Impact of Lipid Environment on Photodamage Activation of Methylene Blue

Effect of stacking interactions on charge transfer states in photoswitches interacting with ion channels

The activity of ion channels can be reversibly photo-controlled via the binding of molecular photoswitches, often based on an azobenzene scaffold. Those azobenzene derivatives interact with aromatic residues of the protein via stacking interactions. In the present work, the effect of face-to-face and t-shaped stacking interactions on the excited state electronic structure of azobenzene and p-diaminoazobenzene integrated into the NaV1.4 channel is computationally investigated. The formation of a charge transfer state, caused by electron transfer from the protein to the photoswitches, is observed. This state is strongly red shifted when the interaction takes place in a face-to-face orientation and electron donating groups are present on the aromatic ring of the amino acids. The low-energy charge transfer state can interfere with the photoisomerization process after excitation to the bright state by leading to the formation of radical species.

MoBioTools: A toolkit to setup quantum mechanics/molecular mechanics calculations

We present a toolkit that allows for the preparation of QM/MM input files from a conformational ensemble of molecular geometries. The package is currently compatible with trajectory and topology files in Amber, CHARMM, GROMACS and NAMD formats, and has the possibility to generate QM/MM input files for Gaussian (09 and 16), Orca (≥4.0), NWChem and (Open)Molcas. The toolkit can be used in command line, so that no programming experience is required, although it presents some features that can also be employed as a python application programming interface. We apply the toolkit in four situations in which different electronic-structure properties of organic molecules in the presence of a solvent or a complex biological environment are computed: the reduction potential of the nucleobases in acetonitrile, an energy decomposition analysis of tyrosine interacting with water, the absorption spectrum of an azobenzene derivative integrated into a voltage-gated ion channel, and the absorption and emission spectra of the luciferine/luciferase complex. These examples show that the toolkit can be employed in a manifold of situations for both the electronic ground state and electronically excited states. It also allows for the automatic correction of the active space in the case of CASSCF calculations on an ensemble of geometries, as it is shown for the azobenzene derivative photoswitch case.

Dual-wavelength photoacoustic atlas method to estimate fractional methylene blue and hemoglobin contents

SIGNIFICANCE

Methylene blue (MB) is an exogenous contrast agent that has the potential to assist with visualization and penetration challenges in photoacoustic imaging. However, monitoring the local concentration between MB and endogenous chromophores is critical for avoiding unnecessary MB accumulations that could lead to adverse effects such as hemolysis when exposed to increased dose and photodamage when exposed to high laser energies.

AIM

We developed a modified version of a previously proposed acoustic-based atlas method to estimate concentration levels from a mixture of two photoacoustic-sensitive materials after two laser wavelength emissions.

APPROACH

Photoacoustic data were acquired from mixtures of 100-μM MB and either human or porcine blood (Hb) injected in a plastisol phantom, using laser wavelengths of 710 and 870 nm. An algorithm to perform linear regression of the acoustic frequency response from an atlas composed of pure concentrations was designed to assess the concentration levels from photoacoustic samples obtained from 11 known MB/Hb volume mixtures. The mean absolute error (MAE), coefficient of determination (i.e., R2), and Spearman's correlation coefficient (i.e., ρ) between the estimated results and ground-truth labels were calculated to assess the algorithm performance, linearity, and monotonicity, respectively.

RESULTS

The overall MAE, R2, and ρ were 12.68%, 0.80, and 0.89, respectively, for the human Hb dataset and 9.92%, 0.86, and 0.93, respectively, for the porcine Hb dataset. In addition, a similarly linear relationship was observed between the acoustic frequency response at 2.3 MHz and 870-nm laser wavelength and the ground-truth concentrations, with R2 and | ρ | values of 0.76 and 0.88, respectively.

CONCLUSIONS

Contrast agent concentration monitoring is feasible with the proposed approach. The potential for minimal data acquisition times with only two wavelength emissions is advantageous toward real-time implementation in the operating room.

Characterization of cisplatin/membrane interactions by QM/MM energy decomposition analysis

We extend for the first time a quantum mechanical energy decomposition analysis scheme based on deformation electron densities to a hybrid electrostatic embedding quantum mechanics/molecular mechanics framework. The implemented approach is applied to characterize the interactions between cisplatin and a dioleyl-phosphatidylcholine membrane, which play a key role in the permeation mechanism of the drug inside the cells. The interaction energy decomposition into electrostatic, induction, dispersion and Pauli repulsion contributions is performed for ensembles of geometries to account for conformational sampling. It is evidenced that the electrostatic and repulsive components are predominant in both polar and non-polar regions of the bilayer.

