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Dinitrogen is inherently inert. This report describes detailed density functional calculations (with a 485+ atom model) of mechanistic steps by which the enzyme nitrogenase activates unreactive N2 at the intact active site FeMo-co, to form a key intermediate with bound HNNH. This mechanism does not bind N2 first and then add H atoms, but rather captures N2 ('N2-ready') that diffuses in through the substrate channel and enters a strategic gallery of H atom donors in the reaction zone, between Fe2 and Fe6. This occurs at the E4 stage of the complete mechanism. Exploration of possible reactions of N2 in this space leads to the conclusion that the first reaction step is transfer of H on Fe7 to one end of N2-ready, soon followed by Fe--N bond formation, and then a second H transfer from bridging S2BH to the other N. Two H--N bonds and one or two N--Fe bonds are formed, in some cases with a single transition state. The vari- able positions and orientations of N2-ready lead to various reaction trajectories and products. The favourable products resulting from this capture, judged by the criteria of reaction energies, reaction barriers, and mechanistic competence for further hydrogenation reactions in the nitrogenase cycle, have Fe2-- NH--NH bonding. The trajectory of one N2 capture reaction is described in detail, and calculations that separate the H atom component and the 'heavy atom' components of the classical activation energy are described, in the context of possible H atom tunneling in the activation of N2-ready. I present arguments for the activation of N2 by the pathway of concerted hydrogenation and binding of N2-ready, alternative to the commonly assumed pathway of binding N2 first, with subsequent hydrogenation. The active site of nitrogenase is well primed for the thermodynamic and kinetic advantages of N2 capture. [ABSTRACT FROM AUTHOR]

In converting N2 to NH3 the enzyme nitrogenase utilises 8 electrons and 8 protons in the complete catalytic cycle. The source of the electrons is an Fe4S4 reductase protein (Fe-protein) which temporarily docks with the MoFe-protein that contains the catalytic active cofactor, FeMo-co, and an electron transfer cluster called the P cluster. The overall mechanism involves 8 repetitions of a cycle in which reduced Fe-protein docks with the MoFe-protein, one electron transfers to the P-cluster, and then to FeMo-co, followed by dissociation of the two proteins and re-reduction of the Fe-protein. Protons are supplied serially to FeMo-co by a Grotthuss proton translocation mechanism from the protein surface along a conserved chain of water molecules (a proton wire) that terminates near S atoms of the FeMo-co cluster [CFe7S9Mo(homocitrate)] where the multiple steps of the chemical conversions are effected. It is assumed that the chemical mechanisms use proton-coupled electron-transfer (PCET) and that H atoms (e− + H+) are involved in each of the hydrogenation steps. However there is neither evidence for, or mechanism proposed, for this coupling. Here I report calculations of cluster charge distribution upon electron addition, revealing that the added negative charge is on the S atoms of FeMo-co, which thereby become more basic, and able to trigger proton transfer from H3O+ waiting at the near end of the proton wire. This mechanism is supported by calculations of the dynamics of the proton transfer step, in which the barrier is reduced by ca. 3.5 kcal mol−1 and the product stabilised by ca. 7 kcal mol−1 upon electron addition. H tunneling is probable in this step. In nitrogenase it is electron transfer that triggers proton transfer. [ABSTRACT FROM AUTHOR]

The binding of N2 to FeMo-co, the catalytic site of the enzyme nitrogenase, is central to the conversion to NH3, but also has a separate role in promoting the N2-dependent HD reaction (D2 + 2H+ + 2e− → 2HD). The protein surrounding FeMo-co contains a clear channel for ingress of N2, directly towards the exo-coordination position of Fe2, a position which is outside the catalytic reaction domain. This led to the hypothesis [I. Dance, Dalton Trans., 2022, 51, 12717] of 'promotional' N2 bound at exo-Fe2, and a second 'reducible' N2 bound in the reaction domain, specifically the endo-coordination position of Fe2 or Fe6. The range of possibilities for the binding of reducible N2 in the presence of bound promotional N2 is described here, using density functional simulations with a 486 atom model of the active site and surrounding protein. The pathway for ingress of the second N2 through protein, past the first N2 at exo-Fe2, and tumbling into the binding domain between Fe2 and Fe6, is described. The calculations explore 24 structures involving 6 different forms of hydrogenated FeMo-co, including structures with S2BH unhooked from Fe2 but tethered to Fe6. The calculations use the most probable electronic states. End-on (η1) binding of N2 at the endo position of either Fe2 or Fe6 is almost invariably exothermic, with binding potential energies ranging up to −18 kcal mol−1. Many structures have binding energies in the range −6 to −14 kcal mol−1. The relevant entropic penalty for N2 binding from a diffusible position within the protein is estimated to be 4 kcal mol−1, and so the binding free energies for reducible N2 are suitably negative. N2 binding at endo-Fe2 is stronger than at endo-Fe6 in three of the six structure categories. In many cases the reaction domain containing reducible N2 is expanded. These results inform computational simulation of the subsequent steps in which surrounding H atoms transfer to reducible N2. [ABSTRACT FROM AUTHOR]

