INDO Molecular Orbital Calculations Research Articles

Ultraviolet photoelectron studies of 5-trifluoromethyluracil: Electronic susceptibility of substituted uracils to nucleophilic attack

UV photoelectron spectroscopy has been employed to investigate the electronic structure of 5-trifluoromethyluracil. Band assignments have been made by comparison with photoelectron results from uracil, thymine, 5-fluorouracil, and 1-methyl-5-trifluoromethyluracil. Spectroscopically measured ionization potentials have also been compared with energy levels predicted by INDO molecular orbital (MO) calculations. The calculations predict the ordering and the spacing of the four uppermost Orbitals in 5-trifluoromethyluracil with good accuracy. They also give a good representation of the shifts observed in the ionization potentials of these orbitals when spectra of uracil, thymine, 5-fluorouracil, 5-trifluoromethyluracil, and 1-methyl-5-trifluoromethyluracil are compared. Descriptions of electronic structure provided by the photoelectron results and the INDO calculations have been examined in conjunction with results from kinetic and equilibrium studies of sulfite attack at the 6 position of uracil and substituted uracils. Results of the comparison indicate that while resonance effects cause 5-fluorouracil to exhibit greater electron density at the 6 position than thymine or uracil, the order of reactivity is 5-fluorouracil ≥ uracil > thymine. The enhanced reactivity of 5-fluorouracil over that expected from considerations of electron density may be ascribed in part to inductive electron withdrawing effects of the F atom, which oppose resonance effects and which stabilize the transition state involved in the addition of an SO2−3 ion.

Transistor performance of a “push-pull”, π-stacked bithiazole-ethylenedioxythiophene co-oligomer

The “push-pull” co-oligomer, 5,5′-bis(4,4′-dibutyl-2,2′-bithiazol-5-yl)-(3,4,3′,4′-bis(ethylenedioxy)-2,2′-dithienyl) (BT2B) was used to construct organic field effect transistors (OFETs) via vacuum evaporation or by solution casting of BT2B crystals. Crystalline OFETs made in either top- or bottom-contact configuration had measured field effect mobilities of (3–4) × 10−3 cm2 V−1 s−1. INDO and EHT molecular orbital calculations show that the HOMO is confined to the central EDOT fragment whereas the LUMO is concentrated on the relatively electron-poor bithiazole rings. This charge confinement, when combined with the molecular offset in the π-stacked crystal structure, leads to relatively small transfer integrals. Even so, the intrinsic hole mobility was computed to be as high as 0.86 cm2 V−1 s−1.

Electronic structure and spectra of linkage isomers of bis(bipyridine)(1,2-dihydroxy-9,10-anthraquinonato)ruthenium(ii) and their redox series.

Linkage isomers of bis(bipyridine)(1,2-dihydroxy-9,10-anthraquinonato)ruthenium(II), 1,2- and 1,9-coordinated complexes, and several of their oxidation products have been prepared chemically and/or electrochemically. For the 1,2-coordinated complex, the one- and two-electron oxidized species have been characterized, and for the 1,9-coordinated complex, the one-electron oxidized species has been characterized. The rich redox activity of these complexes leads to ambiguity in assessing the electronic structure. This paper reports EPR spectra of odd-electron species and detailed analyses of electronic spectra and structure of the complexes, based on INDO molecular orbital calculations. Results of calculations on the related 1-hydroxyanthraquinone complex and the free ligands,1,2-dihydroxy-9,10-anthraquinone (alizarin) and 1-hydroxyanthraquinone, are also briefly discussed.

ESR Spin Trapping Studies of Free Radicals Generated from Nitrofuran Derivative Analogues of Nifurtimox by Electrochemical and Trypanosoma cruzi Reduction

Electron spin resonance (ESR) spectra of radicals obtained from two analogues of the antiprotozoal drug nifurtimox by electrolytic and Trypanosoma cruzi reduction were analyzed. The electrochemistry of these compounds was studied using cyclic voltammetry. STO 3-21G ab initio and INDO molecular orbital calculations were performed to obtain the optimized geometries and spin distribution, respectively. The antioxidant effect of glutathione on the nitroheterocycle radical was evaluated. DMPO spin trapping was used to investigate the possible formation of free radicals in the trypanosome microsomal system. Nitro1 and Nitro2 nitrofuran analogues showed better antiparasitic activity than nifurtimox. Nitro2 produced oxygen redox cycling in T. cruzi epimastigotes. The ESR signal intensities were consistent with the trapping of either the hydroxyl radical or the Nitro2 analogue radicals. These results are in agreement with the biological observation that Nitro2 showed anti-Chagas activity by an oxidative stress mechanism.

