Adjacent versus opposite type di-aromatic ring-fused phthalocyanine derivatives: synthesis,spectroscopy, electrochemistry,and molecular orbital calculations

A series of adjacent and opposite type di-aromatic ring-fused phthalocyanines (Pc's) of varying size have been prepared and characterized spectroscopically and electrochemically, and most of their properties have been reasonably reproduced by molecular orbital (MO) calculations. The adjacent isomers alone were obtained preferentially by using a diphthalonitrile unit linked via a short aryl chain. The main results are summarized as follows. (i) The Q-band shifts to longer wavelength and its intensity increases, but the degree of change decreases, with increasing molecular size. On the bases of the experiments and MO calculations, setting the size of the effect of benzene directly fused to the tetraazaporphyrin (TAP) skeleton at unity, the effect of the second and third benzene units is roughly about 0.75-0.80 and 0.48 +/- 0.06, respectively. As a result of this, among compounds having an isomeric pi-system, the Q-band of a D(4h) type species lies at longer wavelength than those of adjacently and oppositely di-aromatic ring-fused species. (ii) The Q-band of adjacently substituted species does not split appreciably, while that of the oppositely substituted species splits substantially, the extent having a parallel relationship with the ratio of long to short axes in the molecule. In general, the larger the ratio, the larger the splitting. (iii) The Q-band of oppositely dibenzo-fused and bis(dialkyl)-substituted TAP does not show explicit splitting because of the large coefficients of the carbons substituted with alkyl groups in the MOs. (iv) Interestingly, the first oxidation in adjacently and oppositely dibenzo-fused CoTAP occurs at the cobalt and ligand, respectively, although they are isomers to each other.     

Synthesis, spectroscopy, and electrochemistry of tetra-tert-butylated tetraazaporphyrins, phthalocyanines, naphthalocyanines, and anthracocyanines, together with molecular orbital calculations

Tetraazaporphyrins (TAPs), phthalocyanines (Pcs), naphthalocyanines (Ncs), and anthracocyanines (Acs) with four tert-butyl groups attached at similar positions have been synthesized, and their electronic absorption, magnetic circular dichroism (MCD), IR, and voltammetric properties were studied and interpreted with the help of quantum-mechanical calculations. Through the preparation of a series of compounds with the same number of the same substituent, the effects of the increase in the size of the ring system were clearly derived. The main results may be summarized as follows. 1) The Q band shifts to longer wavelength and its intensity increases, but with decreasing degree of change with increasing molecular size. If the size of the effect of benzene directly fused to the TAP skeleton is set at unity, the effects of the second and third benzene units are roughly 0.8 and 0.5, respectively. 2) The splitting of the Q bands in metal-free compounds decreases with increasing molecular size, so that the Q bands of H2Nc and H2Ac appear as single bands. 3) The magnitude of the orbital angular momentum of the excited state of the ligand decreases with increasing molecular size. 4) Interestingly, the ring current, as judged from the positions of pyrrole proton signals in the 1H NMR spectrum, appears to decrease with increasing molecular size. 5) The first reduction potential becomes less negative, but only slightly, whereas the first oxidation potential shows a marked shift to less positive values with increasing molecular size, indicating that the HOMO destabilizes significantly as the molecule becomes larger. 6) In 5), the extent of the HOMO destabilization with molecular size differs depending on the central metal, so metals producing smaller destabilization effects can allow larger macrocycles. Of the metals studied, the most effective is cobalt, and the practical size limit is represented by the Acs. 7) The IR spectra become simpler the larger the molecule, and the main bands were assigned by DFT calculations. 8) The trend in experimentally determined redox potentials and electronic absorption and MCD spectra were reasonably reproduced by MO calculations using the ZINDO/S Hamiltonian. 9) EPR data for several metallocomplexes are also reported.     

Ab initio molecular orbital calculations

A series of non-empirical calculations on furan, pyrrole and 1,2,5-oxadiazole are reported in which the effect of polarisation functions added to the minimal 7s 3p basis on each atom is studied. The effect on these planar molecules is largely through the rather than the-system. A comparison with the results of work with scaled functions is reported. Both series are shown to lead to much improved agreement with the electron spectroscopy energy levels. The effect on the dipole moments of these changes in basis is more variable but, with the exception of furan, the agreement with experiment is improved in the present method.