Nitrogenase is the enzyme that converts N2 to NH3 under ambient conditions. The chemical mechanism of this catalysis at the active site FeMo‐co [Fe7S9CMo(homocitrate)] is unknown. An obligatory co‐product is H2, while exogenous H2 is a competitive inhibitor. Isotopic substitution using exogenous D2 revealed the N2‐dependent reaction D2+2H++2e−→2HD (the 'HD reaction'), together with a collection of additional experimental characteristics and requirements. This paper describes a detailed mechanism for the HD reaction, developed and elaborated using density functional simulations with a 486‐atom model of the active site and surrounding protein. First D2 binds at one Fe atom (endo‐Fe6 coordination position), where it is flanked by H−Fe6 (exo position) and H−Fe2 (endo position). Then there is synchronous transfer of these two H atoms to bound D2, forming one HD bound to Fe2 and a second HD bound to Fe6. These two HD dissociate sequentially. The final phase is recovery of the two flanking H atoms. These H atoms are generated, sequentially, by translocation of a proton from the protein surface to S3B of FeMo‐co and combination with introduced electrons. The first H atom migrates from S3B to exo‐Fe6 and the second from S3B to endo‐Fe2. Reaction energies and kinetic barriers are reported for all steps. This mechanism accounts for the experimental data: (a) stoichiometry; (b) the N2‐dependence results from promotional N2 bound at exo‐Fe2; (c) different N2 binding Km for the HD reaction and the NH3 formation reaction results from involvement of two different sites; (d) inhibition by CO; (e) the non‐occurrence of 2HD→H2+D2 results from the synchronicity of the two transfers of H to D2; (f) inhibition of HD production at high pN2 is by competitive binding of N2 at endo‐Fe6; (g) the non‐leakage of D to solvent follows from the hydrophobic environment and irreversibility of proton introduction. [ABSTRACT FROM AUTHOR]

A procedure is described that allows the total charge state of a complex molecule to be obtained from its redox potential data by comparison with good data for chemically similar reference compounds, the link made by the calculated energies of the Fermi level or highest occupied molecular orbital (HOMO). This method is used to determine the resting redox state of the FeMo cofactor, FeMo-co, which must be protonated in its resting state if the atom at the center is C rather than N.

The migration of H atoms over S and Fe atoms in the reaction domain of FeMo-co, the active site of nitrogenase is described and used to explain mechanistic data on the catalyzed reductions of [N.sub.2] and [C.sub.2][H.sub.2]. The positions of H atoms influence the binding of substrates [N.sub.2] and [C.sub.2][H.sub.2] and the bound substrate blocks further migration of H atoms past the binding site.