The structure of streptonigrin semiquinone in solution

Streptonigrin semiquinone (SQ ·), a free radical intermediate implicated in the biological functioning of the antitumor antibiotic streptonigrin has been prepared and its structural properties in solution have been characterized. Through the use of electron paramagnetic resonance spectroscopy, the spin densities of the unpaired electron have been determined, indicating that the unpaired electron is largely confined to the quinolinesemiquinone moiety of the antibiotic. Unambiguous assignment of the hyperfine coupling constants was achieved employing isotopically labeled semiquinone radical, INDO molecular orbital calculations, and the study of unsubstituted 5,8-quinolinesemiquinone as a reference system. The assignments point to a negative spin density at the carbon para to the pyridine nitrogen in the radicals derived from both streptonigrin and the unsubstituted 5,8-quinolinequinone. Characterization of the properties of the streptonigrin semiquinone in solution indicate that the radical is stable in solution: it can be conveniently studied in 0.1 M methanolic lithium hydroxide or in aqueous organic solvent mixtures buffered with 0.06 M K 3PO 4 at pH 12.0. Under these conditions, the semiquinone shows completely reversible spectral changes between −10 to 60°C. Lowering the pH from 12.0 to 7.0 in aqueous DMSO decreases the lifetime of the radical from two weeks to a few minutes. Changes in structural properties of streptonigrin semiquinone in solution have been found to occur mainly due to variation in solvation and freedom of rotation of the amino group. Decreasing the temperature of SQ · solution in methanol from 60 to −10°C leads to an increase in the hyperfine coupling constant to the amino nitrogen from 1.28 to 1.40 G, and those of the two amino protons from 0.73 and 0.73 to 1.02 and 1.11 G respectively, while the other coupling constants change less than 3%. Greater electron spin delocalization onto the -NH 2 group has been found throughout the solvent systems examined, yet the temperature at which the two amino protons become equivalent changes with the nature of the solvent (e.g., from 25°C in MeOH to 40°C in aq. DMSO). The effective rotational diffusion constant as measured from EPR spectra in a series of solvents with fixed polarity ( E T) follows the Stokes–Einstein equation only in solvent mixtures of low to moderate viscosities (10–12.4 cP) suggesting that in addition to the viscosity of the medium a more specific mechanism (e.g., hydrogen bonding to the solvent) restricts the motion of the amino group. This hydrogen bonding mechanism is further supported by the fact that the degree of inequivalence in the amino proton hyperfine coupling constants varies monotonically with the spin density at the amino nitrogen. Studies of SQ · in aqueous micellar dispersions using neutral, cationic, and anionic sufractants indicate that SQ · is located at the surface of these aggregates. The structure of SQ · changes little at neutral and anionic micellar surfaces; however, more severe structural changes occur in cationic micelles which appear to be consistent with a conformational change induced by the positively charged surface.

EPR study of cation-radicals of cyclic alkenes in chlorofluorocarbon matrices

By gamma irradiation of cycloheptatriene, bicyclo(3.3.0)octene and dehydrodicyclopentadiene in chlorofluorocarbon matrices at 77 K the radical cations generated by electron loss from the parent molecules have been obtained and their electronic structure analyzed by EPR spectroscopy and by INDO and MNDO-PM3 molecular orbital calculations. On warming above 77 K these species undergo deprotonation to form neutral radicals. In the case of dicyclopentadiene the primary radical-cation is not stable at 77 K but decomposes probably by ring opening giving a bis-allylilic type cation-radical.

Indo study of 1,2-fluorine atom migration in 1,1,2,2-tetrafluoroethyl radical, cation and anion

INDO molecular orbital calculations have been carried out to estimate the energy barrier heights of the 1,2-migration of a fluorine atom in 1,1,2,2-tetrafluoroethyl radical, cation, and anion. In addition, the 1,2-hydrogen atom migration in these chemical species has been studied. The results suggest that (1) the 1,2-fluorine atom migration through a fluorine atom bridging intermediate will occur more readily than the 1,2-hydrogen atom migration through a hydrogen atom bridging intermediate in the 1,1,2,2-tetrafluoroethyl radical, (2) on the contrary, the 1,1,2,2-tetrafluoroethyl cation will undergo the 1,2-migration of a hydrogen atom more readily than that of a fluorine atom, and (3) it will be difficult for the 1,1,2,2,-tetrafluoroethyl anion to undergo the 1,2-migration of a fluorine and a hydrogen atom. The enthalpy change associated with the 1,2-fluorine atom migration in the radical was estimated to be 2.5 kcal/mol, which was 1.5 times larger than the corresponding change in the trifluoroethyl radical.

