Synthesis of long Poly(dG).Poly(dC) DNA using enzymatic reaction

Non-defect Poly(dG).Poly(dC) of 500 bp (170 nm) has been synthesized by using enzymatic reactions and was characterized by its UV spectrum, showing that conjugated pi-electrons between base pairs are spread over the DNA molecule suggesting the absence of structural defects.     

On the electronic structure and conduction properties of aperiodic DNA and proteins. IV. Electronic structure of aperiodic proteins

The densities of states (DOS) of 4- and 5-component aperiodic polypeptide chains with 300 units are calculated on the ab initio level using the negative factor counting approach. The amino acid residues were glycine, serine, cysteine, asparagine and histidine. The localization of the wavefunctions belonging to the lowest lying energy levels in the conduction band region are investigated and hopping probabilities are calculated. On the basis of these results the possibility for hopping conduction in proteins is discussed under the assumption of charge transfer from DNA to the peptide chain.     

Crystalline and local vibrations of paired bases in poly(dG)-poly(dC) interacting with the h-b-1 hydrogen bond

Some types of atomic vibrations in a chain of the DNA type constructed of G-C pairs were studied. These are the atomic vibrations of the lateral groups of guanine and N(3)H(1)H(2) of cytosine connected by the hydrogen bond h-b-1 and the vibrations of the centers of masses of bases in the direction parallel to bonds h-b-i, i = 1–3. The vibrations mix partially due to the dependence of the energy of the bond h-b-1 on its length and split into two bands because of the interaction between neighboring base pairs. It was shown that the excitation of the bond h-b-1 results in the splitting off of the two local vibrations and in a small deformation of the chain in the vicinity of the pair with the localized hydrogen bond. The law of the dispersion of band vibrations, values of the split-off frequencies, and degree of poly(dG)-poly(dC) chain deformation were determined. © 1997 John Wiley & Sons, Inc.     

The electronic structure and magnetic properties of poly(m-phenylcarbene)

The electronic structure and the magnetic properties of the ferromagnetic organic polymer poly (m-phenylcarbene ) was studied by application of the unrestricted Hartree-Fock (UHF) crystal orbital (CO) method. In comparison with the restricted Hartree-Fock (RHF) result, it was revealed that the ferromagnetic state is more stable than the non-magnetic state. According to a detailed energy analysis, the stability originates from both the triplet spin configuration at the carbene centre and the delocalized π spins in an antiferromagnetic fashion over the phenyl ring.     

On the electronic structure and conduction properties of aperiodic DNA and proteins. I. Strategy and methods of investigations

The possibilites for applying the ab initio matrix block negative factor counting technique (NFC) for non-periodic nucleotide base stacks and for 4- and 5-component aperiodic model proteins are described. It is outlined how also correlation effects could be taken into account in an approximate way. After a brief summary of the basic equations of the NFC method the inverse iteration technique to study the Anderson localization of the wavefunctions belonging to the different energy levels is shortly reviewed. Also the calculation of hopping probabilities between different localization sites is sketched. Finally, the possibilites are outlined for the experiment verification of hopping conduction in proteins and (in a minor extent) in DNA, assuming the generation of free charge carriers in them through charge transfer.     

On the electronic structure and conduction properties of aperiodic DNA and proteins. III. The band structures of periodic polypeptides

In this paper the calculation of the energy band structure of periodic polypeptides using the ab initio Hartree-Fock crystal orbital method is described. Results are discussed for the twenty homopolypeptides in the β-pleated sheet configuration and for several periodic systems assuming the α-helix structure. The negative factor method in its matrix block form is used to provide density of states curve for periodic two-component polypeptides. The resulting properties of the band structure suggest that homopolypeptides and periodic more-component polyamino acids are in themselves insulators, but may become weak semiconductors if free charge carriers are generated in their valence or conduction bands, respectively, through charge transfer.     

