ABSTRACT
NAD+-reducing [NiFe] hydrogenases are valuable biocatalysts for H2-based energy conversion and the regeneration of nucleotide cofactors. While most hydrogenases are sensitive toward O2 and elevated temperatures, the soluble NAD+-reducing [NiFe] hydrogenase from Hydrogenophilus thermoluteolus (HtSH) is O2-tolerant and thermostable. Thus, it represents a promising candidate for biotechnological applications. Here, we have investigated the catalytic activity and active-site structure of native HtSH and variants in which a glutamate residue in the active-site cavity was replaced by glutamine, alanine, and aspartate. Our biochemical, spectroscopic, and theoretical studies reveal that at least two active-site states of oxidized HtSH feature an unusual architecture in which the glutamate acts as a terminal ligand of the active-site nickel. This observation demonstrates that crystallographically observed glutamate coordination represents a native feature of the enzyme. One of these states is diamagnetic and characterized by a very high stretching frequency of an iron-bound active-site CO ligand. Supported by density-functional-theory calculations, we identify this state as a high-valent species with a biologically unprecedented formal Ni(IV) ground state. Detailed insights into its structure and dynamics were obtained by ultrafast and two-dimensional infrared spectroscopy, demonstrating that it represents a conformationally strained state with unusual bond properties. Our data further show that this state is selectively and reversibly formed under oxic conditions, especially upon rapid exposure to high O2 levels. We conclude that the kinetically controlled formation of this six-coordinate high-valent state represents a specific and precisely orchestrated stereoelectronic response toward O2 that could protect the enzyme from oxidative damage.
Subject(s)
Hydrogenase , Alanine/metabolism , Aspartic Acid/metabolism , Catalytic Domain , Glutamic Acid/metabolism , Glutamine/metabolism , Hydrogenase/chemistry , Hydrogenophilaceae , Iron/chemistry , Ligands , NAD/metabolism , Nickel/chemistry , Oxidation-Reduction , Oxygen/chemistryABSTRACT
Ultrafast two-dimensional infrared (2D-IR) spectroscopy of Escherichia coli Hyd-1 (EcHyd-1) reveals the structural and dynamic influence of the protein scaffold on the Fe(CO)(CN)2 unit of the active site. Measurements on as-isolated EcHyd-1 probed a mixture of active site states including two, which we assign to Nir-SI/II, that have not been previously observed in the E. coli enzyme. Explicit assignment of carbonyl (CO) and cyanide (CN) stretching bands to each state is enabled by 2D-IR. Energies of vibrational levels up to and including two-quantum vibrationally excited states of the CO and CN modes have been determined along with the associated vibrational relaxation dynamics. The carbonyl stretching mode potential is well described by a Morse function and couples weakly to the cyanide stretching vibrations. In contrast, the two CN stretching modes exhibit extremely strong coupling, leading to the observation of formally forbidden vibrational transitions in the 2D-IR spectra. We show that the vibrational relaxation times and structural dynamics of the CO and CN ligand stretching modes of the enzyme active site differ markedly from those of a model compound K[CpFe(CO)(CN)2] in aqueous solution and conclude that the protein scaffold creates a unique biomolecular environment for the NiFe site that cannot be represented by analogy to simple models of solvation.
Subject(s)
Hydrogenase , Hydrogenase/chemistry , Catalytic Domain , Escherichia coli/metabolism , Ligands , Cyanides/chemistry , Spectrophotometry, Infrared/methods , ProteinsABSTRACT
We present a quantitative analysis of the timescales of reactivity that are accessible to a laser pump, NMR probe spectroscopy method using para-hydrogen induced polarisation (PHIP) and identify three kinetic regimes: fast, intermediate and slow. These regimes are defined by the relative rate of reaction, k, compared to δω, the frequency of the NMR signal oscillations associated with the coherent evolution of the hyperpolarised 1H NMR signals created after para-hydrogen (p-H2) addition during the pump-probe delay. The kinetic regimes are quantitatively defined by a NMR dephasing parameter, ε = δω/k. For the fast regime, where k ⫠δω and ε tends to zero, the observed NMR signals are not affected by the chemical evolution of the system and so only an upper bound on k can be determined. In the slow regime, where k ⪠δω and ε tends to infinity, destructive interference leads to the complete dephasing of the coherent NMR signal intensity oscillations. As a result, the observed NMR signal evolution during the pump-probe delay reflects only the chemical change of the system and NMR relaxation. Finally, in the intermediate regime, where k ⼠δω, characteristic partial dephasing of the NMR signal oscillations is predicted. In the limit where the dephasing parameter is small but non-zero, chemical evolution manifests itself as a phase shift in the NMR signal oscillation that is equal to the dephasing parameter. As this phase shift is predicted to persist for pump-probe delays much longer than the timescale of the formation of the product molecules, it provides a route to measure reactivity on micro-to-millisecond timescales through NMR detection. We predict that the most significant fundamental limitations of the accessible reaction timescales are the duration of the NMR excitation pulse (â¼1 µs) and the chemical shift difference (in Hz) between the p-H2-derived protons in the product molecule.
