Enzymatic and catalytic reduction of dinitrogen to ammonia: Density functional theory characterization of alternative molybdenum active sites

We used density functional calculations to model dinitrogen reduction by a FeMo cofactor containing a central nitrogen atom and by a Mo‐based catalyst. Plausible intermediates, reaction pathways, and relative energetics in the enzymatic and catalytic reduction of N₂ to ammonia at a single Mo center are explored. Calculations indicate that the binding of N₂ to the Mo atom and the subsequent multiple proton–electron transfer to dinitrogen and its protonated species involved in the conversion of N₂ are feasible energetically. In the reduction of N₂ the Mo atom experiences a cycled oxidation state from Mo(IV) to Mo(VI) by nitrogenase and from Mo(III) to Mo(VI) by the molybdenum catalyst, respectively, tuning the gradual reduction of N₂. Such a wide range of oxidation states exhibited by the Mo center is crucial for the gradual reduction process via successive proton–electron transfer. Present results suggest that the Mo atom in the N‐centered FeMo cofactor is a likely alternative active site for dinitrogen binding and reduction under mild conditions once there is an empty site available at the Mo site. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Theoretical, spectroscopic, and mechanistic studies on transition-metal dinitrogen complexes: implications to reactivity and relevance to the nitrogenase problem

Dinitrogen complexes of transition metals exhibit different binding geometries of N2 (end-on terminal, end-on bridging, side-on bridging, side-on end-on bridging), which are investigated by spectroscopy and DFT calculations, analyzing their electronic structure and reactivity. For comparison, a bis(mu-nitrido) complex, where the N--N bond has been split, has been studied as well. Most of these systems are highly covalent, and have strong metal-nitrogen bonds. In the present review, particular emphasis is put on a consideration of the activation of the coordinated dinitrogen ligand, making it susceptible to protonation, reactions with electrophiles or cleavage. In this context, theoretical, structural, and spectroscopic data giving informations on the amount of charge on the N2 unit are presented. The orbital interactions leading to a charge transfer from the metals to the dinitrogen ligand and the charge distribution within the coordinated N2 group are analyzed. Correlations between the binding mode and the observed reactivity of N2 are discussed.     

Catalytic reduction of dinitrogen to ammonia by molybdenum: theory versus experiment

Molybdenum complexes that contain the triamidoamine ligand [(RNCH(2)CH(2))(3)N](3-) (R = 3,5-(2,4,6-iPr(3)C(6)H(2))(2)C(6)H(3)) catalyze the reduction of dinitrogen to ammonia at 22 degrees C and 1 atm with protons from 2,6-dimethylpyridinium and electrons from decamethylchromocene. Several theoretical studies have been published that bear on the proposed intermediates in the catalytic dinitrogen reduction reaction and their reaction characteristics, including DFT calculations on [(HIPTNCH(2)CH(2))(3)N]Mo species (HIPT =hexaisopropylterphenyl = 3,5-(2,4,6-iPr(3)C(6)H(2))(2)C(6)H(3)), which contain the actual triamidoamine ligand that is present in catalytic intermediates. Recent theoretical findings are compared with experimental findings for each proposed step in the catalytic reaction.     

Effect of the potential of an external electron donor on C<Subscript>2</Subscript>H<Subscript>2</Subscript> reduction catalyzed by the nitrogenase active center (FeMoco) isolated from the enzyme

The effect of potential value and chemical properties of an external electron donor on C₂H₂ reduction catalyzed by nitrogenase active center (cluster [(₆-N)Fe₇MoS₉·homocitrate] FeMoco isolated from the enzyme) has been investigated in the presence of proton donors of different acidity. The temperature—reaction rate dependences of these reactions have been studied. It has been shown that the rate-limiting steps of the reactions differ depending on the proton donor used. When thiophenol or water are used as proton donors, and electrochemical step — the electron transfer from cathode to adsorbed catalytic cluster — has been found to be a rate-limiting one. The effective activation energy of ethane formation as a product of four-electron C₂H₂ reduction is found to be 1.5 times lower than that of ethylene, namely, 13 kcal mol^–1. When stronger acid, pentafluorothiophenol, is used as a proton donor, the chemical step of intramolecular rearrangement of the catalyst—substrate complex taking place in solution becomes a rate-limiting one. The effective activation energies of both ethylene and ethane become equal to 32 kcal mol^–1.Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1583–1591, August, 2004.     

