Pi-electron Delocalization Research Articles

Enthalpies of Formation of Hydrocarbons by Hydrogen Atom Counting. Theoretical Implications.

Standard enthalpies of formation at 298 K of unstrained alkanes, alkenes, alkynes, and alkylbenzenes can be expressed as a simple sum in which each term consists of the number of hydrogen atoms n of one of eight different types (n1-n8) multiplied by an associated coefficient (c1-c8) derived from the known enthalpy of formation of a typical molecule. Alkylbenzenes require one additive constant for each benzene ring, accounting for a possible ninth term in the sum. Terms are not needed to account for repulsive or attractive 1,3 interactions, hyperconjugation, or for protobranching, rendering them irrelevant. Conjugated eneynes and diynes show thermodynamic stabilizations much smaller than that observed for 1,3-butadiene, bringing into question the usual explanation for the thermodynamic stabilization of conjugated multiple bonds (p orbital overlap, pi electron delocalization, etc.).

Ab Initio Structures for 90°-Twisted s-trans-1,3-Butadiene and Cyclooctatetraene: The Naked sp2−sp2 Bond

The bond length of a carbon-carbon sp2-sp2 sigma-bond without the perturbing effects of pi-interactions has been estimated by high level calculations on two prototypical systems: a 90 degrees -twisted form of butadiene and the tub conformer of cyclooctatetraene. The former system yields a value of 1.4818 A, considerably longer than previous estimates. The corresponding bond length in the latter is slightly shorter due to some pi-electron delocalization.

Optical Detection of DNA and Proteins with Cationic Polythiophenes

In recent years, intense research has been carried out worldwide with the goal of developing simple, sensitive, and specific detection tools for biomedical applications. Along these lines, we reported in 2002 on cationic polythiophene derivatives able to provide ultrasensitive detection levels and the capability to distinguish perfect matches from oligonucleotides having as little as a single base mismatch. It was shown that the intrinsic fluorescence of the random-coil polymers quenches as a result of the planar, highly conjugated conformation adopted by the polymers when complexed with a single-strand DNA (ssDNA) capture probe but increases again after hybridization with the perfectly matched complementary strand. This change in fluorescence intensity is mainly due to a modification in the delocalization of pi electrons along the carbon chain backbone that occurs when switching between the two conformations. Thus, by monitoring, via the change in fluorescence intensity, the hybridization of the complementary ssDNA target with the "duplex", one could detect as little as 220 complementary target molecules in a 150 microL sample volume (0.36 zmol) in less than 1 hour. Building on this initial concept, we then reported that tagging the DNA probe with a suitable fluorophore dramatically increases the detection sensitivity. This novel molecular system involves the self-assembly of aggregates of duplexes in solution, prior to the introduction of the target, which allows a highly efficient resonance energy transfer (RET) between a "donor" (being the complex formed of the DNA double helix and the polymer chain wrapped around it) and a large number of neighboring "acceptors" (the fluorophores attached to the DNA probes). The massive intrinsic signal amplification (fluorescence chain reaction or FCR) provided by this novel integrated molecular system allows the specific detection of as little as five dsDNA copies in a 3 mL sample volume in only 5 minutes, without the need for prior amplification of the target. Clearly, direct and reliable detection of DNA hybridization without prior PCR amplification or chemical tagging of the genetic target is now possible with this methodology. We have also shown that proteins can be detected following a similar strategy. Impressive results have also been reported by direct and specific staining of targeted proteins. All these features have recently allowed the development of responsive polymeric supports for the detection of DNA and proteins. All these assays that do not require any chemical manipulation of the biological targets or sophisticated experimental procedures should soon lead to major advances in genomics and proteomics.

