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 August 2022 | Viewed by 3561

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 (4 papers)

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Research

Article
Energy Transport along α-Helix Protein Chains: External Drives and Multifractal Analysis
Materials 2022, 15(8), 2779; https://doi.org/10.3390/ma15082779 - 10 Apr 2022
Viewed by 375
Abstract
Energy transport within biological systems is critical for biological functions in living cells and for technological applications in molecular motors. Biological systems have very complex dynamics supporting a large number of biochemical and biophysical processes. In the current work, we study the energy [...] Read more.
Energy transport within biological systems is critical for biological functions in living cells and for technological applications in molecular motors. Biological systems have very complex dynamics supporting a large number of biochemical and biophysical processes. In the current work, we study the energy transport along protein chains. We examine the influence of different factors such as temperature, salt concentration, and external mechanical drive on the energy flux through protein chains. We obtain that energy fluctuations around the average value for short chains are greater than for longer chains. In addition, the external mechanical load is the most effective agent on bioenergy transport along the studied protein systems. Our results can help design a functional nano-scaled molecular motor based on energy transport along protein chains. Full article
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Article
LCAO Electronic Structure of Nucleic Acid Bases and Other Heterocycles and Transfer Integrals in B-DNA, Including Structural Variability
Materials 2021, 14(17), 4930; https://doi.org/10.3390/ma14174930 - 30 Aug 2021
Viewed by 743
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 wave function as a linear combination of all valence orbitals, i.e., 2s, 2px, 2py [...] Read more.
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 wave function 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 (also known as on-site energies), we introduce a novel parameterization. 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 Ionization Potential Equation of Motion Coupled Cluster with Singles and Doubles (IP-EOMCCSD)/aug-cc-pVDZ level of theory and Completely Normalized Equation of Motion Coupled Cluster with Singles, Doubles, and non-iterative Triples (CR-EOMCCSD(T))/aug-cc-pVDZ level of theory, respectively, (vertical values), as well as with available experimental data. Similarly, we calculate the transfer integrals between subsequent base pairs, to be used for a Tight-Binding (TB) wire model description of charge transfer and transport along ideal or deformed B-DNA. 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 Hückel approach (i.e., using only 2pz orbitals). We show the effects of structural deformations utilizing a 20mer evolved by Molecular Dynamics. Full article
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Article
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 1189
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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Article
Hole Transfer in Open Carbynes
Materials 2020, 13(18), 3979; https://doi.org/10.3390/ma13183979 - 08 Sep 2020
Cited by 2 | Viewed by 790
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.

1. Controlling the energy transport along a protein chain

Narmin Sefidkar, Samira Fathizadeh, Fatemeh Nemati, Constantinos Simserides

Energy transport within biological systems is important for biological functions in life cell and for technological applications in molecular motors. Biological systems have very complex dynamic supporting a large number of biochemical and biophysical process. In the current work, we have studied the energy transport along the protein chains. Different factors such as the temperature, salt concentration effect, and the external mechanical drive are examined on the energy flux through the protein chains. It is obtained that the external mechanical load is most effective agent on bioenergy transport within our protein systems. The results can be help to design a functional nano-scaled molecular motor based on energy transport along the protein chains.

 

2. Charge movement in Helical Biomolecules:A comparison of appropriate tight-binding variants including helicity.

Sourav Kundu, Constantinos Simserides

We study charge movement in quasi 1D systems having in mind different biomolecules, e.g, DNA and proteins. It has been reported that biomolecules with helical symmetry may contain more than one channel through which charge can move. This provides us with a new way to look into these systems from different modeling points of view.  We are going to employ various appropriate tight-binding variants, e.g., wire fishbone, ladder fishbone (dangling backbone ladder) and extended ladder fishbone models to find the best description. One aim is to find the effects of long- range hopping on charge transport properties for different quasi 1D systems that arises because of helical symmetry. We are going examine various types of long range hopping to find the best possible fit.

 

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