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.

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 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.

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.

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.

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.

[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.

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.

Electronic couplings for singlet fission: Orbital choice and extrapolation to the complete basis set limit.

For the search for promising singlet fission candidates, the calculation of the effective electronic coupling, which is required to estimate the singlet fission rate between the initially excited state (S0S1) and the multiexcitonic state (1TT, two triplets on neighboring molecules, coupled into a singlet), should be sufficiently reliable and fast enough to explore the configuration space. We propose here to modify the calculation of the effective electronic coupling using a nonorthogonal configuration interaction approach by: (a) using only one set of orbitals, optimized for the triplet state of the molecules, to describe all molecular electronic states, and (b) only taking the leading configurations into consideration. Furthermore, we also studied the basis set convergence of the electronic coupling, and we found, by comparison to the complete basis set limit obtained using the cc-pVnZ series of basis sets, that both the aug-cc-pVDZ and 6-311++G** basis sets are a good compromise between accuracy and computational feasibility. The proposed approach enables future work on larger clusters of molecules than dimers.

Efficient Computation of Geometries for Gold Complexes.

Computationally obtaining structural parameters along a reaction coordinate is commonly performed with Kohn-Sham density functional theory which generally provides a good balance between speed and accuracy. However, CPU times still range from inconvenient to prohibitive, depending on the size of the system under study. Herein, the tight binding GFN2-xTB method [C. Bannwarth, S. Ehlert, S. Grimme, J. Chem. Theory Comput. 2019, 15, 1652] is investigated as an alternative to produce reasonable geometries along a reaction path, that is, reactant, product and transition state structures for a series of transformations involving gold complexes. A small mean error (1 kcal/mol) was found, with respect to an efficient composite hybrid-GGA exchange-correlation functional (PBEh-3c) paired with a double-ζ basis set, which is 2-3 orders of magnitude slower. The outlined protocol may serve as a rapid tool to probe the viability of proposed mechanistic pathways in the field of gold catalysis.

The electronic structure of carbones revealed: insights from valence bond theory.

In this contribution, we studied the OC-C bond in carbon suboxide and related allene compounds using the valence bond method. The nature of this bond has been the subject of debate, whether it is a regular, electron sharing bond or a dative bond. We compared the nature of this bond in carbon suboxide with the gold-CO bond in Au(CO)2+, which is a typical dative bond, and we studied its charge-shift bond character. We found that the C-CO bond in carbon suboxide is unique in the sense that it cannot be assigned as either a dative or electron sharing bond, but it is an admixture of electron sharing and dative components, together with a high contribution of ionic character. These findings provide a clear basis for distinguishing the commonly found dative bonds between ligands and transition metals and the present case of what may be described as coordinative bonding to carbon.

Periodoannulenes: A Generalized Annulene-within-an-Annulene Paradigm for Combined σ and π Ring Currents.

Periodoannulene molecules and ions CxIxq in planar geometry offer examples of systems with the potential for outer σ and inner π ring-current double aromaticity, given a sufficient overlap of tangential pσ-orbital manifolds on the large atoms of the outer cycle. Previous theoretical work indicated concentric diatropic currents in the dication C6I62+. Ab initio ipsocentric calculations support an account in terms of frontier-orbital selection rules for current contributions in C6I62+ (and radical C6I6+, implicated in recent experimental work on the oxidation of periodobenzene). A σ/π analogue of the annulene-within-an-annulene model is applied here to periodo systems based on cyclooctatetraene. Model species C8I8q with charges q = 0, +1, +2, +4, -2 and structures constrained to a planar D4h symmetry exhibit maps with all combinations of σ/π con- and counter-rotation, comprising global σ ring currents on the iodine perimeter and central π ring currents on the carbocycle. All can be rationalized by the separate application of the tropicity selection rules to the two subsystems, whether in singlet or triplet states.

Comparing GIPAW with numerically exact chemical shieldings: The role of two-center contributions to the induced current.

In this study, we benchmark density functional theory gauge-including projector-augmented-wave (GIPAW) chemical shieldings against molecular shieldings for which basis set completeness has been achieved [Jensen et al., Phys. Chem. Chem. Phys. 18, 21145 (2016)]. We demonstrate the importance of two-center corrections for GIPAW hydrogen shieldings. For the other nuclei studied, standard GIPAW is sufficiently accurate. We find that GIPAW can be pushed to closely approach the basis set limit. The only source of small inaccuracies lies in the contribution to the shielding that is caused by surface currents, which we estimate comparing GIPAW susceptibilities to converged molecular magnetizabilities.

