DszA Catalyzes C-S Bond Cleavage through N5-Hydroperoxyl Formation.

Due to its detrimental impact on human health and the environment, regulations demand ultralow sulfur levels on fossil fuels, in particular in diesel. However, current desulfurization techniques are expensive and cannot efficiently remove heteroaromatic sulfur compounds, which are abundant in crude oil and concentrate in the diesel fraction after distillation. Biodesulfurization via the four enzymes of the metabolic 4S pathway of the bacterium Rhodococcus erythropolis (DszA-D) is a possible solution. However, the 4S pathway needs to operate at least 500 times faster for industrial applicability, a goal currently pursued through enzyme engineering. In this work, we unveil the catalytic mechanism of the flavin monooxygenase DszA. Surprisingly, we found that this enzyme follows a recently proposed atypical mechanism that passes through the formation of an N5OOH intermediate at the re side of the cofactor, aided by a well-defined, predominantly hydrophobic O2 pocket. Besides clarifying the unusual chemical mechanism of the complex DszA enzyme, with obvious implications for understanding the puzzling chemistry of flavin-mediated catalysis, the result is crucial for the rational engineering of DszA, contributing to making biodesulfurization attractive for the oil refining industry.

Cyclopentene ring effects in cyanine dyes: a handle to fine-tune photophysical properties.

The aim of this study is to investigate the photophysical properties of a cyanine dye analogue by performing first-principles calculations based on density functional theory (DFT) and time dependent-DFT. Cationic cyanine dyes are the subject of great importance due to their versatile applications and the tunability of their photophysical properties, such as by modifying their end groups and chain length. An example of this is the vinylene shift, which is experimentally known for these molecules, and it consists of a bathochromic (red) shift of approximately 100 nm of the 0-0 vibronic transition when a vinyl group is added to the polymethine chain. Our study shows that when the saturated moiety C2H4 of the cyclopentene ring is added to the chain, it interacts with the conjugated π-system, resulting in a smaller HOMO-LUMO gap. Here, we demonstrate the origin of this interaction and how it can be used to fine tune the absorption energies of this class of dyes.

Changes in aromaticity of spin-crossover complexes: a signature for non-innocent ligands.

The influence of the spin state of the metal centre in spin crossover compounds on the aromaticity of the ligands has been investigated for iron(II)tris-bipyridine (Fe(bpy)32+), and Fe(II)(formazanate)2 (as a truncated model and the full phenyl substituted compound). It was found that the aromaticity of the bipyridine ligands is unaffected by changing the spin state of the central iron atom, but that of the formazanate ligands is reduced upon transition to the high-spin state. This change in aromaticity is rationalized using the symmetry selection rules for aromaticity in terms of virtual excitations from occupied to empty orbitals. A further consequence of this loss in aromaticity is a shift to higher energy in the ring vibrations of the formazanate compounds that can be observed in either its IR or Raman spectrum; this prediction has been confirmed here. This change in aromaticity as a consequence of change in spin state can be regarded as an indication for non-innocent ligands.

The Challenging World of Simple Inorganic Rings: Revisiting Roesky's Ketone and Roesky's Sulfoxide.

The surprising differences between the experimental solid-state and calculated gas-phase structures of 5-oxo-1,3,2,4-dithiadiazole (Roesky's ketone, 1) and 1-oxo-1,2,4,3,5-trithiadiazole (Roesky's sulfoxide, 2), identified and studied in a series of papers published between 2004 and 2010 but then never satisfactorily explained, have been revisited, making use of the more advanced computational possibilities currently available. The previous calculations' considerable overestimations of the C-S and S-S bond lengths in 1 and 2, respectively, have been partly explained based on the results of periodic calculations and the application of Valence Bond (VB) Theory. In the case of 1, the crystal environment appears to stabilize a structure with a highly polarized C=O bond, which features a C-S bond with considerable double-bond character - an effect which does not exist for the isolated molecule - explaining the much shorter bond in the solid state. For 2, a similar conclusion can be drawn for the S-S distance. For both compounds, though, packing effects are not the sole source of the differences: the inability of Density Functional Theory (DFT) to properly deal with the electronic structures of these apparently simple main-group systems remains a contributing factor.

