Vibrational markers for the open-shell character of transition metal bis-dithiolenes: an infrared, resonance raman, and quantum chemical study

Multi-wavelength Raman microscopy of nickel-based electron transport in cable bacteria

Cable bacteria embed a network of conductive protein fibers in their cell envelope that efficiently guides electron transport over distances spanning up to several centimeters. This form of long-distance electron transport is unique in biology and is mediated by a metalloprotein with a sulfur-coordinated nickel (Ni) cofactor. However, the molecular structure of this cofactor remains presently unknown. Here, we applied multi-wavelength Raman microscopy to identify cell compounds linked to the unique cable bacterium physiology, combined with stable isotope labeling, and orientation-dependent and ultralow-frequency Raman microscopy to gain insight into the structure and organization of this novel Ni-cofactor. Raman spectra of native cable bacterium filaments reveal vibrational modes originating from cytochromes, polyphosphate granules, proteins, as well as the Ni-cofactor. After selective extraction of the conductive fiber network from the cell envelope, the Raman spectrum becomes simpler, and primarily retains vibrational modes associated with the Ni-cofactor. These Ni-cofactor modes exhibit intense Raman scattering as well as a strong orientation-dependent response. The signal intensity is particularly elevated when the polarization of incident laser light is parallel to the direction of the conductive fibers. This orientation dependence allows to selectively identify the modes that are associated with the Ni-cofactor. We identified 13 such modes, some of which display strong Raman signals across the entire range of applied wavelengths (405-1,064 nm). Assignment of vibrational modes, supported by stable isotope labeling, suggest that the structure of the Ni-cofactor shares a resemblance with that of nickel bis(1,2-dithiolene) complexes. Overall, our results indicate that cable bacteria have evolved a unique cofactor structure that does not resemble any of the known Ni-cofactors in biology.

Characterizing Excited States of a Copper-Based Molecular Qubit Candidate with Correlated Electronic Structure Methods

Molecular spins have a variety of potential advantages as qubits for quantum computation, such as tunability and well-understood design pathways through organometallic synthesis. Organometallic and heavy-metal-based molecular spin qubits can also exhibit rich electronic structures due to ligand field interactions and electron correlation. These features make consistent and reliable modeling of these species a considerable challenge for contemporary electronic structure techniques. Here, we elucidate the electronic structure of a Cu(II) complex analogous to a recently proposed room-temperature molecular spin qubit. Using active space methods to describe the electron correlation, we show the nuanced interaction between the metal d orbitals and ligand σ and π orbitals makes these systems challenging to model, both in terms of the delocalized spin density and the excited state ordering. We show that predicting the correct spin delocalization requires special consideration of the Cu d orbitals and that the excited state spectrum for the Cu(III) complex also requires the explicit inclusion of the π orbitals in the active space. These interactions are rather common in molecular spin qubit motifs and may play an important role in spin-decoherence processes. Our results may lend insight into future studies of the orbital interactions and electron delocalization of similar complexes.

Synthesis and coordination behaviour of 1H-1,2,3-triazole-4,5-dithiolates

The preparative access to and first group 10 metal complexes of novel 1H-1,2,3-triazole-4,5-dithiolate ligands (tazdt^2-) are reported. A set of S-protected 1H-1,2,3-triazole-4,5-dithiol derivatives with R¹ = 2,6-dimethylphenyl (Xy) or benzyl (Bn) at N1 and with R² = Bn or trimethylsilylethyl (TMS-ethyl) at both S atoms were synthesized by a 1,3-dipolar cycloaddition catalysed by either Ru(II) or Cu(I). Extensive investigations on the removal of the protective groups resulted the reductive removal of benzyl groups to be superior in isolating the free 4,5-dithiols of R¹N₃C₂(SH)₂ with R¹ = Xy (H₂-8) or Bn (H₂-9). Coordination of these ligands led to the formation of the metal complexes [(η⁵-C₅H₅)₂Ti(8)], [Ni(dppe)(8)], [Ni(dppe)(9)], [Pd(dppe)(9)] {dppe = bis(diphenylphosphanyl)ethane} and homoleptic (NBu₄)_n[Ni(8)₂] (n = 1, 2). All complexes were fully characterized including structure determination by single crystal XRD. The electronic properties of the Ni and Pd complexes were determined by cyclic voltammetry, UV/vis and EPR spectroscopy supported by DFT calculations. According to the spectral and electrochemical data, the tazdt^2- complexes resemble the corresponding benzene-1,2-dithiolate (bdt^2-) type compounds reflecting the restricted influence of the electron-withdrawing N₃ moiety in the backbone. DSC-TGA measurements with [(η⁵-C₅H₅)₂Ti(8)] and [Ni(dppe)(8)] indicate a well-defined thermal process involving simultaneous elimination of both N₂ and CS.