ABSTRACT
Diazirines are important for photoaffinity labeling, and their photoisomerization is relatively well-known. This work shows how hyperpolarized NMR spectroscopy can be used to characterize an unstable diazo-compound formed via photoisomerization of a 15N2-labeled silyl-ether-substituted diazirine. This diazirine is prepared in a nuclear spin singlet state via catalytic transfer of spin order from para-hydrogen. The active hyperpolarization catalyst is characterized to provide insight into the mechanism. The photochemical isomerization of the diazirine into the diazo-analogue allows the NMR invisible nuclear singlet state of the parent compound to be probed. The identity of the diazo-species is confirmed by trapping with N-phenyl maleimide via a cycloaddition reaction to afford bicyclic pyrazolines that also show singlet state character. The presence of singlet states in the diazirine and the diazo-compound is validated by comparison of experimental nutation behavior with theoretical simulation. The magnetic state lifetime of the diazo-compound is determined as 12 ± 1 s in CD3OD solution at room temperature, whereas its chemical lifetime is measured as 100 ± 5 s by related hyperpolarized NMR studies. Indirect evidence for the generation of the photoproduct para-N2 is presented.
ABSTRACT
Photochemical reactivity associated with metal-hydrogen bonds is widespread among metal hydride complexes and has played a critical part in opening up C-H bond activation. It has been exploited to design different types of photocatalytic reactions and to obtain NMR spectra of dilute solutions with a single pulse of an NMR spectrometer. Because photolysis can be performed on fast time scales and at low temperature, metal-hydride photochemistry has enabled determination of the molecular structure and rates of reaction of highly reactive intermediates. We identify five characteristic photoprocesses of metal monohydride complexes associated with the M-H bond, of which the most widespread are M-H homolysis and R-H reductive elimination. For metal dihydride complexes, the dominant photoprocess is reductive elimination of H2. Dihydrogen complexes typically lose H2 photochemically. The majority of photochemical reactions are likely to be dissociative, but hydride complexes may be designed with equilibrated excited states that undergo different photochemical reactions, including proton transfer or hydride transfer. The photochemical mechanisms of a few reactions have been analyzed by computational methods, including quantum dynamics. A section on specialist methods (time-resolved spectroscopy, matrix isolation, NMR, and computational methods) and a survey of transition metal hydride photochemistry organized by transition metal group complete the Review.
ABSTRACT
The photochemical reactions of Tp'Rh(PMe3)H2 (1) and thermal reactions of Tp'Rh(PMe3)(CH3)H (1a, Tp' = tris(3,5-dimethylpyrazolyl)borate) with substrates containing B-H, Si-H, C-F, and C-H bonds are reported. Complexes 1 and 1a are known activators of C-H bonds, including those of alkanes. Kinetic studies of reactions with HBpin and PhSiH3 show that photodissociation of H2 from 1 occurs prior to substrate attack, whereas thermal reaction of 1a proceeds by bimolecular reaction with the substrate. Complete intramolecular selectivity for B-H over C-H activation of HBpin (pin = pinacolate) leading to Tp'Rh(PMe3)(Bpin)H is observed. Similarly, the reaction with Et2SiH2 shows a strong preference for Si-H over C-H activation, generating Tp'Rh(PMe3)(SiEt2H)H. The Rh(Bpin)H and Rh(SiEt2H)H products were stable to heating in benzene in accord with DFT calculations that showed that reaction with benzene is endoergic. The intramolecular competition with PhSiH3 yields a â¼1:4 mixture of Tp'Rh(PMe3)(C6H4SiH3)H and Tp'Rh(PMe3)(SiPhH2)H, respectively. Reaction with pentafluoropyridine generates Tp'Rh(PMe3)(C5NF4)F, while reaction with 2,3,5,6-tetrafluoropyridine yields a mixture of C-H and C-F activated products. Hexafluorobenzene proves unreactive. Crystal structures are reported for B-H, Si-H, and C-F activated products, but in the latter case a bifluoride complex Tp'Rh(PMe3)(C5NF4)(FHF) was crystallized. Intermolecular competition reactions were studied by photoreaction of 1 in C6F6 with benzene and another substrate (HBpin, PhSiH3, or pentafluoropyridine) employing in situ laser photolysis in the NMR probe, resulting in a wide-ranging map of kinetic selectivities. The mechanisms of intramolecular and intermolecular selection are analyzed.