Enhanced Sorption of Polycyclic Aromatic Hydrocarbons to Tetra-Alkyl Ammonium Modified Smectites via Cation−π Interactions

The objective of this study was to characterize molecular sorptive interactions of polycyclic aromatic hydrocarbons (PAHs) by organoclays modified with quaternary ammonium cations. Three PAHs, naphthalene (NAPH), phenanthrene (PHEN), and pyrene (PYR), and three chlorobenzenes, 1,2-dichlorobenzene (DCB), 1,2,4,5-tetrachlorobenzene (TeCB), and pentachlorobenzene (PtCB), were sorbed from aqueous solution to reference montmorillonite clays (SWy-2) exchanged respectively with tetramethyl ammonium (TMA), tetraethyl ammonium (TEA), tetra-n-butyl ammonium (TBA), and hexadecyltrimethyl ammonium (HDTMA) cations. Solute hydrophobicities are compared between PAHs and chlorobenzenes using the solute n-octanol-water partition coefficient, n-hexadecane-water partition coefficient, and polyethylene-water distribution coefficient. The PAHs show several- to more than 10-fold greater sorption than the chlorobenzenes having close hydrophobicities but fewer delocalized pi electrons (NAPH/DCB, PHEN/TeCB, and PYR/ PtCB) by TEA-, TBA-, and HDTMA-clays. Furthermore, the PAHs show greater trends of solubility enhancement than the compared chlorobenzenes by TMA, TEA, and TBA in aqueous solution. The enhanced sorption and aqueous solubility of PAHs are best described by cation-pi interactions between ammonium cations and PAHs relative to chlorobenzenes that are incapable of such interactions. Cation-pi complexation between PAHs and tetra-alkyl ammonium cations in chloroform was verified by ring-current-induced upfield chemical shifts of the alkyl groups of cations in the 1H NMR spectrum.

Investigation of induced currents in cyclic forms of ortho-acylphenols and lithium analogues: does the lithium cation contribute to aromatic π-electron delocalisation?

Quasi-rings constructed as cyclic beta-ketoenol or lithium beta-ketoenolate moieties fused to aromatic molecules such as benzene, naphthalene and phenanthrene have geometric consequences for the conjoined aromatic similar to those caused by fusion of a benzene ring. This similarity is particularly marked in the case of lithium-bonded derivatives. Energies of bond separation reactions and the HOMA (harmonic-oscillator model of aromaticity) geometry-based index of pi-electron delocalisation show further similarities between quasi-rings and benzene. However, application of the ipsocentric approach to calculation of induced current density, shows that neither hydrogen nor lithium quasi-rings support pi-electron ring currents. It is argued that the geometric effects stem from electrostatic interaction of Li(+), and to a lesser extent H(+), with oxygen neighbours, causing a partial equalisation of CO bond lengths and knock-on effects on CC bonds, in the quasi-ring. The observed geometric effects do not arise from aromatic pi-electron delocalisation in the quasi-ring but are closer to the well-known push-pull effect between the electron-donating -OH and electron-accepting -CO groups, leading to reduction in bond-length alternation.

Pyrido-annellated diazaphospholenes and phospholenium ions

Pyrido-annulated 1,3,2-diazaphospholenium ions and P-bis(trimethylsilyl)amino substituted 1,3,2-diazaphospholenes were synthesised and characterised by spectroscopic methods and single-crystal X-ray diffraction studies. The distribution of bond distances provided evidence for pi-electron delocalisation in the fused ring system. This hypothesis was confirmed by calculations of magnetic (NICS, nucleus independent chemical shift) and geometrical (Bird index, bond shortening index) aromaticity indexes which attest aromatic character of the five-membered rings in the cations that is lost upon introduction of a substituent at the phosphorus atom. Computation of isodesmic reaction energies suggest that the reclamation of aromatic stabilisation energies in the products facilitates reaction of P-amino-substituted annulated diazaphospholenes under cleavage of the fused ring system.