Hydroxylamine as an ammonia equivalent: access to NH-tetrahydroisoquinolonic derivatives from aldoximes by the Castagnoli–Cushman reaction followed by reduction

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Reactivity of tris(acetylacetonato) iron(III) with tridentate [ONO] donor Schiff base as an access to newer mixed-ligand iron(III) complexes

Two new mixed-ligand iron(III) complexes, [Fe(L(n))(acac)(C(2)H(5)OH)] incorporating coordinated ethanol from the reaction solvent were accessed from the reaction of [Fe(acac)(3)] with [ONO] donor dibasic tridentate unsymmetrical Schiff base ligands derived from condensation of 2-hydroxy-1-napthaldehyde with 2-aminophenol (H(2)L(1)) or 2-aminobenzoic acid (H(2)L(2)). The thermal study (TGA-DTA) provided evidence for weakly bound ethanol which is readily substituted by neutral N-donor molecule imidazole, benzimidazole or pyridine to produce an array of newer complexes, [Fe(L(n))(acac)X] (n=1, 2; X=Im, Bim, Py). The compounds were characterized by elemental analyses, FT-IR, UV-vis, solution electrical conductivity, FAB mass, (1)H and (13)C NMR spectroscopy. Room temperature magnetic susceptibility measurements (μ(eff)～5.8 B.M.) are consistent with spin-free octahedral iron(III) complexes. Cyclic voltammetry of ethanol complexes revealed a quasi-reversible one electron redox response (ΔE(p)>100 mV) for the Fe(III)/Fe(II) couple. Low half wave redox potential (E(1/2)) values suggested easy redox susceptibility. The ground state geometries of the ethanol and imidazole complexes have been ascertained to be distorted octahedral by density functional theory using DMol3 program at BLYP/DNP level.     

99Tc NMR as a promising technique for structural investigation of biomolecules: theoretical studies on the solvent and thermal effects of phenylbenzothiazole complex

The phenylbenzothiazole compounds show antitumor properties and are highly selective. In this paper, the ⁹⁹Tc chemical shifts based on the (^99mTc)(CO)₃(NNO) complex conjugated to the antitumor agent 2‐(4′‐aminophenyl)benzothiazole are reported. Thermal and solvent effects were studied computationally by quantum‐chemical methods, using the density functional theory (DFT) (DFT level BPW91/aug‐cc‐pVTZ for the Tc and BPW91/IGLO‐II for the other atoms) to compute the NMR parameters for the complex. We have calculated the ⁹⁹Tc NMR chemical shifts of the complex in gas phase and solution using different solvation models (polarizable continuum model and explicit solvation). To evaluate the thermal effect, molecular dynamics simulations were carried, using the atom‐centered density matrix propagation method at the DFT level (BP86/LanL2dz). The results highlight that the ⁹⁹Tc NMR spectroscopy can be a promising technique for structural investigation of biomolecules, at the molecular level, in different environments. Copyright © 2014 John Wiley & Sons, Ltd.     

New Insights on Glutathione’s Supramolecular Arrangement and Its In Silico Analysis as an Angiotensin-Converting Enzyme Inhibitor

Angiotensin-converting enzyme (ACE) inhibitors are one of the most active classes for cardiovascular diseases and hypertension treatment. In this regard, developing active and non-toxic ACE inhibitors is still a continuous challenge. Furthermore, the literature survey shows that oxidative stress plays a significant role in the development of hypertension. Herein, glutathione’s molecular structure and supramolecular arrangements are evaluated as a potential ACE inhibitor. The tripeptide molecular modeling by density functional theory, the electronic structure by the frontier molecular orbitals, and the molecular electrostatic potential map to understand the biochemical processes inside the cell were analyzed. The supramolecular arrangements were studied by Hirshfeld surfaces, quantum theory of atoms in molecules, and natural bond orbital analyses. They showed distinct patterns of intermolecular interactions in each polymorph, as well as distinct stabilizations of these. Additionally, the molecular docking study presented the interactions between the active site residues of the ACE and glutathione via seven hydrogen bonds. The pharmacophore design indicated that the hydrogen bond acceptors are necessary for the interaction of this ligand with the binding site. The results provide useful information for the development of GSH analogs with higher ACE inhibitor activity.     

Single Si atom supported on defective boron nitride nanosheet as a promising metal‐free catalyst for N2O reduction by CO or SO2 molecule: A computational study

The low‐temperature reduction of N₂O plays a significant role for solving the growing environmental and health issues caused by emission of this greenhouse gas. The aim of this study is to investigate the possible reaction pathways for the reduction of N₂O by CO or SO₂ molecule over Si‐doped boron nitride nanosheet (Si‐BNNS). According to our results, a B or N‐vacancy defect in BN sheet could be able to greatly stabilize the single Si adatom. The relatively large diffusion barrier for the Si atom over the defective BN sheet also indicates Si‐BNNS is stable enough to be utilized in catalytic reduction of N₂O. The large charge‐transfer from the surface to N₂O leads to the spontaneous dissociation of this molecule into N₂ molecule and an activated oxygen atom (O_ads). The O_ads moiety is then eliminated by CO or SO₂ molecule. The calculated activation energies and reaction energies reveal that the Si atom located on top of the B‐vacancy site has a large catalytic activity toward the reduction of N₂O by CO or SO₂.     

