Partitioning of pi-electrons in rings of polycyclic benzenoid hydrocarbons. 2.1. Catacondensed coronoids

Various types of coronoids are examined for finding the partitioning of pi-electrons in individual benzenoid rings of polycyclic aromatic hydrocarbons. A class of catacondensed coronoids, namely fibonacenes, has four pi-electrons in every ring. Most other catacondensed coronoids have more than one type of benzenoid ring, each type with a different partition, but the average per ring is always four pi-electrons. For the class of catacondensed coronoids that have an acenic hole, simple quadratic equations in terms of their number R of rings exist for the partitions of pi-electrons in the three possible ring types.     

Algebraic Kekulé formulas for benzenoid hydrocarbons

By assigning two pi-electrons of CC double bonds in a Kekulé valence structure to a benzene ring if not shared by adjacent rings and one pi-electron if CC double bond is shared by two rings we arrived at numerical valence formulas for benzenoid hydrocarbons. We refer to numerical Kekulé formulas as algebraic Kekulé valence formulas to contrast them to the traditional geometrical Kekulé valences formulas. The average over all numerical Kekulé valence structures results in a single numerical structure when a benzenoid hydrocarbon molecule is considered. By ignoring numerical values the novel quantitative formula transforms into a qualitative one which can replace incorrectly used notation of pi-electron sextets to indicate aromatic benzenoids by placing inscribed circles in adjacent rings-which contradicts Clar's characterization of benzenoid hydrocarbons.     

Homobenzene: homoaromaticity and homoantiaromaticity in cycloheptatrienes

Cycloheptatriene (C(s)) is firmly established to be a neutral homoaromatic molecule based on detailed analyses of geometric, energetic, and magnetic criteria. Substituents at the 7 (methylene) position, ranging from the electropositive BH2 to the electronegative F, favor the equatorial conformation but influence the aromaticity only to a small extent. By the same criteria, the planar transition state (C(2v)) for cycloheptatriene ring inversion is clearly antiaromatic. This is attributed to the involvement of the pseudo-2pi-electrons of the CH2 group with the 6pi-electrons of the ring to give an 8pi-electron system. Similarly, the participation of the CH2 groups into C(2v) cyclopentadiene and cyclononatetraene lead to significant 4n + 2 pi electron aromaticity. The cyclization of cycloheptatriene to norcaradiene proceeds via a highly aromatic transition structure, but norcaradiene itself is less aromatic than cycloheptatriene. An annelated cyclopropane ring does not function as effectively as a double bond in promoting cyclic electron delocalization.     

Numerical Kekulé structures of fullerenes and partitioning of pi-electrons to pentagonal and hexagonal rings

We calculated the partitioning of pi-electrons within individual pentagonal and hexagonal rings of fullerenes for a collection of fullerenes from C20 to C72 by constructing their Kekulé valence structures and averaging the pi-electron content of individual rings over all Kekulé valence structures. The resulting information is collected in Table 2, which when combined with the Schlegel diagram of fullerenes (illustrated in Figure 7) uniquely characterizes each of the 19 fullerenes considered. The results are interpreted as the basic information on the distributions (variation) of the local (ring) pi-electron density.     

Phosphorus-olefin chelation in coordinated atropisomeric chiral auxiliaries

The atropisomeric chelating auxiliaries MeO-Biphep, Binap, MOP and selected monodentate phosphoramidite type ligands are all capable of using differing aromatic fragments as donors to stabilize coordinatively unsaturated 14- or 16-electron species. MeO-Biphep and Binap make use of a double bond immediately adjacent to one of the P-donors to turn these chelate ligands into six-electron donors. In addition to the P-atom, the MOP class uses the pi-electrons of the naphthyl group, not attached to the phosphorus atom, to form a 4e chelate ligand. The MeO-MOP ligands often form weak sigma-bonds, derived from the electrons in this naphthyl ring, rather than pi-olefin complexes. Phosphoramidites, and some related ligands such as "simple-phos", use a pendant phenyl group to form an eta(2)-arene, P-chelate. The various bonding modes have been investigated via X-ray, NMR and DFT studies.     