Revisiting sp2 Dilithio Methandiides: From Geometric Curiosity to Simple Bonding Description.

The reported tetracoordinate dilithio methandiide complex from Liddle and co-workers (1) is investigated from a coordination chemistry perspective, to probe the origin of its intriguing geometry. Through the application of a variety of computational techniques, non-covalent (steric, electrostatic) interactions are found to be dominant. Further, we arrive at a bonding description which emphasizes the tricoordinate sp2 -hybridized nature of the central methandiide carbon, differing somewhat from the original proposal. Thus, 1 is distinct from other dilithio methandiides since it contains only one C-Li σ-bond, and is found to be comparable to a simple aryllithium compound, phenyllithium.

A Predictive Model for the Pd-Catalyzed Site-Selective Oxidation of Diols.

A predictive model, shaped as a set of rules, is presented that predicts site-selectivity in the mono-oxidation of diols by palladium-neocuproine catalysis. For this, the factors that govern this site-selectivity within diols and between different diols have been studied both experimentally and with computation. It is shown that an electronegative substituent antiperiplanar to the C-H bond retards hydride abstraction, resulting in a lower reactivity. This explains the selective oxidation of axial hydroxy groups in vicinal cis-diols. Furthermore, DFT calculations and competition experiments show how the reaction rate of different diols is determined by their configuration and conformational freedom. The model has been validated by the oxidation of several complex natural products, including two steroids. From a synthesis perspective, the model predicts whether a natural product comprising multiple hydroxy groups is a suitable substrate for site-selective palladium-catalyzed oxidation.

Spark Discharge Doping-Achieving Unprecedented Control over Aggregate Fraction and Backbone Ordering in Poly(3-hexylthiophene) Solutions.

The properties of semiconducting polymers are strongly influenced by their aggregation behavior, that is, their aggregate fraction and backbone planarity. However, tuning these properties, particularly the backbone planarity, is challenging. This work introduces a novel solution treatment to precisely control the aggregation of semiconducting polymers, namely current-induced doping (CID). It utilizes spark discharges between two electrodes immersed in a polymer solution to create strong electrical currents resulting in temporary doping of the polymer. Rapid doping-induced aggregation occurs upon every treatment step for the semiconducting model-polymer poly(3-hexylthiophene). Therefore, the aggregate fraction in solution can be precisely tuned up to a maximum value determined by the solubility of the doped state. A qualitative model for the dependences of the achievable aggregate fraction on the CID treatment strength and various solution parameters is presented. Moreover, the CID treatment can yield an extraordinarily high quality of backbone order and planarization, expressed in UV-vis absorption spectroscopy and differential scanning calorimetry measurements. Depending on the selected parameters, an arbitrarily lower backbone order can be chosen using the CID treatment, allowing for maximum control of aggregation. This method may become an elegant pathway to finely tune aggregation and solid-state morphology for thin-films of semiconducting polymers.

The Halogen Bond in Weakly Bonded Complexes and the Consequences for Aromaticity and Spin-Orbit Coupling.

The halogen bond complexes CF3X⋯Y and C2F3X⋯Y, with Y = furan, thiophene, selenophene and X = Cl, Br, I, have been studied by using DFT and CCSD(T) in order to understand which factors govern the interaction between the halogen atom X and the aromatic ring. We found that PBE0-dDsC/QZ4P gives an adequate description of the interaction energies in these complexes, compared to CCSD(T) and experimental results. The interaction between the halogen atom X and the π-bonds in perpendicular orientation is stronger than the interaction with the in-plane lone pairs of the heteroatom of the aromatic cycle. The strength of the interaction follows the trend Cl < Br < I; the chalcogenide in the aromatic ring nor the hybridization of the C−X bond play a decisive role. The energy decomposition analysis shows that the interaction energy is dominated by all three contributions, viz., the electrostatic, orbital, and dispersion interactions: not one factor dominates the interaction energy. The aromaticity of the ring is undisturbed upon halogen bond formation: the π-ring current remains equally strong and diatropic in the complex as it is for the free aromatic ring. However, the spin-orbit coupling between the singlet and triplet π→π* states is increased upon halogen bond formation and a faster intersystem crossing between these states is therefore expected.

