MO visualization of Pi Orbitals

In the spirit of trying to convert people to understanding atomic orbitals centered elsewhere than the origin, we continue the discussion of visualizing molecular orbitals, so called LCAO-MO, using various plotting tricks in Maple.

The synthesis and application of novel profluorescent nitroxides as probes for polymer degradation

This PhD project has expanded the knowledge in the area of profluorescent nitroxides with regard to the synthesis and characterisations of novel profluorescent nitroxide probes as well as physical characterisation of the probe molecules in various polymer/physical environments. The synthesis of the first example of an azaphenalene-based fused aromatic nitroxide TMAO, [1,1,3,3-tetramethyl-2,3-dihydro-2-azaphenalen-2-yloxyl, was described. This novel nitroxide possesses some of the structural rigidity of the isoindoline class of nitroxides, as well as some properties akin to TEMPO nitroxides. Additionally, the integral aromatic ring imparts fluorescence that is switched on by radical scavenging reactions of the nitroxide, which makes it a sensitive probe for polymer degradation. In addition to the parent TMAO, 5 other azaphenalene derivatives were successfully synthesised. This new class of nitroxide was expected to have interesting redox properties when the structure was investigated by high-level ab initio molecular orbitals theory. This was expected to have implications with biological relevance as the calculated redox potentials for the azaphenalene ring class would make them potent antioxidant compounds. The redox potentials of 25 cyclic nitroxides from four different structural classes (pyrroline, piperidine, isoindoline and azaphenalene) were determined by cyclic voltammetry in acetonitrile. It was shown that potentials related to the one electron processes of the nitroxide were influenced by the type of ring system, ring substituents or groups surrounding the moiety. Favourable comparisons were found between theoretical and experimental potentials for pyrroline, piperidine and isoindoline ring classes. Substitution of these ring classes, were correctly calculated to have a small yet predictable effect on the potentials. The redox potentials of the azaphenalene ring class were underestimated by the calculations in all cases by at least a factor of two. This is believed to be due to another process influencing the redox potentials of the azaphenalene ring class which is not taken into account by the theoretical model. It was also possible to demonstrate the use of both azaphenalene and isoindoline nitroxides as additives for monitoring radical mediated damage that occurs in polypropylene as well as in more commercially relevant polyester resins. Polymer sample doped with nitroxide were exposed to both thermo-and photo-oxidative conditions with all nitroxides showing a protective effect. It was found that isoindoline nitroxides were able to indicate radical formation in polypropylene aged at elevated temperatures via fluorescence build-up. The azaphenalene nitroxide TMAO showed no such build-up of fluorescence. This was believed to be due to the more labile bond between the nitroxide and macromolecule and the protection may occur through a classical Denisov cycle, as is expected for commercially available HAS units. Finally, A new profluorescent dinitroxide, BTMIOA (9,10-bis(1,1,3,3- tetramethylisoindolin-2-yloxyl-5-yl)anthracene), was synthesised and shown to be a powerful probe for detecting changes during the initial stages of thermo-oxidative degradation of polypropylene. This probe, which contains a 9,10-diphenylanthracene core linked to two nitroxides, possesses strongly suppressed fluorescence due to quenching by the two nitroxide groups. This molecule also showed the greatest protective effect on thermo-oxidativly aged polypropylene. Most importantly, BTMIOA was found to be a valuable tool for imaging and mapping free-radical generation in polypropylene using fluorescence microscopy.

