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Molybdenum nitrogenase plays a crucial role in the biological nitrogen cycle by catalyzing the reduction of dinitrogen (N 2 ) to ammonia (NH 3 ) under ambient conditions. However, the underlying mechanisms of nitrogenase catalysis, including electron and proton transfer dynamics, remain only partially understood. In this study, we covalently attached molybdenum nitrogenase (MoFe) to gold electrodes and utilized surface-enhanced infrared absorption spectroscopy (SEIRA) coupled with electrochemistry techniques to investigate its catalytic mechanism. Our biohybrid system enabled electron transfer via a mild mediator, likely mimicking the natural electron flow through the P-cluster to FeMoco, the enzyme's active site. For the first time, we experimentally observed both terminal and bridging S-H stretching frequencies, resulting from the protonation of bridging sulfides in FeMoco during turnover conditions providing direct evidence of their role in catalysis. These experimental observations are further supported by QM/MM calculations. Additionally, we investigated CO inhibition, demonstrating both CO binding and unbinding dynamics under electrochemical conditions. These insights not only advance our understanding of the mechanistic cycle of molybdenum nitrogenase but also establish a foundation for studying alternative nitrogenases, including vanadium and iron nitrogenases.

Multiply-bonded main group compounds of groups 13-15 are attracting significant interest not only because they provide fundamental insight into the nature of metal-metal bonding, but also for their potential in small molecule bond activation and catalysis. This includes dialumenes, neutral Al(I) compounds that contain AlAl double bonds, which display high reactivity owing to their intrinsic diradicaloid character. The electronic structure of the simplest dialumene, Al 2 H 2 , is here analyzed up to a practical Full-CI limit using DMRG and selected CI methods for the bond dissociation energy (BDE), geometry and properties of the electron density (difference density, ELF). Acquiring Full-CI reference values for the simplest dialumene (but possessing the highest diradical character) allows for a rigorous benchmarking of simpler correlated wavefunction theory (WFT) methods and density functional methods in treating the electronic structure of such systems. Single-reference coupled cluster theory using a RHF reference is found to reliably converge to the Full-CI limit and CCSD(T) is fully capable of capturing the diradical character, while multi-reference methods offer no clear advantages. Density functional methods struggle to fully describe the electronic structure complexity although non-hybrid functionals such as TPSS come close. Solving the inverse Kohn-Sham problem for a Full-CI-quality density revealed minimal density-driven errors in the TPSS-calculated BDE unlike high-percentage hybrids such as M06-2X. No density functional, however, predicts accurate relative energies. Fractional-occupation density plots at the TPSS level correlate well with WFT-based diradical character metrics, a useful result for determining diradical character in larger systems.

Hydrides are present in the reduced states of the iron-molybdenum cofactor (FeMoco) of Mo nitrogenase and are believed to play a key mechanistic role in the dinitrogen reduction reaction catalyzed by the enzyme. Two hydrides are present in the E4 state according to 1 H ENDOR and there is likely a single hydride in the E2 redox state. The 2-hydride E4 state has been experimentally observed to bind N 2 and it has been speculated that E3 may bind N 2 as well. However, the E3 state has not been directly observed and very little is known about its molecular and electronic structure or reactivity. In recent computational studies, we have explored the energy surfaces of the E2 and E4 by QM/MM modelling, and found that the most stable hydride isomers contain bridging or partially bridging hydrides with an open protonated belt sulfide-bridge. In this work we systematically explore the energy surface of the E3 redox state, comparing single hydride and two-hydride isomers with varying coordination and bridging vs. terminal sulfhydryl groups. We also include a model featuring a triply protonated carbide. The results are only mildly dependent on the QM-region size. The three most stable E3 isomers at the r 2 SCAN level of theory have in common: an open belt sulfide-bridge (terminal sulfhydryl group on Fe6) and either 2 bridging hydrides (between Fe2 and Fe6), 1 bridging-1-terminal hydride (around Fe2 and Fe6) or a dihydrogen ligand bound at the Fe2 site. Analyzing the functional dependency of the results, we find that functionals previously found to predict accurate structures of spin-coupled Fe/Mo dimers and FeMoco (TPSSh, B97-D3, r 2 SCAN, and B3LYP*) are in generally good agreement about the stability of these 3 E3 isomers. However, B3LYP*, similar to its parent B3LYP method, predicts a triply protonated carbide isomer as the most stable isomer, an unlikely scenario in view of the lack of experimental evidence for carbide protonation occurring in reduced FeMoco states. Distinguishing further between the 3 hydride isomers is difficult and this flexible coordination nature of hydrides suggests that multiple hydride isomers could be present during experimental conditions. N 2 binding was explored and resulted in geometries with 2 bridging hydrides and N 2 bound to either Fe 2 or Fe 6 with a local low-spin state on the Fe. N 2 binding is predicted to be mildly endothermic, similar to the E2 state, and it seems unlikely that the E3 state is capable of binding N 2 .

The active site of [NiFe]-hydrogenases contains a strictly-conserved pendant arginine, the guanidine head group of which is suspended immediately above the Ni and Fe atoms. Replacement of this arginine (R479) in hydrogenase-2 from E. coli results in an enzyme that is isolated with a very tightly-bound diatomic ligand attached end-on to the Ni and stabilised by hydrogen bonding to the Nζ atom of the pendant lysine and one of the three additional water molecules located in the active site of the variant. The diatomic ligand is bound under oxidising conditions and is removed only after a prolonged period of reduction with H 2 and reduced methyl viologen. Once freed of the diatomic ligand, the R479K variant catalyses both H 2 oxidation and evolution but with greatly decreased rates compared to the native enzyme. Key kinetic characteristics are revealed by protein film electrochemistry: most importantly, a very low activation energy for H 2 oxidation that is not linked to an increased H/D isotope effect. Native electrocatalytic reversibility is retained. The results show that the sluggish kinetics observed for the lysine variant arise most obviously because the advantage of a more favourable low-energy pathway is massively offset by an extremely unfavourable activation entropy. Extensive efforts to establish the identity of the diatomic ligand, the tight binding of which is an unexpected further consequence of replacing the pendant arginine, prove inconclusive., Competing Interests: The authors report no conflict of interests., (This journal is © The Royal Society of Chemistry.)

The biological conversion of N 2 to NH 3 is accomplished by the nitrogenase family, which is collectively comprised of three closely related but unique metalloenzymes. In the present study, we have employed a combination of the synchrotron-based technique of 57 Fe nuclear resonance vibrational spectroscopy together with DFT-based quantum mechanics/molecular mechanics (QM/MM) calculations to probe the electronic structure and dynamics of the catalytic components of each of the three unique M N 2 ase enzymes (M = Mo, V, Fe) in both the presence (holo-) and absence (apo-) of the catalytic FeMco clusters (FeMoco, FeVco and FeFeco). The results described herein provide vibrational mode assignments for important fingerprint regions of the FeMco clusters, and demonstrate the sensitivity of the calculated partial vibrational density of states (PVDOS) to the geometric and electronic structures of these clusters. Furthermore, we discuss the challenges that are faced when employing NRVS to investigate large, multi-component metalloenzymatic systems, and outline the scope and limitations of current state-of-the-art theory in reproducing complex spectra.

Orange protein (Orp) is a small bacterial metalloprotein of unknown function that harbors a unique molybdenum/copper (Mo/Cu) heterometallic cluster, [S 2 MoS 2 CuS 2 MoS 2 ] 3- . In this paper, the performance of Orp as a catalyst for the photocatalytic reduction of protons into H 2 has been investigated under visible light irradiation. We report the complete biochemical and spectroscopic characterization of holo -Orp containing the [S 2 MoS 2 CuS 2 MoS 2 ] 3- cluster, with docking and molecular dynamics simulations suggesting a positively charged Arg, Lys-containing pocket as the binding site. Holo -Orp exhibits excellent photocatalytic activity, in the presence of ascorbate as the sacrificial electron donor and [Ru(bpy) 3 ]Cl 2 as the photosensitizer, for hydrogen evolution with a maximum turnover number of 890 after 4 h irradiation. Density functional theory (DFT) calculations were used to propose a consistent reaction mechanism in which the terminal sulfur atoms are playing a key role in promoting H 2 formation. A series of dinuclear [S 2 MS 2 M'S 2 MS 2 ] (4 n )- clusters, with M = Mo VI , W VI and M' ( n +) = Cu I , Fe I , Ni I , Co I, Zn II , Cd II were assembled in Orp, leading to different M/M'-Orp versions which are shown to display catalytic activity, with the Mo/Fe-Orp catalyst giving a remarkable turnover number (TON) of 1150 after 2.5 h reaction and an initial turnover frequency (TOF°) of 800 h -1 establishing a record among previously reported artificial hydrogenases.