Theoretical Study of Cooperativity in Biotin

To give a deeper insight into the widely discussed catalytic mechanism of biotin, four representative model molecules and their aggregates hydrogen bonding (H-bonding) to water molecules were investigated by means of ab initio calculations and compared with molecular dynamics simulations. The roles of the ureido group, the sulfur atom, and the side chain of biotin are examined and discussed, respectively. Some significant H-bonding cooperativities are theoretically demonstrated in the ureido group of biotin. The pi-electron delocalization of the ureido group makes the system a good candidate for the H-bonding cooperativities, which in turn increases the covalent character of the corresponding H-bonds and facilitates the electrophilic substitution of the nitrogen atoms in the ureido group. The sulfur of biotin may participate in the delocalized pi-electron system of the ureido group via special sulfur-nitrogen bonding interactions, which reinforces the H-bonding cooperativities of the ureido group. The side chain of biotin not only reduced the accessibility of 3-NH due to steric hindrance but also enhanced the H-bonding cooperativities of the ureido group by folding over to hydrogen bond to more water molecules. The folded states are a probable way of activating 1-NH by strong cooperative effects. In addition, the H-bonding cooperativities may be a significant reason for the strong and specific binding between biotin and streptavidin.

Electronic Structures of Main-Group Carbene Analogues

The electronic structures of 15 group 13-16 carbene analogues are analyzed using various quantum chemical methods and compared to the data obtained for the parent N-heterocyclic carbene (NHC), imidazol-2-ylidene. The results of this study present a uniform analysis of the similarities and differences in the electronic structures of p-block main-group carbene analogues. Though all systems are formally isovalent, the theoretical analyses unambiguously indicate that their electronic structures run the gamut from C=C localized (group 13) to C=N localized (group 16) via intermediate, more delocalized, systems. In particular, neither the stibenium ion nor any of the chalcogenium dications is a direct analogue of imidazol-2-ylidene as they all contain two lone pairs of electrons around the divalent main-group center, instead of the expected one. The reason behind the gradual change in the electronic structure of main-group analogues of imidazol-2-ylidene was traced to the total charge of the systems, which changes from anionic to dicationic when moving from left to right in the periodic table. Results from theoretical analyses of aromaticity show that all group 13-16 analogues of imidazol-2-ylidene display some degree of aromatic character. The heavier group 13 anions benefit the least from pi-electron delocalization, whereas the cationic group 15 systems are on par with the parent carbon system and display only slightly less aromatic character than cyclopentadienide, a true 6pi-electron aromatic species. The sigma-donor and pi-acceptor ability of the different main-group carbene analogues are also evaluated.

Bonding Study in All-Metal Clusters Containing Al4 Units

The nature of the bonding of a series of gas-phase all-metal clusters containing the Al4 unit attached to an alkaline, alkaline earth, or transition metal is investigated at the DFT level using Mulliken, quantum theory of atoms in molecules (QTAIM), and Hirshfeld iterative (Hirshfeld-I) atomic partitionings. The characterization of ionic, covalent, and metallic bonds is done by means of charge polarization and multicenter electron delocalization. This Article uses for the first time Hirshfeld-I multicenter indices as well as Hirshfeld-I based atomic energy calculations. The QTAIM charges are in line with the electronegativity scale, whereas Hirshfeld-I calculations display deviations for transition metal clusters. The Mulliken charges fail to represent the charge polarization in alkaline metal clusters. The large ionic character of Li-Al and Na-Al bonds results in weak covalent bonds. On the contrary, scarcely ionic bonds (Be-Al, Cu-Al and Zn-Al) display stronger covalent bonds. These findings are in line with the topology of the electron density. The metallic character of these clusters is reflected in large 3-, 4- and 5-center electron delocalization, which is found for all the molecular fragments using the three atomic definitions. The previously reported magnetic inactivity (based on means of magnetic ring currents) of the pi system in the Al42- cluster contrasts with its large pi electron delocalization. However, it is shown that the different results not necessary contradict each other.