3,6-Di(furan-2-yl)pyrrolo[3,4-c]pyrrole-1,4(2H,5H)-dione and bithiophene copolymer with rather disordered chain orientation showing high mobility in organic thin film transistors

Pyrrolo[3,4-c]pyrrole-1,4(2H,5H)-dione or diketopyrrolopyrrole (DPP) is a useful electron-withdrawing fused aromatic moiety for the preparation of donor-acceptor polymers as active semiconductors for organic electronics. This study uses a DPP-furan-containing building block, 3,6-di(furan-2-yl)pyrrolo[3,4- c]pyrrole-1,4(2H,5H)-dione (DBF), to couple with a 2,2′-bithiophene unit, forming a new donor-acceptor copolymer, PDBFBT. Compared to its structural analogue, 3,6-di(thiophen-2-yl)pyrrolo[3,4-c]pyrrole-1,4(2H,5H)-dione (DBT), DBF is found to cause blue shifts of the absorption spectra both in solution and in thin films and a slight reduction of the highest occupied molecular orbital (HOMO) energy level of the resulting PDBFBT. Despite the fact that its thin films are less crystalline and have a rather disordered chain orientation in the crystalline domains, PDBFBT shows very high hole mobility up to 1.54 cm 2 V-1 s-1 in bottom-gate, top-contact organic thin film transistors.

Facile dearomatisation of porphyrins using palladium-catalysed hydrazination: the 5,15-diiminoporphodimethenes and their redox products

The synthesis, electronic absorption and 1H NMR spectra of a suite of novel porphyrinoids derived from meso-bromoporphyrins by palladium-catalysed aminations using ethyl and tert-butylcarbazates are reported. Instead of the expected carbazate-substituted porphyrins, a facile oxidative dearomatisation of the porphyrin ring occurs in high yield, especially for the nickel(II) complexes, resulting in high yields of 5,15-diiminoporphodimethenes (DIPDs). The analogous zinc(II) and free base DIPDs were also characterised, the former by X-ray crystallography. The oxidation and reduction reactions of DIPDs and their precursor carbazate porphyrins were studied. Density Functional Theory (DFT) was used to calculate the optimised geometries and frontier molecular orbitals of DIPD Ni8c and bis(azocarboxylate) 19c, and Time Dependent DFT calculations allowed the prediction of electronic absorption spectra, whose characteristics corresponded well with those of the observed solution spectra. In the latter case, the calculated low-energy absorptions were unlike those of a typical porphyrin, due to the near-degeneracy of the highest filled frontier orbitals, and the wide energy separation between the unfilled orbitals. This feature was present in the observed spectrum.

Experimental and theoretical characterization of 5,10- diminoporphodimethenes: Dearomatized porphyrinoids from palladium-catalyzed hydrazinations of 5,10-diarylporphyrins

A new dearomatized porphyrinoid, 5,10-diiminoporphodimethene (5,10-DIPD), has been prepared by palladium-catalyzed hydrazination of 5,10-dibromo-15,20-bis(3,5-di-tert-butylphenyl)porphyrin and its nickel(II) complex, by using ethyl and 4-methoxybenzyl carbazates. The oxidative dearomatization of the porphyrin ring occurs in high yield. Further oxidation with 2,3-dichloro-5,6-dicyanobenzoquinone forms the corresponding 5,10-bis(azocarboxylates), thereby restoring the porphyrin aromaticity. The UV/visible spectra of the NiII DIPDs exhibit remarkable redshifts of the lowest-energy bands to 780 nm, and differential pulse voltammetry reveals a contracted electrochemical HOMO–LUMO gap of 1.44 V. Density functional theory (DFT) was used to calculate the optimized geometries and frontier molecular orbitals of model 5,10-DIPD Ni7c and 5,10-bis(azocarboxylate) Ni8c. The conformations of the carbamate groups and the configurations of the CNZ unit were considered in conjunction with the NOESY spectra, to generate the global minimum geometry and two other structures with slightly higher energies. In the absence of solution data regarding conformations, ten possible local minimum conformations were considered for Ni8c. Partition of the porphyrin macrocycle into tri- and monopyrrole fragments in Ni7c and the inclusion of terminal conjugating functional groups generate unique frontier molecular orbital distributions and a HOMO–LUMO transition with a strong element of charge transfer from the monopyrrole ring. Time-dependent DFT calculations were performed for the three lowest-energy structures of Ni7c and Ni8c, and weighting according to their energies allowed the prediction of the electronic spectra. The calculations reproduce the lower-energy regions of the spectra and the overall forms of the spectra with high accuracy, but agreement is not as good in the Soret region below 450 nm.

