The electronic structure of periodic protein models

The energy band structures of a two-dimensional polyformamide network have been calculated with the aid of the CNDO/2 and MINDO/2 crystal orbital method in the first neighbour's interactions approximation. For comparison also one-dimensional polyformamide chains have been computed with the same methods. The features of the obtained band structures are discussed.

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Zusammenfassung Es wurden die Energiebandenstrukturen eines zweidimensionalen Polyformamid-Netzwerkes in einer Näherung, die die Wechselwirkung der ersten Nachbarn berücksichtigt, mit Hilfe der CNDO/2 und MINDO/2 Kristallorbital-Methoden berechnet. Zum Vergleich wurden auch eindimensionale Polyformamid-Ketten unter Verwendung derselben Methoden berechnet. Die Eigenschaften der erhaltenen Bandenstrukturen werden diskutiert.

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Résumé Calcul de la structure des bandes d'énergie d'un réseau bidimensionnel de polyformamide à l'aide des méthodes d'orbitales cristallines CNDO/2 et MINDO/2 dans l'approximation d'interaction des premiers voisins. A titre de comparaison les chaînes unidimensionnelles de polyformamide ont été calculées avec les mêmes méthodes. Discussion des caractéristiques des structures de bande obtenues.

     

The electronic structure of periodic protein models

The all-valence electron energy band structure has been calculated for β polyglycine in the parallel-chain pleated sheet conformation. The anisotropy of the charge carrier effective masses and mobilities have been investigated. The direction of the polypeptide backbone is found theoretically to be more favourable for electrical conduction than that of the hydrogen bonds.     

Molecular and electronic structure of the dehydroalanine derivatives : The cyclic dipeptide

The molecular structure of the cyclic dipeptide of dehydroalanine(3,6-dimethylene-piperazine-2,5-dione) has been determined from three-dimensional X-ray data. C₆H₆N₂O₂ is monoclinic, space group P2₁, with Z = 2 in a cell of dimensions a = 5.261(3), b = 13.617(4), c = 4.570(3) Å, β = 104.58(5)°. Molecules are planar and they are linked in ribbons by two hydrogen bonds through the amido-groups. The vapour-phase He(I) and He(II) photoelectron spectra are also presented. The assignments are proposed by comparison with simpler related molecules and supported by ab initio calculations. Analogies with respect to the photoelectron results of the corresponding acyclic compound N-acetyldehydroalanine are discussed.     

Halogen versus halide electronic structure

Halide anions X-are known to show a decreasing proton affinity(PA),as X descends in the periodic table along series F,Cl,Br and I.But it is also well-known that,along this series,the halogen atom X becomes less electronegative(or more electropositive).This corresponds to an increasing energy of the valence np atomic orbital(AO) which,somewhat contradictorily,suggests that the electron donor capability and thus the PA of the halides should increase along the series F,Cl,Br,I.To reconcile these contradictory ...     

Pharmacokinetics of Py-Im polyamides depend on architecture: cyclic versus linear

The pharmacokinetic properties of three pyrrole-imidazole (Py-Im) polyamides of similar size and Py-Im content but different shape were studied in the mouse. Remarkably, hairpin and cyclic oligomers programmed for the same DNA sequence 5'-WGGWWW-3' displayed distinct pharmacokinetic properties. Furthermore, the hairpin 1 and cycle 2 exhibited vastly different animal toxicities. These data provide a foundation for design of DNA binding Py-Im polyamides to be tested in vivo.     

Molecular and electronic structure of the dehydroalanine derivatives: The cyclic dipeptide of dehydrophenylalanine

The molecular structure of the cyclic dipeptide of dehydrophenylalanine [3,6-bis(phenylmethylene)-piperazine-2,5-dione] has been determined from three dimensional X-ray data. C₁₈H₁₄ N₂O₂ is monoclinic, space group C2/$\text{c}$, with Z = 12 in a cell of dimensions $\text{a}$=4Ø.774(1), $\text{b}$=6.237(2), $\text{c}$=17.731(3) Å, β=107.76(5)°. Molecules are approximately planar as far as the piperazinedione ring is concerned, and they are linked in two series of hydrogen-bonded ribbons. The vapour phase He(I) and He(II) photoelectron spectra are also presented. Their assignment is proposed by comparison with related molecules and supported by semiempirical quantum mechanical calculations. Analogies and differences with respect to the photoelectron results of the cyclic dipeptide of dehydroalanine and corresponding acyclic compounds are discussed.     

The colors of polydiacetylenes: a commentary

Polydiacetylenes (PDA) can take several colors, mostly "red" and "blue", and blue-to-red color transitions are usually considered as transitions from a well ordered state to a disordered one. Recent work on single isolated PDA chains shows that this is not correct: red chains can be quasi-perfect quantum wires. The transition is between two different chain conformations, and each may, or may not, be perfectly ordered. Disorder, when it occurs, is a side-product of the transformation.     

The electronic structure of peracids. Functional models for cytochrome p-450

An extensive set of ground state ab initio and semiempirical molecular orbital calculations has been performed on both peroxytrifluoroacetic and peroxyacetic acids. The equilibrium geometry of peroxyacetic acid was calculated with the STO-3G and MINDO/3 methods, and peroxide rotational barriers for both peracids were obtained with STO-3G and PCILO. Extended basis set calculations with the 6-31G^** basis were performed for both peracids to compare the electronic structures of these two compounds. Electrostatic potential maps in the region of the peroxide bonds of both peracids were also calculated using INDO wavefunetions. These results are discussed with respect to the enhanced reactivity of peroxytrifluoracetic acid relative to peroxyacetic acid and the nature of the oxygen electrophilicity in these compounds and by analogy in cytochrome P-450, for which peroxytrifluoroacetic acid is considered to be an effective chemical model.     