INDO study of 1,2-fluorine atom migration in 1,2-difluoroethyl and 1,1,2-trifluoroethyl radicals

INDO molecular orbital calculations have been carried out to estimate the barrier heights to the 1,2-migration of fluorine and hydrogen atoms in 1,2-difluoroethyl and 1,1,2-trifluoroethyl radicals. The calculated results suggest that (1) the 1,2-fluorine atom migration through a fluorine atom bridging intermediate will occur more readily than the 1,2-hydrogen atom migration through a hydrogen atom bridging intermediate in both radicals, (2) a fluorine atom will undergo 1,2-migration in 1,1,2-trifluoroethyl radical more readily than in 1,2-difluoroethyl radical. The enthalpy change accompanied by the 1,2-fluorine atom migration in 1,1,2-trifluoroethyl radical was estimated to be 1.7 kcal/mol, which was in good agreement with the value(1.6 kcal/mol) obtained experimentally.

A theoretical study of angiotensin-converting enzyme inhibitors.

INDO molecular orbital calculations are reported for 35 selected angiotensin-converting enzyme inhibitors. QSARs are developed between pI50 data and molecular electronic indices. The QSARs obtained reflect the importance of both charge-charge interactions between inhibitor and receptor and of specific interactions between groups on the inhibitor with points around the molecule which are postulated to correspond to binding sites at the receptor.

Electrically conducting polymers: a review of the electropolymerization reaction, of the effects of chemical structure on polymer film properties, and of applications towards technology

The electrochemical oxidation of aromatic heterocyclic compounds thiophene, pyrrole, and indole and benzenoid and nonbenzenoid polycyclic hydrocarbons azulene, fluorene, and pyrene yield electrically conducting polymers with conductivities of 10−5–10 S/cm. The presence of substituents affects the electrical conductivity of these films and also their electroactive properties. Furthermore, substituents determine whether electropolymerization of these compounds can occur or whether soluble products are formed. The relative importance of these pathways is dependent on the stability of the intermediate radical cation. These effects are investigated by INDO molecular orbital calculations.

Equilibria in complexes of N-heterocyclic molecules. Part 40. Electron densities in orbitals of iron(II) bound by N-heterocycles

Calculated electron densities based on INDO molecular orbital calculations for aromatic carbon atoms and for iron 3d-orbitals in a series of complexes of chelating N-heterocycles (e.g. 2,2′-bipyridyl) form the basis of a discussion for possible sites of nucleophilic substitution. Calculated charges on the ring atoms of quaternized and coordinated 1,10-phenanthroline are also compared.

The electropolymerization of polycyclic hydrocarbons: substituent effects and reactivity/structure correlations

The electrochemical oxidations of pyrene, fluorene and their derivatives yield conducting polymers with electrical conductivities of 10 −1 to 1 S/cm. Their elemental analysis data indicate oxidation levels of 0.06 to 0.31 per monomer unit. Substituents determine whether electropolymerization occurs, or soluble products are formed instead. The relative importance of these pathways is dependent on the stability of the intermediate radical cation, and these are discussed in light of INDO molecular orbital calculations.

Substituent effects on benzylic radical hydrogen hyperfine coupling constants. Part 4. The effect of branching of the alkyl substituent

The effects of substituents in the meta and para positions of the benzyl radical on the α-hydrogen hyperfine coupling constants (hfc's) are discussed. The electron spin resonance (esr) spectra of the para-methyl, ethyl, isopropyl, and tert-butyl substituted benzyl and cumyl radicals are analysed. Hyperconjugation involving the C—C bond is 40–60% as effective as C—H hyperconjugation for delocalizing spin density. This conclusion is supported by INDO molecular orbital calculations. Similar analysis of the 13Cmr spectra of the para-alkyl substituted cumyl carbocations provides evidence that C—C hyperconjugation is 75–90% as effective as C—H hyperconjugation for delocalizing charge density.