The FeMo cofactor (FeMoco) of Mo nitrogenase is responsible for reducing dinitrogen to ammonia, but it requires the addition of 3-4 e - /H + pairs before N 2 even binds. A binding site at the Fe2/Fe3/Fe6/Fe7 face of the cofactor has long been suggested based on mutation studies, with Fe2 or Fe6 nowadays being primarily discussed as possibilities. However, the nature of N 2 binding to the cofactor is enigmatic as the metal ions are coordinatively saturated in the resting state with no obvious binding site. Furthermore, the cofactor consists of high-spin Fe(II)/Fe(III) ions (antiferromagnetically coupled but also mixed-valence delocalized), which are not known to bind N 2 . This suggests that an Fe binding site with a different molecular and electronic structure than the resting state must be responsible for the experimentally known N 2 binding in the E 4 state of FeMoco. We have systematically studied N 2 binding to Fe2 and Fe6 sites of FeMoco at the broken-symmetry QM/MM level as a function of the redox-, spin-, and protonation state of the cofactor. The local and global electronic structure changes to the cofactor taking place during redox events, protonation, Fe-S cleavage, hydride formation, and N 2 coordination are systematically analyzed. Localized orbital and quasi-restricted orbital analysis via diamagnetic substitution is used to get insights into the local single Fe ion electronic structure in various states of FeMoco. A few factors emerge as essential to N 2 binding in the calculations: spin-pairing of d xz and d yz orbitals of the N 2 -binding Fe ion, a coordination change at the N 2 -binding Fe ion aided by a hemilabile protonated sulfur, and finally hydride ligation. The results show that N 2 binding to E 0 , E 1 , and E 2 models is generally unfavorable, likely due to the high-energy cost of stabilizing the necessary spin-paired electronic structure of the N 2 -binding Fe ion in a ligand environment that clearly favors high-spin states. The results for models of E 4 , however, suggest a feasible model for why N 2 binding occurs experimentally in the E 4 state. E 4 models with two bridging hydrides between Fe2 and Fe6 show much more favorable N 2 binding than other models. When two hydrides coordinate to the same Fe ion, an increased ligand-field splitting due to octahedral coordination at either Fe2 or Fe6 is found. This altered ligand field makes it easier for the Fe ion to acquire a spin-paired electronic structure with doubly occupied d xz and d yz orbitals that backbond to a terminal N 2 ligand. Within this model for N 2 binding, both Fe2 and Fe6 emerge as possible binding site scenarios. Due to steric effects involving the His195 residue, affecting both the N 2 ligand and the terminal SH - group, distinguishing between Fe2 and Fe6 is difficult; furthermore, the binding depends on the protonation state of His195.

Open-shell transition metal chemistry presents challenges to contemporary electronic structure methods, based on either density functional or wavefunction theory. While CCSD(T) is the well-trusted gold standard for maingroup thermochemistry, the accuracy and robustness of the method is less clear for open-shell transition metal chemistry, requiring benchmarking of CCSD(T)-based protocols against either higher-level theory or experiment. Ionization energies (IEs) of metallocenes provide an interesting test case with metallocenes being common redox reagents as well as playing roles as redox mediators and cocatalysts in redox catalysis. Using highly accurate ZEKE-MATI experimental measurements of gas phase adiabatic (5.3275 ± 0.0006 eV) and vertical (5.4424 ± 0.0006 eV) ionization energies of cobaltocene, we systematically assessed the accuracy of the local coupled-cluster method DLPNO-CCSD(T) with respect to geometry, reference determinant, basis set size and extrapolation schemes, PNO cut-off and extrapolation, local triples approximation, relativistic effects and core-valence correlation. We show that PNO errors are controllable via the recently introduced PNO extrapolation schemes and that the expensive iterative triples (T 1 ) contribution can be made more manageable by calculating it as a smaller-basis/smaller PNO-cutoff correction. The reference determinant turns out to be a critical aspect in these calculations with the HF determinant resulting in large DLPNO-CCSD(T) errors, likely due to the qualitatively flawed molecular orbital spectrum. The BP86 functional on the other hand was found to provide reference orbitals giving small DLPNO-CCSD(T) errors, likely due to more realistic orbitals as suggested by the more consistent MO spectrum compared to HF. A protocol including complete basis set extrapolations with correlation-consistent basis sets, complete PNO space extrapolations, iterative triples- and core-valence correlation corrections was found to give errors of -0.07 eV and -0.03 eV for adiabatic- and vertical-IE of cobaltocene, respectively, giving close to chemical accuracy for both properties. A computationally efficient DLPNO-CCSD(T) protocol was devised and tested against adiabatic ionization energies of 6 different metallocenes (V, Cr, Mn, Fe, Co, Ni). For the other metallocenes, the iterative triples (T 1 ) and PNO extrapolation contributions turn out to be even more important. The results give errors close to the experimental uncertainty, similar to recent auxiliary-field quantum Monte Carlo results. The quality of the reference determinant orbitals is identified as the main source of uncertainty in CCSD(T) calculations of metallocenes.

[FeFe] hydrogenases are highly efficient metalloenyzmes for hydrogen conversion. Their active site cofactor (the H-cluster) is composed of a canonical [4Fe-4S] cluster ([4Fe-4S] H ) linked to a unique organometallic di-iron subcluster ([2Fe] H ). In [2Fe] H the two Fe ions are coordinated by a bridging 2-azapropane-1,3-dithiolate (ADT) ligand, three CO and two CN - ligands, leaving an open coordination site on one Fe where substrates (H 2 and H + ) as well as inhibitors ( e.g. O 2 , CO, H 2 S) may bind. Here, we investigate two new active site states that accumulate in [FeFe] hydrogenase variants where the cysteine (Cys) in the proton transfer pathway is mutated to alanine (Ala). Our experimental data, including atomic resolution crystal structures and supported by calculations, suggest that in these two states a third CN - ligand is bound to the apical position of [2Fe] H . These states can be generated both by "cannibalization" of CN - from damaged [2Fe] H subclusters as well as by addition of exogenous CN - . This is the first detailed spectroscopic and computational characterisation of the interaction of exogenous CN - with [FeFe] hydrogenases. Similar CN - -bound states can also be generated in wild-type hydrogenases, but do not form as readily as with the Cys to Ala variants. These results highlight how the interaction between the first amino acid in the proton transfer pathway and the active site tunes ligand binding to the open coordination site and affects the electronic structure of the H-cluster., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