Total Synthesis of the Alleged Structure of Crenarchaeol Enables Structure Revision*.

Crenarchaeol is a glycerol dialkyl glycerol tetraether lipid produced exclusively in Archaea of the phylum Thaumarchaeota. This membrane-spanning lipid is undoubtedly the structurally most sophisticated of all known archaeal lipids and an iconic molecule in organic geochemistry. The 66-membered macrocycle possesses a unique chemical structure featuring 22 mostly remote stereocenters, and a cyclohexane ring connected by a single bond to a cyclopentane ring. Herein we report the first total synthesis of the proposed structure of crenarchaeol. Comparison with natural crenarchaeol allowed us to propose a revised structure of crenarchaeol, wherein one of the 22 stereocenters is inverted.

Electronic Control of Spin-Crossover Properties in Four-Coordinate Bis(formazanate) Iron(II) Complexes.

The transition between spin states in d-block metal complexes has important ramifications for their structure and reactivity, with applications ranging from information storage materials to understanding catalytic activity of metalloenzymes. Tuning the ligand field (ΔO) by steric and/or electronic effects has provided spin-crossover compounds for several transition metals in the periodic table, but this has mostly been limited to coordinatively saturated metal centers in octahedral ligand environments. Spin-crossover complexes with low coordination numbers are much rarer. Here we report a series of four-coordinate, (pseudo)tetrahedral Fe(II) complexes with formazanate ligands and demonstrate how electronic substituent effects can be used to modulate the thermally induced transition between S = 0 and S = 2 spin states in solution. All six compounds undergo spin-crossover in solution with T1/2 above room temperature (300-368 K). While structural analysis by X-ray crystallography shows that the majority of these compounds are low-spin in the solid state (and remain unchanged upon heating), we find that packing effects can override this preference and give rise to either rigorously high-spin (6) or gradual spin-crossover behavior (5) also in the solid state. Density functional theory calculations are used to delineate the empirical trends in solution spin-crossover thermodynamics. In all cases, the stabilization of the low-spin state is due to the π-acceptor properties of the formazanate ligand, resulting in an "inverted" ligand field, with an approximate "two-over-three" splitting of the d-orbitals and a high degree of metal-ligand covalency due to metal → ligand π-backdonation. The computational data indicate that the electronic nature of the para-substituent has a different influence depending on whether it is present at the C-Ar or N-Ar rings, which is ascribed to the opposing effect on metal-ligand σ- and π-bonding.

Engineering Long-Range Order in Supramolecular Assemblies on Surfaces: The Paramount Role of Internal Double Bonds in Discrete Long-Chain Naphthalenediimides.

Achieving long-range order with surface-supported supramolecular assemblies is one of the pressing challenges in the prospering field of non-covalent surface functionalization. Having access to defect-free on-surface molecular assemblies will pave the way for various nanotechnology applications. Here we report the synthesis of two libraries of naphthalenediimides (NDIs) symmetrically functionalized with long aliphatic chains (C28 and C33) and their self-assembly at the 1-phenyloctane/highly oriented pyrolytic graphite (1-PO/HOPG) interface. The two NDI libraries differ by the presence/absence of an internal double bond in each aliphatic chain (unsaturated and saturated compounds, respectively). All molecules assemble into lamellar arrangements, with the NDI cores lying flat and forming 1D rows on the surface, while the carbon chains separate the 1D rows from each other. Importantly, the presence of the unsaturation plays a dominant role in the arrangement of the aliphatic chains, as it exclusively favors interdigitation. The fully saturated tails, instead, self-assemble into a combination of either interdigitated or non-interdigitated diagonal arrangements. This difference in packing is spectacularly amplified at the whole surface level and results in almost defect-free self-assembled monolayers for the unsaturated compounds. In contrast, the monolayers of the saturated counterparts are globally disordered, even though they locally preserve the lamellar arrangements. The experimental observations are supported by computational studies and are rationalized in terms of stronger van der Waals interactions in the case of the unsaturated compounds. Our investigation reveals the paramount role played by internal double bonds on the self-assembly of discrete large molecules at the liquid/solid interface.