Interplay between intramolecular resonance-assisted hydrogen bonding and aromaticity in o-hydroxyaryl aldehydes

In this work, we analyze a series of o-hydroxyaryl aldehydes to discuss the interrelation between the resonance-assisted hydrogen bond (RAHB) formation and the aromaticity of the adjacent aromatic rings. As compared to the nonaromatic reference species (malonaldehyde), the studied compounds can be separated into two groups: first, the set of systems that have a stronger RAHB than that of the reference species, for which there is a Kekulé structure with a localized double CC bond linking substituted carbon atoms; and second, the systems having a weaker RAHB than that of the reference species, for which only pi-electrons coming from a localized Clar pi-sextet can be involved in the RAHB. As to aromaticity, there is a clear reduction of aromaticity in the substituted ipso ring for the former group of systems due to the formation of the RAHB, while for the latter group of species only a slight change of local aromaticity is observed in the substituted ipso ring.     

Ab initio study of hydrogen-bond formation between cyclic ethers and selected amino acid side chains

Binding energies for hydrogen-bonded complexes of six cyclic ethers with five hydrogen-bond donor molecules that mimic selected amino acid side chains have been calculated at the MP2/6-31G*, MP2/6-31+G*, MP2/6-311++G**(single point), and MP2/aug-cc-pvtz levels, using geometries obtained with or without counterpoise corrections throughout the geometry optimization. The calculated basis set superposition error (BSSE) amounts to 10-20% and 5-10% of the uncorrected binding energies for the neutral and ionic species, respectively, at the MP2/aug-cc-pvtz level. The authors conclude that the O...H distances in the hydrogen bonds and binding energies for the studied systems may be determined with uncertainties of up to 0.08 A and 1-2 kcal/mol, respectively, in comparison with the MP2/aug-cc-pvtz values at a reasonable computational cost by performing standard geometry optimization at the MP2/6-31+G* level. Hydrogen-bond formation energies are more negative for cyclic ethers compared to their counterparts with a C=C double bond in the ring next to the oxygen atom. The less negative hydrogen-bonding energy and the increased O...H separation have been attributed to the reduced basicity of the ether oxygen when the lone pairs can enter conjugation with the pi-electrons of the Calpha=Cbeta double bond. The present study is the first step toward the development of an affordable computational level for estimating the binding energies of natural product, fused ring ether systems to the human estrogen receptor.     

A resonance Raman investigation on the interaction of styrene and 4-methyl styrene oligomers on sulphated titanium oxide

In order to understand the nature of the interaction that gives rise to the yellow-orange colour observed when styrene or 4-methyl styrene are put in contact with sulphated TiO2, the resonance Raman spectra of such systems, including deuterated styrene (ring-deuterated d5 and perdeuterated d8) and allylbenzene were investigated. In all cases a substantial enhancement of the ring v(CC) stretching mode was observed. A charge transfer process involving a transition from the ring pi-electrons to the empty d-pi orbitals of titanium was ascribed responsible for the absorption in the visible. Two types of resonance Raman spectra were observed depending on the excitation wavelength, which can be explained by the presence of two kinds of oligomers, saturated and unsaturated, on the surface of the oxide with the former giving rise to a Raman enhancement at a higher excitation energy.     

The role of weak hydrogen-bonds on the formation of short-lived molecular associations

Weak molecular homo- and hetero-associations among some ethene derivatives and several common solvents are studied using (1)H NMR spectroscopy. In connection with the aromatic-solvent induced shifts which is a special case of molecular association between aromatic solvents and polar molecules a model for association was suggested that involves the interaction of the positive end of the solute dipole with the aromatic pi-electrons. This model met with certain difficulties. An alternative model for configuration of associated molecules that explains the literature results and the results obtained in this paper is presented. The model is based on interaction of protons of the acceptor molecules with the lone-pair electrons or pi-electrons of the donor molecules. The present model removes the difficulties met with the former model and extends the concept of aromatic-solvent induced shifts to include non-polar molecules besides polar ones. In all cases, the interaction of protons of acceptor molecules with lone-pair electrons of donor molecules gives rise to a deshielding effect, while interaction with aromatic pi-electrons leads to shielding.     