The open-shell electronic structure of iron-sulfur clusters presents considerable challenges to quantum chemistry, with the complex iron-molybdenum cofactor (FeMoco) of nitrogenase representing perhaps the ultimate challenge for either wavefunction or density functional theory. While broken-symmetry density functional theory has seen some success in describing the electronic structure of such cofactors, there is a large exchange-correlation functional dependence in calculations that is not fully understood. In this work, we present a geometric benchmarking test set, FeMoD11, of synthetic spin-coupled Fe-Fe and Mo-Fe dimers, with relevance to the molecular and electronic structure of the Mo-nitrogenase FeMo cofactor. The reference data consists of high-resolution crystal structures of metal dimer compounds in different oxidation states. Multiple density functionals are tested on their ability to reproduce the local geometry, specifically the Fe-Fe/Mo-Fe distance, for both antiferromagnetically coupled and ferromagnetically coupled dimers via the broken-symmetry approach. The metal-metal distance is revealed not only to be highly sensitive to the amount of exact exchange in the functional but also to the specific exchange and correlation functionals. For the antiferromagnetically coupled dimers, the calculated metal-metal distance correlates well with the covalency of the bridging metal-ligand bonds, as revealed via the corresponding orbital analysis, Hirshfeld S/Fe charges, and Fe-S Mayer bond order. Superexchange via bridging ligands is expected to be the dominant interaction in these dimers, and our results suggest that functionals that predict accurate Fe-Fe and Mo-Fe distances describe the overall metal-ligand covalency more accurately and in turn the superexchange of these systems. The best performing density functionals of the 16 tested for the FeMoD11 test set are revealed to be either the nonhybrid functionals r 2 SCAN and B97-D3 or hybrid functionals with 10-15% exact exchange: TPSSh and B3LYP*. These same four functionals are furthermore found to reproduce the high-resolution X-ray structure of FeMoco well according to quantum mechanics/molecular mechanics (QM/MM) calculations. Almost all nonhybrid functionals systematically underestimate Fe-Fe and Mo-Fe distances (with r 2 SCAN and B97-D3 being the sole exceptions), while hybrid functionals with >15% exact exchange (including range-separated hybrid functionals) overestimate them. The results overall suggest r 2 SCAN, B97-D3, TPSSh, and B3LYP* as accurate density functionals for describing the electronic structure of iron-sulfur clusters in general, including the complex FeMoco cluster of nitrogenase.

Carbon monoxide (CO) is a well-known inhibitor of nitrogenase activity. Under turnover conditions, CO binds to FeMoco, the active site of Mo nitrogenase. Time-resolved IR measurements suggest an initial terminal CO at 1904 cm -1 that converts to a bridging CO at 1715 cm -1 , and an X-ray structure shows that CO can displace one of the bridging belt sulfides of FeMoco. However, the CO-binding redox state(s) of FeMoco (E n ) and the role of the protein environment in stabilizing specific CO-bound intermediates remain elusive. In this work, we carry out an in-depth analysis of the CO-FeMoco interaction based on quantum chemical calculations addressing different aspects of the electronic structure. (1) The local electronic structure of the Fe-CO bond is studied through diamagnetically substituted FeMoco. (2) A cluster model of FeMoco within a polarizable continuum illustrates how CO binding may affect the spin-coupling between the metal centers. (3) A QM/MM model incorporates the explicit influence of the amino acid residues surrounding FeMoco in the MoFe protein. The QM/MM model predicts both a terminal and a bridging CO in the E 1 redox state. The scaled calculated CO frequencies (1922 and 1716 cm -1 , respectively) are in good agreement with the experimentally observed IR bands supporting CO binding to the E 1 state. Alternatively, an E 2 state QM/MM model, which has the same atomic structure as the CO-bound X-ray structure, features a semi-bridging CO with a scaled calculated frequency (1718 cm -1 ) similar to the bridging CO in the E 1 model.

The iron-molybdenum cofactor (FeMoco) is responsible for dinitrogen reduction in Mo nitrogenase. Unlike the resting state, E 0 , reduced states of FeMoco are much less well characterized. The E 2 state has been proposed to contain a hydride but direct spectroscopic evidence is still lacking. The E 2 state can, however, relax back the E 0 state via a H 2 side-reaction, implying a hydride intermediate prior to H 2 formation. This E 2 →E 0 pathway is one of the primary mechanisms for H 2 formation under low-electron flux conditions. In this study we present an exploration of the energy surface of the E 2 state. Utilizing both cluster-continuum and QM/MM calculations, we explore various classes of E 2 models: including terminal hydrides, bridging hydrides with a closed or open sulfide-bridge, as well as models without. Importantly, we find the hemilability of a protonated belt-sulfide to strongly influence the stability of hydrides. Surprisingly, non-hydride models are found to be almost equally favorable as hydride models. While the cluster-continuum calculations suggest multiple possibilities, QM/MM suggests only two models as contenders for the E 2 state. These models feature either i) a bridging hydride between Fe 2 and Fe 6 and an open sulfide-bridge with terminal SH on Fe 6 (E 2 -hyd) or ii) a double belt-sulfide protonated, reduced cofactor without a hydride (E 2 -nonhyd). We suggest both models as contenders for the E 2 redox state and further calculate a mechanism for H 2 evolution. The changes in electronic structure of FeMoco during the proposed redox-state cycle, E 0 →E 1 →E 2 →E 0 , are discussed., (© 2021 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)

The aqueous synthesis of Pd(II) complexes with alkylated tripeptides led to the hydrolysis of the peptides at low pH values and mixtures of complexed peptides were formed. A non-aqueous synthetic route allowed the formation and isolation of single products and their characterization. Pd(II) complexes with α-Asp(OR)AlaGly(OR), β-Asp(OR)AlaGly(OR), and TrpAlaGly(OR) (R = H or alkyl) as tri and tetradentate chelates were characterized. The tridentate coordination mode was accompanied by a fourth monodentate ligand that was shown to participate in both ligand exchange reactions and a direct removal to form the tetradentate coordination mode. The tetradentate coordination revealed a rare a hemi labile carbonyl goup coordination mode to Pd(II). Reactivity with small molecules such as ethylene, acids, formate, and episulfide was investigated. Under acidic conditions and in the presence of ethylene; acetaldehyde was formed. The Pd(II) is a soft Lewis acid and thiophilic and the complexes abstract sulfur from episulfide at apparent modest catalytic rates. The complexes adopt a square planar geometry according to a spectroscopic analysis and DFT calculations that were employed to evaluate the most energetically favorable coordination geometry and compared with the observed infrared and NMR data.

The climbing image nudged elastic band method (CI-NEB) is used to identify reaction coordinates and to find saddle points representing transition states of reactions. It can make efficient use of parallel computing as the calculations of the discretization points, the so-called images, can be carried out simultaneously. In typical implementations, the images are distributed evenly along the path by connecting adjacent images with equally stiff springs. However, for systems with a high degree of flexibility, this can lead to poor resolution near the saddle point. By making the spring constants increase with energy, the resolution near the saddle point is improved. To assess the performance of this energy-weighted CI-NEB method, calculations are carried out for a benchmark set of 121 molecular reactions. The performance of the method is analyzed with respect to the input parameters. Energy-weighted springs are found to greatly improve performance and result in successful location of the saddle points in less than a thousand energy and force evaluations on average (about a hundred per image) using the same set of parameter values for all of the reactions. Even better performance is obtained by stopping the calculation before full convergence and complete the saddle point search using an eigenvector following method starting from the location of the climbing image. This combination of methods, referred to as NEB-TS, turns out to be robust and highly efficient as it reduces the average number of energy and force evaluations down to a third, to 305. An efficient and flexible implementation of these methods has been made available in the ORCA software.

Recent Rydberg spectroscopy measurements of a diamine molecule, N , N '-dimethylpiperazine (DMP), indicate the existence of a localized electronic state as well as a delocalized electronic state. This implies that the cation, DMP + , can similarly have its positive charge either localized on one of the N atoms or delocalized over both. This interpretation of the experiments has, however, been questioned based on coupled cluster calculations. In this article, results of high-level multireference configuration interaction calculations are presented where a localized state of DMP + is indeed found to be present with an energy barrier separating it from the delocalized state. The energy difference between the two states is in excellent agreement with the experimental estimate. The results presented here, therefore, support the original interpretation of the experiments and illustrate a rare shortcoming of CCSD(T), the "gold standard" of quantum chemistry. These results have implications for the development of density functionals, as most functionals fail to produce the localized state.

