond critical point and the NH internuclear distance of the RCN—HC1 complexes indicates that the generalization of the bond-length-bond-order relationship of CC bonds due to Bader, Tang, Tal and Biegler-Konig can be extended to intermolecular hydrogen bonding.

Ab initio SCF MO calculations are reported for benzene, s -triazine, borazine and boroxine. The Laplacian of the charge density and the Mulliken population analysis procedure demonstrate that the delocalization of the π electrons decreases and the polarity of the ring bonds increases substantially as the atoms in the ring become more dissimilar. Several other properties, including distortion of the ring angles, puckering of the ring and nuclear quadrupolar coupling constants, emphasize the different chemical properties within the isoelectronic series.

Hartree—Fock wavefunctions and good approximations to the exact wavefunctions are used to demonstrate the effect of electron correlation on the radial density D ( r 1 ) and the contours of the density distribution ϱ( r 1 ) in the He isoelectronic sequence. In general, correlation effects diminish as the charge-cloud becomes less diffuse.

The orbital energies and charge densities in borazine were calculated by the Huckel M.O. method. the Bond Electronegativity Equalization Method for σ and π electrons (BEEM-π) and by the Semi-Emperical All Vallence electron theory with complete neglect of differential overlap (SAVE-CNDO).