Unraveling redox pathways of the disulfide bond in dimethyl disulfide: Ab initio modeling.

Context: In cellular environments, the reduction of disulfide bonds is pivotal for protein folding and synthesis. However, the intricate enzymatic mechanisms governing this process remain poorly understood. This study addresses this gap by investigating a disulfide bridge reduction reaction, serving as a model for comprehending electron and proton transfer in biological systems.

Ultrafast Spectroscopy of Fe(II) Complexes Designed for Solar-Energy Conversion: Current Status and Open Questions.

One major challenge of future sustainable photochemistry is to replace precious and rare transition metals in applications such as energy conversion or electroluminescence by earth-abundant, cheap, and recyclable materials. This involves using coordination complexes of first row transition metals such as Cu, Cr, or Mn. In the case of iron, which is attractive due to its natural abundance, fundamental limitations imposed by the small ligand field splitting energy have recently been overcome.

First-principles characterization of the singlet excited state manifold in DNA/RNA nucleobases.

An extensive theoretical characterization of the singlet excited state manifold of the five canonical DNA/RNA nucleobases (thymine, cytosine, uracil, adenine and guanine) in gas-phase is carried out with time-dependent density functional theory (TD-DFT) and restricted active space second-order perturbation theory (RASPT2) approaches. Both ground state and excited state absorptions are analyzed and compared between these different theoretical approaches, assessing the performance of the hybrid B3LYP and CAM-B3LYP (long-range corrected) functionals with respect to the RASPT2 reference. By comparing the TD-DFT estimates with our reference for high-lying excited states, we are able to narrow down specific energetic windows where TD-DFT may be safely employed to qualitatively reproduce the excited state absorption (ESA) signals registered in non-linear and time-resolved spectroscopy for monitoring photoinduced phenomena.

Localized Molecular Orbital-Based Embedding Scheme for Correlated Methods.

Embedding strategies currently provide the best compromise between accuracy and computational cost in modeling chemical properties and processes of large and complex systems. In this framework, different methods have been proposed all over the years, from the very popular QM/MM approaches to the more recent and very promising density matrix and density functional embedding techniques. Here, we present a further development of the quantum mechanics/extremely localized molecular orbital technique (QM/ELMO) method, a recently proposed multiscale embedding strategy in which the chemically active region of the investigated system is treated at a fully quantum mechanical level, while the rest is described by frozen extremely localized molecular orbitals previously transferred from proper libraries or tailor-made model molecules.

Characterization of Conjugation Effects in the Series of Quinoxaline-2-ones by Means of Vibrational Raman Spectroscopy.

A broad series of quinoxalinone-based π-conjugated donor-acceptor fluoro- and NLO-phores is characterized by means of Raman spectroscopy and single-crystal X-ray analysis supported by quantum chemical computations. Intense Raman spectroscopic markers that allow the differentiation of even closely related structures are identified. The intensities of these bands are shown to be related to the conjugation of the different molecular moieties, and they can provide an estimation of its extent.

Electronic structure and optical properties of isolated and TiO -grafted free base porphyrins for water oxidation: A challenging test case for DFT and TD-DFT.

Seven free base porphyrins employed in dye-sensitized photoelectrosynthetic cells are investigated with the aim of benchmarking the ability of different density functional theory (DFT) and time-dependent DFT approaches in reproducing their structure, vertical, and E excitation energies and the energy levels alignment (red-ox properties) at the interface with the TiO . We find that both vertical and E excitation energies are accurately reproduced by range-separated functionals, among which the ωB97X-D delivers the lowest absolute deviations from experiments. When the dye/TiO interface is modeled, the physical interfacial energetics is only obtained when the B3LYP functional is employed; on the other hand, M06-2X (54% of exchange) and the two long-range corrected approaches tested (CAM-B3LYP and ωB97X-D) excessively destabilize the semiconductor conduction band levels with respect to the dye's lowest unoccupied molecular orbitals (LUMOs), predicting no pathway for electron injection.

2,3-(Dibenzimidazol-2-yl)quinoxalines: Unexpected Dynamical Effect on Steady-State Electronic Absorption Spectra.

We report on the electronic absorption spectra, conformational behavior, and intra- and intermolecular hydrogen bonds of 2,3-(dibenzimidazol-2-yl)-quinoxaline (DBIQ). The experimentally found strong solvent dependence of the absorption spectra of DBIQ solutions cannot be assigned to electronic excitations of the equilibrium ground-state DBIQ structure. Extended consideration including the nonequilibrium structures within the framework of ab initio molecular dynamics (MD) revealed the importance of torsion molecular motions not covered by the static case.

Iron(ii) complexes with diazinyl-NHC ligands: impact of π-deficiency of the azine core on photophysical properties.

