Assessing Configurational Sampling in the Quantum Mechanics/Molecular Mechanics Calculation of Temoporfin Absorption Spectrum and Triplet Density of States

Third-Generation Anticancer Photodynamic Therapy Systems Based on Star-like Anionic Polyacrylamide Polymer, Gold Nanoparticles, and Temoporfin Photosensitizer

Photodynamic therapy (PDT) is a non-invasive anticancer treatment that uses special photosensitizer molecules (PS) to generate singlet oxygen and other reactive oxygen species (ROS) in a tissue under excitation with red or infrared light. Though the method has been known for decades, it has become more popular recently with the development of new efficient organic dyes and LED light sources. Here we introduce a ternary nanocomposite: water-soluble star-like polymer/gold nanoparticles (AuNP)/temoporfin PS, which can be considered as a third-generation PDT system. AuNPs were synthesized in situ inside the polymer molecules, and the latter were then loaded with PS molecules in an aqueous solution. The applied method of synthesis allows precise control of the size and architecture of polymer nanoparticles as well as the concentration of the components. Dynamic light scattering confirmed the formation of isolated particles (120 nm diameter) with AuNPs and PS molecules incorporated inside the polymer shell. Absorption and photoluminescence spectroscopies revealed optimal concentrations of the components that can simultaneously reduce the side effects of dark toxicity and enhance singlet oxygen generation to increase cancer cell mortality. Here, we report on the optical properties of the system and detailed mechanisms of the observed enhancement of the phototherapeutic effect. Combinations of organic dyes with gold nanoparticles allow significant enhancement of the effect of ROS generation due to surface plasmonic resonance in the latter, while the application of a biocompatible star-like polymer vehicle with a dextran core and anionic polyacrylamide arms allows better local integration of the components and targeted delivery of the PS molecules to cancer cells. In this study, we demonstrate, as proof of concept, a successful application of the developed PDT system for in vitro treatment of triple-negative breast cancer cells under irradiation with a low-power LED lamp (660 nm). We consider the developed nanocomposite to be a promising PDT system for application to other types of cancer.

Quantum computing in pharma: A multilayer embedding approach for near future applications

Quantum computers are special purpose machines that are expected to be particularly useful in simulating strongly correlated chemical systems. The quantum computer excels at treating a moderate number of orbitals within an active space in a fully quantum mechanical manner. We present a quantum phase estimation calculation on F₂ in a (2,2) active space on Rigetti's Aspen-11 QPU. While this is a promising start, it also underlines the need for carefully selecting the orbital spaces treated by the quantum computer. In this work, a scheme for selecting such an active space automatically is described and simulated results obtained using both the quantum phase estimation (QPE) and variational quantum eigensolver (VQE) algorithms are presented and combined with a subtractive method to enable accurate description of the environment. The active occupied space is selected from orbitals localized on the chemically relevant fragment of the molecule, while the corresponding virtual space is chosen based on the magnitude of interactions with the occupied space calculated from perturbation theory. This protocol is then applied to two chemical systems of pharmaceutical relevance: the enzyme [Fe] hydrogenase and the photosenzitizer temoporfin. While the sizes of the active spaces currently amenable to a quantum computational treatment are not enough to demonstrate quantum advantage, the procedure outlined here is applicable to any active space size, including those that are outside the reach of classical computation.

Modeling the Electronic Absorption Spectra of the Indocarbocyanine Cy3

Accurate modeling of optical spectra requires careful treatment of the molecular structures and vibronic, environmental, and thermal contributions. The accuracy of the computational methods used to simulate absorption spectra is limited by their ability to account for all the factors that affect the spectral shapes and energetics. The ensemble-based approaches are widely used to model the absorption spectra of molecules in the condensed-phase, and their performance is system dependent. The Franck–Condon approach is suitable for simulating high resolution spectra of rigid systems, and its accuracy is limited mainly by the harmonic approximation. In this work, the absorption spectrum of the widely used cyanine Cy3 is simulated using the ensemble approach via classical and quantum sampling, as well as, the Franck–Condon approach. The factors limiting the ensemble approaches, including the sampling and force field effects, are tested, while the vertical and adiabatic harmonic approximations of the Franck–Condon approach are also systematically examined. Our results show that all the vertical methods, including the ensemble approach, are not suitable to model the absorption spectrum of Cy3, and recommend the adiabatic methods as suitable approaches for the modeling of spectra with strong vibronic contributions. We find that the thermal effects, the low frequency modes, and the simultaneous vibrational excitations have prominent contributions to the Cy3 spectrum. The inclusion of the solvent stabilizes the energetics significantly, while its negligible effect on the spectral shapes aligns well with the experimental observations.