---

Zusammenfassung Für die Moleküle Furan, Pyrrol und 1,2,5-Oxadiazol wurde eine Reihe von nichtempirischen Rechnungen durchgeführt, in denen der Einfluß von zusätzlichen Polarisationsfunktionen zur minimalen 7s 3p-Basis an jedem Atom untersucht wird. Die Ergebnisse werden mehr durch die Art der Beschreibung des Systems der-Elektronen als durch diejenige der-Elektronen beeinflußt. Ein Vergleich mit den Ergebnissen bei Verwendung skalierter Funktionen wird durchgeführt. Beide Reihen von Ergebnissen zeigen eine verbesserte Übereinstimmung zu den Energiemeßwerten der Elektronenspektroskopie. Die Änderungen des berechneten Dipolmoments bei derartigen Basisvariationen sind größer als bei früheren Methoden. Die Übereinstimmung mit dem Experiment wird, mit Ausnahme von Furan, jedoch verbessert.

     

Ab Initio molecular orbital calculations

Linear combinations of Gaussian orbitals were contracted to minimal basis sets. The binding energies (B.E.) obtained for the three compounds furan, pyrrole and 1,2,5-oxadiazole are 0.75, 0.84 and 0.26 a.u. respectively. Correlation of these figures and those obtained in related calculations leads to the relationship (B.E.)_exp.=0.7347 (B.E.)_calc.+633 (Kcal/mole). The photoelectron spectra of these compounds are extended and correlated with the orbital energies; the -electron excitations are given by (I.P.)_exp.=1.00 (I.P.)_calc.–2.20 eV. Mulliken population analyses give dipole moments in reasonable agreement with experiment.

---

Zusammenfassung Linearkombinationen von Gauß-Orbitalen wurden zu minimalen Basissätzen kontrahiert.Die Bindungsenergien (B.E.) für die drei Komponenten Furan, Pyrrol und 1,2,5-Oxadiazol haben die Werte: 0,75, 0,84 und 0,26 a.u. Setzt man diese Werte zu den berechneten in Beziehung, so erhält man die Gleichung: (B.E.)_exp.=0,7347 (B.E.)_calc.+633 (Kcal/Mol).Die Photoelektronenspektren dieser drei Komponenten werden erweitert und mit den Orbitalenergien korreliert; die -Elektronen-Anregungsenergien werden durch die Beziehung: (I.P.)_exp. =1.00 (I.P.)_calc.–2,20 eV gegeben. Mulliken-Populations-Analysen ergeben die Dipolmomente in bemerkenswerter Übereinstimmung mit experimentellen Werten.

     

Semiempirical molecular orbital calculations on boranes

Traditional Pariser-Parr-Pople and variable electronegativity calculations have been carried out on C₆H₅B(OR)₂ and p-CH₃OC₆H₄B(OR)₂, and the results compared with calculations for C₆H₅BR₂. It is concluded that the VE-SCF method offers a real advantage over the simple PPP method for predicting percent charge transfer and transition intensity in cases where excited states possess substantial C.T. character. The restriction that empirically chosen parameters fit the observed transition energies and intensities of both triarylboranes and ArB(OR)₂ requires the choice of a boron VSIP greater than 2.0 eV in the fixed parameter procedure of the usual PPP-SCF-CI method for these molecules. Observed transitions in C₆H₅B(OR)₂ correlate with ¹ L _b, ¹ L _a, ¹ B _b, whereas the first absorption maximum of (C₆H₅)₃B is assigned to C.T. (¹ A ₁¹ A ₁) local C _2v symmetry.

---

Zusammenfassung PPP- und VE SCF-Rechnungen wurden für C₆H₅B(OR)₂ und p-CH₃OC₆H₄(OR)₂ durch- geführt, und die Ergebnisse wurden mit denjenigen für C₆H₅BR₂ verglichen. Es kann der Schluß gezogen werden, daß die VE SCF-Methode einen Vorteil gegenüber der einfachen PPP-Methode bietet, um den prozentualen Charge Transfer und Übergangsintensitäten in Fällen zu bestimmen, in denen die angeregten Zustände einen wesentlichen C.T.-Charakter besitzen. Die Bedingung, daß die empirisch gewählten Parameter den beobachteten Übergangsenergien und -intensitäten von sowohl Triarylboranen als auch ArB(OR)₂ angepaßt sein sollen, erfordert die Wahl eines Bor-VSIP größer als 2,0 eV im Rahmen der üblichen Parametrisierung der PPP-SCF-CI-Methode. Beobachtete Über-gänge in C₆H₅B(OR)₂ korrelieren mit ¹ L _b, ¹ L _a, ¹ B _b, wogegen das erste Absorptionsmaximum des (C₆H₅)₃B einem C.T.-Übergang (¹ A ₁¹ A ₁) lokaler C_2v -Symmetrie zugeordnet wird.

