Special Issue "Electronic Structure, Carrier Transfer and Transport in Polymers and Biopolymers"

A special issue of Materials (ISSN 1996-1944).

Deadline for manuscript submissions: 31 March 2022.

Special Issue Editor

Ass. Prof. Dr. Constantinos Simserides
E-Mail Website
Guest Editor
Department of Physics, National and Kapodistrian University of Athens, Athens, Greece
Interests: biophysics; spintronics; quantum optics; nanostructures; ab initio calculations

Special Issue Information

Dear Colleagues,

Today, many members of the scientific community are interested in charge transfer and transport in organic and biological systems such as carbon nanotubes, carbynes, porphyrins, proteins, enzymes, π-conjugated systems, nucleic acids (DNA, RNA), chromophores, to name just a few. Their electronic structure and their charge transfer and transport properties are being studied with the aim to understand their biological functions and their potential applications in nanotechnology. Transport implies the use of electrodes between which electric voltage is applied. Transfer means that the electron or hole, created, e.g., by reduction or oxidation at a specific site, moves to more favorable sites. Usually, a donor and an acceptor are connected at the ends of a system, which acts as a bridge. For example, DNA can be used as a molecular wire for charge transfer and transport. Favoring geometries and base-pair sequences, the use of non-natural bases, isomers and tautomers of the bases, among others, are being investigated. Structural fluctuation is another important factor which influences carrier movement through these systems. Charge transfer is, for example, relevant in DNA damage and repair and in discrimination between pathogenic and nonpathogenic mutations at an early stage. Charge transport can be used to probe DNA of different origin or organisms, mutations, and diseases. Charge transport in damaged DNA and under structural fluctuations has also been investigated.

In this Special Issue of Materials, "Electronic Structure, Carrier Transfer and Transport in Polymers and Biopolymers", researchers are invited to submit their recent work on this and related subjects. We hope that this issue will become a fruitful forum for all of us and other interested colleagues. We welcome full papers, communications, and reviews.

Keywords

  • charge transfer
  • charge transport
  • polymers
  • biopolymers
  • carbon nanotubes
  • carbynes
  • porphyrins
  • proteins
  • enzymes
  • π-conjugated systems
  • nucleic acids
  • DNA
  • RNA
  • chromophores

Published Papers (2 papers)