Ligand field enhancing N-heterocyclic carbene (NHC) ligands were recently shown to prevent photo-induced spin crossover in Fe(ii) complexes due to their intricate effects on the electronic excited state structure. Due to their pico- to nanosecond lifetimes, these complexes are now good candidates for photo-sensitizing applications. Herein we report the synthesis and photophysical characterization of a new family of homoleptic Fe(ii) complexes with C^N^C ligands involving diazines as the central N-heteroaromatic ligand.

Impact of the fac/ mer Isomerism on the Excited-State Dynamics of Pyridyl-carbene Fe(II) Complexes.

The control of photophysical properties of iron complexes and especially of their excited states decay is a great challenge in the search for sustainable alternatives to noble metals in photochemical applications. Herein we report the synthesis and investigations of the photophysics of mer and fac iron complexes bearing bidentate pyridyl-NHC ligands, coordinating the iron with three ligand-field-enhancing carbene bonds. Ultrafast transient absorption spectroscopy reveals two distinct excited state populations for both mer and fac forms, ascribed to the populations of the T and the T states, respectively, which decay to the ground state via parallel pathways.

Synthesis and Computational Study of a Pyridylcarbene Fe(II) Complex: Unexpected Effects of fac/ mer Isomerism in Metal-to-Ligand Triplet Potential Energy Surfaces.

The synthesis and the steady-state absorption spectrum of a new pyridine-imidazolylidene Fe(II) complex (Fe-NHC) are presented. A detailed mechanism of the triplet metal-to-ligand charge-transfer states decay is provided on the basis of minimum energy path (MEP) calculations used to connect the lowest-lying singlet, triplet, and quintet state minima. The competition between the different decay pathways involved in the photoresponse is assessed by analyzing the shapes of the obtained potential energy surfaces.

Steady-State Linear and Non-linear Optical Spectroscopy of Organic Chromophores and Bio-macromolecules.

Bio-macromolecules as DNA, lipid membranes and (poly)peptides are essential compounds at the core of biological systems. The development of techniques and methodologies for their characterization is therefore necessary and of utmost interest, even though difficulties can be experienced due to their intrinsic complex nature. Among these methods, spectroscopies, relying on optical properties are especially important to determine their macromolecular structures and behaviors, as well as the possible interactions and reactivity with external dyes-often drugs or pollutants-that can (photo)sensitize the bio-macromolecule leading to eventual chemical modifications, thus damages.

Resolving the Singlet Excited State Manifold of Benzophenone by First-Principles Simulations and Ultrafast Spectroscopy.

Accurate characterization of the high-lying excited state manifolds of organic molecules is of fundamental importance for the interpretation of the rich response detected in time-resolved nonlinear electronic spectroscopies. Here, we have characterized the singlet excited state manifold of benzophenone (BP), a versatile organic photoinitiator and a well-known DNA photosensitizer. Benchmarks of various multiconfigurational/multireference (RASSCF/PT2) and time-dependent density functional theory (TD-DFT) approaches allowed assignments of experimental linear absorption signals of BP in the ultraviolet (UV) region, with unprecedented characterization of ground state absorptions in the far UV.

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

Benzophenone (BP) despite its relatively simple molecular structure is a paradigmatic sensitizer, featuring both photocatalytic and photobiological effects due to its rather complex photophysical properties. In this contribution we report an original theoretical approach to model realistic, ultra-fast spectroscopy data, which requires describing intra- and intermolecular energy and structural relaxation. In particular we explicitly simulate time-resolved pump-probe spectra using a combination of state-of-the art hybrid quantum mechanics/molecular mechanics dynamics to treat relaxation and vibrational effects.

Unveiling the nature of post-linear response Z-vector method for time-dependent density functional theory.

We report a theoretical study on the analysis of the relaxed one-particle difference density matrix characterizing the passage from the ground to the excited state of a molecular system, as obtained from time-dependent density functional theory. In particular, this work aims at using the physics contained in the so-called Z-vector, which differentiates between unrelaxed and relaxed difference density matrices to analyze excited states' nature. For this purpose, we introduce novel quantum-mechanical quantities, based on the detachment/attachment methodology, for analysing the Z-vector transformation for different molecules and density functional theory functionals.

Iterative stochastic subspace self-consistent field method.

We propose a new self-consistent field (SCF) algorithm based on an iterative, partially stochastic "Divide & Conquer"-type approach. This new SCF algorithm is a simple variant of the usual SCF procedure and can be easily implemented in parallel. A detailed description of the algorithm is reported.

Interfacial charge separation and photovoltaic efficiency in Fe(ii)-carbene sensitized solar cells.

The first combined theoretical and photovoltaic characterization of both homoleptic and heteroleptic Fe(ii)-carbene sensitized photoanodes in working dye sensitized solar cells (DSSCs) has been performed. Three new heteroleptic Fe(ii)-NHC dye sensitizers have been synthesized, characterized and tested. Despite an improved interfacial charge separation in comparison to the homoleptic compounds, the heteroleptic complexes did not show boosted photovoltaic performances.