---

Résumé Des calculs traditionnels Pariser-Parr-Pople et des calculs d'électronégativité variable ont été effectués sur C₆H₅B(OR)₂ et p-CH₃OC₆H₄B(OR)₂ avec comparison aux résultats obtenus pour C₆H₅BR₂. La conclusion est que la méthode VE-SCF offre un réel avantage sur la méthode PPP simple en ce qui concerne la prédiction du transfert de charge et de l'intensité de transition pour les états excités possédant un net caractère de transfert de charge. La restriction selon laquelle les paramètres empiriques doivent permettre de reproduire les énergies de transition et les intensités des deux triarylboranes et de ArB(OR)₂, nécessite le choix d'un potential d'ionisation de l'état de valence du bore supérieur de 2 eV à celui employé dans les méthodes ordinaires. Les transitions observées dans C₆H₅B(OR)₂ sont reliées à ¹ L _b, ¹ L _a, ¹ B _b, tandis que la première absorption de (C₆H₅)₃B est attribuée à un transfert de charge (¹ A ₁¹ A ₁) de symétrie locale C_2v.

     

Flavin enzymes: molecular orbital calculations

Molecular orbital calculations were obtained for one hundred and forty-four versions of the flavin group contained in oxidase enzymes. Ten different structures were considered and the results indicate that the flavin group changes its identity from a pi electron acceptor to a pi electron donor after reduction occurs, regardless of the inductive effect of the attached protein. Furthermore, the calculations suggest both the site for reduction and the mechanism by which it proceeds.     

Synthesis, mechanism of formation, and molecular orbital calculations of arylamidoximes

Abstract  

A simple and easy synthesis of ten arylamidoximes from arylnitriles and hydroxylamine is described. The formation of the arylamides has been observed to a much lesser extent in the present work. A new mechanism for the formation of arylamidoximes, as well as arylamides, from arylnitriles and hydroxylamine is suggested. Quantum mechanical calculations have been carried out to support this mechanism. The enthalpy of formation in conjunction with atomic charges of the reactants and intermediates helped to understand more about the generation of the products.     

Semi-empirical molecular orbital calculations for pyridinealdoximes and acetamidopyridines

Tautomerism of pyridinealdoximes and acetamidopyridines is discussed with regard to their electronic absorption spectra. The spectra of both neutral and ionic forms of the molecules are interpreted by means of the Pariser—Parr—Pople type of calculation in a satisfactory way.The stability of 2- and 4-pyridinealdoxime tautomers is investigated using the CNDO/2 method. The lactim are more stable than the lactam forms of the molecules. The molecules having the substituent group of the syn-configuration are more stable than the molecules with other configurations of the substituent.     

Self-consistent molecular orbital calculations on organoboron compounds

The Pariser-Parr-Pople method has been used to calculate the electronic structures and spectra of three methylvinylboranes. Two separate calculational models of the methyl group are considered and the agreement between observed and calculated spectral quantities is good. The reorganisation energies of these molecules are also evaluated.

---

Zusammenfassung Mit der Methode von Pariser, Pople und Parr werden Struktur und Spektren der -Elektronensysteme von drei Methylvinylboranen berechnet, ebenso ihre Reorganisationsenergien. Für die Methylgruppe werden zwei verschiedene Modelle verwendet. Die übereinstimmung zwischen berechneten und experimentellen Werten ist gut.

---

Résumé A l'aide de la méthode Pariser-Parr-Pople nous avons calculé les structures et les spectres -électroniques de trois méthylvinylboranes. Nous considérons deux modèles du groupe méthyl; les spectres observés et calculés s'accordent bien. En plus, les énergies de réorganisation de ces molécules sont évaluées.

---

---

One of us (D.R.A.) wishes to thank the S.R.C. for a maintenance grant.     

Self-consistent molecular orbital calculations on organoboron compounds

The PPP-SCMO-method is used to calculate the energies of the ground and lower excited states of triphenylborane and tri-p-tolylborane for which both planar and propellor models are considered. It is found necessary to include a large measure of configuration interaction in the excited states in order to produce satisfactory agreement with published u.v. spectra. However the calculations are not diagnostic for the detailed geometry of these compounds. The electronic spectra may be interpreted in terms of ring exciton states and interring and phenyl-boron charge-resonance states. The electron density on the central atom and the B-C bond orders are small and so the phenyl rings are but little perturbed by their bonding to boron.