The role of specific interactions in the self-assembly process of low molecular weight gelators (LMWGs) was studied by altering the nonbonding interactions responsible for gel formation via structural modification of the gelator/nongelator. This was achieved by modifying pyridyl moieties of bis(pyridyl) urea-based hydrogelator ( 4-BPU ) and the isomer ( 3-BPU ) to pyridyl N -oxide compounds ( L 1 and L 2 , respectively). The modification of the functional groups resulted in the tuning of the gelation properties of the parent gelator, which induced/enhanced the gelation properties. The modified compounds displayed better mechanical and thermal stabilities and the introduction of the N -oxide moieties had a prominent effect on the morphologies of the gel network, which was evident from the scanning electron microscopy (SEM) images. The effect of various interactions due to the introduction of N -oxide moieties in the gel network formation was analyzed by comparing the solid-state interactions of the compounds using single crystal X-ray diffraction and computational studies, which were correlated with the enhanced gelation properties. This study shows the importance of specific nonbonding interactions and the spatial arrangement of the functional groups in the supramolecular gel network formation.

[FeFe] hydrogenases are the most active H 2 converting catalysts in nature, but their extreme oxygen sensitivity limits their use in technological applications. The [FeFe] hydrogenases from sulfate reducing bacteria can be purified in an O 2 -stable state called H inact . To date, the structure and mechanism of formation of H inact remain unknown. Our 1.65 Å crystal structure of this state reveals a sulfur ligand bound to the open coordination site. Furthermore, in-depth spectroscopic characterization by X-ray absorption spectroscopy (XAS), nuclear resonance vibrational spectroscopy (NRVS), resonance Raman (RR) spectroscopy and infrared (IR) spectroscopy, together with hybrid quantum mechanical and molecular mechanical (QM/MM) calculations, provide detailed chemical insight into the H inact state and its mechanism of formation. This may facilitate the design of O 2 -stable hydrogenases and molecular catalysts., (© 2020 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.)

Candida albicans is one of the most prevalent fungal pathogens involved in hospital acquired infections. It binds to glycans at the surface of epithelial cells and initiates infection. This process can be blocked by synthetic carbohydrates that mimic the structure of cell surface glycans. Herein we report the evaluation of a series of divalent glycosides featuring aromatic (benzene, squaramide) and bicyclic aliphatic (norbornene) scaffolds, with the latter being the first examples of their kind as small molecule anti-adhesion glycoconjugates. Galactosides 1 and 6 , built on an aromatic core, were most efficient inhibitors of adhesion of C. albicans to buccal epithelial cells, displacing up to 36% and 48%, respectively, of yeast already attached to epithelial cells at 138 μM. Remarkably, cis-endo -norbornene 21 performed comparably to benzene-core derivatives. Conformational analysis reveals a preference for compounds 1 and 21 to adopt folded conformations. These results highlight the potential of norbornenes as a new class of aliphatic scaffolds for the synthesis of anti-adhesion compounds., Competing Interests: The authors declare no conflict of interest., (This journal is © The Royal Society of Chemistry.)

The nitrogenase enzymes are responsible for all biological nitrogen reduction. How this is accomplished at the atomic level, however, has still not been established. The molybdenum-dependent nitrogenase has been extensively studied and is the most active catalyst for dinitrogen reduction of the nitrogenase enzymes. The vanadium-dependent form, on the other hand, displays different reactivity, being capable of CO and CO 2 reduction to hydrocarbons. Only recently did a crystal structure of the VFe protein of vanadium nitrogenase become available, paving the way for detailed theoretical studies of the iron-vanadium cofactor (FeVco) within the protein matrix. The crystal structure revealed a bridging 4-atom ligand between two Fe atoms, proposed to be either a CO 3 2- or NO 3 - ligand. Using a quantum mechanics/molecular mechanics model of the VFe protein, starting from the 1.35 Å crystal structure, we have systematically explored multiple computational models for FeVco, considering either a CO 3 2- or NO 3 - ligand, three different redox states, and multiple broken-symmetry states. We find that only a [VFe 7 S 8 C(CO 3 )] 2- model for FeVco reproduces the crystal structure of FeVco well, as seen in a comparison of the Fe-Fe and V-Fe distances in the computed models. Furthermore, a broken-symmetry solution with Fe2, Fe3, and Fe5 spin-down (BS7-235) is energetically preferred. The electronic structure of the [VFe 7 S 8 C(CO 3 )] 2- BS7-235 model is compared to our [MoFe 7 S 9 C] - BS7-235 model of FeMoco via localized orbital analysis and is discussed in terms of local oxidation states and different degrees of delocalization. As previously found from Fe X-ray absorption spectroscopy studies, the Fe part of FeVco is reduced compared to FeMoco, and the calculations reveal Fe5 as locally ferrous. This suggests resting-state FeVco to be analogous to an unprotonated E 1 state of FeMoco. Furthermore, V-Fe interactions in FeVco are not as strong compared to Mo-Fe interactions in FeMoco. These clear differences in the electronic structures of otherwise similar cofactors suggest an explanation for distinct differences in reactivity.

Nitrogenases are responsible for biological nitrogen fixation, a crucial step in the biogeochemical nitrogen cycle. These enzymes utilize a two-component protein system and a series of iron-sulfur clusters to perform this reaction, culminating at the FeMco active site (M = Mo, V, Fe), which is capable of binding and reducing N 2 to 2NH 3 . In this review, we summarize how different spectroscopic approaches have shed light on various aspects of these enzymes, including their structure, mechanism, alternative reactivity, and maturation. Synthetic model chemistry and theory have also played significant roles in developing our present understanding of these systems and are discussed in the context of their contributions to interpreting the nature of nitrogenases. Despite years of significant progress, there is still much to be learned from these enzymes through spectroscopic means, and we highlight where further spectroscopic investigations are needed.

The elucidation of magnetostructural correlations between bridging ligand substitution and strength of magnetic coupling is essential to the development of high-temperature molecule-based magnetic materials. Toward this end, we report the series of tetraoxolene-bridged Fe II 2 complexes [(Me 3 TPyA) 2 Fe 2 ( R L)] n + (Me 3 TPyA = tris(6-methyl-2-pyridylmethyl)amine; n = 2: OMe LH 2 = 3,6-dimethoxy-2,5-dihydroxo-1,4-benzoquinone, Cl LH 2 = 3,6-dichloro-2,5-dihydroxo-1,4-benzoquinone, Na 2 [ NO 2 L] = sodium 3,6-dinitro-2,5-dihydroxo-1,4-benzoquinone; n = 4: SMe 2 L = 3,6-bis(dimethylsulfonium)-2,5-dihydroxo-1,4-benzoquinone diylide) and their one-electron-reduced analogues. Variable-temperature dc magnetic susceptibility data reveal the presence of weak ferromagnetic superexchange between Fe II = +1.2(2) (R = OMe, Cl) and +0.3(1) (R = NO J = +1.2(2) (R = OMe, Cl) and +0.3(1) (R = NO 2 , SMe 2 ) cm -1 . In contrast, X-ray diffraction, cyclic voltammetry, and Mössbauer spectroscopy establish a ligand-centered radical in the reduced complexes. Magnetic measurements for the radical-bridged species reveal the presence of strong antiferromagnetic metal-radical coupling, with J for R = OMe, Cl, NO -1 for R = OMe, Cl, NO 2 , and SMe 2 , respectively. The minimal effects of substituents in the 3- and 6-positions of R L x -• on the magnetic coupling strength is understood through electronic structure calculations, which show negligible spin density on the substituents and associated C atoms of the ring. Finally, the radical-bridged complexes are single-molecule magnets, with relaxation barriers of U for R = OMe, Cl, NO eff = 50(1), 41(1), 38(1), and 33(1) cm -1 for R = OMe, Cl, NO 2 , and SMe 2 , respectively. Taken together, these results provide the first examination of how bridging ligand substitution influences magnetic coupling in semiquinoid-bridged compounds, and they establish design criteria for the synthesis of semiquinoid-based molecules and materials.

In this study, we present experimental and theoretical results on dissociative electron attachment and dissociative ionisation for the potential FEBID precursor cis-Pt(CO) 2 Cl 2 . UHV surface studies have shown that high purity platinum deposits can be obtained from cis-Pt(CO) 2 Cl 2 . The efficiency and energetics of ligand removal through these processes are discussed and experimental appearance energies are compared to calculated thermochemical thresholds. The present results demonstrate the potential effectiveness of electron-induced reactions in the deposition of this FEBID precursor, and these are discussed in conjunction with surface science studies on this precursor and the design of new FEBID precursors.