Spectroscopic Manifestations and Implications for Catalysis of Quasi-d10 Configurations in Formal Gold(III) Complexes.

Several gold +I and +III complexes are investigated computationally and spectroscopically, focusing on the d-configuration and physical oxidation state of the metal center. Density functional theory calculations reveal the non-negligible electron-sharing covalent character of the metal-to-ligand σ-bonding framework. The bonding of gold(III) is shown to be isoelectronic to the formal CuIII complex [Cu(CF3 )4 ]1- , in which the metal center tries to populate its formally unoccupied 3dx2-y2 orbital via σ-bonding, leading to a reduced d10 CuI description. However, Au L3 -edge X-ray absorption spectroscopy reveals excitation into the d-orbital of the AuIII species is still possible, showing that a genuine d10 configuration is not achieved. We also find an increased electron-sharing nature of the σ-bonds in the AuI species, relative to their AgI and CuI analogues, due to the low-lying 6s orbital. We propose that gold +I and +III complexes form similar bonds with substrates, owing primarily to participation of the 5dx2-y2 or 6s orbital, respectively, in bonding, indicating why AuI and AuIII complexes often have similar reactivity.

Strategies for Enhancing the Dielectric Constant of Organic Materials.

High dielectric constant organic semiconductors, often obtained by the use of ethylene glycol (EG) side chains, have gained attention in recent years in the efforts of improving the device performance for various applications. Dielectric constant enhancements due to EGs have been demonstrated extensively, but various effects, such as the choice of the particular molecule and the frequency and temperature regime, that determine the extent of this enhancement require further understanding. In this work, we study these effects by means of polarizable molecular dynamics simulations on a carefully selected set of fullerene derivatives with EG side chains. The selection allows studying the dielectric response in terms of both the number and length of EG chains and also the choice of the group connecting the fullerene to the EG chain. The computed time- and frequency-dependent dielectric responses reveal that the experimentally observed rise of the dielectric constant within the kilo/megahertz regime for some molecules is likely due to the highly stretched dielectric response of the EGs: the initial sharp increase over the first few nanoseconds is followed by a smaller but persistent increase in the range of microseconds. Additionally, our computational protocol allows the separation of different factors that contribute to the overall dielectric constant, providing insights to make several molecular design guides for future organic materials in order to enhance their dielectric constant further.

Toward Detection of the Molecular Parity Violation in Chiral Ru(acac)3 and Os(acac)3.

We present a theory-experiment investigation of the helically chiral compounds Ru(acac)3 and Os(acac)3 as candidates for next-generation experiments for detection of molecular parity violation (PV) in vibrational spectra. We used relativistic density functional theory calculations to identify optimal vibrational modes with expected PV effects exceeding by up to 2 orders of magnitude the projected instrumental sensitivity of the ultrahigh resolution experiment under construction at the Laboratoire de Physique des Lasers in Paris. Preliminary measurements of the vibrational spectrum of Ru(acac)3 carried out as the first steps toward the planned experiment are presented.

Modelling structural properties of cyanine dye nanotubes at coarse-grained level.

Self-assembly is a ubiquitous process spanning from biomolecular aggregates to nanomaterials. Even though the resulting aggregates can be studied through experimental techniques, the dynamic pathways of the process and the molecular details of the final structures are not necessarily easy to resolve. Consequently, rational design of self-assembling aggregates and their properties remains extremely challenging. At the same time, modelling the self-assembly with computational methods is not trivial, because its spatio-temporal scales are usually beyond the limits of all-atom based simulations. The use of coarse-grained (CG) models can alleviate this limitation, but usually suffers from the lack of optimised parameters for the molecular constituents. In this work, we describe the procedure of parametrizing a CG Martini model for a cyanine dye (C8S3) that self-assembles into hollow double-walled nanotubes. First, we optimised the model based on quantum mechanics calculations and all-atom reference simulations, in combination with available experimental data. Then, we conducted random self-assembly simulations, and the performance of our model was tested on preformed assemblies. Our simulations provide information on the time-dependent local arrangement of this cyanine dye, when aggregates are being formed. Furthermore, we provide guidelines for designing and optimising parameters for similar self-assembling nanomaterials.