---

Zusammenfassung PPP-SCMO-Rechnungen wurden für Triphenyl- und Tri-p-tolylboran durchgeführt. Ohne ausgedehnte Konfigurationenwechselwirkung erhält man keine befriedigende Übereinstimmung mit veröffentlichten UV-Spektren. Die Deutung der Elektronenspektren geschieht mit Hilfe der Begriffe der einzelnen Einganregung sowie des Ring-Ring- und des Ring-Bor-Ladungsaustausches. Ob die Molekeln in einer planaren oder einer Propeller-Konformation vorliegen, kann aufgrund dieser Rechnungen nicht entschieden werden. Bor--Ladung und B-C--Bindungsordnung sind gering; die Phenylringe werden durch ihre Bindung an Bor kaum beeinflußt.

---

Résumé La méthode SCMO-PPP a été utilisée pour calculer les énergies de l'état fondamental et des plus bas états excités du triphènylborane et du tri-p-tolylborane pour lequel on a considéré les modèles plan et en hêlice de bâteau. L'inclusion d'une interaction de configurations étendue entre états excités est nécessaire pour obtenir un accord satisfaisant avec les spectres UV publiés. Mais les calculs ne permettent pas de préciser la géométrie détaillée de ces composés. Les spectres électroniques peuvent être interprétés en termes d'états excitoniques du cycle et d'états de résonance de charge entre cycles et entre le phényl et le bore. La densité électronique sur l'atome central et les indices de liaison sur les liaisons B-C sont faibles ce qui montre que les noyaux phényliques sont peu perturbés par leur liaison au bore.

     

Self-consistent molecular orbital calculations on organoboron compounds

The electronic structures of three dihalogenophenylboranes have been investigated by the Pariser-Parr-Pople method. The agreement between the observed and calculated electronic spectra is quite good.

---

Zusammenfassung Die -Elektronen-Strukturen von drei Dihalogenphenylboranen wurden mit der PPP-Methode untersucht. Beobachtete und berechnete Elektronenspektren stimmen recht gut überein.

---

Résumé On a étudié par la méthode de Pariser-Parr-Pople les structures électroniques de trois dihalogénophenylboranes. L'accord entre les spectres électroniques observés et calculés est assez satisfaisant.

     

Aggregation mechanism of polyglutamine diseases revealed using quantum chemical calculations, fragment molecular orbital calculations, molecular dynamics simulations, and binding free energy calculations

Polyglutamine (polyQ) diseases, including Huntington’s disease (HD), are caused by expansion of polyQ-encoding repeats within otherwise unrelated gene products. The aggregation mechanism of polyQ diseases, the inhibition mechanism of Congo red, and the alleviation mechanism of trehalose were proposed here based on quantum chemical calculations and molecular dynamics simulations. The calculations and simulations revealed the following. The effective molecular bonding is between glutamine (Gln) and Gln (Gln + Gln), between Gln and Congo red (Gln + Congo red), and between Gln and trehalose (Gln + trehalose). The bonding strength is −13.1 kcal/mol for Gln + Gln, −24.4 kcal/mol for Gln + Congo red, and −12.0 kcal/mol for Gln + trehalose. In the polyQ region, both the number of intermolecular Gln + Gln formations and the total calories generated by the Gln + Gln formation are proportional to the number of repetitions of Gln. We propose an aggregation mechanism whose heat generated by the intermolecular Gln + Gln formation causes the pathogeny of polyQ disease. In our aggregation mechanism, this generated heat collapses the host protein and promotes fibrillogenesis. Without contradiction, our mechanism can explain all the experimental results reported to date. Our mechanism can also explain the inhibition mechanism by Congo red as an inhibitor of polyglutamine-induced protein aggregation and the alleviation mechanism by trehalose as an alleviator of that aggregation. The inhibition mechanism by Congo red is explained by the strong interaction with Gln and by the characteristic structure of Congo red.     

Second-row molecular orbital calculations: II. Semi-empirical calculations of dipole moments

The ability of four semi-empirical methods to predict dipole moments of molecules containing atoms in the second row of the periodic table is investigated. None of the methods is capable of consistently reproducing either magnitudes or qualitative trends; however, the CNDO method of Santry gives the best agreement overall. The original CNDO method of Santry and Segal emphasizes the importance of d orbitals to a greater extent than does the Santry method. Comparisons are presented with non-empirical results when possible.     