Molybdenum nitrogenase is one of the most intriguing metalloenzymes in nature, featuring an exotic iron-molybdenum-sulfur cofactor, FeMoco, whose mode of action remains elusive. In particular, the molecular and electronic structure of the N 2 -binding E 4 state is not known. In this study we present theoretical QM/MM calculations of new structural models of the E 4 state of molybdenum-dependent nitrogenase and compare to previously suggested models for this enigmatic redox state. We propose two models as possible candidates for the E 4 state. Both models feature two hydrides on the FeMo cofactor, bridging atoms Fe 2 and Fe 6 with a terminal sulfhydryl group on either Fe 2 or Fe 6 (derived from the S2B bridge) and the change in coordination results in local lower-spin electronic structure at Fe 2 and Fe 6 . These structures appear consistent with the bridging hydride proposal put forward from ENDOR studies and are calculated to be lower in energy than other proposed models for E 4 at the TPSSh-QM/MM level of theory. We critically analyze the DFT method dependency in calculations of FeMoco that has resulted in strikingly different proposals for this state. Importantly, dinitrogen binds exothermically to either Fe 2 or Fe 6 in our models, contrary to others, an effect rationalized via the unique ligand field (from the hydrides) at the Fe with an empty coordination site. A low-spin Fe site is proposed as being important to N 2 binding. Furthermore, the geometries of these states suggest a feasible reductive elimination step that could follow, as experiments indicate. Via this step, two electrons are released, reducing the cofactor to yield a distorted 4-coordinate Fe 2 or Fe 6 that partially activates N 2 . We speculate that stabilization of an N 2 -bound Fe(i) at Fe 6 (not found for Fe 2 model) via reductive elimination is a crucial part of N 2 activation in nitrogenases, possibly aided by the apical heterometal ion (Mo or V). By using protons from the sulfhydryl group (to regenerate the sulfide bridge between Fe 2 and Fe 6 ) and the nearby homocitrate hydroxy group, we calculate a plausible route to yield a diazene intermediate. This is found to be more favorable with the Fe 6 -bound model than the Fe 2 -bound model; however, this protonation is uphill in energy, suggesting protonation of N 2 might occur later in the catalytic cycle or via another mechanism., (This journal is © The Royal Society of Chemistry 2019.)

Biological nitrogen fixation is predominately accomplished through Mo nitrogenase, which utilizes a complex MoFe 7 S 9 C catalytic cluster to reduce N 2 to NH 3 . This cluster requires the accumulation of three to four reducing equivalents prior to binding N 2 ; however, despite decades of research, the intermediate states formed prior to N 2 binding are still poorly understood. Herein, we use Mo and Fe K-edge X-ray absorption spectroscopy and QM/MM calculations to investigate the nature of the E 1 state, which is formed following the addition of the first reducing equivalent to Mo nitrogenase. By analyzing the extended X-ray absorption fine structure (EXAFS) region, we provide structural insight into the changes that occur in the metal clusters of the protein when forming the E 1 state, and use these metrics to assess a variety of possible models of the E 1 state. The combination of our experimental and theoretical results supports that formation of E 1 involves an Fe-centered reduction combined with the protonation of a belt-sulfide of the cluster. Hence, these results provide critical experiment and computational insight into the mechanism of this important enzyme., (This journal is © The Royal Society of Chemistry 2019.)

We present a combined theoretical and experimental study on the ionization and primary fragmentation channels of the mono-halogenated biphenyls; 2-chlorobiphenyl, 2-bromobiphenyl and 2-iodobiphenyl. The ionization energies (IEs) of the 2-halobiphenyls and the appearance energies (AEs) of the principal fragments are determined through electron impact ionization, while quantum mechanical calculations at the coupled cluster level of theory are used to elucidate the observed processes and the associated dynamics. The primary fragmentation channels are the direct loss of the halogen upon ionization, the loss of the respective hydrogen halides (HX) as well as loss of the hydrogen halide and an additional hydrogen. We find that the dihedral angle strongly influences the relative potential energy of the neutral and the cation on their respective ground state surfaces, an effect caused by the strong influence of the nuclear motion on the conjugation between the phenyl rings. For the principal dissociative ionization channels from the mono-halogenated biphenyls we reason that these can not be described as statistical decay from the ground state cation, but must rather be understood as direct, state-selective processes from specific excited cationic states characterized through local ionization of either the halogenated or the non-substituted phenyl ring.

Molybdenum-dependent nitrogenase is the most active biological catalyst for dinitrogen reduction. This reaction is catalyzed by a [MoFe 7 S 9 C] cofactor (FeMoco). FeMoco can be described as a double-cubane, with [MoFe 3 S 3 ] and [Fe 4 S 3 ] parts, bound via an interstitial carbide and three bridging sulfides. Model compounds have been synthesized since early studies of the enzyme and Coucouvanis and co-workers demonstrated that [MoFe 3 S 4 ] cubanes are active catalysts for many substrates catalyzed by nitrogenase. These reactions include hydrazine reduction to ammonia and cis-dimethyldiazene reduction to methylamine. Experiments implicated molybdenum as the binding site but the mechanisms have not been studied by theoretical calculations before. Here we present a DFT study of the catalytic reaction mechanisms of hydrazine and cis-dimethyldiazene reduction with a [MoFe 3 S 4 ] cubane. Like in the experiments, molybdenum is revealed as the likely substrate binding site, likely due to the labile ligand on Mo. For the hydrazine mechanism, a reduction event is centered on Fe, specifically on the Fe antiferromagnetically coupled to the mixed-valence pair. After protonation of the distal hydrazine nitrogen, the N-N bond can be cleaved to yield NH 3 and a Mo-bound -NH 2 intermediate. This is followed by another protonation/reduction step to give an -NH 3 intermediate, and finally substituted by the substrate to complete the cycle. The computed mechanisms shed light on the bimetallic cooperativity in these systems where the reduction steps are localized on Fe while the substrate binds to Mo and the reductions require only a free coordination site (on Mo) and a favorable reduction event (to Fe). Although both substrates easily displace the weakly bound acetonitrile ligand, one reduction event is required for hydrazine activation and N-N bond cleavage to give an integer-spin -NH 2 intermediate. An integer-spin -NH 2 intermediate has been observed as a common intermediate for the enzyme reduction of hydrazine and diazene, suggesting a possible link to the enzyme chemistry.

The calculation of molecular redox potentials in aqueous solution presents a challenge to quantum chemistry due to the need to calculate charged, open-shell species experiencing large solvent effects. Traditionally, redox potentials are calculated via the use of density functional theory and continuum solvation methods, but such protocols have been found to often suffer from large errors, particularly in the case of aqueous solution. While explicit solvation models hold promise of higher accuracy to describe solvent effects in general, their complicated use and lack of well-defined, reliable protocols has hindered their adoption. In this study, we present an explicit-solvation-based approach for the calculation of molecular redox potentials. We combine the use of affordable semiempirical QM/MM molecular dynamics (making use of the recently proposed GFN-xTB method by Grimme et al.) for both redox states and use the linear response approximation to relate vertical ionization energies to the adiabatic redox potential. Simulation length, averaging over snapshots, and accounting for bulk and polarization effects are systematically evaluated using phenol as a working example. We find that it is crucial to reliably account for bulk solvation effects in these calculations, as well as polarization effects which we divide up into short-range and long-range contributions. The short-range polarization contribution is accounted for via QM-region expansion, while the long-range contribution is accounted for via Drude-polarizable QM/MM. Our multistep protocol has been coded to be used in a fully automatic way in a local version of Chemshell. It has been evaluated on a test set of oxidation potentials of organic molecules and found to give gas-solution redox shifts with a mean absolute error of 0.13 eV with respect to experiment, compared to mean absolute errors of 0.26 and 0.21 eV with CPCM and SMD continuum models, respectively.