A New Mechanism For Ferromagnetism In C-60-TDAE

Based on the topology of C-60 and the resulting non-disjoint nature of the lowest unoccupied molecular orbitals, Ne propose a new model for ferromagnetic exchange in C-60-TDAE. Within the Hubbard model, we find that the ferromagnetic exchange integral is stabilized to first order in the inter-ball transfer integral, while the antiferromagnetic coupling is stabilized only to second order. This difference is adequate to counter the larger phase space available for stabilizing the antiferromagnetic state. Thus, the ground state is found to be ferromagnetic for reasonable inter-ball transfer integrals.

Hydrogen bonding with mono- and di-carbonyls

The electronic absorption and i.r. spectroscopic studies are reported for the hydrogen bonding systems involving alcohol and various ketones. It is shown that the hydrogen bonding abilities of ketones are determined by the extent of delocalization of the lone pair electrons in their non-bonding molecular orbitals. Evidence for the formation of very weak intermolecular hydrogen bonds between alcohol and the π-electron part of the dicarbonyls has also been presented from the i.r. studies in the 3400–3700 cm−1 region.

Ab initio studies on the tri- and diphosphate fragments of adenosine triphosphate

Pyrophosphate prototypes such as methyl triphosphate and methyl diphosphate molecules in their different protonation states have been investigated at high levels of quantum chemical calculations. The optimized geometries, the thermochemistry of the hydrolysis and the molecular orbitals contributing to the high energy of these compounds have been analyzed. These investigations provide insights into the "high energy" character of ATP molecule. Further, the dependence of vibrational frequencies on the number of phosphate groups and the charged states has also been presented. These results can aid the interpretation of spectra obtained by experiments on complexes containing pyrophosphate prototypes.

Ab initio studies on the tri- and diphosphate fragments of adenosine triphosphate

Pyrophosphate prototypes such as methyl triphosphate and methyl diphosphate molecules in their different protonation states have been investigated at high levels of quantum chemical calculations. The optimized geometries, the thermochemistry of the hydrolysis and the molecular orbitals contributing to the high energy of these compounds have been analyzed. These investigations provide insights into the ``high energy'' character of ATP molecule. Further, the dependence of vibrational frequencies on the number of phosphate groups and the charged states has also been presented. These results can aid the interpretation of spectra obtained by experiments on complexes containing pyrophosphate prototypes. (c) 2005 Elsevier B.V. All rights reserved.

The short range interactions between two rare gas atoms

The short range interactions in He2, Ne2 and Ar2 have been studied in terms of the electronic forces as functions of their internuclear separations employing their single configuration SCF wave functions. The results show that the constituent molecular orbitals behave differently in terms of the forces they exert on the nuclei during the interaction process. The different behaviour of the orbitals is also reflected in the redistribution of charges.

Patterning Nanoroads and Quantum Dots on Fluorinated Graphene

Using ab initio methods we have investigated the fluorination of graphene and find that different stoichiometric phases can be formed without a nucleation barrier, with the complete “2D-Teflon” CF phase being thermodynamically most stable. The fluorinated graphene is an insulator and turns out to be a perfect matrix-host for patterning nanoroads and quantum dots of pristine graphene. The electronic and magnetic properties of the nanoroads can be tuned by varying the edge orientation and width. The energy gaps between the highest occupied and lowest unoccupied molecular orbitals (HOMO-LUMO) of quantum dots are size-dependent and show a confinement typical of Dirac fermions. Furthermore, we study the effect of different basic coverage of F on graphene (with stoichiometries CF and C4F) on the band gaps, and show the suitability of these materials to host quantum dots of graphene with unique electronic properties.