Efficient long-range conduction in cable bacteria through nickel protein wires

Filamentous cable bacteria display long-range electron transport, generating electrical currents over centimeter distances through a highly ordered network of fibers embedded in their cell envelope. The conductivity of these periplasmic wires is exceptionally high for a biological material, but their chemical structure and underlying electron transport mechanism remain unresolved. Here, we combine high-resolution microscopy, spectroscopy, and chemical imaging on individual cable bacterium filaments to demonstrate that the periplasmic wires consist of a conductive protein core surrounded by an insulating protein shell layer. The core proteins contain a sulfur-ligated nickel cofactor, and conductivity decreases when nickel is oxidized or selectively removed. The involvement of nickel as the active metal in biological conduction is remarkable, and suggests a hitherto unknown form of electron transport that enables efficient conduction in centimeter-long protein structures.

Proton and Electron Transfer in the Formation of a Copper Dithiolene-Based Coordination Polymer

Metal bis(dithiolene) complexes are promising building blocks for electrically conductive coordination polymers. N-Heterocyclic dithiolene complexes allow their cross-linking via the coordination of N-donor atoms to additional transition metal ions. In this study, we present the formal copper(II) and copper(III) 6,7-quinoxalinedithiolene complexes [Cu(qdt)₂]^- and [Cu(qdt)₂]^2- (qdt^2-: 6,7-quinoxalinedithiolate), as well as the 2D coordination polymer Cu[Cu(Hqdt)(qdt)] (3). The dithiolene complexes were isolated as (Bu₄N)₂[Cu(qdt)₂] (1), Na[Cu(qdt)₂]·4H₂O (2a), [Na(acetone)₄][Cu(qdt)₂] (2b), and [Ni(MeOH)₆][Cu(qdt)₂]₂·2H₂O (2c). Their crystal structures reveal nearly planar complexes with a high tendency of π-stacking. For a better understanding of their coordination behavior, the electronic properties are investigated by UV-vis-NIR spectroscopy, cyclic voltammetry, and DFT simulations. The synthesis of the 2D coordination polymer 3 involves the reduction and protonation of the monoanionic copper(III) complex. A combination of powder X-ray diffraction, magnetic susceptibility measurements, as well as IR and EPR spectroscopy confirm that formal [Cu^II(Hqdt)(qdt)]^- units link trigonal planar copper(I) atoms to a dense 2D coordination polymer. The electrical conductivity of 3 at room temperature is 2 × 10^-7 S/cm. Temperature dependent conductivity measurements confirm the semiconducting behavior of 3 with an Arrhenius derived activation energy of 0.33 eV. The strong absorption of 3 in the visible and NIR regions of the spectrum is caused by the small optical band gap of E_g,opt = 0.65 eV, determined by diffuse reflectance spectroscopy. This study sheds light on the coordination chemistry of N-heterocyclic dithiolene complexes and may serve as a reference for the future design and synthesis of dithiolene-based coordination polymers with interesting electrical and magnetic properties.

What Does Ectoine Do to DNA? A Molecular-Scale Picture of Compatible Solute-Biopolymer Interactions

Compatible solutes accumulate in the cytoplasm of halophilic microorganisms, enabling their survival in a high-salinity environment. Ectoine is such a compatible solute. It is a zwitterionic molecule that strongly interacts with surrounding water molecules and changes the dynamics of the local hydration shell. Ectoine interacts with biomolecules such as lipids, proteins, and DNA. The molecular interaction between ectoine and biomolecules, in particular the interaction between ectoine and DNA, is far from being understood. In this paper, we describe molecular aspects of the interaction between ectoine and double-stranded DNA (dsDNA). Two 20 base pairs-long dsDNA fragments were immobilized on a gold surface via a thiol-tether. The interaction between the dsDNA monolayers with diluted and concentrated ectoine solutions was examined by means of X-ray photoelectron and polarization modulation infrared reflection absorption spectroscopies (PM IRRAS). Experimental results indicate that the ability of ectoine to bind water reduces the strength of hydrogen bonds formed to the ribose-phosphate backbone in the dsDNA. In diluted (0.1 M) ectoine solution, DNA interacts predominantly with water molecules. The sugar-phosphate backbone is involved in the formation of strong hydrogen bonds to water, which, over time, leads to a reorientation of the planes of nucleic acid bases. This reorientation destabilizes the strength of hydrogen bonds between the bases and leads to a partial dehybridization of the dsDNA. In concentrated ectoine solution (2.5 M), almost all water molecules interact with ectoine. Under this condition, ectoine is able to interact directly with DNA. Density functional theory (DFT) calculations demonstrate that the direct interaction involves the nitrogen atoms in ectoine and phosphate groups in the DNA molecule. The results of the quantum-chemical calculations show that rearrangements in the ribose-phosphate backbone, caused by a direct interaction with ectoine, facilitates contacts between the O atom in the phosphate group and H atoms in a nucleic acid base. In the PM IRRA spectra, an increase in the number of IR absorption modes in the base pair frequency region proves that the hydrogen bonds between bases become weaker. Thus, a sequence of reorientations caused by interaction with ectoine leads to a breakdown of hydrogen bonds between bases in the double helix.