Multiconfigurational Quantum Chemistry Determinations of Absorption Cross Sections (σ) in the Gas Phase and Molar Extinction Coefficients (ε) in Aqueous Solution and Air-Water Interface

Theoretical determinations of absorption cross sections (σ) in the gas phase and molar extinction coefficients (ε) in condensed phases (water solution, interfaces or surfaces, protein or nucleic acids embeddings, etc.) are of interest when rates of photochemical processes, J = ∫ ϕ(λ) σ(λ) I(λ) dλ, are needed, where ϕ(λ) and I(λ) are the quantum yield of the process and the irradiance of the light source, respectively, as functions of the wavelength λ. Efficient computational strategies based on single-reference quantum-chemistry methods have been developed enabling determinations of line shapes or, in some cases, achieving rovibrational resolution. Developments are however lacking for strongly correlated problems, with many excited states, high-order excitations, and/or near degeneracies between states of the same and different spin multiplicities. In this work, we define and compare the performance of distinct computational strategies using multiconfigurational quantum chemistry, nuclear sampling of the chromophore (by means of molecular dynamics, ab initio molecular dynamics, or Wigner sampling), and conformational and statistical sampling of the environment (by means of molecular dynamics). A new mathematical approach revisiting previous absolute orientation algorithms is also developed to improve alignments of geometries. These approaches are benchmarked through the nπ* band of acrolein not only in the gas phase and water solution but also in a gas-phase/water interface, a common situation for instance in atmospheric chemistry. Subsequently, the best strategy is used to compute the absorption band for the adduct formed upon addition of an OH radical to the C6 position of uracil and compared with the available experimental data. Overall, quantum Wigner sampling of the chromophore with molecular dynamics sampling of the environment with CASPT2 electronic-structure determinations arise as a powerful methodology to predict meaningful σ(λ) and ε(λ) band line shapes with accurate absolute intensities.

Optical properties of photodynamic therapy drugs in different environments: the paradigmatic case of temoporfin

Computational tools have been used to study the photophysical and photochemical features of photosensitizers in photodynamic therapy (PDT) - a minimally invasive, less aggressive alternative for cancer treatment. PDT is mainly based on the activation of molecular oxygen through the action of a photoexcited sensitizer (photosensitizer). Temoporfin, widely known as mTHPC, is a second-generation photosensitizer, which produces the cytotoxic singlet oxygen when irradiated with visible light and hence destroys tumor cells. However, the bioavailability of the mostly hydrophobic photosensitizer, and hence its incorporation into cells, is fundamental to achieve the desired effect on malignant tissues via PDT. In this study, we focus on the optical properties of the temoporfin chromophore in different environments -in vacuo, in solution, encapsulated in drug delivery agents, namely cyclodextrin, and interacting with a lipid bilayer.

Adiabatic-Molecular Dynamics Generalized Vertical Hessian Approach: A Mixed Quantum Classical Method To Compute Electronic Spectra of Flexible Molecules in the Condensed Phase

We present a general mixed quantum classical method that couples classical molecular dynamics (MD) and vibronic models to compute the shape of electronic spectra of flexible molecules in the condensed phase without, in principle, any phenomenological broadening. It is based on a partition of the nuclear motions of the solute + solvent system in "soft" and "stiff" vibrational modes and an adiabatic hypothesis that assumes that stiff modes are much faster than soft ones. In this framework, the spectrum is rigorously expressed as a conformational integral of quantum vibronic spectra along the stiff coordinates only. Soft modes enter at the classical level through the conformational distribution that is sampled with classical MD runs. In each configuration, reduced-dimensionality quadratic Hamiltonians are built in the space of the stiff coordinates only, thanks to a generalization of the Vertical Hessian harmonic model and an iterative application of projectors in internal coordinates to remove soft modes. Quantum vibronic spectra, specific for each sampled configuration of the soft coordinates, are then computed at the desired temperature with efficient time-dependent techniques, and the global spectrum simply arises from their average. For consistency of the whole procedure, classical MD runs are performed with quantum-mechanically derived force fields, parameterized at the same level of theory selected for generating the quadratic Hamiltonians along the stiff coordinates. Application to N-methyl-6-oxyquinolinium betaine in water, dithiophene in ethanol, and cyanidine in water is presented to show the performance of the method.

QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra

Cyanobacteriochromes are compact and spectrally diverse photoreceptor proteins that are promising candidates for biotechnological applications. Computational studies can contribute to an understanding at a molecular level of their wide spectral tuning and diversity. In this contribution, we benchmark methods to model a 110 nm shift in the UV/Vis absorption spectrum from a red- to a green-absorbing form of the cyanobacteriochrome Slr1393g3. Based on an assessment of semiempirical methods to describe the chromophore geometries of both forms in vacuo, we find that DFTB2+D leads to structures that are the closest to the reference method. The benchmark of the excited state calculations is based on snapshots from quantum mechanics/molecular mechanics molecular dynamics simulations. In our case, the methods RI-ADC(2) and sTD-DFT based on CAM-B3LYP ground state calculations perform the best, whereas no functional can be recommended to simulate the absorption spectra of both forms with time-dependent density functional theory. Furthermore, the difference in absorption for the lowest energy absorption maxima of both forms can already be modelled with optimized structures, but sampling is required to improve the shape of the absorption bands of both forms, in particular for the second band. This benchmark study can guide further computational studies, as it assesses essential components of a protocol to model the spectral tuning of both cyanobacteriochromes and the related phytochromes.