Molecular structure and benzene ring deformation of three cyanobenzenes from gas-phase electron diffraction and quantum chemical calculations

The molecular structures of cyanobenzene, p-dicyanobenzene, and 1,2,4,5-tetracyanobenzene have been accurately determined by gas-phase electron diffraction and ab initio/DFT MO calculations. The equilibrium structures of these molecules are planar, but their average geometries in the gaseous phase are nonplanar because of large-amplitude vibrational motions of the substituents out of the plane of the benzene ring. The use of nonplanar models in electron diffraction analysis is necessary to yield ring angles consistent with the results of MO calculations. The angular deformation of the benzene ring in the three molecules is found to be much smaller than obtained from previous electron diffraction studies, as well as from microwave spectroscopy studies of cyanobenzene. While the deformation of the ring CC bonds and CCC angles in p-dicyanobenzene is well interpreted as arising from the superposition of independent effects from each substituent, considerable deviation from additivity occurs in 1,2,4,5-tetracyanobenzene. The changes in the ring geometry and C ipso-C cyano bond lengths in this molecule indicate an enhanced ability of the cyano group to withdraw pi-electrons from the benzene ring, compared with cyanobenzene and p-dicyanobenzene. In particular, gas-phase electron diffraction and MP2 or B3LYP calculations show a small but consistent increase in the mean length of the ring CC bonds for each cyano group and a further increase in 1,2,4,5-tetracyanobenzene. Comparison with accurate results from X-ray and neutron crystallography indicates that in p-dicyanobenzene the internal ring angle at the place of substitution opens slightly as the molecule is frozen in the crystal. The small geometrical change, about 0.6 degrees , is shown to be real and to originate from intermolecular C identical withN...HC interactions in the solid state.     

Relation between pi-electron localization/delocalization and H-bond strength in derivatives of omicron-hydroxy-schiff bases

Detailed investigations of electronic effects taking place within the molecular system of o-hydroxy Schiff bases have been performed. The analysis of geometry, local and global aromaticity, selected AIM-based parameters, and finally, pi-electron currents induced in the systems under consideration have been performed on the basis of quantum chemical calculations at the B3LYP/6-311+G** level of theory. The relation between localization/delocalization of pi-electrons within the whole system has been described. It has been shown that the character of the bond which is common to the phenylic ring and the quasi-ring formed as a result of H-bond formation has a crucial impact on the strength of H-bonding. The strongest H-bonds can be observed for the systems in which the sequence of formally single and double bonds within the H-bridged quasi-ring enable a pi-electronic coupling. These observations indicate that pi-electron effects play a fundamental role in the stabilization of the hydrogen bridge within omicron-hydroxy Schiff bases. Analysis of pi-ring currents induced by a magnetic field perpendicular to the molecular plane of selected analyzed systems confirms these conclusions.     

Quantification of the (anti)aromaticity of fulvalenes subjected to pi-electron cross-delocalization

Fulvalenes 3-12 were theoretically studied at the ab initio level of theory. For the global minima structures, the occupation of the bonding (pi)C=C orbital of the interring C=C double bond obtained by NBO analysis quantitatively proves pi-electron cross-delocalization resulting in, at least partially, 2- or 6pi-electron aromaticity and 8pi-electron antiaromaticity for appropriate moieties. The cross-conjugation was quantified by the corresponding occupation numbers and lengths of the interring C=C double bonds, while the aromaticity or antiaromaticity due to cross-delocalization of the pi-electrons was visualized and quantified by through-space NMR shielding surfaces.     

Clar valence bond representation of pi-bonding in carbon nanotubes

The application of the Clar aromatic sextet valence bond (VB) model to extended, defect-free single-walled carbon nanotubes (CNTs) with roll-up vectors (m, n) provides a real space model of their electronic structure. If m - n = 3k, where k is an integer, then all pi-electrons can be represented by aromatic sextets, and the CNT is fully benzenoid; the converse is also true. Since m - n = 3k is known to be a necessary criterion for conductivity in CNTs, only fully benzenoid CNTs are metallic, and only potentially metallic CNTs are fully benzenoid. This behavior contrasts with that of planar polycyclic aromatic hydrocarbons, in which the fully benzenoid structures are known to have large HOMO-LUMO gaps. For CNTs that are not fully benzenoid, e.g., m - n = 3k + l, where l = 1 or 2 and k is an integer, a seam of double bonds wraps about an otherwise benzenoid CNT at the chiral angle - 60 degrees or the chiral angle, respectively. Nucleus-independent chemical shift calculations on hydrogen-terminated CNT segments support this, and show that the magnetic manifestation of aromatic sextets is not due to electron correlation. The resonance hybrid of the Clar VB structures corresponds to patterns occasionally observed in scanning tunneling microscopy images of CNTs.     