ABSTRACT
We report pump-probe experiments employing laser-synchronized reactions of para-hydrogen (para-H2) with transition metal dihydride complexes in conjunction with nuclear magnetic resonance (NMR) detection. The pump-probe experiment consists of a single nanosecond laser pump pulse followed, after a precisely defined delay, by a single radio frequency (rf) probe pulse. Laser irradiation eliminates H2 from either Ru(PPh3)3(CO)(H)2 1 or cis-Ru(dppe)2(H)2 2 in C6D6 solution. Reaction with para-H2 then regenerates 1 and 2 in a well-defined nuclear spin state. The rf probe pulse produces a high-resolution, single-scan (1)H NMR spectrum that can be recorded after a pump-probe delay of just 10 µs. The evolution of the spectra can be followed as the pump-probe delay is increased by micro- or millisecond increments. Due to the sensitivity of this para-H2 experiment, the resulting NMR spectra can have hydride signal-to-noise ratios exceeding 750:1. The spectra of 1 oscillate in amplitude with frequency 1101 ± 3 Hz, the chemical shift difference between the chemically inequivalent hydrides. The corresponding hydride signals of 2 oscillate with frequency 83 ± 5 Hz, which matches the difference between couplings of the hydrides to the equatorial (31)P nuclei. We use the product operator formalism to show that this oscillatory behavior arises from a magnetic coherence in the plane orthogonal to the magnetic field that is generated by use of the laser pulse without rf initialization. In addition, we demonstrate how chemical shift imaging can differentiate the region of laser irradiation thereby distinguishing between thermal and photochemical reactivity within the NMR tube.
ABSTRACT
The [CpFe(CO)(CN)2]- unit is an excellent structural model for the Fe(CO)(CN)2 moiety of the active site found in [NiFe] hydrogenases. Ultrafast infrared (IR) pump-probe and 2D-IR spectroscopy have been used to study K[CpFe(CO)(CN)2] (M1) in a range of protic and polar solvents and as a dry film. Measurements of anharmonicity, intermode vibrational coupling strength, vibrational relaxation time, and solvation dynamics of the CO and CN stretching modes of M1 in H2O, D2O, methanol, dimethyl sulfoxide, and acetonitrile reveal that H-bonding to the CN ligands plays an important role in defining the spectroscopic characteristics and relaxation dynamics of the Fe(CO)(CN)2 unit. Comparisons of the spectroscopic and dynamic data obtained for M1 in solution and in a dry film with those obtained for the enzyme led to the conclusion that the protein backbone forms an important part of the bimetallic active site environment via secondary coordination sphere interactions.
