Modeling the temperature dependence of the fluorescence properties of Indole in aqueous solution.

In a recent paper, we proposed a scheme to describe the relaxation mechanism of the excited Indole in aqueous solution, involving the fluctuations among the diabatic electronic states 1Lb, 1La and 1πσ∗. Such a theoretical and computational model reproduced accurately the available experimental data at room temperature. Following these results, in the present work, we model the complex temperature dependence of the fluorescence properties of Indole in aqueous solution, with results further validating the proposed relaxation scheme. This scheme is able to explain the temperature effects on the fluorescence behavior indicating the water fluctuations as the main cause of (i) the stabilization of the dark state (1πσ∗) and (ii) the increase in temperature of the kinetics of the irreversible transition towards such a state.

Unveiling the Excited State Dynamics of Indole in Solution.

In this paper, we reconstruct in detail the dynamics of the emitting electronic excited state of aqueous indole, investigating its relaxation mechanism and kinetics to be related to the time-dependent fluorescence signal. Taking advantage of the results shown in a very recent paper, we were able to model the relaxation process in solution in terms of the transitions between two gas-phase singlet electronic states (1La and 1Lb), subsequently irreversibly relaxing to the gas-phase singlet dark state (1πσ*). A comparison of the results with the available experimental data shows that the relaxation mechanism we obtain by our theoretical-computational model is reliable, reproducing rather accurately all the experimental observables.

A study of cyanidin/alginate complexation: Influence of pH in assembly and chiral properties.

Cyanidin 3-O-glucoside (CND) is a frequently-used anthocyanin that has excellent antioxidant properties but a limited bioavailability in bloodstream. Complexation of CND with alginate can improve its therapeutic outcome. Here we have studied the complexation of CND with alginate under a range of pH values from 2.5 to 5. CND is positively charged at low pH, and becomes neutral, and then negatively charged as pH increases. CND/alginate complexation was studied by dynamic light scattering, transmission electron microscopy, small angle X-ray scattering, STEM, UV-Vis spectroscopy and circular dichroism (CD). CND/alginate complexes at pH 4.0 and 5.0 form chiral fibres with a fractal structure. At these pH values, CD spectra show very intense bands, which are inverted compared with free CND. Complexation at lower pH results in disordered polymer structures and CD spectra show the same features as for CND in solution. Molecular dynamics simulations suggest the formation of parallel CND dimers through complexation with alginate at pH 3.0, while at pH 4.0 CND dimers form in a cross like arrangement.

PyMM: An Open-Source Python Program for QM/MM Simulations Based on the Perturbed Matrix Method.

Quantum mechanical/molecular mechanics (QM/MM) methods are important tools in molecular modeling as they are able to couple an extended phase space sampling with an accurate description of the electronic properties of the system. Here, we describe a Python software package, called PyMM, which has been developed to apply a QM/MM approach, the perturbed matrix method, in a simple and efficient way. PyMM requires a classical atomic trajectory of the whole system and a set of unperturbed electronic properties of the ground and electronic excited states. The software output includes a set of the most common perturbed properties, such as the electronic excitation energies and the transitions dipole moments, as well as the eigenvectors describing the perturbed electronic states, which can be then used to estimate whatever electronic property. The software is composed of a simple and complete command-line interface, a set of internal input validation, and three main analyses focusing on (i) the perturbed eigenvector behavior, (ii) the calculation of the electronic absorption spectrum, and (iii) the estimation of the free energy differences along a reaction coordinate.

A Simplified Treatment for Efficiently Modeling the Spectral Signal of Vibronic Transitions: Application to Aqueous Indole.

In this paper, we introduce specific approximations to simplify the vibronic treatment in modeling absorption and emission spectra, allowing us to include a huge number of vibronic transitions in the calculations. Implementation of such a simplified vibronic treatment within our general approach for modelling vibronic spectra, based on molecular dynamics simulations and the perturbed matrix method, provided a quantitative reproduction of the absorption and emission spectra of aqueous indole with higher accuracy than the one obtained when using the existing vibronic treatment. Such results, showing the reliability of the approximations employed, indicate that the proposed method can be a very efficient and accurate tool for computational spectroscopy.

Complexation and organization of doxorubicin on polystyrene sulfonate chains: impacts on doxorubicin dimerization and quenching.