A new 1.2 Å crystal structure of vanadium nitrogenase, isolated under turnover conditions, recently revealed a light atom ligand (OH or NH) replacing the bridging S2B sulfide of the FeV cofactor. QM/MM calculations on the new structure now reveal the light-atom ligand to be a bridging hydroxo group, probably derived from water binding to the cofactor.

The production of alloyed nanostructures presents a unique problem in focused electron beam induced deposition (FEBID). Deposition of such structures has historically involved the mixing of two or more precursor gases in situ or via multiple channel gas injection systems, thereby making the production of precise, reproducible alloy compositions difficult. Promising recent efforts to address this problem have involved the use of multi-centred, heterometallic FEBID precursor species. In this vein, we present here a study of low-energy electron interactions with cyclopentadienyl iron dicarbonyl manganese pentacarbonyl ((η 5 -Cp)Fe(CO) 2 Mn(CO) 5 ), a bimetallic species with a polyhapto ligand (Cp) and seven terminal carbonyl ligands. Gas phase studies and coupled cluster calculations of observed low-energy electron-induced reactions were conducted in order to predict the performance of this precursor in FEBID. In dissociative electron attachment, we find single CO loss and cleavage of the Fe-Mn bond, leading to the formation of [Mn(CO) 5 ] - , to be the two dominant channels. Contributions through further CO loss from the intact core and the formation of [Mn(CO) 4 ] - are minor channels. In dissociative ionization (DI), the fragmentation is significantly more extensive and the DI spectra are dominated by fragments formed through the loss of 5 and 6 CO ligands, and fragments formed through cleavage of the Fe-Mn bond accompanied by substantial CO loss. The gas phase fragmentation channels observed are discussed in relation to the underlying processes and their energetics, and in context to related surface studies and the likely performance of this precursor in FEBID.

In the current contribution we present a comprehensive study on the heteronuclear carbonyl complex H 2 FeRu 3 (CO) 13 covering its low energy electron induced fragmentation in the gas phase through dissociative electron attachment (DEA) and dissociative ionization (DI), its decomposition when adsorbed on a surface under controlled ultrahigh vacuum (UHV) conditions and exposed to irradiation with 500 eV electrons, and its performance in focused electron beam induced deposition (FEBID) at room temperature under HV conditions. The performance of this precursor in FEBID is poor, resulting in maximum metal content of 26 atom % under optimized conditions. Furthermore, the Ru/Fe ratio in the FEBID deposit (≈3.5) is higher than the 3:1 ratio predicted. This is somewhat surprising as in recent FEBID studies on a structurally similar bimetallic precursor, HFeCo 3 (CO) 12 , metal contents of about 80 atom % is achievable on a routine basis and the deposits are found to maintain the initial Co/Fe ratio. Low temperature (≈213 K) surface science studies on thin films of H 2 FeRu 3 (CO) 13 demonstrate that electron stimulated decomposition leads to significant CO desorption (average of 8-9 CO groups per molecule) to form partially decarbonylated intermediates. However, once formed these intermediates are largely unaffected by either further electron irradiation or annealing to room temperature, with a predicted metal content similar to what is observed in FEBID. Furthermore, gas phase experiments indicate formation of Fe(CO) 4 from H 2 FeRu 3 (CO) 13 upon low energy electron interaction. This fragment could desorb at room temperature under high vacuum conditions, which may explain the slight increase in the Ru/Fe ratio of deposits in FEBID. With the combination of gas phase experiments, surface science studies and actual FEBID experiments, we can offer new insights into the low energy electron induced decomposition of this precursor and how this is reflected in the relatively poor performance of H 2 FeRu 3 (CO) 13 as compared to the structurally similar HFeCo 3 (CO) 12 .

A combination of two elements' (Au, Zn) X-ray absorption spectroscopy (XAS) and time-dependent density functional theory (TD-DFT) allowed the elucidation of differential substitution pathways of Au(I) and Au(III) compounds reacting with biologically relevant zinc fingers (ZnFs). Gold L 3 -edge XAS probed the interaction of gold and the C-terminal Cys 2 HisCys finger of the HIV-1 nucleocapsid protein NCp7, and the Cys 2 His 2 human transcription factor Sp1. The use of model compounds helped assign oxidation states and the identity of the gold-bound ligands. The computational studies accurately reproduced the experimental XAS spectra and allowed the proposition of structural models for the interaction products at early time points. The direct electrophilic attack on the ZnF by the highly thiophilic Au(I) resulted in a linear P-Au-Cys coordination sphere after zinc ejection whereas for the Sp1, loss of PEt 3 results in linear Cys-Au-Cys or Cys-Au-His arrangements. Reactions with Au(III) compounds, on the other hand, showed multiple binding modes. Prompt reaction between [AuCl(dien)] 2+ and [Au(dien)(DMAP)] 3+ with Sp1 showed a partially reduced Au center and a final linear His-Au-His coordination. Differently, in the presence of NCp7, [AuCl(dien)] 2+ readily reduces to Au(I) and changes from square-planar to linear geometry with Cys-Au-His coordination, while [Au(dien)(DMAP)] 3+ initially maintains its Au(III) oxidation state and square-planar geometry and the same first coordination sphere. The latter is the first observation of a "noncovalent" interaction of a Au(III) complex with a zinc finger and confirms early hypotheses that stabilization of Au(III) occurs with N-donor ligands. Modification of the zinc coordination sphere, suggesting full or partial zinc ejection, is observed in all cases, and for [Au(dien)(DMAP)] 3+ this represents a novel mechanism for nucleocapsid inactivation. The combination of XAS and TD-DFT presents the first direct experimental observation that not only compound reactivity, but also ZnF core specificity, can be modulated on the basis of the coordination sphere of Au(III) compounds.

Nitrogenase is one of the most fascinating enzymes in nature, being responsible for all biological nitrogen reduction. Despite decades of research, it is among the enzymes in bioinorganic chemistry whose mechanism is the most poorly understood. The MoFe protein of nitrogenase contains an iron-molybdenum-sulfur cluster, FeMoco, where N 2 reduction takes place. The resting state of FeMoco has been characterized by crystallography, multiple spectroscopic techniques, and theory (broken-symmetry density functional theory), and all heavy atoms are now characterized. The cofactor charge, however, has been controversial, the electronic structure has proved enigmatic, and little is known about the mechanism. While many computational studies have been performed on FeMoco, few have taken the protein environment properly into account. In this study, we put forward QM/MM models of the MoFe protein from Azotobacter vinelandii, centered on FeMoco. By a detailed analysis of the FeMoco geometry and comparison to the atomic resolution crystal structure, we conclude that only the [MoFe 7 S 9 C] 1- charge is a possible resting state charge. Further, we find that of the three lowest energy broken-symmetry solutions of FeMoco, the BS7-235 spin isomer (where 235 refers to Fe atoms that are "spin-down") is the only one that can be reconciled with experiment. This is revealed by a comparison of the metal-metal distances in the experimental crystal structure, a rare case of spin-coupling phenomena being visible through the molecular structure. This could be interpreted as the enzyme deliberately stabilizing a specific electronic state of the cofactor, possibly for tuning specific reactivity on specific metal atoms. Finally, we show that the alkoxide group on the Mo-bound homocitrate must be protonated under resting state conditions, the presence of which has implications regarding the nature of FeMoco redox states as well as for potential substrate reduction mechanisms.

In single electron collisions with the heteronuclear metal carbonyl compound HFeCo 3 (CO) 12 we observe the formation of long-lived negative ion states up to about 20 eV, 11 eV above its ionization energy. These transient negative ions (TNIs) relax through dissociation (dissociative electron attachment, DEA), losing up to all 12 CO ligands, demonstrating their resilience towards reemission of the captured electron - even at such very high energies. This is unique in DEA and we hypothesize that this phenomenon is rooted in the orbital structure enabling a scaffold of multi-particle, electronically excited resonances. We support this with calculated MO-diagrams revealing dense bands of energy levels near the HOMO-LUMO gap. HFeCo 3 (CO) 12 is a promising focused electron beam induced deposition (FEBID) precursor and we argue that its unusual DEA behavior relates to its exceptional performance in FEBID. This may be general to a class of molecules with high potential for nano-fabrication by FEBID.

