Tetranuclear, Oxygen Centered Copper(II) Clusters Linked Together with Guanidine-Guanidinate Ligands

The reaction of copper(I) chloride with Htbo (1,4,6-triazabicyclo[3.3.0]oct-4-ene) under reflux in THF with oxidation by oxygen, produces a neutral cluster comprising two oxo-tetra-copper(II) units connected by six tbo⁻ bridges three of them bind two and the other three bind four metals; each unit also contains three chlorine bridges and a Htbo terminal ligand. Two different X-ray crystal structures (1a, 1b) have been determined and the magnetic behavior has been studied. The molar magnetic susceptibility measurements indicate strong exchange interactions within an oxo cluster with coupling constants of J ₁ = −163 cm⁻¹ and J ₂ = −1.1 cm⁻¹, and a weak interaction across the guanidinate bridges of J ₃ = −5.2 cm⁻¹ of the octa-Cu^II cluster.     

Structural and spectroscopic models of the A-cluster of acetyl coenzyme a synthase/carbon monoxide dehydrogenase: Nature's Monsanto acetic acid catalyst

Acetyl coenzyme A synthase/carbon monoxide dehydrogenase (ACS/CODH) is a bifunctional enzyme present in a number of anaerobic bacteria. The enzyme catalyzes two separate reactions namely, the reduction of atmospheric CO₂ to CO (CODH activity at the C-cluster) and the synthesis of acetyl coenzyme A (ACS activity at the A-cluster) from CO, CH₃ from a corrinoid iron-sulfur protein, and the thiol coenzyme A. The structure(s) of the A-cluster of ACS/CODH from Moorella thermoacetica revealed an unprecedented structure with three different metallic subunits linked to each other through bridging Cys-S residues comprising the active site. In these structure(s) a Fe₄S₄ cubane is bridged via Cys-S to a bimetallic metal cluster. This bimetallic cluster contains a four-coordinate Ni, Cu, or Zn as the proximal metal (to the Fe₄S₄ cluster; designated M_p), which in turn is bridged through two Cys-S residues to a terminal square planar Ni(II) (Ni_d, distal to Fe₄S₄) ligated by two deprotonated carboxamido nitrogens from the peptide backbone. It is now established that Ni is required at the M_p site for the ACS activity. Over the past several years modeling efforts by several groups have provided clues towards understanding the intrinsic properties of the unique site in ACS. To date most studies have focused on dinuclear compounds that model the M_p-Ni_d subsite. Synthesis of such models have revealed that the Ni_p sites (a) are readily removed when mixed with 1,10-phenanthroline (phen) and (b) can be reduced to the Ni(I) and/or Ni(0) oxidation state (deduced by EPR or electrochemical studies) and bind CO in terminal fashion with ν_co value similar to the enzyme. In contrast, the presence of Cu(I) centers at these M_p sites do not bind CO and are not removable with phen supporting a non-catalytic role for Cu(I) at the M_p site in the enzyme. The Ni_d site (coordinated by carboxamido-N/thiolato-S) in these models are very stable in the +2 oxidation state and not readily removed upon treatment with phen suggesting that the source of ‘labile Ni’ and the NiFeC signal arises from the presence of Ni at the M_p site in ACS. This review includes the results and implications of the modeling studies reported so far.     

Pressure enhancement of gas-phase water oligomer populations: A RRHO MCY-B/EPEN computational study

Existing theoretical data, including the recently suggested MCY-B water pair potential and EPEN data on water oligomers in conjunction with rigid-rotor and harmonic-oscillator (RRHO) partition functions, are combined to evaluate equilibrium constants of water associate, (H₂O) _i , formation. The equilibrium constant set obtained is employed to study water cluster populations under various temperatures and pressures. Within the model it is shown that the pressure dependence of the mole fraction of a cluster in the equilibrium steam exhibits a maximum. The maximum with increasing temperature is shifted towards higher pressure values, however, its height is increasing, too. The importance of the finding for an assessment of optimum conditions for a cluster observation as well as reliability of the RRHO MCY-B model of steam are discussed.     

Charge exchange in alkali cluster collisions

Collisional charge exchange between mass selected alkali cluster ions and Cs has been studied and cross sections have been determined for the processes Na _n ⁺ + Cs and K _n ⁺ + Cs, withn=1–21 andn=1–14, respectively. A strong dependence of the cross sections on the energy defect as well as on cluster size and collision energy is found. The results are analysed by a coupled two state density matrix model, taking account of the relaxation of electronic amplitudes due to interaction with the nuclear motion in the cluster.     