A new record excited state (3)MLCT lifetime for metalorganic iron(ii) complexes.

Herein we report the synthesis and time-resolved spectroscopic characterization of a homoleptic Fe(ii) complex exhibiting a record (3)MLCT lifetime of 26 ps promoted by benzimidazolylidene-based ligands. Time dependent density functional molecular modeling of the triplet excited state manifold clearly reveals that, at equilibrium geometries, the lowest (3)MC state lies higher in energy than the lowest (3)MLCT one. This unprecedented energetic reversal in a series of iron complexes, with the stabilization of the charge-transfer state, opens up new perspectives towards iron-made excitonic and photonic devices, hampering the deactivation of the excitation via metal centered channels.

Circular Dichroism of DNA G-Quadruplexes: Combining Modeling and Spectroscopy To Unravel Complex Structures.

We report on the comparison between the computational and experimental determination of electronic circular dichroism spectra of different guanine quadruplexes obtained from human telomeric sequences. In particular the difference between parallel, antiparallel, and hybrid structures is evidenced, as well as the induction of transitions between the polymorphs depending on the solution environment. Extensive molecular dynamics simulations (MD) are used to probe the conformational space of the different quadruplexes, and subsequently state-of-the-art hybrid quantum mechanics/molecular mechanics (QM/MM) techniques coupled with excitonic semiempirical Hamiltonian are used to simulate the macromolecular induced circular dichroism.

Interaction of Iron II Complexes with B-DNA. Insights from Molecular Modeling, Spectroscopy, and Cellular Biology.

We report the characterization of the interaction between B-DNA and three terpyridin iron II complexes. Relatively long time-scale molecular dynamics (MD) is used in order to characterize the stable interaction modes. By means of molecular modeling and UV-vis spectroscopy, we prove that they may lead to stable interactions with the DNA duplex.

Resolving the Benzophenone DNA-Photosensitization Mechanism at QM/MM Level.

Benzophenone, the parent of the diarylketone family, is a versatile compound commonly used as a UV blocker. It may also trigger triplet-based DNA photosensitization. Therefore, benzophenone is involved in DNA photodamage induction.

New Insight into the Topology of Excited States through Detachment/Attachment Density Matrices-Based Centroids of Charge.

In parallel with the derivation of a novel descriptor (ϕS) related to chromophores' electronic excited states topology, the present article emphasizes some congruence of significance between our ϕS index and formerly developed centroid-related indices. We especially point out the possibility to formally adapt a barycenter (centroid) approach to the use of detachment/attachment densities. While the reciprocity of the two approaches can be mathematically evidenced, we will show that some difficulties brought by the use of ground and excited states electron densities in direct space can be overcome by undertaking some operations on the Hilbert space-related detachment/attachment matrices.

Toward a Quantitative Assessment of Electronic Transitions' Charge-Transfer Character.

We hereby report studies devoted to a topological descriptor of photoinduced electronic charge density variation. Our novel index, symbolized as ϕS, consists in the detachment and attachment densities overlap, where the detachment density physically depicts the electron density removed from the ground state of a molecule during the transition while the attachment density consists in the rearranged density in the excited state. Our method provides a simple and efficient way to quantitatively evaluate how easy the charge-separation is made upon the chromophore's light absorption.

Photophysical properties of ruthenium(II) polypyridyl DNA intercalators: effects of the molecular surroundings investigated by theory.

The environmental effects on the structural and photophysical properties of [Ru(L)2 (dppz)](2+) complexes (L=bpy=2,2'-bipyridine, phen=1,10-phenanthroline, tap=1,4,5,8-tetraazaphenanthrene; dppz=dipyrido[3,3-a:2',3'-c]phenazine), used as DNA intercalators, have been studied by means of DFT, time-dependent DFT, and quantum mechanics/molecular mechanics calculations. The electronic characteristics of the low-lying triplet excited states in water, acetonitrile, and DNA have been investigated to decipher the influence of the environment on the luminescent behavior of this class of molecules. The lowest triplet intra-ligand (IL) excited state calculated at λ≈800 nm for the three complexes and localized on the dppz ligand is not very sensitive to the environment and is available for electron transfer from a guanine nucleobase.

Lipid Peroxidation in Membranes: The Peroxyl Radical Does Not "Float".

Lipid peroxidation is a fundamental phenomenon in biology and medicine involved in a wide range of diseases. Some key microscopic aspects of this reaction in cell membranes are still poorly studied. In particular, it is commonly accepted that the propagation of the radical reaction in lipid bilayers is hampered by the rapid diffusion of peroxyl intermediates toward the water interface, that is, out of the reaction region.