Here we present a combined experimental and theoretical study on the fragmentation of o- and p-tetrafluorohydroquinone upon low energy electron attachment. Despite an identical ring-skeleton and identical functional groups in these constitutional isomers, they show distinctly different fragmentation patterns, a phenomenon that cannot be explained by distinct resonances or different thermochemistry. Using high-level quantum chemical calculations with the computationally affordable domain localized pair natural orbital approach, DLPNO-CCSD(T), we are able to provide a complete and accurate description of the respective reaction dynamics, revealing proton shuttling and transition states for competing channels as the explanation for the different behavior of these isomers. The results represent a "schoolbook example" of how the combination of experiment and modern high-level theory may today provide a thorough understanding of complex reaction dynamics by computationally affordable means.

An investigation of the active site cofactors of the molybdenum and vanadium nitrogenases (FeMoco and FeVco) was performed using high-resolution X-ray spectroscopy. Synthetic heterometallic iron-sulfur cluster models and density functional theory calculations complement the study of the MoFe and VFe holoproteins using both non-resonant and resonant X-ray emission spectroscopy. Spectroscopic data show the presence of direct iron-heterometal bonds, which are found to be weaker in FeVco. Furthermore, the interstitial carbide is found to perturb the electronic structures of the cofactors through highly covalent Fe-C bonding. The implications of these conclusions are discussed in light of the differential reactivity of the molybdenum and vanadium nitrogenases towards various substrates. Possible functional roles for both the heterometal and the interstitial carbide are detailed.

Despite decades of research, the structure-activity relationship of nitrogenase is still not understood. Only recently was the full molecular structure of the FeMo cofactor (FeMoco) revealed, but the charge and metal oxidation states of FeMoco have been controversial. With the recent identification of the interstitial atom as a carbide and the more recent revised oxidation-state assignment of the molybdenum atom as Mo(III), here we revisit the Mössbauer properties of FeMoco. By a detailed error analysis of density functional theory-computed isomer shifts and computing isomer shifts relative to the P-cluster, we find that only the charge of [MoFe 7 S 9 C] 1- fits the experimental data. In view of the recent Mo(III) identification, the charge of [MoFe 7 S 9 C] 1- corresponds to a formal oxidation-state assignment of Mo(III)3Fe(II)4Fe(III), although due to spin delocalization, the physical oxidation state distribution might also be interpreted as Mo(III)1Fe(II)4Fe(2.5)2Fe(III), according to a localized orbital analysis of the M S = 3/2 broken symmetry solution. These results can be reconciled with the recent spatially resolved anomalous dispersion study by Einsle et al. that suggests the Mo(III)3Fe(II)4Fe(III) distribution, if some spin localization (either through interactions with the protein environment or through vibronic coupling) were to take place.

The threshold photoelectron spectra and threshold photoionization mass spectra of 1-halogenated-1-silacyclohexanes, for the halogens X = F, Cl, Br, and I, have been obtained using synchrotron vacuum ultraviolet radiation and photoelectron photoion coincidence spectroscopy. As confirmed by a similar ionization onset and density functional theory molecular orbitals, the ionization to the ground state is dominated by electron removal from the silacyclohexane ring for X = F, Cl, and Br, and from the halogen lone pair for X = I. The breakdown diagrams show that the dissociative photoionization mechanism is also different for X = I. Whereas the parent ions decay by ethylene loss for X = F to Br in the low-energy regime, the iodine atom is lost for X = I. The first step is followed by a sequential ethylene loss at higher internal energies in each of the compounds. It is argued that the tendency of silicon to lower bond angles stabilizes the complex cation in which C 2 H 4 is η 2 -coordinated to it, and which precedes ethylene loss. Together with the relatively strong silicon-halogen bonds and the increased inductive effect of the silacyclohexane ring in stabilizing the cation, this explains the main differences observed in the fragmentation of the halogenated silacyclohexane and halogenated cyclohexane ions. The breakdown diagrams have been modeled taking into account slow dissociations at threshold and the resulting kinetic shift. The 0 K appearance energies have been obtained to within 0.08 eV for the ethylene loss for X = F to Br (10.56, 10.51, and 10.51 eV, respectively), the iodine atom loss for X = I (10.11 eV), the sequential ethylene loss for X = F to I (12.29, 12.01, 11.94, and 11.86 eV, respectively), and the minor channels of H loss for X = F (10.56 eV) and propylene loss in X = Cl (also at 10.56 eV). The appearance energies for the major channels likely correspond to the dissociative photoionization reaction energy.

Herein, a systematic study of [L2Fe2S2](n) model complexes (where L = bis(benzimidazolato) and n = 2-, 3-, 4-) has been carried out using iron and sulfur K-edge X-ray absorption (XAS) and iron Kβ and valence-to-core X-ray emission spectroscopies (XES). These data are used as a test set to evaluate the relative strengths and weaknesses of X-ray core level spectroscopies in assessing redox changes in iron-sulfur clusters. The results are correlated to density functional theory (DFT) calculations of the spectra in order to further support the quantitative information that can be extracted from the experimental data. It is demonstrated that due to canceling effects of covalency and spin state, the information that can be extracted from Fe Kβ XES mainlines is limited. However, a careful analysis of the Fe K-edge XAS data shows that localized valence vs delocalized valence species may be differentiated on the basis of the pre-edge and K-edge energies. These findings are then applied to existing literature Fe K-edge XAS data on the iron protein, P-cluster, and FeMoco sites of nitrogenase. The ability to assess the extent of delocalization in the iron protein vs the P-cluster is highlighted. In addition, possible charge states for FeMoco on the basis of Fe K-edge XAS data are discussed. This study provides an important reference for future X-ray spectroscopic studies of iron-sulfur clusters.

The first direct evidence is provided for the presence of an interstitial carbide in the Fe-V cofactor of Azotobacter vinelandii vanadium nitrogenase. As for our identification of the central carbide in the Fe-Mo cofactor, we employed Fe Kβ valence-to-core X-ray emission spectroscopy and density functional theory calculations, and herein report the highly similar spectra of both variants of the cofactor-containing protein. The identification of an analogous carbide, and thus an atomically homologous active site in vanadium nitrogenase, highlights the importance and influence of both the interstitial carbide and the identity of the heteroatom on the electronic structure and catalytic activity of the enzyme., (© 2015 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution Non-Commercial NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.)

The molecular structure of 1,2-bis(trifluoromethyl)-1,1,2,2-tetramethyldisilane has been determined in three different phases (solid, liquid, and gas) using various spectroscopic and diffraction techniques. Both the solid-state and gas-phase investigations revealed only one conformer to be present in the sample analyzed, whereas the liquid phase revealed the presence of three conformers. The data have been reproduced using computational methods and a rationale is presented for the observation of three conformers in the liquid state.

Biological nitrogen fixation is enabled by molybdenum-dependent nitrogenase enzymes, which effect the reduction of dinitrogen to ammonia using an Fe7MoS9C active site, referred to as the iron molybdenum cofactor or FeMoco. In this mini-review, we summarize the current understanding of the molecular and electronic structure of FeMoco. The advances in our understanding of the active site structure are placed in context with the parallel evolution of synthetic model studies. The recent discovery of Mo(III) in the FeMoco active site is highlighted with an emphasis placed on the important role that model studies have played in this finding. In addition, the reactivities of synthetic models are discussed in terms of their relevance to the enzymatic system.