Application of AIM Parameters at Ring Critical Points for Estimation of π‐Electron Delocalization in Six‐Membered Aromatic and Quasi‐Aromatic Rings

The AIM parameters at the ring critical point (the electron density and its Laplacian, the total electron energy density and both its components, potential and kinetic electron energy densities), have been intercorrelated with aromaticity indices: the geometry-based HOMA and the magnetism-based NICS, NICS(1), and NICS(1)(zz). A set of 33 phenylic rings having possibly a diversified aromatic character, and a set of 20 quasi-rings formed by intramolecular hydrogen and lithium bonds, have been taken into consideration. It has been found that the density of total electron energy, H, may serve as a new quantitative characteristic of pi-electron delocalization. The dependences between H values and aromaticity indices are correlated (cc(H/HOMA)=0.99, cc(H/NICS(1)zz)=0.95).

A Spectroscopic and Computational Study of the Neutral and Radical Cation Species of Conjugated Aryl-Substituted 2,5-Bis(2-thien-2-ylethenyl)thiophene-Based Oligomers

A spectroscopic and computational study of a series of 2,5-bis(2-thien-2-ylethenyl) thiophene-based oligomers with a para-R-arylethenyl substituent is reported. The primary aim of this investigation is to increase understanding of how charge moves through these molecules by comparing the neutral and oxidized structures for each molecule. To this end, the B3LYP/6-31G(d) computational method was used to calculate the geometry and vibrational spectra for all molecules considered and their oxidation products. For vibrational data, mean absolute deviations for frequencies between experimental and theoretical results ranging from 2 to 18 cm-1 were obtained. Experimental Raman spectroscopy, in conjunction with calculated bond length analyses, was used to gain an insight into the position and delocalization of the charged defect on the oxidized oligomers. The relative frequencies of different ethylene stretching modes served as a particularly useful probe in this regard. It was found that the ethenyl spacers do not impede pi-electron delocalization and, therefore, give rise to a longer conjugation length relative to the corresponding terthiophenes. Furthermore, the para-R-arylethenyl substituent was found to orientate the charged defect toward a specific region of the 2,5-bis(2-thien-2-ylethenyl)thiophene conjugation path.

Influence of Bond Fixation in Benzo-Annulated N-Salicylideneanilines and Their ortho-C(O)X Derivatives (X = CH3, NH2, OCH3) on Tautomeric Equilibria in Solution

1H, 13C, and 15N NMR spectra show that an ortho-C(=O)X group present in the molecules of N-salicylideneanthranilamide (X = NH2), methyl N-salicylideneanthranilate (X = OCH3), N-salicylidene-o-aminoacetophenone (X = CH3), and their benzo analogues have only a minor effect on the tautomeric OH/NH-equilibrium in solution. Only two of three possible tautomers were detected. Lability of the absent form was proved by theoretical calculations. Calculated energies show that the enolimino form (OH) is less stable than the enaminone (NH) form only for dibenzo-annulated N-salicylideneanilines. The population of each species in the tautomeric mixture was found to be inversely proportional to its energy. Application of the geometry-based aromaticity index HOMA shows that the effectiveness of the pi-electron delocalization in different rings in the molecule depends mostly on the position of benzo-annulation. Both the NH...O and N...HO hydrogen bonds present in the NH and OH tautomers, respectively, increase the aromaticity of the quasirings H-O-C=C-C=N and O=C-C=C-N-H and decrease the aromatic character of the fused benzene ring. These results seem to be reliable when N-salicylideneanilines studied are compared with naphthalene and their benzo-annulated derivatives, i.e., phenanthrene, anthracene, and triphenylene. An analysis of the effectiveness of pi-electron delocalization confirms that in all cases studied, the OH form is more stable. Although the HOMA values and calculated energies are not a criterion that allows determination of the dominating tautomer, both of these parameters correctly show the effect of changes in the molecular topology on tautomeric preferences.

