Absorption Spectrum of Hydroperoxymethyl Thioformate: A Computational Chemistry Study.

Hydroperoxymethyl thioformate (or HPMTF) is a compound relevant to the chemistry of sulfur in the marine atmosphere. The chemical cycling of this molecule in the atmosphere is still uncertain due in part to the lack of accurate knowledge of its photolytic behavior. Only approximations based on the properties of its chromophores are used in previous studies.

DNA Triplet Energies by Free Energy Perturbation Theory.

Determining the energetics of triplet electronic states of nucleobases in the biological macromolecular environment of nucleic acids is essential for an accurate description of the mechanism of photosensitization and the design of drugs for cancer treatment. In this work, we aim at developing a methodological approach to obtain accurate free energies of triplets in DNA beyond the state of the art, able to reproduce the decrease of triplet energies measured experimentally for in DNA (270 kJ/mol) vs in the isolated nucleotide in aqueous solution (310 kJ/mol). For such purposes, we adapt the free energy perturbation method to compute the free energy related to the transformation of a pure singlet state into a pure triplet state via "alchemical" intermediates with mixed singlet-triplet nature.

Role of the stratosphere in the global mercury cycle.

Mercury (Hg) is a global pollutant with substantial risks to human and ecosystem health. By upward transport in tropical regions, mercury enters into the stratosphere, but the contribution of the stratosphere to global mercury dispersion and deposition remains unknown. We find that between 5 and 50% (passing through the 400-kelvin isentropic surface and tropopause, respectively) of the mercury mass deposited on Earth's surface is chemically processed in the lower stratosphere.

The Photophysics and Photochemistry of Phenylalanine, Tyrosine, and Tryptophan: A CASSCF/CASPT2 Study.

Among all amino acids, the three aromatic systems including phenylalanine, tyrosine, and tryptophan are known to manifest UV light absorption at the higher wavelengths. Their fluorescent properties are important for protein detection and determination of the spatial structure. Based on quantum chemical calculations, the absorption spectra in the 0-12 eV UV range of these aromatic amino acids were interpreted, and the photochemistry of the lowest-lying excited states was studied.

Kinetic Study and Reaction Mechanism of the Gas-Phase Thermolysis Reaction of Methyl Derivatives of 1,2,4,5-Tetroxane.

Tetroxane derivatives are interesting drugs for antileishmaniasis and antimalaric treatments. The gas-phase thermal decomposition of 3,6,-dimethyl-1,2,4,5-tetroxane (DMT) and 3,3,6,6,-tetramethyl-1,2,4,5-tetroxane (acetone diperoxide (ACDP)) was studied at 493-543 K by direct gas chromatography by means of a flow reactor. The reaction is produced in the injector chamber at different temperatures.

Photolytic splitting of homodimeric quinone-derived oxetanes studied by ultrafast transient absorption spectroscopy and quantum chemistry.

The photoinduced cycloreversion of oxetane derivatives is of considerable biological interest since these compounds are involved in the photochemical formation and repair of the highly mutagenic pyrimidine (6-4) pyrimidone DNA photoproducts ((6-4)PPs). Previous reports have dealt with the photoreactivity of heterodimeric oxetanes composed mainly of benzophenone (BP) and thymine (Thy) or uracil (Ura) derivatives. However, these models are far from the non-isolable Thy〈º〉Thy dimers, which are the real precursors of (6-4)PPs.

Quantum-Chemistry Study of the Photophysical Properties of 4-Thiouracil and Comparisons with 2-Thiouracil.

DNA in living beings is constantly damaged by exogenous and endogenous agents. However, in some cases, DNA photodamage can have interesting applications, as it happens in photodynamic therapy. In this work, the current knowledge on the photophysics of 4-thiouracil has been extended by further quantum-chemistry studies to improve the agreement between theory and experiments, to better understand the differences with 2-thiouracil, and, last but not least, to verify its usefulness as a photosensitizer for photodynamic therapy.

Electronic spectroscopy of gemcitabine and derivatives for possible dual-action photodynamic therapy applications.