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Research

Open AccessArticle
Base-Pairs’ Correlated Oscillation Effects on the Charge Transfer in Double-Helix B-DNA Molecules
Materials 2020, 13(22), 5119; https://doi.org/10.3390/ma13225119 - 13 Nov 2020
Cited by 1 | Viewed by 669
Abstract
By introducing a suitable renormalization process, the charge carrier and phonon dynamics of a double-stranded helical DNA molecule are expressed in terms of an effective Hamiltonian describing a linear chain, where the renormalized transfer integrals explicitly depend on the relative orientations of the [...] Read more.
By introducing a suitable renormalization process, the charge carrier and phonon dynamics of a double-stranded helical DNA molecule are expressed in terms of an effective Hamiltonian describing a linear chain, where the renormalized transfer integrals explicitly depend on the relative orientations of the Watson–Crick base pairs, and the renormalized on-site energies are related to the electronic parameters of consecutive base pairs along the helix axis, as well as to the low-frequency phonons’ dispersion relation. The existence of synchronized collective oscillations enhancing the π-π orbital overlapping among different base pairs is disclosed from the study of the obtained analytical dynamical equations. The role of these phonon-correlated, long-range oscillation effects on the charge transfer properties of double-stranded DNA homopolymers is discussed in terms of the resulting band structure. Full article
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Open AccessArticle
Hole Transfer in Open Carbynes
Materials 2020, 13(18), 3979; https://doi.org/10.3390/ma13183979 - 08 Sep 2020
Cited by 1 | Viewed by 488
Abstract
We investigate hole transfer in open carbynes, i.e., carbon atomic nanowires, using Real-Time Time-Dependent Density Functional Theory (RT-TDDFT). The nanowire is made of N carbon atoms. We use the functional B3LYP and the basis sets 3-21G, 6-31G*, cc-pVDZ, cc-pVTZ, cc-pVQZ. We also utilize [...] Read more.
We investigate hole transfer in open carbynes, i.e., carbon atomic nanowires, using Real-Time Time-Dependent Density Functional Theory (RT-TDDFT). The nanowire is made of N carbon atoms. We use the functional B3LYP and the basis sets 3-21G, 6-31G*, cc-pVDZ, cc-pVTZ, cc-pVQZ. We also utilize a few Tight-Binding (TB) wire models, a very simple model with all sites equivalent and transfer integrals given by the Harrison ppπ expression (TBI) as well as a model with modified initial and final sites (TBImod) to take into account the presence of one or two or three hydrogen atoms at the edge sites. To achieve similar site occupations in cumulenes with those obtained by converged RT-TDDFT, TBImod is sufficient. However, to achieve similar frequency content of charge and dipole moment oscillations and similar coherent transfer rates, the TBImod transfer integrals have to be multiplied by a factor of four (TBImodt4times). An explanation for this is given. Full geometry optimization at the B3LYP/6-31G* level of theory shows that in cumulenes bond length alternation (BLA) is not strictly zero and is not constant, although it is symmetrical relative to the molecule center. BLA in cumulenic cases is much smaller than in polyynic cases, so, although not strictly, the separation to cumulenes and polyynes, approximately, holds. Vibrational analysis confirms that for N even all cumulenes with coplanar methylene end groups are stable, for N odd all cumulenes with perpendicular methylene end groups are stable, and the number of hydrogen atoms at the end groups is clearly seen in all cumulenic and polyynic cases. We calculate and discuss the Density Functional Theory (DFT) ground state energy of neutral molecules, the CDFT (Constrained DFT) “ground state energy” of molecules with a hole at one end group, energy spectra, density of states, energy gap, charge and dipole moment oscillations, mean over time probabilities to find the hole at each site, coherent transfer rates, and frequency content, in general. We also compare RT-TDDFT with TB results. Full article
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

LCAO electronic structure of nucleic acid bases and other heterocycles and charge transfer parameters in B-DNA: effects of structural variability

Marilena Mantela^1 Constantinos Simserides^1 and Rosa Di Felice^2

1 National and Kapodistrian University of Athens, Department of Physics, Panepistimiopolis, Zografos, GR-15784, Athens, Greece
2 University of Southern California, Department of Physics and Astronomy, Department of Quantitative and Computational Biology, 920 Bloom Walk, Los Angeles, CA 90089, USA

Abstract To describe the molecular electronic structure of nucleic acid bases and other heterocycles, we employ the linear
combination of atomic orbitals (LCAO) method, considering the molecular wavefunction as a linear combination of all valence
orbitals, i.e., 2s, 2px, 2py, 2pz orbitals for C, N and O atoms and 1s orbital for H atoms. Regarding the diagonal matrix
elements (aka on-site energies), we introduce a novel parametrization. For the non-diagonal matrix elements referring
to neighboring atoms, we employ  the Slater-Koster two-center interaction transfer integrals. We use Harrison-type expressions
with factors slightly modified relative to the original. We compare our LCAO predictions for the ionization and excitation
energies of heterocycles with those obtained from IP-EOMCCSD/aug-cc-pVDZ and CR-EOMCCSD(T)/aug-cc-pVDZ level of
theory as well as with available experimental values. Similarly, we calculate the transfer integrals between subsequent base
pairs. Taking into account all valence orbitals, we are in the position to treat deflection from the planar geometry, e.g., DNA
structural variability, a task impossible for the plane Hueckel LCAO (i.e., using only 2pz orbitals). We show a structural deformation example utilizing a 20mer evolved by own Molecular
Dynamics.

 

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