On the molecular structure of uranium dicarbide: T-shape versus linear isomers

A theoretical study of the molecular structure of uranium dicarbide has been carried out employing DFT, coupled cluster, and multiconfigurational methods. A triangular species, corresponding to a (5)A(2) electronic state, has been found to be the most stable UC(2) species. A triplet linear CUC species, which has been observed in recent infrared spectroscopy experiments, lies much higher in energy. A topological analysis of the electronic density has also been carried out. The triangular species is shown to be in fact a T-shape structure with a U-C interaction which can be considered to be a closed-shell interaction.     

The electronic structure of benzvalene : Photoelectronspectroscopic studies

The photoelectron(PE)spectrum of tricyclo[3.1.0.0^2,6] hex-2-ene(benzvalene 1) has been recorded. The first four bands in the PE spectrum of 1 can be assigned to transitions to ²B₂, ²A₁, ²A₂ and ²B₁ states of 1¹. This assignment is discussed in terms of the results of semiempirical and ab initio calculations on 1. Furthermore the highest occupied MO's of 1 are derived qualitatively from an interaction diagram between a distorted bicyclobutane and an ethylene moiety.     

The electronic structure of dibenzotetrathiafulvalene

The electronic polarization spectrum in stretched polyethylene film and the photoelectron spectrum of dibenzotetrathiafulvalene are reported. The spectra are compared with those of tetrathiafulvalene, and discussed in terms of semi-empirical calculations.     

The electronic structure of C-nitroso-compounds

The electronic absorption spectra of nitroso-methane, nitroso-ethylene and nitroso-benzene were investigated by the PPP and CNDO/2 method. The unusual energy level spacing may lead to an interesting photophysical behaviour making fluorescence from the second excited singlet state of aromatic nitroso-compounds conceivable. The source of intensity of the forbidden low-frequency transition at 13 kK in nitroso-benzene is also discussed.     

The electronic structure of tetra-azapentalene

The ultraviolet absorption spectra in various solvents and a study of the electronic structure of 1, 3a, 4, 6a-tetra-azapentalene are reported. The ASMO-SCF-CI method in the Pariser-Parr-Pople approximation has been used with different alternatives for evaluating the _pq and the (A: pp) integrals. Only two out of the six different set of calculations have given an acceptable prediction of the first * transition; moreover the introduction of penetration integrals is found necessary for a correct prediction of the sequence of the N-N bond lengths based on the sequence of the bond orders.

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Zesummenfassung Die UV-Absorptionsspektren von 1, 3a, 4, 6a-Tetraazapentalen in verschiedenen Lösungsmitteln werden angegeben. Die Elektronenstruktur dieser Verbindung wurde mittels SCF-CI-Rechnungen mit den Näherungen von Pariser-Parr-Pople and verschiedenen Sätzen von _pq und (A: pp)-Integralen ermittelt, wobei zwei der sechs Sätze einen annehmbaren -*-Über-gang liefern. Sollen sich die Werte der N-N-Bindungsordnungen in Übereinstimmung mit denentsprechenden Bindungslängen ergeben, so können die Durchdringungsintegrale nicht vernachlässigt werden.

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Resume Les spectres d'absorption ultraviolet dans des differents solvents et un étude sur la structure électronique du 1, 3a, 4, 6a-tetra-azapentalene sont exposés. La méthode ASMO-SCF-CI dans l'approximation de Pariser-Parr-Pople, a été employée avec plusieures alternatives pour 1e calcul des intégrales _pq et (A: pp). Entre les six differents calculs accomplis, deux seulement ont donné une prédiction acceptable pour la prémière transition* On a trouvé que pour une correcte prédiction de la séquence des longueures N-N sur la base des indices de liaison il faut introduir dans les calculs les integrales de pénetration.

     

PNA versus DNA: effects of structural fluctuations on electronic structure and hole-transport mechanisms

The effects of structural fluctuations on charge transfer in double-stranded DNA and peptide nucleic acid (PNA) are investigated. A palindromic sequence with two guanine bases that play the roles of hole donor and acceptor, separated by a bridge of two adenine bases, was analyzed using combined molecular dynamics (MD) and quantum-chemical methods. Surprisingly, electronic structure calculations on individual MD snapshots show significant frontier orbital electronic population on the bridge in approximately 10% of the structures. Electron-density delocalization to the bridge is found to be gated by fluctuations of the covalent conjugated bond structure of the aromatic rings of the nucleic bases. It is concluded, therefore, that both thermal hopping and superexchange should contribute significantly to charge transfer even in short DNA/PNA fragments. PNA is found to be more flexible than DNA, and this flexibility is predicted to produce larger rates of charge transfer.     

Electronic structure of the polydiacetylenes: effect of bond length variations in a model system

SCF Xα calculations are reported for a cyclic molecule whose bonding sequence is a model for the backbone bonding sequence in the polydiacetylenes. The electronic structure of the model molecule, with particular emphasis on the two lowest energy optical transitions, is determined in conjunction with a systematic variation in bonding sequence. Transition energies are in fair agreement with experiment for polydiacetylenes with the acetylene linkage,

, and for the model molecule in solution. The same analysis predicts a substantial red shift on going to the butatriene linkage,

, whereas a small blue-shift is observed experimentally. This qualitative disagreement between theory and experiment is attributed to the inability of the present scheme to represent excitonic excitations and/or the neglect of interchain interactions. The transition energies from the SCF Xα treatment can be satisfactorily represented in a simple Hückel model with the following resonance integral-bond length relationship:β_ij = 67.28 exp (-d_ij/0.424) eV.