The Permeation Mechanism of Cisplatin Through a Dioleoylphosphocholine Bilayer*

The investigation of the intermolecular interactions between platinum-based anticancer drugs and lipid bilayers is of special relevance to unveil the mechanisms involved in different steps of the anticancer mode of action of these drugs. We have simulated the permeation of cisplatin through a model membrane composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine lipids by means of umbrella sampling classical molecular dynamics simulations. The initial physisorption of cisplatin into the polar region of the lipid membrane is controlled by long-range electrostatic interactions with the choline groups in a first step and, in a second step, by long-range electrostatic and hydrogen bond interactions with the phosphate groups. The second half of the permeation pathway, in which cisplatin diffuses through the nonpolar region of the bilayer, is characterized by the drop of the interactions with the polar heads and the rise of attractive interactions with the non-polar tails, which are dominated by van der Waals contributions. The permeation free-energy profile is explained by a complex balance between the drug/lipid interactions and the energy and entropy contributions associated with the dehydration of the drug along the permeation pathway and with the decrease and increase of the membrane ordering along the first and second half of the mechanism, respectively.

A Galactose Dendritic Silicon (IV) Phthalocyanine as a Photosensitizing Agent in Cancer Photodynamic Therapy

Two protected galacto-dendritic units have been axially coordinated to the central ion of a silicon(IV) phthalocyanine to afford SiPcPGal₄ containing four units of galactose per macrocycle. These biological moieties provided better solubility in aqueous medium and a sensitizer with higher absorption peaks at 680-690 nm. The photodynamic activity of SiPcPGal₄ was evaluated against UM-UC-3 human bladder cancer cell line and the results were compared with the activity of the reported SiPcPGal₂ and SiPc(OH)₂ . SiPcPGal₄ had a better uptake and it was a better toxicity inducer than SiPcPGal₂ and SiPc(OH)₂ owing to its four galactose units, protected by isopropylidene groups, which can act as targeted micelles.

Vibrational Sampling and Solvent Effects on the Electronic Structure of the Absorption Spectrum of 2-Nitronaphthalene

The influence of vibrational motion on electronic excited state properties is investigated for the organic chromophore 2-nitronaphtalene in methanol. Specifically, the performance of two vibrational sampling techniques - Wigner sampling and sampling from an ab initio molecular dynamics trajectory- is assessed, in combination with implicit and explicit solvent models. The effects of the different sampling/solvent combinations on the energy and electronic character of the absorption bands are analyzed in terms of charge transfer and exciton size, computed from the electronic transition density. The absorption spectra obtained using sampling techniques and its underlying properties are compared to those of the electronic excited states calculated at the Franck-Condon equilibrium geometry. It is found that the absorption bands of the vibrational ensembles are red-shifted compared to the Franck-Condon bright states, and this red-shift scales with the displacement from the equilibrium geometry. Such displacements are found larger and better described when using ensembles from the harmonic Wigner distribution than snapshots from the molecular dynamics trajectory. Particularly relevant is the torsional motion of the nitro group that quenches the charge transfer character of some of the absorption bands. This motion, however, is better described in the molecular dynamics trajectory. Thus, none of the vibrational sampling approaches can satisfactorily capture all important aspects of the nuclear motion. The inclusion of solvent also red-shifts the absorption bands with respect to the gas phase. This red-shift scales with the charge-transfer character of the bands and is found larger for the implicit than for the explicit solvent model. The advantages and drawbacks of the different sampling and solvent models are discussed to guide future research on the calculation of UV-vis spectra of nitroaromatic compounds.

Exciton Localization on Ru-Based Photosensitizers Induced by Binding to Lipid Membranes

The characterization of electronic properties of metal complexes embedded in membrane environments is of paramount importance to develop efficient photosensitizers in optogenetic applications. Molecular dynamics and QM/MM simulations together with quantitative wave function analysis reveal a directional electronic redistribution of the exciton formed upon excitation of [Ru(bpy)₂(bpy-C17)]²⁺ when going from water to a lipid bilayer, despite the fact that the media influence neither the metal-to-ligand charge-transfer character nor the excitation energy of the absorption spectra. When the photosensitizer is embedded into the DOPC lipid membrane, exciton population is mainly located in the bypyridyl sites proximal to the positively charged surface of the bilayer due to electrostatic interactions. This behavior shows that the electronic structure of metal complexes can be controlled through the binding to external species, underscoring the crucial role of the environment in directing the electronic flow upon excitation and thus helping rational tuning of optogenetic agents.

The effect of solvent relaxation in the ultrafast time-resolved spectroscopy of solvated benzophenone

Modeling time-resolved spectra to unravel ultra fast solvent reorganization.

Deciphering the photosensitization mechanisms of hypericin towards biological membranes

Molecular modeling and simulation allow unravelling the molecular basis of the photosensitization of biological membranes by the hypericin drug used in photodynamic therapy.