Molecular orbital calculation of the electronic structure of poly(N-vinylcarbazole)

Energy levels and molecular orbital wave functions of π-electrons in a carbazole ring are calculated by the ω-method. The result agrees well with observed optical absorption spectra of carbazole and poly(N-vinylcarbazole) (PVCA). Molecular orbital wave functions are obtained for a PVCA chain in a 3/1 helix. The overlap integral between adjacent carbazole rings is evaluated for each molecular orbital of the ring. The result affords evidence for hole conduction in PVCA and explains the photoconductivity spectrum under high de field.     

The Fourier space restricted Hartree-Fock method for the electronic structure calculation of linear poly(tetrafluoroethylene)

Building on the pioneering work of Jean-Marie André and working in the laboratory he founded, the authors have developed a code called FT-1D to make Hartree-Fock electronic structure computations for stereoregular polymers using Ewald-type convergence acceleration methods. That code also takes full advantage of all line-group symmetries to calculate only the minimal set of two-electron integrals and to optimize the computation of the Fock matrix. The present communication reports a benchmark study of the FT-1D code using polytetrafluoroethylene(PTFE) as a test case. Our results not only confirm the algorithmic correctness of the code through agreement with other studies where they are applicable, but also show that the use of convergence acceleration enables accurate results to be obtained in situations where other widely-used codes(e.g., PLH and Crystal) fail. It is also found that full attention to the line-group symmetry of the PTFE polymer leads to an increase of between one and two orders of magnitude in the speed of computation. The new code can therefore be viewed as extending the range of electronic-structure computations for stereoregular polymers beyond the present scope of the successful and valuable code Crystal.     

First-principle calculations of the electronic properties of poly(p-phenylenevinylene), polyacetylene, and their derivatives

Results of density-functional studies of the electronic properties of poly(p-phenylene-vinylene) (PPV) and polybutadiene are presented. The calculations were performed using a single-chain, full-potential, linearized muffin-tin orbital (LMTO)-based method. In particular, we analyze the effects on the electronic properties due to the addition of substituents to the vinylene linkage. As substituents, we concentrate on cyano and amine groups. It is found that these groups induce large changes in the band structures of these systems, particularly of the bands closest to the Fermi level. Further, the effects on the band gap and on the total energy due to the bond-length alternation of the polymer backbones, are analyzed both for unsubstituted and substituted polybutadiene. It is found that both properties depend sensitively on both the substituents attached to the chain and on the precise structure of the polymer. The substituents lead to overall redistributions of the electrons and, in particular, the disubstituted PPV is found to have a large dipole moment perpendicular to the polymer axis. For disubstituted polybutadiene we find a stronger C–C bond-length alternation than for the unsubstituted compound (polyacetylene), and the results for this compound indicate that the band gap of substituted and unsubstituted PPV depends strongly on the bond-length alternation.     

Structural and electronic properties of ZrX2)and HfX2 (X=S and Se) from first principles calculations

Early transition metal dichalcogenides (TMDC), characterized by their quasi-two-dimensional layered structure, have attracted intensive interest due to their versatile chemical and physical properties, but a comprehensive understanding of their structural and electronic properties from a first-principles point of view is still lacking. In this work, four simple TMDC materials, MX(2) (M = Zr and Hf, X = S and Se), are investigated by the Kohn-Sham density functional theory (KS-DFT) with different local or semilocal exchange-correlation (xc) functionals and many-body perturbation theory in the GW approximation. Although the widely used Perdew-Burke-Ernzelhof (PBE) generalized gradient approximation (GGA) xc functional overestimates the interlayer distance dramatically, two newly developed GGA functionals, PBE-for-solids (PBEsol) and Wu-Cohen 2006 (WC06), can reproduce experimental crystal structures of these TMDC materials very well. The GW method, currently the most accurate first-principles approach for electronic band structures of extended systems, gives the fundamental band gaps of all these materials in good agreement with the experimental values obtained from optical absorption. The minimal direct gaps from GW are systematically larger than those measured from thermoreflectance by about 0.1-0.3 eV, implying that excitonic effects may be stronger than previously estimated. The calculated density of states from GW quasi-particle band energies agrees very well with photo-emission spectroscopy data. Ionization potentials of these materials are also computed by combining PBE calculations based on the slab model and GW quasi-particle corrections. The calculated absolute band energies with respect to the vacuum level indicate that that ZrS(2) and HfS(2), although having suitable band gaps for visible light absorption, cannot be used for overall water splitting as a result of mismatch of the conduction band minimum with the redox potential of H(+)/H(2).     

