Molecular Simulations Guidelines for Biological Nanomaterials: From Peptides to Membranes

In studying biological processes and focusing on the molecular mechanisms at the basis of these, molecular dynamics (MD) simulations have demonstrated to be a very useful tool for the past 50 years. This suite of computational methods calculates the time-dependent evolution of a molecular system using physics-based first principles. In this chapter, we give a brief introduction to the theory and practical use of molecular dynamics simulations, highlighting the different models and algorithms that have been developed to tackle specific problems, with a special focus on classical force fields. Some examples of how simulations have been used in the past will help the reader in discerning their power, limitations, and significance.

Microwave-assisted synthesis of rhodamine derivatives

The microwave synthesis of 12 rhodamine-derived imines is described. The present work involves condensation of rhodamine hydrazide with various aromatic aldehydes in ethanol under microwave irradiation. The results obtained indicate that, unlike classical heating, microwave irradiation results in higher yields, shorter reaction time, mild reaction condition and simple work-up procedure. The structures of synthesized compounds were confirmed by 1H-NMR, 13C-NMR, FT-IR and high-resolution mass spectra data.

Development of a Reagentless Biosensor for Inorganic Phosphate, Applicable over a Wide Concentration Range

A fluorescent reagentless biosensor for inorganic phosphate (Pi), based on the E. coli PstS phosphate binding protein, was redesigned to allow measurements of higher Pi concentrations and at low, substoichiometric concentrations of biosensor. This was achieved by weakening Pi binding of the previous biosensor, and different approaches are described that could enable this change in properties. The readout, providing response to the Pi concentration, is delivered by tetramethylrhodamine fluorescence. In addition to two cysteine mutations for rhodamine labeling at positions 17 and 197, the final variant had an I76G mutation in the hinge region between the two lobes that make up the protein. Upon Pi binding, the lobes rotate on this hinge and the mutation on the hinge lowers affinity ∼200-fold, with a dissociation constant now in the tens to hundreds micromolar range, depending on solution conditions. The signal change on Pi binding was up to 9-fold, depending on pH. The suitability of the biosensor for steady-state ATPase assays was demonstrated with low biosensor usage and its advantage in ability to cope with Pi contamination.

Absorption and Emission Spectra of a Flexible Dye in Solution: a Computational Time-Dependent Approach

The spectroscopic properties of the organic chromophore 4-naphthoyloxy-1-methoxy-2,2,6,6-tetramethylpiperidine (NfO-TEMPO-Me) in toluene solution are explored through an integrated computational strategy combining a classical dynamic sampling with a quantum mechanical description within the framework of the time-dependent density functional theory (TDDFT) approach. The atomistic simulations are based on an accurately parametrized force field, specifically designed to represent the conformational behavior of the molecule in its ground and bright excited states, whereas TDDFT calculations are performed through a selected combination of hybrid functionals and basis sets to obtain optical spectra closely matching the experimental findings. Solvent effects, crucial to obtain good accuracy, are taken into account through explicit molecules and polarizable continuum descriptions. Although, in the case of toluene, specific solvation is not fundamental, the detailed conformational sampling in solution has confirmed the importance of a dynamic description of the molecular geometry for a reliable description of the photophysical properties of the dye. The agreement between theoretical and experimental data is established and a robust protocol for the prediction of the optical behaviour of flexible fluorophores in solution is set.