Correlated electronic states of C-60 fragments

We have studied electronic states of various fragments of C-60 within the Pariser-Parr-Pople (PPP) model and have obtained structural, magnetic and spectral properties of these molecules. The fragments studied include corannulene, fluoranthene and pyracylene. Pyracylene is studied using the exact valence bond (VB) approach while fluoranthene and corannulene are studied using a novel restricted CI technique which employs molecular orbitals for constructing the VB functions. The electronic excitations, bond order and ring currents are calculated for these systems. From these studies, the wide range of absorptions in C-60 can be viewed as those localized on pyracylene units or on the corannulene/fluoranthene units. The bond orders and ring currents show the hexagons to be similar to benzene rings. The pentagon-hexagon bonds are also found to be longer than the hexagon-hexagon bonds.

meso-substituted octabromoporphyrins: Synthesis, spectroscopy, electrochemistry and electronic structure

The free-base, copper(II) and zinc(II) derivatives of 5,10,15,20-tetraarylporphyrin (aryl = phenyl, 4-methylphenyl or 4-chlorophenyl) and the corresponding brominated 2,3,7,8,12,13,17,18-octabromo-5,10,15,20-tetraarylporphyrin derivatives have been synthesized and their spectral and redox properties compared by UV/VIS, H-1 NMR, ESR and cyclic voltammetric methods. Substitution with the electron-withdrawing bromine groups at the pyrrole carbons has a profound influence on the UV/VIS and H-1 NMR spectral features and also on the redox potentials of these systems. On the other hand, electron-withdrawing chloro or electron-donating methyl groups at the para positions of the four phenyl rings have only a marginal effect on the spectra and redox potentials of both the brominated and the non-brominated derivatives. The ESR data for the copper(II) derivatives of ail these systems reveal that substitution at either the beta-pyrrole carbons and/or the para positions of the meso-phenyl groups does not significantly affect the spin-Hamiltonian parameters that describe the metal centre in each case. Collectively, these observations suggest that the highest-occupied (HOMO) and lowest-unoccupied molecular orbitals (LUMO) of the octabromoporphyrins involve the porphyrin pi-ring system as is the case with the non-brominated derivatives.-Investigations have been carried out to probe the electronic structures of these systems by three different approaches involving spectral and redox potential data as well as AMI calculations. The results obtained suggest that the electron-withdrawing beta-bromine substituents stabilize the LUMOs and, to a lesser degree, the HOMOs and that the extent of these changes can be fine-tuned, in a subtle way, by substituting at the meso-aryl rings of a given porphyrin.

K(2)O(2): The most stable oxide of K

We have analyzed the stability of various oxides of K and find that K(2)O(2) is the most stable one. The additional stability is traced to the presence of oxygen dimers in K(2)O(2) which interact to form molecular orbitals. Other oxides such as KO(2) and KO(3) which also have dimers/trimers of oxygens are found to be less stable. This is traced to the shorter O-O bonds that one finds in them which gives rise to a significant coulomb repulsion between the electrons on the oxygen atoms making up the dimer/trimer, making them less stable.

Quantum and variational monte-carlo interaction potentials for li2 (x1-sigma-g+)

Optimized trial functions are used in quantum Monte Carlo and variational Monte Carlo calculations of the Li₂(X ¹Σ⁺_g) potential curve. The trial functions used are a product of a Slater determinant of molecular orbitals multiplied by correlation functions of electron—nuclear and electron—electron separation. The parameters of the determinant and correlation functions are optimized simultaneously by reducing the deviations of the local energy E_L (E_L  Ψ⁻¹_THΨ_T, where Ψ_T denotes a trial function) over a fixed sample. At the equilibrium separation, the variational Monte Carlo and quantum Monte Carlo methods recover 68% and 98% of the correlation energy, respectively. At other points on the curves, these methods yield similar accuracies.