13C NMR relaxation study of molecular motions in tetraphenyltin and tetra(p-tolyl)tin in solution

The Woessner approach is applied to the 13C relaxation data for tetraphenyltin (1) and tetra(p-tolyl)tin (2) in CDCl3 solution over the temperature range 5-42 degrees C to obtain correlation times for rotational motions and hence the activation barriers. Quantum mechanical computations were carried out to obtain the rotational energy barriers for comparison. For 2 the relaxation data indicate (1) slower ring rotation than in 1, (2) highly hindered internal rotation of the methyl group. IR and chemical shift data support the hypothesis of hyperconjugation of the methyl correlated with interaction between the pi-electrons and the 5d orbitals of tin in the (p-tolyl)Sn moiety to account for the hindrances to the rotations of the ring and the methyl. The activation barrier for the tolyl group rotation is found to be much higher than that for the phenyl rotation. However, the Woessner approach yields an anomalously high barrier for the methyl rotation. An explanation based on correlated rotations of the tolyl ring and the methyl is offered.     

Comparative photophysical properties of free-base, bis-Zn(II), bis-Cu(II), and bis-Co(II) doubly N-confused hexaphyrins(1.1.1.1.1.1)

We have comparatively investigated the photophysics of a series of bis-metal doubly N-confused hexaphyrins(1.1.1.1.1.1) using time-resolved fluorescence, femtosecond transient absorption, two-photon absorption measurements, and geometry-optimized ab initio calculations. Bis-Zn(II) and free-base doubly N-confused hexaphyrins exhibit well-resolved and red-shifted B- and Q-like absorption bands compared with porphyrins. Their allowed transitions are (pi,pi) transitions of the hexaphyrin ring, as confirmed by the HOMO and LUMO frontier orbitals based on ab initio calculations at the B3LYP/6-31G level. On the other hand, the absorption spectra of bis-Cu(II) and bis-Co(II) doubly N-confused hexaphyrins are relatively broad, presumably due to large couplings between the metal d-orbitals and pi-electrons of the hexaphyrin ring. Owing to these couplings, bis-Cu(II) and bis-Co(II) doubly N-confused hexaphyrins have much shorter excited-state lifetimes of 9.4 +/- 0.3 ps and 670 fs, respectively, than those (267 +/- 16 and 62.4 +/- 1.2 ps, respectively) of bis-Zn(II) and free-base doubly N-confused hexaphyrins. The two-photon absorption cross section (sigma(2)) values, which are believed to depend strongly on the ring planarity (pi-conjugation), are in line with the excited-state lifetime trends.     

An ab initio theoretical prediction: an antiaromatic ring pi-dihydrogen bond accompanied by two secondary interactions in a "wheel with a pair of pedals" shaped complex FH . . . C4H4 . . . HF

By the counterpoise-correlated potential energy surface method (interaction energy optimization), the structure of the pi H-bond complex FH cdots, three dots, centered FH . . . C4H4 . . . HF has been obtained at the second-order M?ller-Plesset perturbation theory (MP2/aug-cc-pVDZ) level. Intermolecular interaction energy of the complex is calculated to be -7.8 kcal/mol at the coupled-cluster theory with single, double substitutions and perturbatively linked triple excitations CCSD (T)/aug-cc-pVDZ level. The optimized structure is a "wheel with a pair of pedals" shaped (1mid R:1) structure in which both HF molecules almost lie on either vertical line passing through the middle-point of the C[Double Bond]C bond on either side of the horizontal plane of the C4 ring for cyclobutadiene. In the structure, an antiaromatic ring pi-dihydrogen bond is found, in which the proton acceptor is antiaromatic 4 electron and 4 center pi bond and the donors are both acidic H atoms of HF molecules. In accompanying with the pi-dihydrogen bond, two secondary interactions are exposed. The first is a repulsive interaction between an H atom of HF and a near pair of H atoms of C4H4 ring. The second is the double pi-type H bond between two lone pairs on a F atom and a far pair of H atoms.     

Single-conformation ultraviolet and infrared spectroscopy of model synthetic foldamers: beta-peptides Ac-beta3-hPhe-beta3-hAla-NHMe and Ac-beta3-hAla-beta3-hPhe-NHMe