An approximate method of self-consistent electronic structure calculations of a crystal surface. The Ir(111) surface

The Slater approximation for atomic electron energies is employed to calculate the electronic structure of the Ir(111) surface. The results are used to estimate the shift of the 4f_7/2 level on the surface relative to its position in the volume. The electron state densities in the neighborhood of the center of the surface Brillouin zone (SBZ) are compared with photoelectronic spectra for emission normal to the Ir(111) surface. On this basis, the accuracy of this approximation is estimated. Institute of Catalysis, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 35, No. 1, pp. 17–24, January–February, 1994. Translated by O. Kharlamova     

Effect of poly(ethylene oxide) on the structure and properties of poly(vinyl alcohol)

To improve the drawability of poly(vinyl alcohol) (PVA) thermal products, poly(ethylene oxide) (PEO), a special resin with good flexibility, excellent lubricity, and compatibility with many resins, was applied, and the Fourier transform infrared spectroscopy, dynamic mechanical analysis (DMA), differential scanning calorimetry (DSC), and wide‐angle X‐ray diffraction (WXRD) were adopted to study the hydrogen bonds, water states, thermal properties, crystal structure, and nonisothermal crystallization of modified PVA. It was found that PEO formed strong hydrogen bonds with water and PVA, thus weakened the intra‐ and inter‐hydrogen bonds of PVA, changed the aggregation states of PVA chains, and decreased its melting point and crystallinity. Moreover, the interactions among PVA, water, and PEO retarded the water evaporation and made more water remain in the system to plasticize PVA. The existence of PEO also slowed down the melt crystallization process of PVA, however, increased the nucleation points of system, thus made more and smaller spherulites formed. The weakened crystallization capability of PVA and the lubrication of PEO made PVA chains to have more mobility under the outside force and obtain high mechanical properties. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 1946–1954, 2010     

The electronic structure of polymers by the FSGO (Floating Spherical Gaussian Orbital) method

Non-empirical band-structure calculations have been performed on polyethylene using two basis sets introduced by Christoffersen. Both basis sets had to be optimised with respect to the carbon-carbon framework bond in order to yield solutions within the nearest-neighbour approximations. The valence bands of polyethylene are well reproduced by both basis sets whilst the conduction bands are only in fair agreement with those produced by conventional gaussian calculations. The use of the unsplit basis set was considered unsatisfactory for the representation of the core bands. The effect of increasing the number of interacting unit cells on the energy terms is discussed. Some of the energy terms converge when five unit cells are used and almost all of the terms reach a constant value when nine unit cells are employed.     

Quantum chemical investigation of the electronic structure of poly(2,4-dioxocyclobuta-1,3-diylidene)

The electronic structure of poly(2,4-dioxocyclobuta-1,3-diylidene) molecule is calculated by the semiempirical CNDO/S3 method. The calculated Wiberg indices and the additive occupancies of interatomic bonds determine the structural formula, which includes the C=C and C=O conjugated double bonds and corresponds to the name of the compound. Polarization of C=O bonds and πelectron conjugation do not lead to a zwitterionic structure with positive aromatic fourmembered cycles. The indices and occupancies of carboncarbon bonds 1– 3 and 2– 4 are σelectronic, negative, and negligibly small. The band structure corresponds to strong electronaccepting properties of the polymer; the MO of the bottom of the lowlying vacant band contains 2pπorbitals of all atoms of the compound. The occupied π-electronic bands do not overlap, and their widths are relatively small. Translated fromZhurnal Strukturnoi Khimii, Vol. 39, No. 5, pp. 781–786, September–October, 1998.     

