A computational study on the electronic and optical properties of boron-nitride circumacenes

First-Principles Investigation of the Optical Properties of Eumelanin Protomolecules

Using first-principles calculations, we investigate the absorption spectra (in the near-infrared, visible, and first UV range) of the two most probable eumelanin tetrameric molecules exhibiting either a linear open-chain or a cyclic porphyrine-like configuration. In order to simulate a realistic molecular system, an implicit solvent model is used in our calculations to mimic the effect of the solvated environment around the eumelanin molecule. Although the presence of solvent is found not to significantly affect the absorption pattern of both molecules, the onset of the spectra are shifted toward higher energies, especially for the linear tetramer. Interestingly, the absorption spectra and optical onsets of the two molecules differ significantly both in a vacuum and in ethanol. However, the two predicted spectra do not allow us to definitely discriminate between the two configurations when comparing the theoretical predictions with the available experimental spectrum. In addition, a mix of the two eumelanin configurations (close to fifty-fifty) leads to a maximum overlap between theoretical and experimental spectra. Consequently, this theoretical research shows that deeper insight can be gained using beyond DFT techniques on the real form of eumelanin protomolecules present in living systems as well as on their possible use in hybrid solar cells.

Optical properties of nanostructured antiviral and anticancer drugs

We present a computational study on the optical absorption properties of some systems of interest in the field of drug delivery. In particular we considered as drug molecules favipiravir (T705, an antiviral molecule) and 5-fluorouracil (5FU, an anticancer molecule) and, on the other hand, pure fullerenes (C24, B12N12, Ga12N12) and doped fullerenes (C23B, CB11N12) are considered as nanocarriers. Some combined configurations between the drug molecules and the carrier nanostructures have been then studied. The optical absorption properties of the above mentioned drug molecules and their carrier nanostructures in the free and bound states are obtained by a TD-DFT method, in gas phase and in aqueous solution. We perform a detailed analysis of the modifications arising in the absorption spectra that take place in some linked configurations between the drug molecules and the carrier nanostructures. These changes could be of importance as an optical fingerprint of the realized drug/carrier link.

A combined molecular dynamics simulation and DFT study on mercapto-benzamide inhibitors for the HIV NCp7 protein

Molecular dynamics and quantum simulations are performed to elucidate some aspects of the action mechanism of mercapto-benzamides, a proposed class of antivirals against HIV-1. These molecules act as prodrugs that, after modifications in the biological environment, are able to denature the HIV nucleocapsid protein 7, a metal binder protein, with two zinc finger motifs, vital for RNA maturation and viral replication. Despite their attractive features, these molecules and their biological target are not well understood. Simulations were performed to support a proposed action mechanism, based on the activation of mercapto-benzamides by acetylation, targeting a relatively rare protein hydrolyzed state, followed by trans-molecular acetylation from the molecule to the protein and finally the direct interaction of the molecular sulphur atom of mercapto-benzamides with the zinc atom coordinated by the protein. Our simulation results are in agreement with the NMR data about the zinc finger binding protein equilibrium configurations.

An investigation into the structural, electronic, and non-linear optical properties in CN (N = 20, 24, 26, 28, 30, 32, 34, 36, and 38) fullerene cages

The present study attempts to investigate the structural, electronic, and non-linear optical properties of C_N (N = 20, 24, 26, 28, 30, 32, 34, 36, and 38) fullerene cages based on Density Functional Theory (DFT). In the DFT calculations, the B3LYP/6-311G(d,p) and CAM-B3LYP/6-311 +  + G(d,p) level of theories were used. The isomers of each fullerene have been received from the Fullerene Structure Library. These isomers have optimized using the B3LYP/6-311G(d,p). The results included optimization of the neutral and ionic state structures according to their multiplicity. Geometries, optimization energies, relative energies, frequencies, HOMO, LUMO, and HOMO-LUMO gap of these stable fullerene cages have been predicted by B3LYP/6-311G(d,p). Afterwards, the most stable structures have been re-optimized using the CAM-B3LYP /6-311 +  + G(d,p). Finally, non-linear optical properties, Fukui functions, density of state, electron affinity, and ionization potential values of the most stable fullerene cages have been found out by the DFT/ CAM-B3LYP /6-311 +  + G(d,p) level of theory. All calculation results have been compared with both C60 fullerene and the relevant literature on corresponding fullerenes.