Recent Advances in Planar Tetracoordinate Carbon Chemistry

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Phenolic esters with potential anticancer activity - the structural variable

The conformational preferences of several potential anticancer dihydroxycinnamic esters with a variable length alkyl chain were studied by quantum-mechanical (DFT) calculations (both for the isolated molecule and for aqueous solutions). The orientation of the hydroxyl ring substituents and of the alkyl ester moiety relative to the carbonyl group showed these to be the most determinant factors for the overall stability of this type of phenolic systems, strongly dependent on an effective pi-electron delocalization. Compared to the parent caffeic acid (dihydroxycinnamic acid), esterification was found to lead to a higher conformational freedom, and to affect mainly the energy barrier corresponding to the (O=)C-OR internal rotation. No particular differences were verified to occur upon lengthening of the ester alkyl chain, except when this is branched instead of linear. The vibrational spectra of the whole series of compounds were simulated, based on their calculated harmonic vibrational frequencies, and a preliminary assignment was performed.

The Conversion among Various B4C Clusters: A Density Functional Theoretical Study

Geometry optimizations and vibration frequencies of B4C clusters were performed with Becke-3LYP method using 6-31G(d) basis set. We have found 14 stable isomers, and the most stable structure among them is the five-member ring containing two three-member boron rings. We also analyzed these stable isomers in detail, and the results show that the structures containing three-member boron rings are predominant in energy for B4C clusters. In terms of MO and NBO analysis, the three-centered bond and the pi-electron delocalization play an important role in stabilizing the planar five-member rings of these B4C clusters. Our calculations suggest that isomer4 can be converted into isomer7 with only an energy barrier of 0.31 kJ mol(-1) at the B3LYP/6-311G+(3df) level. Although the planar structures of the five-member rings (isomers12-14) can be converted with each other, the conversions of isomer14 to isomer13 and isomer13 to isomer12 have high-energy barriers of 70.99 and 68.51 kJ mol(-1) at the B3LYP/6-31G(d) level, respectively.

7-Amino-2-tert-butyl-5-methylpyrazolo[1,5-a]pyrimidine: a three-dimensional framework structure built from two N—H...N hydrogen bonds

The bond distances in the title compound, C11H16N4, provide evidence for peripheral delocalization of pi electrons. The molecules are linked by two independent N-H...N hydrogen bonds into a three-dimensional framework structure.

Recent advances in planar tetracoordinate carbon chemistry

We summarize our contributions on the quest of new planar tetracoordinate carbon entities (new carbon molecules with exotic chemical structures and strange bonding schemes). We give special emphasis on the rationalization why in this type of molecules the planar configuration is favored over the tetrahedral one. We will concentrate on the latter and will show that molecules containing planar tetracoordinate carbons have a stabilizing system of delocalized pi electrons, which shows similar properties as pi systems in aromatic molecules.

Enhancement of the Curie Temperature by Isomerization of Diarylethene (DAE) for an Organic−Inorganic Hybrid System: Co4(OH)7(DAE)0.5·3H2O

Intercalation of an organic photochromic molecule into layered magnetic systems may provide multifunctional properties such as photomagnetism. To build up a photosensitive multifunctional magnet, an organic-inorganic hybrid system coupled with a photochromic diarylethene anion, 2,2'-dimethyl-3,3'-(perfluorocyclopentene-1,2-diyl)bis(benzo[b]thiophene-6-sulfonate) (DAE), and cobalt LDHs (layered double hydroxides), Co4(OH)7(DAE)0.5.3H2O, was synthesized by the anion exchange reaction between Co2(OH)3(CH3COO).H2O and DAE. In the dark and under UV-irradiated (313 nm) conditions, Co4(OH)7(DAE)0.5.3H2O with open and closed forms of DAE were obtained, respectively. The magnetic susceptibility measurements elucidated ferromagnetic intra- and interlayer interactions and Curie temperatures of TC = 9 and 20 K for cobalt LDHs with the open and closed forms of DAE, respectively. The enhancement of the Curie temperature from 9 to 20 K by substitution of the open form of DAE with the closed form of DAE as an intercalated molecule is attributed to the delocalization of the pi-electrons in the closed form of DAE, which enhances the interlayer magnetic interaction. The enhancement of the interlayer magnetic interaction induced by the delocalization of pi-electrons in intercalated molecules is strongly supported by the fact that the Curie temperature (26.0 K) of cobalt LDHs with (E,E)-2,4-hexadienedioate having a conjugated pi-electron system is enormously higher than that (7.0 K) of the cobalt LDHs with hexanedioate. By UV irradiation at 313 nm, Co4(OH)7(DAE)0.5.3H2O shows the photoisomerization of DAE from the open form to the closed one in the solid state, which leads to the enhancement of Curie temperature.