In this paper, we explore the molecular basis of combining photodynamic therapy (PDT), a light-triggered targeted anticancer therapy, with the traditional chemotherapeutic properties of the well-known cytotoxic agent gemcitabine. A photosensitizer prerequisite is significant absorption of biocompatible light in the visible/near IR range, ideally between 600 and 1000 nm. We use highly accurate multiconfigurational CASSCF/MS-CASPT2/MM and TD-DFT methodologies to determine the absorption properties of a series of gemcitabine derivatives with the goal of red-shifting the UV absorption band toward the visible region and facilitating triplet state population.

Reductive Photocycloreversion of Cyclobutane Dimers Triggered by Guanines.

The quest for simple systems achieving the photoreductive splitting of four-membered ring compounds is a matter of interest not only in organic chemistry but also in biochemistry to mimic the activity of DNA photorepair enzymes. In this context, 8-oxoguanine, the main oxidatively generated lesion of guanine, has been shown to act as an intrinsic photoreductant by transferring an electron to bipyrimidine lesions and provoking their cycloreversion. But, in spite of appropriate photoredox properties, the capacity of guanine to repair cyclobutane pyrimidine dimer is not clearly established.

The OpenMolcas : A Community-Driven Approach to Advancing Computational Chemistry.

The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.

Accurate Calculation of Excited-State Absorption for Small-to-Medium-Sized Conjugated Oligomers: Multiconfigurational Treatment vs Quadratic Response TD-DFT.

Excited-state absorption (ESA) spectra of π-conjugated compounds are frequently calculated by (quadratic response) time-dependent density functional theory, (QR) TD-DFT, often giving a reasonable representation of the experimental results despite the (known) incomplete electronic description. To investigate whether this is inherent to the method, we calculate here the ESA spectra of small-to-medium-sized oligophenylenevinylenes (PV) and oligothiophenes (T) using QR TD-DFT as well as CASPT2 based on CASSCF geometries. CASPT2 gives indeed a reliable, theoretically correct description of the ESA features for all compounds; the computational effort can be reduced without significant loss of accuracy using TD-DFT geometries.

Photochemical and thermochemical pathways to S and polysulfur formation in the atmosphere of Venus.

Polysulfur species have been proposed to be the unknown near-UV absorber in the atmosphere of Venus. Recent work argues that photolysis of one of the (SO) isomers, cis-OSSO, directly yields S with a branching ratio of about 10%. If correct, this pathway dominates polysulfur formation by several orders of magnitude, and by addition reactions yields significant quantities of S, S, and S.

The Chemistry of Mercury in the Stratosphere.

Mercury, a global contaminant, enters the stratosphere through convective uplift, but its chemical cycling in the stratosphere is unknown. We report the first model of stratospheric mercury chemistry based on a novel photosensitized oxidation mechanism. We find two very distinct Hg chemical regimes in the stratosphere: in the upper stratosphere, above the ozone maximum concentration, Hg oxidation is initiated by photosensitized reactions, followed by second-step chlorine chemistry.

Reaction of SO with HONO and Implications for Sulfur Partitioning in the Atmosphere.

Sulfur trioxide is a critical intermediate for the sulfur cycle and the formation of sulfuric acid in the atmosphere. The traditional view is that sulfur trioxide is removed by water vapor in the troposphere. However, the concentration of water vapor decreases significantly with increasing altitude, leading to longer atmospheric lifetimes of sulfur trioxide.

Reconstruction of Nuclear Ensemble Approach Electronic Spectra Using Probabilistic Machine Learning.

The theoretical prediction of molecular electronic spectra by means of quantum mechanical (QM) computations is fundamental to gain a deep insight into many photophysical and photochemical processes. A computational strategy that is attracting significant attention is the so-called Nuclear Ensemble Approach (NEA), that relies on generating a representative ensemble of nuclear geometries around the equilibrium structure and computing the vertical excitation energies (Δ) and oscillator strengths () and each transition with a line-shaped function with empirical full-width δ. Frequently, the choice of δ is carried out by visually finding the trade-off between artificial vibronic features (small δ) and over-smoothing of electronic signatures (large δ).