Why Does a B12H12 Icosahedron Need Two Electrons to be Stable: A First-Principles Electron-Correlated Investigation of B12Hn (n = 6, 12) Clusters

In this work, we present large-scale electron-correlated computations on various conformers of B₁₂H₁₂ and B₁₂H₆ clusters to understand the reasons behind the high stability of dianion icosahedron (I_h) and cage-like B₁₂H₆ geometries. Although the B₁₂ icosahedron is the basic building block in some structures of bulk boron, it is unstable in its free form. Furthermore, its H-passivated entity, i.e., a B₁₂H₁₂ icosahedron, is also unstable in the free form. However, dianion B₁₂H₁₂ has been predicted to be stable as a perfect icosahedron in the free-standing form. To capture the correct picture for the stability of B₁₂H₁₂^2- and B₁₂H₆ clusters, we optimized these structures by employing the coupled-cluster singles and doubles (CCSD) approach and the cc-pVDZ basis set. We also performed the vibrational frequency analysis of the isomers of these clusters using the same level of theory to ensure the stability of the structures. For all of the stable geometries obtained from the vibrational frequency analysis, we additionally computed their optical absorption spectra using the time-dependent density functional theory (TDDFT) approach at the B3LYP/6-31G* level of theory. Our calculated absorption spectra could be probed in future experiments on these clusters.

Chemical bonding between thorium atoms and a carbon hexagon in carbon nanomaterials

We explore the unusual nature of chemical bonding of thorium atoms with a ring of six carbon atoms (hexagon) in novel carbon materials. Our ab initio calculations of Th-based metallofullerenes (Th@C60 and Th@C20) and Th bound to benzene or coronene at the Hartree-Fock level with the second order perturbation (MP2) correction accounting for the van der Waals interactions demonstrate that the optimal position of the thorium atom is where it faces the center of a hexagon and is located at a distance of 2.01-2.07 Å from the center. For Th encapsulated in C60 it is found at 2.01 Å, whereas the other local energy minima are shifted to larger energies (0.22 eV and higher). Inside C60 the highest local minimum at 1.17 eV is observed when Th faces the center of the five member carbon ring (pentagon). Based on our calculations for Th with benzene and coronene where the global minimum for Th corresponds to its position at 2.05 Å (benzene) or 2.02 Å (coronene) from the hexagon center, we conclude that a well pronounced minimum is likely to be present in graphene and in a single wall carbon nanotube. The ground state of Th is singlet, and other high spin states (triplet and quintet) lie higher in energy (>1.62 eV). We discuss a potential use of carbon nanomaterials with the 229Th isotope having its nuclear transition in the optical range, for metrological purposes.

Electronic and Optical Properties of Small Metal Fluoride Clusters

We report a systematic investigation on the electronic and optical properties of the smallest stable clusters of alkaline-earth metal fluorides, namely, MgF₂, CaF₂, SrF₂, and BaF₂. For these clusters, we perform density functional theory (DFT) and time-dependent DFT (TDDFT) calculations with a localized Gaussian basis set. For each molecule ((MF₂) _n , n = 1-3, M = Mg, Ca, Sr, Ba), we determine a series of molecular properties, namely, ground-state energies, fragmentation energies, electron affinities, ionization energies, fundamental energy gaps, optical absorption spectra, and exciton binding energies. We compare electronic and optical properties between clusters of different sizes with the same metal atom and between clusters of the same size with different metal atoms. From this analysis, it turns out that MgF₂ clusters have distinguished ground-state and excited-state properties with respect to the other fluoride molecules. Sizeable reductions of the optical onset energies and a consistent increase of excitonic effects are observed for all clusters under study with respect to the corresponding bulk systems. Possible consequences of the present results are discussed with respect to applied and fundamental research.