The crystallization of cadmium bis(1,3-thiazolidine-2-thionate), Cd[([C.sub.3][H.sub.4]N[S.sub.2]).sub.2] (1), is reported. Freshly prepared 1 reacts with [Ph.sub.4][P.sup.+][X.sup.-] in a 1:2 ratio to give [([Ph.sub.4]P).sub.2][[[Cd.sub.2]([C.sub.3][H.sub.4]N[S.sub.2]).sub.2] [X.sub.4]](X = I (4) or Br (5)). Crystallization of 1 from pyridine produces a solvate 7. which loses pyridine readily. X-ray analyses show that 1 has a polymeric sheet structure in which the [C.sub.3][H.sub.4]N[S.sub.2-] ligands act as bidentate bridges through N and the exocyclic S and the Cd has a Cd[N.sub.2][S.sub.2] kernel; 5 is isomorphous with 4, which contains a dimeric anion again with bridging through the N and exocyclic S of the heterocyclic ligands: and 7 is Cd([[C.sub.3][H.sub.4]N[S.sub.2]).sub.2][([C.sub.5][H.sub.5]N).sub.3] x [C.sub.5][H.sub.5]N, containing trigonal bipyramidal Cd[([C.sub.3][H.sub.4] N[S.sub.2]).sub.2] [([C.sub.5][H.sub.5]N).sub.3] molecules, in which the [C.sub.3][H.sub.4]N [S.sub.2-] ligands, both of which are monodentate and in equatorial positions, occur as a unique combination of S- and N-bound. Cadmium-113 NMR data for 1 in pyridine solution and solid-state CP-MAS [sup.113]Cd data for 1, 7, bis(pyridinium-4-thiolate)cadmium, and tetrakis(pyridinium-2-thiolate)cadmium nitrate are reported and discussed. The compound 1 has chemical and NMR spectroscopic properties that make it a useful standard for solid-state CP-MAS [sup.113]Cd NMR spectroscopy. Key words: cadmium, 1,3-thiazolidine-2-thionate, X-ray analysis, solid-state [sup.113]Cd NMR, [sup.113]Cd NMR standard compound.

The chemical mechanism by which the enzyme nitrogenase effects the reduction of N2 to NH3 under ambient conditions and the site and geometry of binding of alkyne and alkene substrates and intermediates is described. Alternate binding sites and geometries for ethyne and ethene, relevant to the wild-type protein, are described.

Research discusses the preparation of metal cyanide ions in the gas phase by laser ablation of cyano-metalate complexes. Results show that excepting the complexes containing zinc or cadmium metal component, other cyano-metalate complexes, used as precursors, yield a lower metal oxidation state than that of the precursors.

Research has been conducted on the diol synthesis. Results indicate that their X-ray crystal structures have been determined and the role of the crystal engineering in the hydroxy group hydrogen bonding has been investigated.

Research has been conducted on the M (super)+ (sub)g transition metal ions. The reactions of these ions with phosphane investigated via the use of the Fourier transform ion cyclotron resonance spectrometry are described.

A density functional investigation of 100 isomers of 28 clusters, ranging in size, calculated as both neutral and monocation species is reported. Vertical ionization energies and normalized binding energies are provided for all isomers and the most probable structures of the 28[Nb(sub x)C(sub y)] clusters are assigned.

Research has been conducted on the crystal structure of (Ph (sub)3 PCl) (sub)2 [Cu (sub)3 Cl (sub)8]. A new supramolecular motif for Ph (sub)3 PY (super)+ cations is described.

The chemical reactions occurring at the Fe7MoS9C(homocitrate) cluster, FeMo-co, the active site of the enzyme nitrogenase (N2 → NH3), are enigmatic. Experimental information collected over a long period reveals aspects of the roles of N2 and H2, each with more than one type of reactivity. This paper reports investigations of the binding of H2 and N2 at intact FeMo-co, using density functional simulations of a large 486 atom relevant portion of the protein, resulting in 27 new structures containing H2 and/or N2 bound at the exo and endo coordination sites of the participating Fe atoms, Fe2 and Fe6. Binding energies and transition states for association/dissociation are determined, and trajectories for the approach, binding and separation of H2/N2 are described, including diffusion of these small molecules through proximal protein. Influences of surrounding amino acids are identified. FeMo-co deforms geometrically when binding H2 or N2, and a procedure for calculating the energy cost involved, the adaptation energy, is introduced here. Adaptation energies, which range from 7 to 36 kcal mol−1 for the reported structures, are influenced by the protonation state of the His195 side chain. Seven N2 structures and three H2 structures have negative binding free energies, which include the estimated entropy penalties for binding of N2, H2 from proximal protein. These favoured structures have N2 bound end-on at exo-Fe2, exo-Fe6 and endo-Fe2 positions of FeMo-co, and H2 bound at the endo-Fe2 position. Various postulated structures with N2 bridging Fe2 and Fe6 revert to end-on-N2 at endo positions. The structures are also assessed via the calculated potential energy barriers for association and dissociation. Barriers to the binding of H2 range from 1 to 20 kcal mol−1 and barriers to dissociation of H2 range from 3 to 18 kcal mol−1. Barriers to the binding of N2, in either side-on or end-on mode, range from 2 to 18 kcal mol−1, while dissociation of bound N2 encounters barriers of 3 to 8 kcal mol−1 for side-on bonding and 7 to 18 kcal mol−1 for end-on bonding. These results allow formulation of mechanisms for the H2/N2 exchange reaction, and three feasible mechanisms for associative exchange and three for dissociative exchange are identified. Consistent electronic structures and potential energy surfaces are maintained throughout. Changes in the spin populations of Fe2 and Fe6 connected with cluster deformation and with metal–ligand bond formation are identified. [ABSTRACT FROM AUTHOR]