Molecular Recognition: Preorganization of a Bis(pyrrole) Schiff Base Derivative for Tight Dimerization by Hydrogen Bonding

Multiple techniques have been used to delineate the self-assembly of a bis(pyrrole) Schiff base derivative (compound 4, C(16)H(14)N(4)), which forms an unusual dimer through complementary N-H...N=C hydrogen bonds between twisted, C2-symmetric monomer units. The asymmetric unit of the crystal structure comprises one and a half dimer units, with one dimer exhibiting approximate D2 point-group symmetry and the other exact D2 symmetry (space group C2/c). The dimers pack into columns whose axes are collinear with the a axis of the unit cell. The columns assemble into discrete layers with two distinct types of hydrogen-sized voids residing between the layers. Despite the promising architecture of the voids within the lattice of 4, the absence of genuine channels to interconnect the voids precludes the uptake of hydrogen gas, even at elevated pressures (10 bar). AM1 calculations of the structure of dimeric 4 indicate that self-recognition through hydrogen bonding depends primarily on favorable electrostatic interactions. The potential-energy surface for monomeric 4 mapped by counter-rotation of an adjacent pair of C=C-N=C torsion angles indicates that the X-ray structures of the four monomeric units are global minima with highly nonplanar conformations that are preorganized for self-recognition by hydrogen bonding. The in vacuo enthalpy of association for the dimer was calculated to be significantly exergonic (DeltaG(assoc)=-21.9 kJ mol(-1), 298 K) and in excellent agreement with that determined by 1H NMR spectroscopy in CDCl3 (DeltaG(assoc)=-16.6(4) kJ mol(-1), 298 K). Using population and bond order analyses, in conjunction with the conformation dependence of the frontier MO energies, we have been able to show that pi-electron delocalization is only marginally diminished in the nonplanar conformers of 4 and that the electronic structures of the constituent monomers of the dimer are well mixed.

Triply Fused ZnII–Porphyrin Oligomers: Synthesis, Properties, and Supramolecular Interactions with Single‐Walled Carbon Nanotubes (SWNTs)

The photophysical, electrochemical, and self-assembly properties of a novel triply fused Zn(II)-porphyrin trimer were investigated and compared to the properties of a triply fused porphyrin dimer and the analogous monomer. The trimer exhibited significantly red-shifted absorption bands relative to the corresponding monomer and dimer. Electrochemical investigations indicated a clear trend in redox properties amongst the three porphyrin structures, with the lowest oxidation potential and the lowest HOMO-LUMO gap exhibited by the triply fused trimer. This electrochemical behavior is attributed to the extensive pi-electron delocalization in the trimeric structure relative to the monomer and dimer. Additionally, it was found that the trimer forms extremely strong and nearly irreversible supramolecular interactions with single-walled carbon nanotubes (SWNTs), resulting in stable solutions of porphyrin-nanotube complexes in THF. Formation of these complexes required the addition of trifluoroacetic acid (TFA) to the solvent. This allowed the oligomers to make close contact with the nanotubes, enabling the formation of stable supramolecular assemblies. Atomic force microscopy (AFM) was used to observe the supramolecular porphyrin-nanotube complexes and revealed that the porphyrin trimer formed a uniform coating on the SWNTs. Height profiles indicated that nanotube bundles could be exfoliated into either individual tubes or very small bundles by exposure to the porphyrin trimer during sonication.