Length-dependent symmetry in narrow chevron-like graphene nanoribbons.

We report the structural and electronic properties of narrow chevron-like graphene nanoribbons (GNRs), which depending on their length are either mirror or inversion symmetric. Additionally, GNRs of different length can form molecular heterojunctions based on an unusual binding motif.

[Fe4S4] cubane in sulfite reductases: new insights into bonding properties and reactivity.

The dissimilatory sulfite reductase enzyme has very characteristic active site where the substrate binds to an iron site, ligated by a siroheme macrocycle and a thiol directly connected to a [Fe4S4] cluster. This arrangement gives the enzyme remarkable efficiency in reducing sulfite and nitrite all the way to hydrogen sulfide and ammonia. For the first time we present a theoretical study where substrate binding modalities and activation are elucidated using active site models containing proton supply side chains and the [Fe4S4] cluster. Density functional theory (DFT) was deployed in conjunction with the energy decomposition scheme (as implemented in AMS), the quantum theory of atoms in molecules (QTAIM), and conceptual DFT (cDFT) descriptors. We quantified the role of the electrostatic interactions inside the active site created by the side chains as well as the influence of the [Fe4S4] cluster on the substrate binding. Furthermore, using conceptual DFT results we shed light of the activation process, thus, laying foundation for further mechanistic studies. We found that the bonding of the ligands to the iron complex is dominated by electrostatic interactions, but the presence of the [Fe4S4] cubane leads to substantial changes in electronic interaction. The spin state of the cubane, however, affects the binding energy only marginally. The conceptual DFT results show that the presence of the [Fe4S4] cubane affects the reactivity of the active site as it is involved in electron transfer. This is corroborated by an increase in the electrophilicity index, thus making the active site more prone to react with the ligands. The interaction energies between the ligand and the siroheme group are also increased upon the presence of the cubane group, thus, suggesting that the siroheme group is not an innocent spectator but plays an active role in the reactivity of the dSIR active site.

How reduced are nucleophilic gold complexes?

Nucleophilic formal gold(-I) and gold(I) complexes are investigated via Intrinsic Bond Orbital analysis and Energy Decomposition Analysis, based on density functional theory calculations. The results indicate gold(0) centres engaging in electron-sharing bonding with Al- and B- based ligands. Multiconfigurational (CASSCF) calculations corroborate the findings, highlighting the gap between the electonic structures and the oxidation state formalism.

Gold-Aluminyl and Gold-Diarylboryl Complexes: Bonding and Reactivity with Carbon Dioxide.

The unconventional carbon dioxide insertion reaction of a gold-aluminyl [tBu3PAuAl(NON)] complex has been recently shown to be related to the electron-sharing character of the Au-Al bond that acts as a nucleophile and stabilizes the insertion product through a radical-like behavior. Since a gold-diarylboryl [IPrAuB(o-tol)2] complex with similar reactivity features has been recently reported, in this work we computationally investigate the reaction of carbon dioxide with [LAuX] (L = phosphine, N-heterocyclic carbene (NHC); X = Al(NON), B(o-tol)2) complexes to get insights into the Al/B anionic and gold ancillary ligand effects on the Au-Al/B bond nature, electronic structure, and reactivity of these compounds. We demonstrate that the Au-Al and Au-B bonds possess a similar electron-sharing nature, with diarylboryl complexes displaying a slightly more polarized bond as Au(δ+)-B(δ-). This feature reduces the radical-like reactivity toward CO2, and the Al/B anionic ligand effect is found to favor aluminyls over boryls, despite the greater oxophilicity of B. Remarkably, the ancillary ligand of gold has a negligible electronic trans effect on the Au-X bond and only a minor impact on the formation of the insertion product, which is slightly more stable with carbene ligands. Surprisingly, we find that the modification of the steric hindrance at the carbene site may exert a sizable control over the reaction, with more sterically hindered ligands thermodynamically disfavoring the formation of the CO2 insertion product.

