LCAO Electronic Structure of Nucleic Acid Bases and Other Heterocycles and Transfer Integrals in B-DNA, Including Structural Variability
| Autor: | Constantinos Simserides, Marilena Mantela, Rosa Di Felice |
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| Rok vydání: | 2021 |
| Předmět: |
Technology
Linear Combination of Atomic Orbitals (LCAO) Electronic structure Molecular physics Article Matrix (mathematics) Atomic orbital charge transfer DNA nucleic acids Molecular Dynamics (MD) Tight Binding (TB) heterocycles General Materials Science Wave function Physics Microscopy QC120-168.85 Valence (chemistry) QH201-278.5 Engineering (General). Civil engineering (General) TK1-9971 Coupled cluster Descriptive and experimental mechanics Linear combination of atomic orbitals Computer Science::Programming Languages Electrical engineering. Electronics. Nuclear engineering Ionization energy TA1-2040 |
| Zdroj: | Materials Materials, Vol 14, Iss 4930, p 4930 (2021) Materials (Basel) 14 (2021): 4930-1–4930-20. doi:10.3390/ma14174930 info:cnr-pdr/source/autori:Mantela M.; Simserides C.; Di Felice R./titolo:Lcao electronic structure of nucleic acid bases and other heterocycles and transfer integrals in b-dna, including structural variability/doi:10.3390%2Fma14174930/rivista:Materials (Basel)/anno:2021/pagina_da:4930-1/pagina_a:4930-20/intervallo_pagine:4930-1–4930-20/volume:14 Materials; Volume 14; Issue 17; Pages: 4930 |
| ISSN: | 1996-1944 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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