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. Six potential mechanisms for reducing the dimethyl disulfide (DMDS) bridge through electron and proton capture were explored. Thermodynamic and kinetic analyses elucidated the sequence of proton and electron addition. MD-PMM, a method that combines molecular dynamics simulations and quantum-chemical calculations, was employed to compute the redox potential of the mechanism. This research provides valuable insights into the mechanisms and redox potentials involved in disulfide bridge reduction within proteins, offering an understanding of phenomena that are challenging to explore experimentally. METHODS: All calculations used the Gaussian 09 software package at the MP2/6-311 + g(d,p) theory level. Visualization of the molecular orbitals and electron densities was conducted using Gaussview6. Molecular dynamics simulations were performed using GROMACS with the CHARMM36 force field. The PyMM program (Python Program for QM/MM Simulations Based on the Perturbed Matrix Method) is used to apply the Perturbed Matrix Method to MD simulations.

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. In this review article, we briefly summarize the present knowledge and understanding of the structure-property relationships of Fe(II) and Fe(III) complexes with excited state lifetimes in the nanosecond range. However, our main focus is to examine to which extent the ultrafast spectroscopy methods used so far provided insight into the excited state structure and the photo-induced dynamics of these complexes. Driven by the main question of how to spectroscopically, i. e. in energy and concentration, differentiate the population of ligand- vs. metal-centered states, the hitherto less exploited ultrafast vibrational spectroscopy is suggested to provide valuable complementary insights.

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. Our results show a qualitative agreement between the RASPT2 reference and the B3LYP computed ESAs of pyrimidines in the near-IR/Visible spectral probing window while for purines the agreement is limited to the near-IR ESAs, with generally larger discrepancies obtained with the CAM-B3LYP functional. This outcome paves the way for appropriate application of cost-effective TD-DFT approaches to simulate linear and non-linear spectroscopies of realistic multichromophoric DNA/RNA systems with biological and nanotechnological relevance.

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. In particular, in this work we discuss and assess in detail the extension of the QM/ELMO approach to density functional theory and post-Hartree-Fock techniques by evaluating its performances when it is used to describe chemical reactions, bond dissociations, and intermolecular interactions. The preliminary test calculations have shown that, in the investigated cases, the new embedding strategy enables the results of the corresponding fully quantum mechanical computations to be reproduced within chemical accuracy in almost all the cases but with a significantly reduced computational cost, especially when correlated post-Hartree-Fock strategies are used to describe the quantum mechanical subsystem. In light of the obtained results, we already envisage the future application of the new correlated QM/ELMO techniques to the investigation of more challenging problems, such as the modeling of enzyme catalysis, the study of excited states of biomolecules, and the refinement of macromolecular X-ray crystal structures.

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. The intensity redistribution between these markers serves as a source of auxiliary structural information capable of pointing to a distortion of the conjugation or to the influence of aggregation effects in the condensed state. A simple relation between the intensity of the marker and the position and oscillator strength of the lowest-energy electronic absorption band of quinoxalinones allows a linking of the Raman effect with the optical properties of these compounds, which can be used for the rational design of novel species with improved optical characteristics.

Electronic structure and optical properties of isolated and TiO2 -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 E0-0 excitation energies and the energy levels alignment (red-ox properties) at the interface with the TiO2 . We find that both vertical and E0-0 excitation energies are accurately reproduced by range-separated functionals, among which the ωB97X-D delivers the lowest absolute deviations from experiments. When the dye/TiO2 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. © 2019 Wiley Periodicals, Inc.

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. For these four carbene bond complexes, ultrafast transient absorption spectroscopy revealed a significant improvement of the excited-state lifetime. A record 32 ps lifetime was measured for a complex bearing a ligand combining a π-deficient pyrazine nucleus and a benzimidazolylidene as NHC. When compared to other azine-based ligands investigated, we argue that the lifetimes are modulated by a small excited state barrier expressing the ability of the ligand to reach the Fe-N distance needed for internal conversion to the ground state.

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. The strong impact of solute-solvent hydrogen bonding on stabilization of these nonequilibrium structures and on conformational composition of DBIQ was demonstrated. A presence of twisted nonplanar geometries along the whole MD trajectory was shown to drastically influence not only energies but also characters of electronic excitations, resulting in a change of local π-π* character in a solution of 1,2-dichloroethane to charge-transfer character in polar dimethylsulfoxide.

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 T1 and the T2 states, respectively, which decay to the ground state via parallel pathways. We find 3-4 ps and 15-20 ps excited-state lifetimes, with respective amplitudes depending on the isomer. The longer lifetime exceeds the one reported for iron complexes with tridentate ligands analogues involving four iron-carbene bonds. By combining experimental and computational results, a mechanism based on the differential trapping of the triplet states in spin-crossover regions is proposed for the first time to explain the impact of the fac/ mer isomerism on the overall excited-state lifetimes. Our results clearly highlight the impact of bidentate pyridyl-NHC ligands on the photophysics of iron complexes, especially the paramount role of fac/ mer isomerism in modulating the overall decay process, which can be potentially exploited in the design of new Fe(II)-based photoactive compounds.