An efficient molecular orbital approach for self-consistent calculations of molecular junctions

To model electron transport through a molecular junction, we propose an efficient method using an ab initio self-consistent nonequilibrium Green's function theory combined with density functional theory. We have adopted a model close to the extended molecule approach, due to its flexibility, but have improved on the problems relating to molecule-surface couplings and the long-range potential via a systematic procedure for the same ab initio level as that of Green's function. The resulting algorithm involves three main steps: (i) construction of the embedding potential; (ii) perturbation expansion of Green's function in the molecular orbital basis; and (iii) truncation of the molecular orbital space by separating it into inactive, active, and virtual spaces. The above procedures directly reduce the matrix size of Green's function for the self-consistent calculation step, and thus, the algorithm is suitable for application to large molecular systems.     

Synthesis,characterization and electrochemistry of a new organosoluble metal-free and metallophthalocyanines

4-[2-(Phenylthio)ethoxy]phthalonitrile 3 was synthesized by nucleophilic displacement of nitro group in 4-nitrophthalonitrile with 2-(phenylthio)ethanol 1. The metal-free phthalocyanine 4 was prepared by the reaction of a dinitrile monomer with 2-(dimethylamino)ethanol. Ni(II), Co(II), Cu(I) phthalocyanines 5, 7, 8 were prepared by reaction of the dinitrile compound with the chlorides of Ni(II), Co(II), Cu(I) in DMAE. Zn(II) phthalocyanine 6, was prepared by reaction of the dinitrile compound with the acetates of Zn(II) in DMAE. Electrochemical behaviours of novel metal-free, Co(II) and Zn(II) phthalocyanines were investigated by cyclic voltammetry, potential differential pulse voltammetry techniques. The new compounds were characterized by a combination of IR, ¹H NMR, ¹³C NMR, UV–Vis, elemental analysis and MS spectral data.     

Second row molecular orbital calculations: III. Semi-empirical calculations of geometries

The ability of four semi-empirical methods to predict geometries of molecules containing atoms in the second row of the periodic table is investigated for about 80 molecules. Non-empirical, minimal basis set calculations, with and without optimization of valence orbital exponents, are carried out for a number of diatomic molecules. While none of the methods are capable of predicting geometries with an accuracy comparable to the first row parametrization, the SPD' method of Santry and the related INDO method of Benson and Hudson appear to be the most consistent. The ab initio calculations do not suffer from the drawbacks exhibited by the latter two semi-empirical methods. From this it is concluded that the failure of such methods lies in the parametrization rather than in the use of a minimal basis set.     

Synthesis and electrochemistry of new octa-substituted metal-free and metallophthalocyanines

The synthesis and characterization of metal-free (H₂-Pc) and metal-containing (Zn, Co, and Cu) derivatives of a symmetrically octa-substituted phthalocyanine derived from 4,5-bis[2-(phenylthio)ethoxy]phthalonitrile were carried out by microwave irradiation. The electrochemical properties of the metal-free phthalocyanine 4 and metallophthalocyanine complexes 5 and 6 were investigated by cyclic voltammetry and differential pulse voltammetry. We have previously investigated the electrochemical properties of the tetra substituted 2-(phenylthio)ethoxy phthalocyanines. The reduction potential of the octa-substituted metal-free phthalocyanine shifted to more negative potential as a result of the electron donating of the 2-(phenylthio)ethoxy groups on the periphery compared to those of tetra substituted. The H₂Pc and ZnPc demonstrated ligand-based electron transfer processes, while CoPc complex has a metal-based reduction process. Similar aggregation behavior was observed for octa-substituted phthalocyanines. The compounds were characterized using IR, ¹H NMR, ¹³C NMR, elemental analysis, and MS spectral data.     

Molecular conformation of bilirubin from semiempirical molecular orbital calculations

Semiempirical methods were utilized in the computation of a fully optimized structure of bilirubin. Bond lengths and bond angles obtained using either AM1 or PM3 calculations showed excellent agreement with those obtained by X-ray diffraction. This indicated that molecular orbital methods satisfactory reproduced the complex conjugation found in bilirubin. Dihedral angles of the crucial “hinge” and the dihedral angles of the propionic acid side chains agreed well with those found by X-ray diffraction. Calculated hydrogen- bond parameters (distance and angles) showed substantial differences from experimental values, probably due to inherent weakness in the parameterization of the molecular orbital techniques. Conformational studies were carried out using AM1 by rotating the C9? C10 bond in 5° increments showed that the most stable structure exhibited a minimum at about 125° and exhibited a structure similar to those postulated from X-ray and NMR experiments. The hydrogen bonds showed remarkable tenacity during rotation of the C9? C10 bond and resisted breaking until the molecule was under extreme strain. © 1992 John Wiley & Sons, Inc.