ABSTRACT
Three ruthenium complexes Λ-[cis-Ru((R,R)-Me-BPE)(2)(H)(2)] Λ-R,R-Ru1H(2), Δ-[cis-Ru((S,S)-Me-DuPHOS)(2)(H)(2)] Δ-S,S-Ru2H(2), and Λ-[cis-Ru((R,R)-Me-DuPHOS)(2)(H)(2)] Λ-R,R-Ru2H(2) (1 = (Me-BPE)(2), 2 = (Me-DuPHOS)(2)) were characterized by multinuclear NMR and CD spectroscopy in solution and by X-ray crystallography. The chiral ligands allow the full control of stereochemistry and enable mechanistic studies not otherwise available. Oxidative addition of E-H bonds (E = H, B, Si, C) was studied by steady state and laser flash photolysis in the presence of substrates. Steady state photolysis shows formation of single products with one stereoisomer. Solid state structures and circular dichroism spectra reveal a change in configuration at ruthenium for some Δ-S,S-Ru2H(2)/Λ-R,R-Ru2H(2) photoproducts from Λ to Δ (or vice versa) while the configuration for Λ-R,R-Ru1H(2) products remains unchanged as Λ. The X-ray structure of silyl hydride photoproducts suggests a residual H(1)···Si(1) interaction for Δ-[cis-Ru((R,R)-Me-DuPHOS)(2)(Et(2)SiH)(H)] and Δ-[cis-Ru((R,R)-Me-DuPHOS)(2)(PhSiH(2))(H)] but not for their Ru(R,R-BPE)(2) analogues. Molecular structures were also determined for Λ-[cis-Ru((R,R)-Me-BPE)(2)(Bpin)(H)], Λ-[Ru((S,S)-Me-DuPHOS)(2)(η(2)-C(2)H(4))], Δ-[Ru((R,R)-Me-DuPHOS)(2)(η(2)-C(2)H(4))], and trans-[Ru((R,R)-Me-DuPHOS)(2)(C(6)F(5))(H)]. In situ laser photolysis in the presence of p-H(2) generates hyperpolarized NMR spectra because of magnetically inequivalent hydrides; these experiments and low temperature photolysis with D(2) reveal that the loss of hydride ligands is concerted. The reaction intermediates [Ru(DuPHOS)(2)] and [Ru(BPE)(2)] were detected by laser flash photolysis and have spectra consistent with approximate square-planar Ru(0) structures. The rates of their reactions with H(2), D(2), HBpin, and PhSiH(3) were measured by transient kinetics. Rate constants are significantly faster for [Ru(BPE)(2)] than for [Ru(DuPHOS)(2)] and follow the substrate order H(2) > D(2) > PhSiH(3) > HBpin.
ABSTRACT
Vibrational spectroscopy is an important tool in chemical and biological analysis. A key issue when applying vibrational spectroscopy to dilute liquid samples is the inherently low sensitivity caused by short interaction lengths and small extinction coefficients, combined with low target molecule concentrations. Here, we introduce a novel type of surface-enhanced infrared absorption spectroscopy based on the resonance of a dielectric metasurface. We demonstrate that the method is suitable for probing vibrational bands of dilute analytes with a range of spectral linewidths. We observe that the absorption signal is enhanced by 1-2 orders of magnitude and show that this enhancement leads to a lower limit of detection compared to attenuated total reflection (ATR). Overall, the technique provides an important addition to the spectroscopist's toolkit especially for probing dilute samples.
ABSTRACT
Ultrafast 2D-IR spectroscopy is a powerful tool for understanding the spectroscopy and dynamics of biological molecules in the solution phase. A number of recent studies have begun to explore the utility of the information-rich 2D-IR spectra for analytical applications. Here, we report the application of ultrafast 2D-IR spectroscopy for the detection and classification of bacterial spores. 2D-IR spectra of Bacillus atrophaeus and Bacillus thuringiensis spores as dry films on CaF2 windows were obtained. The sporulated nature of the bacteria was confirmed using 2D-IR diagonal and off-diagonal peaks arising from the calcium dipicolinate CaDP·3H2O biomarker for sporulation. Distinctive peaks, in the protein amide I region of the spectrum were used to differentiate the two types of spore. The identified marker modes demonstrate the potential for the use of 2D-IR methods as a direct means of spore classification. We discuss these new results in perspective with the current state of analytical 2D-IR measurements, showing that the potential exists to apply 2D-IR spectroscopy to detect the spores on surfaces and in suspensions as well as in dry films. The results demonstrate how applying 2D-IR screening methodologies to spores would enable the creation of a library of spectra for classification purposes.