Photoswitching activation of a ferrocenyl-stilbene analogue by its covalent grafting to gold.

Until now, surface-deposited stilbenes have been much less studied than other photochromic systems. Here, an asymmetrically substituted styrene incorporating a redox-active ferrocene moiety and a terminal alkyne group has been synthesised to investigate its photoisomerization in solution, and upon the formation of chemisorbed self-assembled monolayers through a carbon-gold bond formation. Charge transport measurements across the monolayers reveal that upon chemical linkage to the gold substrate there is an alteration of the isomerization pathway, which favours the to conversion, which is not observed in solution.

Quantum-chemistry study of the ground and excited state absorption of distyrylbenzene: Multi vs single reference methods.

State-of-the-art complete active space self-consistent field/complete active space second order perturbation theory (CASPT2) calculations are used to investigate the role of double excitations on the ground state absorption (GSA) and excited state absorption (ESA) spectra of distyrylbenzene, an important prototype medium-sized π-conjugated organic compound for optoelectronics. The multi-reference results are compared with linear and quadratic response time-dependent density functional theory (DFT) results, revealing an incomplete description of the electronic transitions in the latter. Careful selection of the active space and basis set in the CASPT2 approach allows for a reliable description of the GSA and ESA features; cost-effective DFT-based geometries can be utilized without a significant loss of accuracy.

Photochemistry of HOSO and SO and Implications for the Production of Sulfuric Acid.

Sulfur trioxide (SO) and the hydroxysulfonyl radical (HOSO) are two key intermediates in the production of sulfuric acid (HSO) on Earth's atmosphere, one of the major components of acid rain. Here, the photochemical properties of these species are determined by means of high-level quantum chemical methodologies, and the potential impact of their light-induced reactivity is assessed within the context of the conventional acid rain generation mechanism. Results reveal that the photodissociation of HOSO occurs primarily in the stratosphere through the ejection of hydroxyl radicals (OH) and sulfur dioxide (SO).

Light-Induced On/Off Switching of the Surfactant Character of the o-Cobaltabis(dicarbollide) Anion with No Covalent Bond Alteration.

Cobaltabis(dicarbollide) anion ([o-COSAN] ) is a well-known metallacarborane with multiple applications in a variety of fields. In aqueous solution, the cisoid rotamer is the most stable disposition in the ground state. The present work provides theoretical evidence on the possibility to photoinduce the rotation from the cisoid to the transoid rotamer, a conversion that can be reverted when the ground state is repopulated.

Building a Functionalizable, Potent Chemiluminescent Agent: A Rational Design Study on 6,8-Substituted Luminol Derivatives.

Luminol is a prominent chemiluminescent (CL) agent, finding applications across numerous fields, including forensics, immunoassays, and imaging. Different substitution patterns on the aromatic ring can enhance or decrease its CL efficiency. We herein report a systematic study on the synthesis and photophysics of all possible 6,8-disubstituted luminol derivatives bearing H, Ph, and/or Me substituents.

Photochemistry and Non-adiabatic Photodynamics of the HOSO Radical.

Hydroxysulfinyl radical (HOSO) is important due to its involvement in climate geoengineering upon SO injection and generation of the highly hygroscopic HSO. Its photochemical behavior in the upper atmosphere is, however, uncertain. Here we present the ultraviolet-visible photochemistry and photodynamics of this species by simulating the atmospheric conditions with high-level quantum chemistry methods.

Theoretical Study on the Photo-Oxidation and Photoreduction of an Azetidine Derivative as a Model of DNA Repair.

Photocycloreversion plays a central role in the study of the repair of DNA lesions, reverting them into the original pyrimidine nucleobases. Particularly, among the proposed mechanisms for the repair of DNA (6-4) photoproducts by photolyases, it has been suggested that it takes place through an intermediate characterized by a four-membered heterocyclic oxetane or azetidine ring, whose opening requires the reduction of the fused nucleobases. The specific role of this electron transfer step and its impact on the ring opening energetics remain to be understood.

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, = ∫ ϕ(λ) σ(λ) (λ) dλ, are needed, where ϕ(λ) and (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.