Spectroscopic and Electronic Properties of Molybdacarborane Complexes with Non-innocently Acting Ligands

The molybdacarboranes [3-{L-κ² N,N}-3-(CO)₂ -closo-3,1,2-MoC₂ B₉ H₁₁ ] (L=2,2'-bipyridine (2,2'-bpy, 1 a) or 1,10-phenanthroline (1,10-phen, 1 b)) incorporating well-known potentially non-innocent ligands (CO, 2,2'-bpy, 1,10-phen) and the "non-spectator" nido-carborane ([η⁵ -C₂ B₉ H₁₁ ]^2- ) ligand were prepared and fully characterised. High-resolution mass spectrometry, single-crystal X-ray diffraction methods, spectroscopy (IR, (resonance) Raman, NMR), cyclic voltammetry and spectroelectrochemistry (electrochemical properties) were supported by theoretical investigations of the electronic structure (DFT, CAS-SCF, TD-DFT).

Strategic design of thiophene-fused nickel dithiolene derivatives for efficient NLO response

The zwitterionic donor–acceptor group significantly reduces the HOMO–LUMO energy gap resulting in an enormous increase in the first hyperpolarizability values.

Calixsmaragdyrin: A Versatile Ligand for Coordination Complexes

The Ru(II) and BF₂ complexes of calixsmaragdyrin were prepared under simple reaction conditions and characterized by HR-MS, 1D and 2D NMR spectroscopy, optical spectroscopy, and electrochemistry, and the structure of the Ru(II) complex of calixsmaragdyrin was elucidated by X-ray crystallography. The crystal structure of the Ru(II) complex revealed that the Ru(II) ion is hexacoordinate with the three pyrrole nitrogen ligands from the tripyrrin unit of the calixsmaragdyrin macrocycle, and the remaining coordination sites of Ru(II) ion were occupied by two carbonyl groups and one hydroxyl (-OH) group. The calixsmaragdyrin macrocycle in the Ru(II) complex was distorted with a dome-like structure. In the BF₂ complex of calixsmaragdyrin, the BF₂ unit was bound to two pyrrolic nitrogens of the dipyrrin moiety of calixsmaragdyrin as deduced by detailed 1- and 2-dimensional NMR spectroscopy studies. The Ru(II) complex displayed a strong Soret-like absorption band at 449 nm with the absence of Q-bands, whereas the BF₂ complex showed a Soret-like band at 475 nm with two well-defined Q-bands at 787 and 883 nm, respectively. Quantum mechanical DFT calculations yielded relaxed equilibrium structures that were similar to the X-ray crystal structures, and the related charge density distributions indicated that the d orbital of the Ru(II) ion was contributing to the HOMO and LUMO states. In addition, TD-DFT calculations successfully reproduced the large bathochromic shifts, oscillator strengths, and electronic transitions that were observed in the experimental absorption spectra of all three complexes. Both the Ru(II) and the BF₂ complexes of calixsmaragdyrin were stable under redox conditions.

Experimental and DFT Investigations Reveal the Influence of the Outer Coordination Sphere on the Vibrational Spectra of Nickel-Substituted Rubredoxin, a Model Hydrogenase Enzyme

Nickel-substituted rubredoxin (NiRd) is a functional enzyme mimic of hydrogenase, highly active for electrocatalytic and solution-phase hydrogen generation. Spectroscopic methods can provide valuable insight into the catalytic mechanism, provided the appropriate technique is used. In this study, we have employed multiwavelength resonance Raman spectroscopy coupled with DFT calculations on an extended active-site model of NiRd to probe the electronic and geometric structures of the resting state of this system. Excellent agreement between experiment and theory is observed, allowing normal mode assignments to be made on the basis of frequency and intensity analyses. Both metal-ligand and ligand-centered vibrational modes are enhanced in the resonance Raman spectra. The latter provide information about the hydrogen bonding network and structural distortions due to perturbations in the secondary coordination sphere. To reproduce the resonance enhancement patterns seen for high-frequency vibrational modes, the secondary coordination sphere must be included in the computational model. The structure and reduction potential of the Ni^IIIRd state have also been investigated both experimentally and computationally. This work begins to establish a foundation for computational resonance Raman spectroscopy to serve in a predictive fashion for investigating catalytic intermediates of NiRd.