The conformational preferences and infrared and ultraviolet spectral signatures of two model beta-peptides, Ac-beta3-hPhe-beta3-hAla-NHMe (1) and Ac-beta3-hAla-beta3-hPhe-NHMe (2), have been explored under jet-cooled, isolated-molecule conditions. The mass-resolved, resonant two-photon ionization spectra of the two molecules were recorded in the region of the S0-S1 origin of the phenyl substituents (37,200-37,800 cm(-1)). UV-UV hole-burning spectroscopy was used to determine the ultraviolet spectral signatures of five conformational isomers of both 1 and 2. Transitions due to two conformers (labeled A and B) dominate the R2PI spectra of each molecule, while the other three are minor conformers (C-E) with transitions a factor of 3-5 smaller. Resonant ion-dip infrared spectroscopy was used to obtain single-conformation infrared spectra in the 3300-3700 cm(-1) region. The infrared spectra showed patterns of NH stretch transitions characteristic of the number and type of intramolecular H-bonds present in the beta-peptide backbone. For comparison with experiment, full optimizations of low-lying minima of both molecules were carried out at DFT B3LYP/6-31+G*, followed by single point MP2/6-31+G* and selected MP2/aug-cc-pVDZ calculations at the DFT optimized geometries. Calculated harmonic vibrational frequencies and infrared intensities for the amide NH stretch vibrations were used to determine the beta-peptide backbone structures for nine of the ten observed conformers. Conformers 1B, 1D, and 2A were assigned to double ring structures containing two C6 H-bonded rings (C6a/C6a), conformers 1A and 2B are C10 single H-bonded rings, conformers 1C and 2D are double ring structures composed of two C8 H-bonded rings (C8/C8), and conformers 1E and 2E are double ring/double acceptor structures in which two NH groups H-bond to the same C=O group, thereby weakening both H-bonds. Both 1E and 2E are tentatively assigned to C6/C8 double ring/double acceptor structures, although C8/C12 structures cannot be ruled out unequivocally. Finally, no firm conformational assignment has been made for conformer 2C whose unusual infrared spectrum contains one very strong H-bond with NH stretch frequency at 3309 cm(-1), a second H-bonded NH stretch fundamental of more typical value (3399 cm(-1)), and a third fundamental at 3440 cm(-1), below that typical of a branched-chain free NH. The single conformation spectra provide characteristic wavenumber ranges for the amide NH stretch fundamentals ascribed to C6 (3378-3415 cm(-1)), C8 (3339-3369 cm(-1)), and C10 (3381-3390 cm(-1)) H-bonded rings.     

Molecular modeling and 3D-QSAR studies in 2-aziridinyl-and 2,3-bis(aziridinyl)-1,4-naphthoquinonyl sulfonate and acylate derivatives as potential antimalarial agents

Malaria is still continuing to be one of the most dreadful diseases of the tropical countries particularly due to the development of resistance to the existing antimalarials. From observed, antimalarial activity of 2-aziridinyl- and 2,3-bis(aziridinyl)-1,4-naphthoquinonyl sulfonate and acylate derivatives acting through redox cycling mechanism, molecular modeling and three dimensional-quantitative structure activity relationship (3D-QSAR) studies have been carried out on a set of 63 compounds to identify important pharmacophors. Among several 3D-QSAR models generated, three models with correlation coefficient r > 0.82, match > 0.60 and chance = 0.00 have shown two common biophoric sites: one being the oxygen atom at position 1 of the naphthoquinone ring in terms of pi-population, charge and electron donating ability while the second being the center of the phenyl ring in terms of its 6pi-electrons. In addition to these sites, the models also share two common secondary sites: one positively contributing H-acceptor site while the second site contributing negatively in terms of steric refractivity. All these models showed good agreement between the experimental, calculated and predicted antimalarial activities.     

Synthesis of indaphyrins: meso-tetraarylsecochlorin-based porphyrinoids containing direct o-phenyl-to-beta-linkages

The synthesis of indaphyrins, novel meso-tetraarylsecochlorin-derived chromophores incorporating o-phenyl-to-beta-linkages, is described. Oxidative diol cleavage of meso-tetraaryl-2,3-dihydroxy-2,3-chlorins results in the formation of a secochlorin bisaldehyde. Depending on the reaction conditions during the ring cleavage reaction, one or two of the aldehyde groups react with the adjacent o-phenyl positions, leading to an intramolecular electrophilic aromatic substitution of the o-phenyl proton, and the establishment of a direct o-phenyl-to-beta-linkage. The initially formed carbinol is spontaneously oxidized to the corresponding ketone. This modification forces the aryl groups into co-planarity with the macrocycle, allowing for interactions between the pi-electrons of the aryl groups, the ketone linkage, and those of the chromophore, resulting in a significant electronic modulation of the porphyrinic pi-system. The UV-vis spectroscopic properties of the free base, CuII, NiII, and ZnII indaphyrins are discussed.