An electron spin, ENDOR, and TRIPLE resonance and INDO study of fluorine-substituted N,N′-diphenyl-4,4′-bipyridylium radical cations

E.s.r., ENDOR, and TRIPLE resonance results are reported for the radical cation of N,N′-diphenyl-4,4′-bipyridylium dichloride and a series of its fiuorophenyl analogues. The effect of ortho-, meta-, and para-substitution on the spin density distribution within the molecule is discussed and the observed coupling constants for the fluorine-substituted phenyl derivatives are analysed with the aid of INDO molecular orbital calculations. The magnitude of the spin delocalised into the phenyl rings when ortho-substituted suggests that these rings are substantially twisted with respect to the plane of the bipyridylium rings.

Endor studies of free radicals trapped in X-ray irradiated single crystals of caffeine hydrochloride dihydrate

ENDOR spectroscopy has been used to identify two different radical species in caffeine hydrochloride dihydrate X-irradiated at room temperature. One radical was identified as that formed by the net abstraction of a hydrogen atom from N(9). This radical is equivalent to that which would be produced by the loss of an electron from a neutral caffeine molecule, the caffeine cation. The other radical, which dominated the EPR spectrum, was identified as that resulting from net addition of a hydrogen atom to C(8) of the protonated caffeine molecule. The identification of this radical was based on the analysis of four different proton hyperfine couplings. Both the nitrogen ( 14N) hyperfine and quadrupole coupling tensors for a ring nitrogen atom were also obtained from the ENDOR spectra, and are attributed to the N(7) nucleus. The observation of 14N ENDOR lines, provided a second, independent estimate of the unpaired spin density centred on N(7). An indirect second-order effect, giving rise to a non-crossing phenomenon, was observed between the methylene protons, which were also found to be non-equivalent. The structure of this radical agrees with those determined previously by EPR and by INDO molecular orbital calculations for the analogous species in other purine derivatives.

Dipole moments of fluorobenzenes by CNDO and INDO methods

The dipole moments of fluorobenzenes are evaluated by CNDO/2 and INDO molecular orbital calculations from reasonably assumed geometries. The results are compared with experimentally obtained values. It is found that both methods overestimate the dipole moments, the overestimation being more for INDO calculations. The disparity between the observed and calculated values of dipole moments increases with the addition of fluorines. To a good approximation, the charge densities at different positions in monofluorobenzene are sufficient to generate the electronic distribution pattern in higher members of the series.

Dipole moments of fluorobenzenes by CNDO and INDO methods

The dipole moments of fluorobenzenes are evaluated by CNDO/2 and IN DO molecular orbital calculations from reasonably assumed geometries. The results are compared with experimentally obtained values. It is found that both methods overestimate the dipole moments, the overestimation being more for INDO calculations. The disparity between the observed and calculated values of dipole moments increases with the addition of fluorines. To a good approximation, the charge densities at different positions in monofluorobenzene are sufficient to generate the electronic distribution pattern in higher members of the series.

The assignment of the hyperfine coupling constants for the pyridyl protons in aryl and alkyl n-substituted bipyridylium radical cations

The coupling constants for the pyridyl protons of the radical cations of N,N'-dimethyl-4,4'-bipyridylium dichloride PQ + and N,N'-diphenyl-4,4'-bipyridylium dichloride DPQ + have been unambiguously assigned from an ENDOR study of selectively deuterated compounds. The experimental results confirm the early theoretical assignments for PQ + made by Johnson and Gutowsky; however subsequent assignments for DPQ + based on this work have now been revised. The revision of the assignments and the difference between the two compounds are discussed using INDO molecular orbital calculations.

7Li–13C n.m.r. coupling constants and the nature of the carbon–lithium bond: INDO MO calculations

INDO molecular orbital calculations suggest that the 7Li–13C n.m.r. coupling constant for the methyl-lithium monomer should be very large; this indicates the predominantly covalent character of the C–Li bond.

ENDOR studies on X-irradiated single crystals of acridine and phenazine

Stable radicals formed by room temperature X-irradiation of single crystals of acridine and phenazine have been identified and their structures determined by detailed ENDOR studies at 77 K. The E.S.R. spectra are of little assistance in the identification of these radicals. However, the high resolution of ENDOR has made it possible to study all the proton hyperfine interactions in detail. The radicals investigated in this study are formed as a result of the addition of atomic hydrogen to the nitrogen atom of the acridine and phenazine molecules. ENDOR lines of all the protons have been identified and analysed. Spin densities have been deduced from the proton hyperfine tensors. Although the unpaired electron is extensively delocalized throughout the molecule, there are large spin densities (0·475 and 0·584, respectively) on C9 in acridine and the second nitrogen in phenazine. Excellent agreement has been obtained between the observed spin densities and those computed by INDO molecular orbital calculations....