Homolytic X-H Bond Cleavage at a Gold(III) Hydroxide: Insights into One-Electron Events at Gold.

C(sp3 )-H and O-H bond breaking steps in the oxidation of 1,4-cyclohexadiene and phenol by a Au(III)-OH complex were studied computationally. The analysis reveals that for both types of bonds the initial X-H cleavage step proceeds via concerted proton coupled electron transfer (cPCET), reflecting electron transfer from the substrate directly to the Au(III) centre and proton transfer to the Au-bound oxygen. This mechanistic picture is distinct from the analogous formal Cu(III)-OH complexes studied by the Tolman group (J. Am. Chem. Soc. 2019, 141, 17236-17244), which proceed via hydrogen atom transfer (HAT) for C-H bonds and cPCET for O-H bonds. Hence, care should be taken when transferring concepts between Cu-OH and Au-OH species. Furthermore, the ability of Au-OH complexes to perform cPCET suggests further possibilities for one-electron chemistry at the Au centre, for which only limited examples exist.

Revisiting Formal Copper(III) Complexes: Bridging Perspectives with Quasi-d 10 Configurations.

The formal Cu(III) complex [Cu(CF3)4]1- has often served as a paradigmatic example of challenging oxidation state assignment - with many reports proposing conflicting descriptions. Here we report a computational analysis of this compound, employing Energy Decomposition Analysis and Intrinsic Bond Orbital Analysis. We present a quasi-d 10 perspective of the metal centre, resulting from ambiguities in d-electron counting. The implications for describing reactions which undergo oxidation state changes, such as the formal reductive elimination from the analogous [Cu(CF3)3(CH2Ph)]1- complex (Paeth et al. J. Am. Chem. Soc. 2019, 141, 3153), are probed. Electron flow analysis finds that the changes in electronic structure may be understood as a quasi-d 10 to d 10 transition at the metal centre, rendering this process essentially redox neutral. This is reminiscent of a previously studied formal Ni(IV) complex (Steen et al., Angew. Chem. Int. Ed. 2019, 58, 13133-13139), and indicates that our description of electronic structure has implications for the understanding of elementary organometallic reaction steps.

Fullerene derivatives with oligoethylene-glycol side chains: an investigation on the origin of their outstanding transport properties.

For many years, fullerene derivatives have been the main n-type material of organic electronics and optoelectronics. Recently, fullerene derivatives functionalized with ethylene glycol (EG) side chains have been showing important properties such as enhanced dielectric constants, facile doping and enhanced self-assembly capabilities. Here, we have prepared field-effect transistors using a series of these fullerene derivatives equipped with EG side chains of different lengths. Transport data show the beneficial effect of increasing the EG side chain. In order to understand the material properties, full structural determination of these fullerene derivatives has been achieved by coupling the X-ray data with molecular dynamics (MD) simulations. The increase in transport properties is paired with the formation of extended layered structures, efficient molecular packing and an increase in the crystallite alignment. The layer-like structure is composed of conducting layers, containing of closely packed C60 balls approaching the inter-distance of 1 nm, that are separated by well-defined EG layers, where the EG chains are rather splayed with the chain direction almost perpendicular to the layer normal. Such a layered structure appears highly ordered and highly aligned with the C60 planes oriented parallel to the substrate in the thin film configuration. The order inside the thin film increases with the EG chain length, allowing the systems to achieve mobilities as high as 0.053 cm2 V-1 s-1. Our work elucidates the structure of these interesting semiconducting organic molecules and shows that the synergistic use of X-ray structural analysis and MD simulations is a powerful tool to identify the structure of thin organic films for optoelectronic applications.