The reaction between transition metal ions and gaseous S8 forms a series of product ions, (MS(sub y))+, where M = metal ion and y = 4, 8, 10, 12, 16 or 21. The proposed mechanism of the reaction involves the formation of the reactive MS8+ encounter complex which undergoes S-S bond cleavage and rearrangement around the metal. The metals in the third row react twice as fast as metals in the first row and the early transition metals are more reactive than the later ones. All 29 metals except Tc react with S.

Density functionals computations were carried out to model the geometric and electronic configurations of Ti14C13 and Ti8C13 as uncharged metal-carbon clusters and as positive ions. The intermediates Ti13C13, Ti12C13, Ti11C13, Ti10C13 and Ti9C13 formed during the conversion of Ti14C13 to Ti8C13 were also characterized. The models demonstrated the geometrical linkage between titanium extrusion or photodissociation process and the carbon-carbon bond formation process.

The crystals of 2,6-dimethylbicyclo(3.3.1)nonane-exo-2,exo-6-diol (1) constitute a series of spiral hydrogen bonded spines ...OH...OH...OH...OH... surrounding parallel canals. The compounds of 1 have guests trapped in the canals along c. In some compounds the guests affect the structure of the resulting inclusion compounds. The helical tubuland structures are present in the samples of the guest-free compounds of 1.

Fourier transform ion cyclotron resonance mass spectrometry reveals the formation of Cu(I) and Ag(I) cyanide clusters of the types (M(n)(CN)n+1)- and (M(n)(CN)n-1)+ during the ablation of solid MCN by a focused Nd-YAG laser. Both species undergo dissociation during reaction with gaseous NH3, H2S and CO, while addition reaction occurs only in cations, producing bis-adducts. Analysis of the structures of these species by density functional theory reveals that these gaseous ions exhibit linear structures with spear topology.

Plasma desorption (PD) mass spectroscopy is used for the structural characterization of various cadmium arenethiolates and bis(phenyl-methanethiolato) cadmium. These crystals are nonmolecular but are made of large quasi molecular units. Relatively large fragments are excised from the complex which involve dissociative processes through an intermediate energetic state. A staircase structure explains all the fragmentation processes.

Copper K-edge X-ray absorption spectroscopy is used to study structurally characterized cuprous-thiolate model compounds consisting of varying proportion of digonal and trigonal copper sites, to explore the presence of digonal coordination in silver-substituted metallothionein. The nature of the 8983 electron volt edge feature in the edge spectrum, is not as good a porphyrin spectroscopic indicator as the mean Cu-S bond distance.

Laser ablation-Fourier transform ion cyclotron resonance experiments on FeS, KFeS2 and CoS were described. Under the conditions CoS yields a series of 83 gaseous ions (CoxSy)-, ranging in size from (CoS2)- to (Co38S24)-. The iron compounds yield two series of (FexSy)- clusters that are distinctly separate in composition. There is increased concentrations of metal atoms and metal-metal bonding in the cores of larger clusters.

The structure and electronic properties of three compounds containing the (S4Cd10 SPh 16)4- cluster were determined using solid-state Cd nuclear magnetic resonance spectroscopy and chemical shift anisotropy. The results showed that the occurrence of isomerism led to observable distortions and changes in the pseudotetrahedral Cd coordination. Furthermore, chemical shift anisotropy was successfully used in characterizing the molecular orientation and local structure of the compounds.