Optical response of the Cu2 S2 diamond core in Cu2II(NGuaS)2 Cl2

Density functional theory (DFT) and time-dependent DFT calculations are presented for the dicopper thiolate complex Cu2 (NGuaS)2 Cl2 [NGuaS=2-(1,1,3,3-tetramethylguanidino) benzenethiolate] with a special focus on the bonding mechanism of the Cu2 S2 Cl2 core and the spectroscopic response. This complex is relevant for the understanding of dicopper redox centers, for example, the CuA center. Its UV/Vis absorption is theoretically studied and found to be similar to other structural CuA models. The spectrum can be roughly divided in the known regions of metal d-d absorptions and metal to ligand charge transfer regions. Nevertheless the chloride ions play an important role as electron donors, with the thiolate groups as electron acceptors. The bonding mechanism is dissected by means of charge decomposition analysis which reveals the large covalency of the Cu2 S2 diamond core mediated between Cu dz2 and S-S π and π* orbitals forming Cu-S σ bonds. Measured resonant Raman spectra are shown for 360- and 720-nm excitation wavelength and interpreted using the calculated vibrational eigenmodes and frequencies. The calculations help to rationalize the varying resonant behavior at different optical excitations. Especially the phenylene rings are only resonant for 720 nm. © 2016 Wiley Periodicals, Inc.

Bioinspired design of redox-active ligands for multielectron catalysis: effects of positioning pyrazine reservoirs on cobalt for electro- and photocatalytic generation of hydrogen from water

Mononuclear metalloenzymes in nature can function in cooperation with precisely positioned redox-active organic cofactors in order to carry out multielectron catalysis. Inspired by the finely tuned redox management of these bioinorganic systems, we present the design, synthesis, and experimental and theoretical characterization of a homologous series of cobalt complexes bearing redox-active pyrazines. These donor moieties are locked into key positions within a pentadentate ligand scaffold in order to evaluate the effects of positioning redox non-innocent ligands on hydrogen evolution catalysis. Both metal- and ligand-centered redox features are observed in organic as well as aqueous solutions over a range of pH values, and comparison with analogs bearing redox-inactive zinc(ii) allows for assignments of ligand-based redox events. Varying the geometric placement of redox non-innocent pyrazine donors on isostructural pentadentate ligand platforms results in marked effects on observed cobalt-catalyzed proton reduction activity. Electrocatalytic hydrogen evolution from weak acids in acetonitrile solution, under diffusion-limited conditions, reveals that the pyrazine donor of axial isomer 1-Co behaves as an unproductive electron sink, resulting in high overpotentials for proton reduction, whereas the equatorial pyrazine isomer complex 2-Co is significantly more active for hydrogen generation at lower voltages. Addition of a second equatorial pyrazine in complex 3-Co further minimizes overpotentials required for catalysis. The equatorial derivative 2-Co is also superior to its axial 1-Co congener for electrocatalytic and visible-light photocatalytic hydrogen generation in biologically relevant, neutral pH aqueous media. Density functional theory calculations (B3LYP-D2) indicate that the first reduction of catalyst isomers 1-Co, 2-Co, and 3-Co is largely metal-centered while the second reduction occurs at pyrazine. Taken together, the data establish that proper positioning of non-innocent pyrazine ligands on a single cobalt center is indeed critical for promoting efficient hydrogen catalysis in aqueous media, akin to optimally positioned redox-active cofactors in metalloenzymes. In a broader sense, these findings highlight the significance of electronic structure considerations in the design of effective electron-hole reservoirs for multielectron transformations.

Revealing the thermodynamic driving force for ligand-based reductions in quinoids; conceptual rules for designing redox active and non-innocent ligands

Metal and ligand-based reductions have been modeled in octahedral ruthenium complexes revealing metal-ligand interactions as the profound driving force for the redox-active behaviour of orthoquinoid-type ligands. Through an extensive investigation of redox-active ligands we revealed the most critical factors that facilitate or suppress redox-activity of ligands in metal complexes, from which basic rules for designing non-innocent/redox-active ligands can be put forward. These rules also allow rational redox-leveling, i.e. the moderation of redox potentials of ligand-centred electron transfer processes, potentially leading to catalysts with low overpotential in multielectron activation processes.