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. A qualitative difference between facial ( fac) and meridional ( mer) isomers' potential energy surface (PES) topologies is evidenced for the first time in iron-based complexes. Indeed, the mer complex shows a steeper triplet path toward the corresponding 3MC minimum, which lies at a lower energy as compared to the fac isomer, thus pointing to a faster triplet decay of the former. Furthermore, while a major role of the metal-centered quintet state population from the triplet 3MC region is excluded, we identify the enlargement of iron-nitrogen bonds as the main normal modes driving the excited-state decay.

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. Experimental transient absorption spectra obtained by UV-vis pump-probe spectroscopy at very short time delays are shown to be directly comparable to theoretical estimates of excited state absorptions (from the low-lying nOπ* and ππ* singlet states) in the Franck-Condon region. Multireference computations provided reliable interpretation of the PP spectra, with TD-DFT results yielding a fair agreement as long as electronic transitions featuring double excitations contributions are not involved. These results lay the groundwork for further computational studies and interpretation of experimental nonlinear electronic spectra of benzophenone in more complex systems, such as BP/DNA adducts.

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. In this review, we will focus on the theoretical simulation of electronic spectroscopies of bio-macromolecules, considering their secondary structure and including their interaction with different kind of (photo)sensitizers. Namely, absorption, emission and electronic circular dichroism (CD) spectra are calculated and compared with the available experimental data. Non-linear properties will be also taken into account by two-photon absorption, a highly promising technique (i) to enhance absorption in the red and infra-red windows and (ii) to enhance spatial resolution. Methodologically, the implications of using implicit and explicit solvent, coupled to quantum and thermal samplings of the phase space, will be addressed. Especially, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are explored for a comparison with solely QM methods, in order to address the necessity to consider an accurate description of environmental effects on spectroscopic properties of biological systems.

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. The comparison with experimental transient absorption data demonstrates the efficiency and accuracy of our approach. Furthermore the explicit inclusion of the solvent, water for simulation and methanol for experiment, allows us, despite the inherent different behavior of the two, to underline the role played by the H-bonding relaxation in the first hundreds of femtoseconds after optical excitation. Finally we predict for the first time the two-dimensional electronic spectrum (2DES) of BP taking into account the vibrational effects and hence modelling partially symmetric and asymmetric ultrafast broadening.

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. A derivation pathway of these novel descriptors is reported, involving a numerical integration to be performed in the Euclidean space on the density functions. This topological analysis is then applied to two sets of chromophores, and the correlation between the level of theory and the behavior of our descriptors is properly rationalized. In particular, the effect of range-separation on the relaxation amplitude is discussed. The relaxation term is finally shown to be system-specific (for a given level of theory) and independent of the number of electrons (i.e., the relaxation amplitude is not simply the result of a collective phenomenon).

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. We illustrate this new method on one-dimensional hydrogen chains and three-dimensional hydrogen clusters. Graphical Abstract Stochastic partition of the molecular orbitals.

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. The ab initio quantitative analysis of the interfacial electron and hole transfers and the measured photovoltaic data clearly evidenced fast recombination reactions for heteroleptics, even associated with un unfavorable directional electron flow, and hence slower injection rates, in the case of homoleptics. Notably, quantum mechanics calculations revealed that deprotonation of the not anchored carboxylic function in the homoleptic complex can effectively accelerate the electron injection rate and completely suppress the electron recombination to the oxidized dye. This result suggests that introduction of strong electron-donating substituents on the not-anchored carbene ligand in heteroleptic complexes, in such a way of mimicking the electronic effects of the carboxylate functionality, should yield markedly improved interfacial charge generation properties. The present results, providing for the first time a detailed understanding of the interfacial electron transfers and photovoltaic characterization in Fe(ii)-carbene sensitized solar cells, open the way to a rational molecular engineering of efficient iron-based dyes for photoelectrochemical applications.

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. The coupling of spectroscopy and molecular simulation allows an efficient one-to-one mapping between structures and optical properties, offering a way to disentangle the rich, yet complicated, quantity of information embedded in circular dichroism spectra. We show that our methodology is robust and efficient and allows us to take into account subtle conformational changes. As such, it could be used as an efficient tool to investigate structural modification upon DNA/drug interactions.

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. In the absence of experimentally resolved structure, the mechanism of DNA damage production remains elusive. Employing a hybrid quantum mechanics/molecular mechanics approach, here we address the spin transfer mechanism between this drug and proximal thymine, that is, the DNA nucleobase most prone to suffer triplet damages.