scholarly journals LCAO Electronic Structure of Nucleic Acid Bases and Other Heterocycles and Transfer Integrals in B-DNA, Including Structural Variability

Materials ◽  
2021 ◽  
Vol 14 (17) ◽  
pp. 4930
Author(s):  
Marilena Mantela ◽  
Constantinos Simserides ◽  
Rosa Di Felice
Keyword(s):  
Electronic Structure ◽  
Nucleic Acid ◽  
Linear Combination ◽  
Equation Of Motion ◽  
Diagonal Matrix ◽  
Coupled Cluster ◽  
Matrix Elements ◽  
Nucleic Acid Bases ◽  
Structural Variability ◽  
Transfer Integrals

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.

scholarly journals General Framework for Calculating Spin–orbit Couplings Using Spinless One-Particle Density Matrices: Theory and Application to the Equation-of-Motion Coupled-Cluster Wave Functions

2019 ◽  
Author(s):  
Pavel Pokhilko ◽  
Evgeny Epifanovsky ◽  
Anna I. Krylov
Keyword(s):  
Degrees Of Freedom ◽  
Particle Density ◽  
Mean Field ◽  
Transition Density ◽  
Open Shell ◽  
Equation Of Motion ◽  
Wave Functions ◽  
Coupled Cluster ◽  
Spin Orbit ◽  
Matrix Elements

Standard implementations of non-relativistic excited-state calculations compute only one component of spin multiplets (i.e., Ms =0 triplets), however, matrix elements for all components are necessary for calculations of experimentally relevant spin-dependent quantities. To circumvent explicit calculations of all multiplet components, we employ Wigner–Eckart’s theorem. Applied to a reduced one-particle transition density matrix computed for a single multiplet component, Wigner–Eckart’s theorem generates all other spin–orbit matrix elements. In addition to computational efficiency, this approach also resolves the phase issue arising within Born–Oppenheimer’s separation of nuclear and electronic degrees of freedom. A general formalism and its application to the calculations of spin–orbit couplings using equation-of-motion coupled-cluster wave functions is presented. The two-electron contributions are included via the mean-field spin–orbit treatment. Intrinsic issues of constructing spin–orbit mean-field operators for open-shell references are discussed and a resolution is proposed. The method is benchmarked by using several radicals and diradicals. The merits of the approach are illustrated by a calculation of the barrier for spin inversion in a high-spin tris(pyrrolylmethyl)amine Fe(II) complex.

Third Neighbor Analytic Tight-Binding Solutions for Electronic Structure of Carbon Nanosystems

2010 ◽  
Vol 659 ◽  
pp. 197-202
Author(s):  
István László
Keyword(s):  
Electronic Structure ◽  
Tight Binding ◽  
Electronic Structure Calculations ◽  
Diagonal Matrix ◽  
Graphene Sheets ◽  
Matrix Elements ◽  
Structure Calculations

Third neighbor analytic tight-binding formulae were obtained for graphene sheets and nanotubes. After fitting the corresponding of-diagonal matrix elements can be used in numerical electronic structure calculations of nanotubes and corrugated graphene.

scholarly journals Electronic Structure and Spectroscopy of Nucleic Acid Bases: Ionization Energies, Ionization-Induced Structural Changes, and Photoelectron Spectra

2010 ◽  
Vol 114 (46) ◽  
pp. 12305-12317 ◽  
Author(s):  
Ksenia B. Bravaya ◽  
Oleg Kostko ◽  
Stanislav Dolgikh ◽  
Arie Landau ◽  
Musahid Ahmed ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Nucleic Acid ◽  
Structural Changes ◽  
Photoelectron Spectra ◽  
Nucleic Acid Bases ◽  
Ionization Energies

scholarly journals General Framework for Calculating Spin–orbit Couplings Using Spinless One-Particle Density Matrices: Theory and Application to the Equation-of-Motion Coupled-Cluster Wave Functions

2019 ◽  
Author(s):  
Pavel Pokhilko ◽  
Evgeny Epifanovsky ◽  
Anna I. Krylov
Keyword(s):  
Degrees Of Freedom ◽  
Particle Density ◽  
Mean Field ◽  
Transition Density ◽  
Open Shell ◽  
Equation Of Motion ◽  
Wave Functions ◽  
Coupled Cluster ◽  
Spin Orbit ◽  
Matrix Elements

Standard implementations of non-relativistic excited-state calculations compute only one component of spin multiplets (i.e., Ms =0 triplets), however, matrix elements for all components are necessary for calculations of experimentally relevant spin-dependent quantities. To circumvent explicit calculations of all multiplet components, we employ Wigner–Eckart’s theorem. Applied to a reduced one-particle transition density matrix computed for a single multiplet component, Wigner–Eckart’s theorem generates all other spin–orbit matrix elements. In addition to computational efficiency, this approach also resolves the phase issue arising within Born–Oppenheimer’s separation of nuclear and electronic degrees of freedom. A general formalism and its application to the calculations of spin–orbit couplings using equation-of-motion coupled-cluster wave functions is presented. The two-electron contributions are included via the mean-field spin–orbit treatment. Intrinsic issues of constructing spin–orbit mean-field operators for open-shell references are discussed and a resolution is proposed. The method is benchmarked by using several radicals and diradicals. The merits of the approach are illustrated by a calculation of the barrier for spin inversion in a high-spin tris(pyrrolylmethyl)amine Fe(II) complex.

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