Kinetic studies on the reduction of a nickel (III) oxime-imine complex by sulphur(IV) and selenium(IV)

The kinetics of the reduction of [Ni^III(L¹)]²⁺ (where HL¹ = 15-amino-3-methyl-4,7,10,13-tetraazapentadec-3-en-2-one oxime) by sulphur(IV) and selenium (IV) over the regions pH 2.50–8.02 and 2.01–4.00 respectively have been investigated at 30°C. Attempts were made to evaluate the reactivity of all the reacting species, of sulphur(IV) and selenium(IV) by considering suitable pH ranges. The oxidation of SC₂·H₂O and HSO ₃ ⁻ is proposed to proceed through the formation of a hydrogen-bonded adduct. The reaction with SO ₃ ²⁻ seems to follow a direct outer-sphere route which is well supported by Marcus crossrelation calculation. The oxidation of HSeO _l3 ⁻ is ≈ 10³ times slower than that of H₂SeO₃. The kinetic data indicate that the oxidation of sulphur(IV) by [Ni^IIIL¹)]²⁺ is much more favourable as compared to the corresponding oxidation of selenium(IV).     

Mechanistic studies on peroxide activation by a water-soluble iron(III)-porphyrin: implications for O-O bond activation in aqueous and nonaqueous solvents

The reactions of a water-soluble iron(III)-porphyrin, [meso-tetrakis(sulfonatomesityl)porphyrinato]iron(III), [Fe(III)(tmps)] (1), with m-chloroperoxybenzoic acid (mCPBA), iodosylbenzene (PhIO), and H(2)O(2) at different pH values in aqueous methanol solutions at -35 degrees C have been studied by using stopped-flow UV/Vis spectroscopy. The nature of the porphyrin product resulting from the reactions with all three oxidants changed from the oxo-iron(IV)-porphyrin pi-cation radical [Fe(IV)(tmps(*+))(O)] (1(++)) at pH<5.5 to the oxo-iron(IV)-porphyrin [Fe(IV)(tmps)(O)] (1(+)) at pH>7.5, whereas a mixture of both species was formed in the intermediate pH range of 5.5-7.5. The observed reactivity pattern correlates with the E degrees' versus pH profile reported for 1, which reflects pH-dependent changes in the relative positions of E degrees'(Fe(IV)/Fe(III) ) and E degrees'(P(*+)/P) for metal- and porphyrin-centered oxidation, respectively. On this basis, the pH-dependent redox equilibria involving 1(++) and 1(+) are suggested to determine the nature of the final products that result from the oxidation of 1 at a given pH. The conclusions reached are extended to water-insoluble iron(III)-porphyrins on the basis of literature data concerning the electrochemical and catalytic properties of [Fe(III)(P)(X)] species in nonaqueous solvents. Implications for mechanistic studies on [Fe(P)]-catalyzed oxidation reactions are briefly addressed.     

Asymmetric reduction of acetophenone and propiophenone by NaAl(IPTOLate)H2 combined with enantiomeric enrichment of the reaction product as an inclusion complex with IPTOL

An improved procedure was developed for asymmetric reduction of acetophenone and propiophenone by the chiral reagent NaAl(IPTOLate)H₂. This procedure is based on isolation of the chiral alcohol that formed as a crystalline host—guest complex with the IPTOL ligand. The enantiomeric enrichment of the product was as high as 97% ee. The ability of IPTOL and its analogs to form host—guest complexes with a number of ether-type solvents, 1-phenylethanol, and 1-phenylpropan-1-ol as well as thermal stabilities of IPTOL-containing complexes with these alcohols were studied.     

Mechanistic studies on the oxidation of pyruvic acid by an oxo-bridged diiron(III,III) complex in aqueous acidic media

In aqueous solution [Fe₂(μ-O)(phen)₄(H₂O)₂]⁴⁺ (1, phen = 1,10-phenanthroline) equilibrates with its conjugate bases [Fe₂(μ-O)(phen)₄(H₂O)(OH)]³⁺ (2) and [Fe₂(μ-O)(phen)₄(OH)₂]²⁺ (3). In the presence of excess phen and in the pH range 2.5–5.5, the dimer quantitatively oxidizes pyruvic acid to acetic acid and carbon dioxide, the end iron species being ferroin, [Fe(phen)₃]²⁺. The observed reaction rate shows a bell-shaped curve as pH increases, but is independent of added phen. Kinetic analysis shows that (3) is non-reactive and (1) has much higher reactivity than (2) in oxidizing pyruvic acid. The basicity of the bridging oxygen increases with deprotonation of the aqua ligands. The reaction rate decreases significantly in media enriched with D₂O in comparison to that in H₂O, with a greater retardation at higher pH, suggesting the occurrence of proton coupled electron transfer (PCET; 1e, 1H⁺), which possibly drags the energetically unfavorable reaction to completion in presence of excess phen.     