A molybdenum L-edge X-ray absorption spectroscopy (XAS) study is presented for native and oxidized MoFe protein of nitrogenase as well as Mo-Fe model compounds. Recently collected data on MoFe protein (in oxidized and reduced forms) is compared to previously published Mo XAS data on the isolated FeMo cofactor in NMF solution and put in context of the recent Mo K-edge XAS study, which showed a Mo III assignment for the molybdenum atom in FeMoco. The L 3 -edge data are interpreted within a simple ligand-field model, from which a time-dependent density functional theory (TDDFT) approach is proposed as a way to provide further insights into the analysis of the molybdenum L 3 -edges. The calculated results reproduce well the relative spectral trends that are observed experimentally. Ultimately, these results give further support for the Mo III assignment in protein-bound FeMoco, as well as isolated FeMoco.

X-ray absorption spectroscopy (XAS) is a widely used experimental technique capable of selectively probing the local structure around an absorbing atomic species in molecules and materials. When applied to heavy elements, however, the quantitative interpretation can be challenging due to the intrinsic spectral broadening arising from the decrease in the core-hole lifetime. In this work we have used high-energy resolution fluorescence detected XAS (HERFD-XAS) to investigate a series of molybdenum complexes. The sharper spectral features obtained by HERFD-XAS measurements enable a clear assignment of the features present in the pre-edge region. Time-dependent density functional theory (TDDFT) has been previously shown to predict K-pre-edge XAS spectra of first row transition metal compounds with a reasonable degree of accuracy. Here we extend this approach to molybdenum K-edge HERFD-XAS and present the necessary calibration. Modern pure and hybrid functionals are utilized and relativistic effects are accounted for using either the Zeroth Order Regular Approximation (ZORA) or the second order Douglas-Kroll-Hess (DKH2) scalar relativistic approximations. We have found that both the predicted energies and intensities are in excellent agreement with experiment, independent of the functional used. The model chosen to account for relativistic effects also has little impact on the calculated spectra. This study provides an important calibration set for future applications of molybdenum HERFD-XAS to complex catalytic systems.

The molecular structures of axial and equatorial conformers of cyclo -C 5 H 10 SiHX (X = Cl, Br, I) as well as the thermodynamic equilibrium between these species was investigated by means of gas electron diffraction, dynamic nuclear magnetic resonance, temperature-dependent Raman spectroscopy, and quantum-chemical calculations applying CCSD(T), MP2, and DFT methods. According to the experimental and calculated results, all three compounds exist as a mixture of two chair conformers of the six-membered ring. The two chair forms of C s symmetry differ in the axial or equatorial position of the X atom. In all cases, the axial conformer is preferred over the equatorial one. When the experimental uncertainties are taken into account, all of the experimental and theoretical results for the conformational energy ( E axial - E equatorial ) fit into a remarkably narrow range of -0.50 ± 0.15 kcal mol -1 . It was found by NBO analysis that the axial conformers are unfavorable in terms of steric energy and conjugation effects and that they are stabilized mainly by electrostatic interactions. The conformational energies for C 6 H 11 X and cyclo -C 5 H 10 SiHX (X = F, Cl, Br, I, At) were compared using CCSD(T) calculations. In both series, fluorine is predicted to have a lower conformational preference (cyclohexane equatorial, silacyclohexane axial) than Cl, Br, and I. It is predicted that astatine would behave very similarly to Cl, Br, and I within each series.

The 1'-organyl-1,2,3,4-tetrahydrospiro[naphthalene-1,4'-piperidine] derivatives 1 a-4 a [for which organyl=benzyl (1 a), 4-methoxybenzyl (2 a), 2-phenylethyl (3 a), or 3-methylbut-2-enyl (4 a)] are high-affinity, selective σ₁ ligands. The corresponding sila-analogues 1 b-4 b (replacement of the carbon spirocenter with a silicon atom) were synthesized in multistep syntheses, starting from dichlorodivinylsilane, and were isolated as the hydrochlorides 1 b⋅HCl-4 b⋅HCl. Compounds 1 a⋅HCl-4 a⋅HCl and 1 b⋅HCl-4 b⋅HCl were structurally characterized by NMR spectroscopy (¹H, ¹³C, ²⁹Si) in solution, and the C/Si analogues 3 a⋅HCl and 3 b⋅HCl were studied by single-crystal X-ray diffraction. These structural investigations were complemented by computational studies. The σ₁ and σ₂ receptor affinities of the C/Si pairs 1 a/1 b-4 a/4 b were studied with radioligand binding assays. The σ₁ receptor affinity of the silicon compounds 1 b-4 b is slightly higher than that of the corresponding carbon analogues 1 a-4 a. Because affinity for the σ₂ receptor is decreased by the C/Si exchange, the σ₁/σ₂ selectivity of the silicon compounds is considerably improved, indicating that the C→Si switch strategy is a powerful tool for modulating both pharmacological potency and selectivity., (Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

We present an approach to model molecular crystals using an adaptive quantum mechanics/molecular mechanics (QM/MM) based protocol. The molecule of interest (or a larger cluster thereof) is described at an appropriate QM level and is embedded in a large array of MM atoms built up from crystal structure information. The nonbonded MM force field consists of atom-centered point charges and Lennard-Jones potentials using van der Waals parameters from the UFF force field. The point charges are initially derived from a single molecule DFT calculation and are then updated self-consistently in the field of point charges. Additional charges are fitted around the MM cluster to correct for missing long-range electrostatic effects. The geometry of the central complex can then be relaxed by quantum chemical calculations in the surrounding MM reaction field, hence capturing solid-state effects on the geometry. We demonstrate the accuracy of this approach for geometry optimization by successful modeling of the huge gas-to-solid bond contraction of HCN-BF3, the ability to reproduce periodic-DFT quality local geometries of solid VOCl3, and the geometry of [Ru(η(5)-Cp*)(η(3)-CH2CHCHC6H5)(NCCH3)2](2+), a difficult ruthenium allyl complex in the solid state. We further show that this protocol is well suited for subsequent molecular property calculations in the solid state (where accurate relaxed geometries are often required) as exemplified by transition metal NMR and EFG calculations of VOCl3 and a vanadium catechol complex in the solid state.

The conformations and relative stabilities of folded and extended 3-fluoro-γ-aminobutyric acid (3F-GABA) conformers were studied using explicit solvation models. Geometry optimisations in the gas phase with one or two explicit water molecules favour folded and neutral structures containing intramolecular NH···O-C hydrogen bonds. With three or five explicit water molecules zwitterionic minima are obtained, with folded structures being preferred over extended conformers. The stability of folded versus extended zwitterionic conformers increases on going from a PCM continuum solvation model to the microsolvated complexes, though extended structures become less disfavoured with the inclusion of more water molecules. Full explicit solvation was studied with a hybrid quantum-mechanical/molecular-mechanical (QM/MM) scheme and molecular dynamics simulations, including more than 6000 TIP3P water molecules. According to free energies obtained from thermodynamic integration at the PM3/MM level and corrected for B3LYP/MM total energies, the fully extended conformer is more stable than folded ones by about -4.5 kJ mol(-1). B3LYP-computed (3)J(F,H) NMR spin-spin coupling constants, averaged over PM3/MM-MD trajectories, agree best with experiment for this fully extended form, in accordance with the original NMR analysis. The seeming discrepancy between static PCM calculations and experiment noted previously is now resolved. That the inexpensive semiempirical PM3 method performs so well for this archetypical zwitterion is encouraging for further QM/MM studies of biomolecular systems., (Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

(51)V NMR parameters have been calculated for VOCl(3), the reference compound in (51)V NMR spectroscopy, in order to capture environmental effects in both the neat liquid and the solid state. Using a combination of periodic geometry optimizations and Car-Parrinello molecular dynamics simulations with embedded cluster NMR calculations, we are able to test the ability of current computational approaches to reproduce (51)V NMR properties (isotropic shifts, anisotropic shifts and quadrupole coupling constants) in the gas, liquid and solid states, for direct comparison with liquid and solid-state experimental data. The results suggest that environmental effects in the condensed phases can be well captured by an embedded cluster approach and that the remaining discrepancy with experiment may be due to the approximate density functionals in current use. The predicted gas-to-liquid shift on the isotropic shielding constant is small, validating the common practice to use a single VOCl(3), molecule as reference in (51)V NMR computations.