Synthesis and characterization of mononuclear, pseudotetrahedral cobalt(III) compounds

The preparation and characterization of two mononuclear cobalt(III) tropocoronand complexes, [Co(TC-5,5)](BF4) and [Co(TC-6,6)](BPh4), are reported. The cobalt(III) centers exist in rare pseudotetrahedral conformations, with twist angles of 65° and 74° for the [Co(TC-5,5](+) and [Co(TC-6,6)](+) species, respectively. Structural and electrochemical characteristics are compared with those of newly synthesized [Ga(TC-5,5)](GaCl4) and [Ga(TC-6,6)](GaCl4) analogues. The spin state of the pseudotetrahedral [Co(TC-6,6)](BPh4) compound was determined to be S = 2, a change in spin state from the value of S = 1 that occurs in the square-planar and distorted square-planar complexes, [Co(TC-3,3)](X) (X = BPh4, BAr'4) and [Co(TC-4,4)](BPh4), respectively.

Charge transfer in MOH(H2O)+ (M = Mn, Fe, Co, Ni, Cu, Zn) complexes revealed by vibrational spectroscopy of mass-selected ions

The hydroxide frequency in MOH(H₂O)⁺ is a sensitive probe of charge transfer.

An electroactive porous network from covalent metal–dithiolene links

Direct reaction between a hexathiol and PtCl₂ leads to the formation of a covalent metal–organic framework (CMOF) featuring substantial porosity, redox activity and ion exchange capability.

DFT studies of structure and vibrational spectra of 4-benzylidene-1-phenyl-2-selenomorpholino-1H-imidazol-5(4H)-one and its derivatives

The Raman spectra and FT-IR spectra of 4-benzylidene-1-phenyl-2-selenomorpholino-1H-imidazol-5(4H)-one and its derivatives have been measured and their ground-state geometries and vibrational spectra are studied by DFT at B3LYP/6-31G(d) level. Comparing the optimized geometries of compounds 1-6, we find that different substituent and substitution site on benzene rings result in very small changes on the imidazoline skeleton, the changes on bond length are within 0.005 Å and on bond angle are within 0.5°. Calculated spectra are well consistent with the experimental one and the deviations are smaller than 30 cm-1. The influence of substituent on IR and Raman spectrum must not be neglected. Electron-withdrawing chlorine atom makes the stretching vibration of carbonyl group shift 4-16 cm(-1) towards higher wavenumber, but electron-donating methoxyl group and dioxole group make it shift 6-10 cm(-1) in IR and 9-13 cm(-1) in Raman spectrum towards lower wavenumber, respectively. Dioxole substitution makes the C=C stretching vibration of phenyl shift to a higher position at 1617-1618 cm(-1). The influence of intermolecular weak interaction on vibrational spectrum is studied by two models (dimer and monomer inclusion van del Waals correction). Dimer model presents a better accuracy, but van del Waals correction on B3LYP hybrid function does not produce a significant change on accuracy in this system.

Synthetic approaches to (smif)2Ti (smif = 1,3-di-(2-pyridyl)-2-azaallyl) reveal redox non-innocence and C-C bond-formation

Attempted syntheses of (smif)(2)Ti (smif =1,3-di-(2-pyridyl)-2-azaallyl) based on metatheses of TiCl(n)L(m) (n = 2-4) with M(smif) (M = Li, Na), in the presence of a reducing agent (Na/Hg) when necessary, failed, but several apparent Ti(II) species were identified by X-ray crystallography and multidimensional NMR spectroscopy: (smif){Li(smif-smif)}Ti (1, X-ray), [(smif)Ti](2)(μ-κ(3),κ(3)-N,N(py)(2)-smif,smif) (2), (smif)Ti(κ(3)-N,N(py)(2)-smif,(smif)H) (3), and (smif)Ti(dpma) (4, dpma = di-2-pyridylmethyl-amide). NMR spectroscopy and K-edge XAS showed that each compound possesses ligands that are redox noninnnocent, such that d(1) Ti(III) centers AF-couple to ligand radicals: (smif){Li(smif-smif)(2-)}Ti(III) (1), [(smif(2-))Ti(III)](2)(μ-κ(3),κ(3)-N,N(py)(2)-smif,smif) (2), [(smif(2-))Ti(III)](κ(3)-N,N(py)(2)-smif,(smif)H) (3), and (smif(2-))Ti(III)(dpma) (4). The instability of (smif)(2)Ti relative to its C-C coupled dimer, 2, is rationalized via the complementary nature of the amide and smif radical dianion ligands, which are also common to 3 and 4. Calculations support this contention.