Determination of calcium, iron and manganese in moss by automated discrete sampling flame atomic absorption spectrometry as an alternative to the ICP-MS analysis

An automated, fast and reliable procedure has been developed for flame atomic absorption analysis of Ca, Fe and Mn in moss. The method is suitable for routine analysis of a large number of moss samples and allows sequential determination of all three elements in the same solution. In order to inhibit the matrix interference on Ca and to level the diverse analytical behaviour of the moss matrix, approximately 1% La was added to both samples and standard solutions as well. An integrated system of ‘sandwich-type’ air segmented discrete sample introduction and flame atomic absorption detection (ASDI-FAAS) was successfully applied. It works at ‘solvent-air-sample-air-solvent’ mode, which tolerates the introduction of high salt content solutions, reduces reagent and sample consumption and allows the application of data treatment models to pseudo-steady state signals for bettering the repeatability. For moss samples containing high Ca and Fe concentrations, equivalent procedure was used by turned on 45° burner head without worsening the analytical characteristics. Concerning these three elements, the method is suggested as a cheaper, easier and more trustworthy alternative with a better precision to the inductively coupled plasma-mass spectrometry (ICP-MS) one. The ASDI-FAAS results were used for selection of appropriate isotopes and correction procedures for ICP-MS determination. Both methods show good agreement of the Ca, Fe and Mn results that correspond to the moss reference materials tested.     

From allylic alcohols to aldols by using iron carbonyls as catalysts: computational study on a novel tandem isomerization-aldolization reaction

The tandem isomerization-aldolization reaction between allyl alcohol and formaldehyde mediated by [Fe(CO)3] was studied with the density functional B3LYP method. Starting from the key [(enol)Fe(CO)3] complex, several reaction paths for the reaction with formaldehyde were explored. The results show that the most favorable reaction path involves first an enol/allyl alcohol ligand-exchange process followed by direct condensation of formaldehyde with the free enol. During this process, formation of the new C-C bond takes place simultaneously with a proton transfer between the enol and the aldehyde. Therefore, the role of [Fe(CO)3] is to catalyze the allyl alcohol to enol isomerization affording the free enol, which adds to the aldehyde in a carbonyl-ene type reaction. Similar results were obtained for the reaction between allyl alcohol and acetaldehyde.     

Synthesis,characterization, density functional theory calculations,and in vitro antibacterial activity of novel transition metal complexes containing an O3-tridentate amoxicillin-based Schiff base: A silver(II) complex as alternative against Pseudomonas aeruginosa resistant to amoxicillin

Transition metal complexes containing an amoxicillin-based Schiff base (H₂L, 3 ) obtained from the condensation of amoxicillin 1 with salicylaldehyde 2 were prepared. Spectroscopic and physicochemical techniques, namely, UV–visible, Fourier-transform infrared spectroscopy, ¹H NMR, electron paramagnetic resonance, transmission electron microscopy, mass spectrometry, magnetic susceptibility, molar conductance, density functional theory (DFT) calculations, together with elemental and thermal analyses were used to characterize the synthesized complexes. Based on these studies, the general formulae [ML(H₂O)₃], where M = Mn 4 , Ni 5 , Zn 6 , and [ML(H₂O)], where M = Cu 7 , Ag 8 , were proposed for the complexes. The amoxicillin-based Schiff base ligand behaved as a dianionic O₃-tridentate chelating agent. DFT studies and magnetic and spectral data revealed octahedral geometries for Mn, Ni, and Zn atoms and distorted tetrahedral geometries for Cu(II) and Ag(II) complexes. Synthesized compounds were tested for antibacterial activity by both agar disk diffusion method and the minimum inhibitory concentration. in vitro bacterial viability revealed that complex 5 had similar antibacterial activity as 1 against Staphylococcus aureus and Staphylococcus epidermidis, whereas Pseudomonas aeruginosa, resistant to amoxicillin, was sensitive to complex 8 . The antibacterial activity of complex 8 could be attributed to its greater catalytic activity as shown by DFT calculations. Toxicity bioassay of the tested compounds showed LC₅₀ values > 1000 ppm, indicating their nontoxicity against brine shrimp nauplii (Artemia salina).