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Register a new userRT-TDDFT study of hole oscillations in B-DNA monomers and dimers
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We employ Real-Time Time-Dependent Density Functional Theory to study hole oscillations within a B-DNA monomer (one base pair) or dimer (two base pairs). Placing the hole initially at any of the bases which make up a base pair, results in THz oscillations, albeit of negligible amplitude. Placing the hole initially at any of the base pairs which make up a dimer is more interesting: For dimers made of identical monomers, we predict oscillations with frequencies in the range $f approx$ 20-80 THz, with a maximum transfer percentage close to 1. For dimers made of different monomers, $f approx$ 80-400 THz, but with very small or small maximum transfer percentage. We compare our results with those obtained recently via our Tight-Binding approaches and find that they are in good agreement.
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The interaction of heavy charged particles with DNA is of interest for several areas, from hadrontherapy to aero-space industry. In this paper, a TD-DFT study on the interaction of a 4 keV proton with an isolated DNA base pair was carried out. Ehrenfest dynamics was used to study the evolution of the system during and after the proton impact up to about 193 fs. This time was long enough to observe the dissociation of the target, which occurs between 80-100 fs. The effect of base pair linking to the DNA double helix was emulated by fixing the four O3 atoms responsible for the attachment. The base pair tends to dissociate into its main components, namely the phosphate groups, sugars and nitrogenous bases. A central impact with energy transfer of 17.9 eV only produces base damage while keeping the backbone intact. An impact on a phosphate group with energy transfer of about 60 eV leads to backbone break at that site together with base damage, while the opposite backbone site integrity is kept is this situation. As the whole system is perturbed during such a collision, no atom remains passive. These results suggest that base damage accompanies all backbone breaks since hydrogen bonds that keep bases together are much weaker that those between the other components of the DNA.
A necessary first step in the development of technologies such as artificial photosynthesis is understanding the photoexcitation process within the basic building blocks of naturally-occurring light harvesting complexes (LHCs). The most important of these building blocks in biological LHCs such as LHC II from green plants are the chlorophyll $a$ (Chl $a$) and chlorophyll $b$ (Chl $b$) chromophores dispersed throughout the protein matrix. However, efforts to describe such systems are still hampered by the lack of computationally efficient and accurate methods that are able to describe optical absorption in large biomolecules. In this work we employ a highly efficient linear combination of atomic orbitals (LCAOs) to represent the Kohn--Sham (KS) wave functions at the density functional theory (DFT) level and perform time dependent density functional theory (TDDFT) in either the reciprocal space and frequency domain (LCAO-TDDFT-$k$-$omega$) or real space and time (LCAO-TDDFT-$r$-$t$) calculations of the optical absorption spectra of Chl $a$ and $b$ monomers and dimers. We find our LCAO-TDDFT-$k$-$omega$ and LCAO-TDDFT-$r$-$t$ calculations reproduce results obtained with a plane wave (PW) representation of the KS wave functions (PW-TDDFT-$k$-$omega$), but with a significant reduction in computational effort. Moreover, by applying the GLLB-SC derivative discontinuity correction $Delta_x$ to the KS eigenenergies, with both LCAO-TDDFT-$k$-$omega$ and LCAO-TDDFT-$r$-$t$ methods we are able to semi-quantitatively reproduce the experimentally measured photoinduced dissociation (PID) results. This work opens the path to first principles calculations of optical excitations in macromolecular systems.
Low-lying excited states for indeno[1,2-b]fluorene homo dimers with or without benzene spacers are calculated using the Density Matrix Renormalization group (DMRG) approach within Pariser-Parr-Pople (PPP) model Hamiltonian. DMRG calculations suggest that all the dimers studied here satisfy the essential energy conditions for SF. SF is a multiexciton generation process. As it is spin allowed, the process is very fast. By generating multiple exciton at a time SF underestimate SQ limit to enhance photo-conversion efficiency of single junction solar cells. Frontier orbital calculation through Density Functional Theory (DFT) depicts orbital localization of triplets on either side of the covalent spacers. Which supports the entangled triplet-triplet state $^1(TT)$. Here the process is intramolecular (iSF), which has many advantages over the intermolecular (xSF) process, as in intermolecular process the SF process is highly dependent on the crystal packing, defects, dislocations etc. The entangled $^1(TT)$ state for xSF is localized on both of the chromophores, thus the appropriate crystal packing is essential for xSF. However iSF does not depend on the crystal packing. Our DMRG calculation and TDDFT calculation are in well agreement with experimental results found in the literature. Thus indeno[1,2-b]fluorene homo dimers can be applicable in iSF application.
We consider a monomer-dimer system with a strong attractive dimer-dimer interaction that favors alignment. In 1979, Heilmann and Lieb conjectured that this model should exhibit a nematic liquid crystal phase, in which the dimers are mostly aligned, but do not manifest any translational order. We prove this conjecture for large dimer activity and strong interactions. The proof follows a Pirogov-Sinai scheme, in which we map the dimer model to a system of hard-core polymers whose partition function is computed using a convergent cluster expansion.
Ion beam therapy is one of the most progressive methods in cancer treatment. Studies of the water radiolysis process show that the most long-living species that occur in the medium of a biological cell under the action of ionizing irradiation are hydrogen peroxide (H$_2$O$_2$) molecules. But the role of H$_2$O$_2$ molecules in the DNA deactivation of cancer cells in ion beam therapy has not been determined yet. In the present paper, the competitive interaction of hydrogen peroxide and water molecules with atomic groups of non-specific DNA recognition sites (phosphate groups PO$_4$) is investigated. The interaction energies and optimized spatial configurations of the considered molecular complexes are calculated with the help of molecular mechanics method and quantum chemistry approach. The results show that the H$_2$O$_2$ molecule can form a complex with the PO$_4$ group (with and without a sodium counterion) that is more energetically stable than the same complex with the water molecule. Formation of such complexes can block genetic information transfer processes in cancer cells and can be an important factor during ion beam therapy treatment.
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