X-ray spectral and quantum chemical analyses of the electronic structure of poly(monofluorocarbon)

The electronic structure of poly(monofluorocarbon) has been studied by X-ray spectral and quantum chemical methods. Calculations were performed in terms of the MNDO method, with the fluorographite layer modeled by clusters of different sizes. The high-resolution CK_a and FK_a spectra have been obtained; the calculated spectra are consistent with the experimental ones. It has been shown that carbon and fluorine are bonded mainly through the σ bonds. The p orbitals of fluorine atoms that are perpendicular to the C-F bond are not involved in the chemical bond, while the transitions from the molecular orbitals consisting of these p orbitals are responsible for the main maximum in the FK_a spectrum. Deceased. Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 4, pp. 630–635, July–August, 1995. Translated by I. Izvekova     

Modification of the electrochemical and electronic properties of electrogenerated poly(3,4-ethylenedioxythiophene) by hydroxymethyl and oligo(oxyethylene) substituents

Ethylenedioxythiophene (EDOT) derivatives with hydroxymethyl and oligo(oxyethylene) groups covalently attached at the ethylenedioxy bridge have been synthesized. The hydroxymethyl group considerably increases the ability of EDOT to electropolymerize in water and the electroactivity of the polymer in aqueous media. The electrochemical and optical properties of the oligo(oxyethylene)-substituted polymer reveal a negative shift of the oxidation potential and a significant enhancement of the effective conjugation length with a 0.10 eV decrease of the bandgap. The optical spectra of the polymer undoped in the presence and absence of oxygen indicate a high sensitivity of the polymer towards molecular oxygen, suggesting possible spontaneous doping by molecular oxygen.     

First-principle calculations on the structures and electronic properties of the CO-adsorbed (SnO2)2 clusters

To clear the adsorption site of CO on the surface of the nanosized SnO₂ film, the structures, stability, and electronic characteristics of the CO-adsorbed (SnO₂)₂ clusters have been investigated by using PW91 functional. The more stable configurations of these CO(SnO₂)₂ clusters derive from CO are adsorbed on the lower energy excited-state (SnO₂)₂ clusters rather than on the ground-state (SnO₂)₂ clusters. The calculated adsorption energies for CO on the lower energy excite-state (SnO₂)₂ clusters are up to 1.363–1.454 eV which is transferred from physical adsorption to chemical adsorptions. CO adsorption increases the kinetic stability and decreases the conductivity of the lower energy excited-states (SnO₂)₂ clusters.

     

Investigation of the electronic spectra and excited-state geometries of poly(para-phenylene vinylene) (PPV) and poly(para-phenylene) (PP) by the symmetry-adapted cluster configuration interaction (SAC-CI) method

The symmetry-adapted cluster-configuration interaction (SAC-CI) method has been used to investigate the optical and geometric properties of the oligomers of poly(para-phenylene vinylene) (PPV) and poly(para-phenylene) (PP). Vertical singlet and triplet absorption spectra and emission spectra have been calculated accurately; the mean average deviation from available experimental results lies within 0.2 eV. The chain length dependence of the transition energies has been improved in comparison to earlier TDDFT and MRSDCI calculations. The present analysis suggests that conventional TDDFT with the B3LYP functional should be used carefully, as it can provide inaccurate estimates of the chain length dependence of the excitation energies of these molecules with long pi conjugation. The T1 state was predicted to be at a lower energy, by 1.0-1.5 eV for PPV and by 0.9-1.7 eV for PP, than the S1 state, which indicates a localized T1 state with large exchange energy. By calculating the SAC-CI electron density difference between the ground and excited states, the geometry relaxations due to excitations can be analyzed in detail using electrostatic force theory. For trans-stilbene, the doubly excited 21Ag state was studied, and the calculated transition energy of 4.99 eV agrees very well with the experimental value of 4.84 eV. In contrast to previous ab initio calculations, we predict this doubly excited 21Ag state to lie above the 11Bu state.     

Calculation of the electronic structure of molecules by the method of two electron orbitals (geminals)

Journal of Structural Chemistry -