M. Seel

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

Abstract 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.

Quantum chemistry of polymers--solid state aspects

Towards Specific AB Initio Programs for Polymer Calculations.- Theoretical Interpretation of Valence XPS Spectra of Stereoregular Organic Polymers.- AB Initio Studies on the Structure and Phonon Spectra of Simple Polymers.- Theory of Excitons in Organic Solids.- Theory of the Electronic Structure and Optical Properties of Organic Solids: Collective Effects.- Calculation of the Mechanical and Optical Properties of Polyethylene Including Electron Correlation Effects.- Synthesis and Properties of Conducting Bridged Macro-Cyclic Metal Complexes.- Carrier Generation, Recombination, and Transport in Organic Crystals.- Electrical Transport Properties of Polyacetylene and Related Compounds.- The Preparation and Properties of Ordered and Disordered Diacetylene Polymers.- Doped Conjugated Polymers: Theory and Experiment.- Resonant Interaction Between Laser Pulses and Surface Layers.- Energy Transfer and Molecular Weight Effects on Polymer Luminescence.- Calculational Methods for Disordered Quasi-One-Dimensional Systems.- Effect of Local Perturbations on the Electronic Structure of Organic Polymers.- Electronic Localization and Delocalization in Organic Metals and Semiconductors.- Electronic Structure of Highly Conducting Polymers and Biopolymers Solid State Aspects.- Large Scale AB Initio Band Structure Calculations of Polynucleotides and Polypeptides.- Index of Authors.- Index of Subjects.

Electronic spectra of aperiodic protein model chains

Abstract Energy eigenvalue spectra for large disordered two-component chains of length 1000 respectively 10000 units containing glycine and alanine residues are calculated in the tight-binding approximation using the direct numerical approach. Starting from the valence band of polyglycine it is shown how alanine residues produce localized states and influence and destroy the band structure of the host system. These preliminary results indicate that the band description is inappropriate for proteins with different side groups and that charge transport is most probably best described not by a band type but by a hopping type conduction mechanism.

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

Abstract Electronic density of states (DOS) curves of single stranded periodic and aperiodic DNA base stacks (in B conformation) and of a fragment of a human gene, obtained with the help of ab initio matrix block negative factor counting (NFC) method are presented. The calculated large values of band gap obtained for these systems rule out the possibility of intrinsic conduction in them. It is also found that in contrast to the corresponding period systems, the peaks in the DOS curves of aperiodic systems are broader. The probable effects of these changes in the DOS on the possibility of hopping conduction in DNA are also discussed.

Electronic structure of high pressure phase of AlN

Results of ab initio Hartree–Fock calculations for the electronic structure of aluminum nitride in the (high-pressure) rocksalt phase are reported. In the rocksalt phase, the calculated lattice constant is 3.982 A with the bulk modulus of 329 GPa. The band structure is predicted to be indirect at the X point with a gap of 8.9 eV. In this phase, the bonding is shown to be essentially ionic between Al and N. The direct gap shows a stronger linear dependence on pressure with a pressure derivative of 68 meV/GPa compared to that of the indirect gap with a pressure derivative of 31.7 meV/GPa.

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

Abstract 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.

The high-pressure phase transitions of silicon and gallium nitride: a comparative study of Hartree - Fock and density functional calculations

All-electron Hartree - Fock and density functional calculations are performed to study the high-pressure phase transitions in gallium nitride and silicon within the framework of the linear combination of atomic orbitals using the Gaussian basis sets. Under high pressure, GaN makes a transition from the wurtzite (semiconducting) to the rock-salt (semiconducting) phase, whereas Si makes a transition from the cubic (semiconducting) to the -tin (metallic) phase. The calculated results suggest that the lattice constants and the bulk moduli can be accurately described by both the methodologies for GaN and Si. Furthermore, both the calculations yield a phase transition pressure for GaN which is in reasonable agreement with the experimental data. However, the transition pressure for Si calculated in the closed-shell (restricted) Hartree - Fock approximation differs significantly from the one calculated using the density functional theory and the experimental data. This is primarily due to the fact that the energy difference between a semiconducting and a metallic state of Si is not well produced in the closed-shell Hartree - Fock approximation.

Influence of substitutional impurities on soliton dynamics in trans‐polyacetylene

For different chains of trans‐polyacetylene with various substituents the equations of motion of the coupled electron–phonon system are integrated within the Su–Schrieffer–Heeger model. NH+, N, and O+ as isoelectronic substitutions for a CH group as well as the effect of an NH and a CO group are investigated. The calculations for the time evolution of an end‐generated kink show that neutral solitons can pass a nitrogen atom and an oxygen ion, but not an NH+, NH, or CO group. The negatively charged soliton is not able to pass any of the investigated substitutions. The CO unit, which is of special interest in the light of recent experimental results for acetylene–CO–copolymers with similar properties as trans‐polyacetylene, represents a trap for both neutral and negatively charged kinks and a repulsive barrier for a positively charged kink. The limitations of the soliton model are discussed.

The role of self-consistency in quantum-mechanical studies of disordered quasi-one-dimensional systems

Abstract A self-consistent-field numerical approach is proposed to calculate the density of states for large quasi-one-dimensional systems. The initial Fock matrix is built up from blocks of small-cluster calculations. A part of the density matrix constructed from a selected number of occupied orbitals is kept constant during the iteration. Illustrative numerical calculations on model polymers are presented.

Soliton trapping and repulsion due to a co-group in trans-polyacetylene

Abstract For a chain of trans-polyacetylene with one CO substitution the equations of motion of the couples electron phonon system are integrated within the Su-Schrieffer-Heeger model. The calculations for the time-evolution of an end generated kink show that a -C(=O)- unit presents a trap for both a neutral and a negatively charged kink and a repulsive barrier for a positively charged kink. The limitations of the soliton model are discussed.