Subject(s)
Bacillus , Spores, Bacterial , Bacteria , Spectrophotometry, InfraredABSTRACT
Upon ex situ UV-visible light irradiation, complex cis-bis(N,N-diethyl-N'-naphthoylthioureato)-palladium(ii), cis-[Pd(L-κS,O)2], undergoes isomerization in acetonitrile-d3 and chloroform-d to yield trans-[Pd(L-κS,O)2] which then rearranges thermally to novel trans-[Pd(L-κS,N)2] prior to reverting thermally to the cis isomer in the absence of light. The thermal isomerization rate is highly solvent dependent and harnessed to enable each of these three geometric isomers to be isolated and characterized by 1H NMR spectroscopy, X-ray crystallography, melting point and thermal analysis. The formation of the trans-[Pd(L-κS,N)2] isomer as part of this isomerization has only been observed with the sterically demanding cis-bis(N,N-diethyl-N'-(naphthoylthioureato)palladium(ii) precursor based on our knowledge to date. In situ irradiation with monochromatic laser light (λ = 355 nm) coupled to 1H NMR spectroscopy of solutions of cis-[Pd(L-κS,O)2] in acetonitrile-d3 supports the ex situ photo-induced isomerization experiments.
ABSTRACT
The 3-cyano-N-methylquinolinium perchlorate (3-CN-NMQ(+)ClO4(-))-photosensitized oxidation of phenyl alkyl sulfoxides (PhSOCR1R2R3, 1, R1 = R2 = H, R3 = Ph; 2, R1 = H, R2 = Me, R3 = Ph; 3, R1 = R2 = Ph, R3 = H; 4, R1 = R2 = Me, R3 = Ph; 5, R1 = R2 = R3 = Me) has been investigated by steady-state irradiation and nanosecond laser flash photolysis (LFP) under nitrogen in MeCN. Steady-state photolysis showed the formation of products deriving from the heterolytic C-S bond cleavage in the sulfoxide radical cations (alcohols, R1R2R3COH, and acetamides, R1R2R3CNHCOCH3) accompanied by sulfur-containing products (phenyl benzenethiosulfinate, diphenyl disulfide, and phenyl benzenethiosulfonate). By laser irradiation, the formation of 3-CN-NMQ(*) (lambda(max) = 390 nm) and sulfoxide radical cations 1(*+) , 2(*+), and 5(*+) (lambda(max) = 550 nm) was observed within the laser pulse. The radical cations decayed by first-order kinetics with a process attributable to the heterolytic C-S bond cleavage leading to the sulfinyl radical and an alkyl carbocation. The radical cations 3(*+) and 4(*+) fragment too rapidly, decaying within the laser pulse. The absorption band of the cation Ph2CH(+) (lambda(max) = 440 nm) was observed with 3 while the absorption bands of 3-CN-NMQ(*) and PhSO(*) (lambda(max) = 460 nm) were observed just after the laser pulse in the LFP experiment with 4. No competitive beta-C-H bond cleavage has been observed in the radical cations from 1-3. The C-S bond cleavage rates were measured for 1(*+), 2(*+), and 5(*+). For 3(*+) and 4(*+), only a lower limit (ca. >3 x 10(7) s(-1)) could be given. Quantum yields (Phi) and fragmentation first-order rate constants (k) appear to depend on the structure of the alkyl group and on the bond dissociation free energy (BDFE) of the C-S bond of the radical cations determined by a thermochemical cycle using the C-S BDEs for the neutral sulfoxides 1-5 obtained by DFT calculations. Namely, Phi and k increase as the C-S BDFE becomes more negative, that is in the order 1 < 5 < 2 < 3, 4, which is also the stability order of the alkyl carbocations formed in the cleavage. An estimate of the difference in the C-S bond cleavage rate between sulfoxide and sulfide radical cations was possible by comparing the fragmentation rate of 5(*+) (1.4 x 10(6) s(-1)) with the upper limit (10(4) s(-1)) given for tert-butyl phenyl sulfide radical cation (Baciocchi, E.; Del Giacco, T.; Gerini, M. F.; Lanzalunga, O. Org. Lett. 2006, 8, 641-644). It turns out that sulfoxide radical cations undergo C-S bond breaking at a rate at least 2 orders of magnitude faster than that of corresponding sulfide radical cations.
