Structural Investigation of DHICA Eumelanin Using Density Functional Theory and Classical Molecular Dynamics Simulations.

Eumelanin is an important pigment, for example, in skin, hair, eyes, and the inner ear. It is a highly heterogeneous polymer with 5,6-dihydroxyindole-2-carboxylic acid (DHICA) and 5,6-dihydroxyindole (DHI) building blocks, of which DHICA is reported as the more abundant in natural eumelanin. The DHICA-eumelanin protomolecule consists of three building blocks, indole-2-carboxylic acid-5,6-quinone (ICAQ), DHICA and pyrrole-2,3,5-tricarboxylic acid (PTCA).

Free Energy and Stacking of Eumelanin Nanoaggregates.

Eumelanin, a member of the melanin family, is a black-brown insoluble pigment. It possesses a broad range of properties such as antioxidation, free radical scavenging, photoprotection, and charge carrier transportation. Surprisingly, the exact molecular structure of eumelanin remains undefined.

Neural evolution structure generation: High entropy alloys.

We propose a neural evolution structure (NES) generation methodology combining artificial neural networks and evolutionary algorithms to generate high entropy alloy structures. Our inverse design approach is based on pair distribution functions and atomic properties and allows one to train a model on smaller unit cells and then generate a larger cell. With a speed-up factor of ∼1000 with respect to the special quasi-random structures (SQSs), the NESs dramatically reduce computational costs and time, making possible the generation of very large structures (over 40 000 atoms) in few hours.

Experimental and Computational Observations of Immunogenic Cobalt Porphyrin Lipid Bilayers: Nanodomain-Enhanced Antigen Association.

Cobalt porphyrin phospholipid (CoPoP) can incorporate within bilayers to enable non-covalent surface-display of antigens on liposomes by mixing with proteins bearing a polyhistidine tag (his-tag); however, the mechanisms for how this occurs are poorly understood. These were investigated using the his-tagged model antigen Pfs25, a protein antigen candidate for malaria transmission-blocking vaccines. Pfs25 was found to associate with the small molecule aquocobalamin, a form of vitamin B12 and a cobalt-containing corrin macrocycle, but without particle formation, enabling comparative assessment.

Probing alkylsilane molecular structure on amorphous silica surfaces by sum frequency generation vibrational spectroscopy: First-principles calculations.

The sum frequency generation (SFG) signatures of octadecyl-trichlorosilane (OTS) and dodecyl-dimethyl-chlorosilane (DDCS) monolayers on silica were simulated in the C-H stretching region for three polarization combinations (ppp, sps, and ssp), showing the impact of the additional Si-linked methyl groups of DDCS on its SFG signatures. These simulations are based on a two-step procedure where (i) the molecular properties (vibrational frequencies, IR and Raman intensities) are evaluated using first principles methods and (ii) the three-layer model is employed to calculate the macroscopic responses using these molecular responses, the geometry of the experimental setup, and the optical properties of the layers. These first principles calculations adopt the own N-layered integrated orbital molecular mechanics (ONIOM) approach, which divides the system and enables different levels of approximation to be applied to its different parts.

Coupled-cluster sum-frequency generation nonlinear susceptibilities of methyl (CH) and methylene (CH) groups.

The first vibrational sum frequency generation (SFG) spectra based on molecular properties calculated at the coupled cluster singles and doubles (CCSD) level of approximation have been simulated for interfacial model alkyl chains, providing benchmark data for comparisons with approximate methods, including density functional theory (DFT). The approach proceeds in three steps. In the first two steps, the molecular spectral properties are determined: the vibrational normal modes and frequencies and then the derivatives of the dipole moment and of the polarizability with respect to the normal coordinates.

Analyzing the vibrational signatures of thiophenol adsorbed on small gold clusters by DFT calculations.

Using density functional theory, we calculate the IR and Raman signatures of the thiophenol (TP) molecule adsorbed on gold clusters by mimicking the different types of adsorption sites, and we analyze these signatures by using advanced tools implemented into the pyvib2 program. First, we follow the evolution of the vibrational normal modes from the isolated TP molecule to those of TP adsorbed on different clusters to highlight the influence of the site of adsorption on the vibrational motions. The use of the overlap matrix between the modes enables mode permutations, mode mixings, and mode splittings to be highlighted, all of which depend not only on the adsorption but also on the type of cluster and its symmetry.

Towards modelling the vibrational signatures of functionalized surfaces: carboxylic acids on H-Si(111) surfaces.

In this work, we investigate the adsorption process of two carboxylic acids (stearic and undecylenic) on a H-Si(111) surface via the calculation of structural and energy changes as well as the simulation of their IR and Raman spectra. The two molecules adsorb differently at the surface since the stearic acid simply physisorbs while the undecylenic acid undergoes a chemical reaction with the hydrogen atoms of the surface. This difference is observed in the change of geometry during the adsorption.