Anthracycline doxorubicin hydrochloride (DX) is a positively charged fluorescent drug, which in water self-associates into non-fluorescent antiparallel dimers upon increasing concentration and/or ionic strength. The positive charge of DX allows for complexation with negatively charged polymers and drug carriers. The fluorescence of DX following complexation with polyanion polystyrene sulfonate (PSS) is studied here. The fluorescence emission of DX decreases in the presence of PSS, being almost completely quenched when the ratio (R) of PSS monomers-to-DX molecules is larger than 10. Increasing R values over 30 results in a progressive recovery of fluorescence. The circular dichroism of PSS-DX complexes shows inverted characteristic bands of DX dimers suggesting the presence of parallel dimers at a concentration of DX below dimerization in water. Molecular dynamics studies corroborate a preferential orientation of DX into parallel dimers when interacting with PSS and show that DX molecules interact with a binding pocket of PSS monomers rather than with one single monomer. Increasing the ionic strength results in a recovery of fluorescence without an apparent release of DX from the PSS-DX complex as shown by DOSY NMR. PSS acts as a template for concentrating DX, triggering dimerisation and orienting DX molecules with their charged groups facing the negatively charged PSS monomers.

Computational Modeling of the Thermodynamics of the Mesophilic and Thermophilic Mutants of Trp-Cage Miniprotein.

We characterize the folding-unfolding thermodynamics of two mutants of the miniprotein Trp-cage by combining extended molecular dynamics simulations and an advanced statistical-mechanical-based approach. From a set of molecular dynamics simulations in an explicit solvent performed along a reference isobar, we evaluated the structural and thermodynamic behaviors of a mesophilic and a thermophilic mutant of the Trp-cage and their temperature dependence. In the case of the thermophilic mutant, computational data confirm that our theoretical-computational approach is able to reproduce the available experimental estimate with rather good accuracy. On the other hand, the mesophilic mutant does not show a clear two-state (folded and unfolded) behavior, preventing us from reconstructing its thermodynamics; thus, an analysis of its structural behavior along a reference isobar is presented. Our results show that an extended sampling of these kinds of systems coupled to an advanced statistical-mechanical-based treatment of the data can provide an accurate description of the folding-unfolding thermodynamics along a reference isobar, rationalizing the discrepancies between the simulated and experimental systems.

Absorption behavior of doxorubicin hydrochloride in visible region in different environments: a combined experimental and computational study.

The experimental absorption measurements in the interval 350-600 nm (Vis), molecular dynamics simulations, quantum-mechanics calculations and an advanced molecular treatment of simulation data are here combined to provide a complete picture of the absorption behavior in the visible portion of the electromagnetic spectrum of the doxorubicin hydrochloride (DX) molecule in different environments. By such an approach, we have shown that it is possible to characterize the effect of the environment on the DX absorption behavior - including the vibronic contributions - as well as to interpret such differences in terms of molecular electronic excited states, which are found to be strongly influenced by the environment.

Theoretical Modeling of Redox Potentials of Biomolecules.

The estimation of the redox potentials of biologically relevant systems by means of theoretical-computational approaches still represents a challenge. In fact, the size of these systems typically does not allow a full quantum-mechanical treatment needed to describe electron loss/gain in such a complex environment, where the redox process takes place. Therefore, a number of different theoretical strategies have been developed so far to make the calculation of the redox free energy feasible with current computational resources. In this review, we provide a survey of such theoretical-computational approaches used in this context, highlighting their physical principles and discussing their advantages and limitations. Several examples of these approaches applied to the estimation of the redox potentials of both proteins and nucleic acids are described and critically discussed. Finally, general considerations on the most promising strategies are reported.

Point Mutations at a Key Site Alter the Cytochrome P450 OleP Structural Dynamics.

Substrate binding to the cytochrome P450 OleP is coupled to a large open-to-closed transition that remodels the active site, minimizing its exposure to the external solvent. When the aglycone substrate binds, a small empty cavity is formed between the I and G helices, the BC loop, and the substrate itself, where solvent molecules accumulate mediating substrate-enzyme interactions. Herein, we analyzed the role of this cavity in substrate binding to OleP by producing three mutants (E89Y, G92W, and S240Y) to decrease its volume. The crystal structures of the OleP mutants in the closed state bound to the aglycone 6DEB showed that G92W and S240Y occupied the cavity, providing additional contact points with the substrate. Conversely, mutation E89Y induces a flipped-out conformation of this amino acid side chain, that points towards the bulk, increasing the empty volume. Equilibrium titrations and molecular dynamic simulations indicate that the presence of a bulky residue within the cavity impacts the binding properties of the enzyme, perturbing the conformational space explored by the complexes. Our data highlight the relevance of this region in OleP substrate binding and suggest that it represents a key substrate-protein contact site to consider in the perspective of redirecting its activity towards alternative compounds.