Subject(s)
Benzene Derivatives/chemistry , Carbon/chemistry , Photosensitizing Agents/chemistry , Sulfur/chemistry , Alkylation , Cations/chemistry , Free Radicals/chemistry , Molecular Structure , Oxidation-Reduction , Photolysis , SpectrophotometryABSTRACT
We recently reported a pump-probe method that uses a single laser pulse to introduce parahydrogen (p-H2) into a metal dihydride complex and then follows the time-evolution of the p-H2-derived nuclear spin states by NMR. We present here a theoretical framework to describe the oscillatory behaviour of the resultant hyperpolarised NMR signals using a product operator formalism. We consider the cases where the p-H2-derived protons form part of an AX, AXY, AXYZ or AA'XX' spin system in the product molecule. We use this framework to predict the patterns for 2D pump-probe NMR spectra, where the indirect dimension represents the evolution during the pump-probe delay and the positions of the cross-peaks depend on the difference in chemical shift of the p-H2-derived protons and the difference in their couplings to other nuclei. The evolution of the NMR signals of the p-H2-derived protons, as well as the transfer of hyperpolarisation to other NMR-active nuclei in the product, is described. The theoretical framework is tested experimentally for a set of ruthenium dihydride complexes representing the different spin systems. Theoretical predictions and experimental results agree to within experimental error for all features of the hyperpolarised 1H and 31P pump-probe NMR spectra. Thus we establish the laser pump, NMR probe approach as a robust way to directly observe and quantitatively analyse the coherent evolution of p-H2-derived spin order over micro-to-millisecond timescales.
ABSTRACT
On reaction of IrI(CO)(PPh3)21 with para-hydrogen (p-H2), Ir(H)2I(CO)(PPh3)22 is formed which exhibits strongly enhanced 1H NMR signals for its hydride resonances. Complex 2 also shows similar enhancement of its NMR spectra when it is irradiated under p-H2. We report the use of this photochemical reactivity to measure the kinetics of H2 addition by laser-synchronized reactions in conjunction with NMR. The single laser pulse promotes the reductive elimination of H2 from Ir(H)2I(CO)(PPh3)22 in C6D6 solution to form the 16-electron precursor 1, back reaction with p-H2 then reforms 2 in a well-defined nuclear spin-state. The build up of this product can be followed by incrementing a precisely controlled delay (τ), in millisecond steps, between the laser and the NMR pulse. The resulting signal vs. time profile shows a dependence on p-H2 pressure. The plot of kobs against p-H2 pressure is linear and yields the second order rate constant, k2, for H2 addition to 1 of (3.26 ± 0.42) × 102 M-1 s-1. Validation was achieved by transient-UV-vis absorption spectroscopy which gives k2 of (3.06 ± 0.40) × 102 M-1 s-1. Furthermore, irradiation of a C6D6 solution of 2 with multiple laser shots, in conjunction with p-H2 derived hyperpolarization, allows the detection and characterisation of two minor reaction products, 2a and 3, which are produced in such low yields that they are not detected without hyperpolarization. Complex 2a is a configurational isomer of 2, while 3 is formed by substitution of CO by PPh3.
ABSTRACT
Pt(PCyp3)2 (Cyp = cyclopentyl) undergoes C-O oxidative addition with 2,3,5,6-tetrafluoro-4-methoxypyridine, pentafluoroanisole, 2,3,5,6-tetrafluoroanisole and 2,3,6-trifluoroanisole yielding platinum methyl derivatives. The reactions occur in preference to C-H or C-F activation.
ABSTRACT
Irradiation of CpRh(PMe3)(C2H4) (1; Cp = η5-C5H5) in the presence of pentafluoropyridine in hexane solution at low temperature yields an isolable η2-C,C-coordinated pentafluoropyridine complex, CpRh(PMe3)(η2-C,C-C5NF4) (2). The molecular structure of 2 was determined by single-crystal X-ray diffraction, showing coordination by C3-C4, unlike previous structures of pentafluoropyridine complexes that show N-coordination. Corresponding experiments with 2,3,5,6-tetrafluoropyridine yield the C-H oxidative addition product CpRh(PMe3)(C5NF4)H (3). In contrast, UV irradiation of 1 in hexane, in the presence of 4-substituted tetrafluoropyridines C5NF4X, where X = NMe2, OMe, results in elimination of C2H4 and HF to form the metallacycles CpRh(PMe3)(κ2-C,C-CH2N(CH3)C5NF3) (4) and CpRh(PMe3)(κ2-C,C-CH2OC5NF3) (5), respectively. The X-ray structure of 4 shows a planar RhCCNC-five-membered ring. Complexes 2-5 may also be formed by thermal reaction of CpRh(PMe3)(Ph)H with the respective pyridines at 50 °C.