Peptide structural analysis using continuous Ar cluster and C60 ion beams

A novel application of time-of-flight secondary ion mass spectrometry (ToF-SIMS) with continuous Ar cluster beams to peptide analysis was investigated. In order to evaluate peptide structures, it is necessary to detect fragment ions related to multiple neighbouring amino acid residues. It is, however, difficult to detect these using conventional ToF-SIMS primary ion beams such as Bi cluster beams. Recently, C₆₀ and Ar cluster ion beams have been introduced to ToF-SIMS as primary ion beams and are expected to generate larger secondary ions than conventional ones. In this study, two sets of model peptides have been studied: (des-Tyr)-Leu-enkephalin and (des-Tyr)-Met-enkephalin (molecular weights are approximately 400 Da), and [Asn¹ Val⁵]-angiotensin II and [Val⁵]-angiotensin I (molecular weights are approximately 1,000 Da) in order to evaluate the usefulness of the large cluster ion beams for peptide structural analysis. As a result, by using the Ar cluster beams, peptide molecular ions and large fragment ions, which are not easily detected using conventional ToF-SIMS primary ion beams such as Bi₃ ⁺, are clearly detected. Since the large fragment ions indicating amino acid sequences of the peptides are detected by the large cluster beams, it is suggested that the Ar cluster and C₆₀ ion beams are useful for peptide structural analysis.     

A comparison of the on-top dissociation of H2 on Ni(100) and Cu(100)

The on-top dissociations of H₂ on Ni(100) and Cu(100) are studied using a cluster approach. Correlation effects are accounted for through the use of CASSCF and CCI methods. The central metal atom is treated with all its electrons whereas the other cluster atoms are described by recently developed one electron ECP's. A molecular chemisorbed H₂ state on nickel, similar to that recently observed experimentally, was identified in the cluster calculations and also for the triatomic NiH₂. No such state was found on copper. The large differences found for the on top dissociation of H₂ on nickel and copper are attributed solely to the difference in 3d orbital occupation. The parallel between the on top dissociation reaction on the cluster and the dissociation on a single atom is also studied. While the neutral triatomic NiH₂ represents a qualitatively correct model in the nickel case, the negatively charged CuH ₂ ^– is required as a model in the copper case.     

The Nitrogenase FeMo‐Cofactor Precursor Formed by NifB Protein: A Diamagnetic Cluster Containing Eight Iron Atoms

The biological activation of N₂ occurs at the FeMo‐cofactor, a 7Fe–9S–Mo–C–homocitrate cluster. FeMo‐cofactor formation involves assembly of a Fe_6–8–S_X–C core precursor, NifB‐co, which occurs on the NifB protein. Characterization of NifB‐co in NifB is complicated by the dynamic nature of the assembly process and the presence of a permanent [4Fe–4S] cluster associated with the radical SAM chemistry for generating the central carbide. We have used the physiological carrier protein, NifX, which has been proposed to bind NifB‐co and deliver it to the NifEN protein, upon which FeMo‐cofactor assembly is ultimately completed. Preparation of NifX in a fully NifB‐co‐loaded form provided an opportunity for Mössbauer analysis of NifB‐co. The results indicate that NifB‐co is a diamagnetic (S=0) 8‐Fe cluster, containing two spectroscopically distinct Fe sites that appear in a 3:1 ratio. DFT analysis of the ⁵⁷Fe electric hyperfine interactions deduced from the Mössbauer analysis suggests that NifB‐co is either a 4Fe²⁺–4Fe³⁺ or 6Fe²⁺–2Fe³⁺ cluster having valence‐delocalized states.     

Guest‐Directed Supramolecular Architectures of {W36} Polyoxometalate Crowns

The {W₃₆} isopolyoxotungstate cluster provides a stable inorganic molecular platform for the binding of inorganic and organic guest molecules. This is achieved by a binding pocket formed by six terminal oxo ligands located in the central cavity of the all‐inorganic cation binding host. Previously it was shown that the cluster can specifically bind primary amines and importantly, functionalized diamines through a combination of electrostatic and hydrogen bonding interactions. Here we transform this assembly strategy to utilize the binding of long‐chain alkyldiammonium guest cations to physically define the supramolecular structure of the clusters with respect to each other and demonstrate the structure direction as a function of alkyl chain length. The systematic variation of the chain length gives access to five supramolecular assemblies which were all fully characterized using single crystal XRD, TGA, ¹H NMR, and elemental analysis. In compound 1 , diprotonated 1,8‐diaminooctane molecules link the {W₃₆} clusters into infinite 1D zigzag chains, whereas compounds 2 and 3 feature trimeric {W₃₆} assemblies directly connected through protonated 1,9‐diaminononane ( 2 ) or 1,10‐diaminodecane ( 3 ) linkers . Compound 4 contains dumb‐bell shaped dimeric units as a result of direct center‐to‐center linkages between the {W₃₆} clusters formed by protonated 1,12‐diaminododecane. In compound 5 , triply protonated bis(hexamethylene)triamine was employed to obtain linear 1D chains of directly connected {W₃₆} cluster units.     

Die Bindungsverhältnisse in der Clusterverbindung CZr6I14

Summary The electronic properties of the cluster compound CZr₆I₁₄ are discussed on the basis of EHT results. In the model cluster CZr₆I ₁₈ ^4– the calculated Zr-Zr distance in the metal octahedron is enlarged by encapsulation of the interstitial C as well as by the surrounding ligands. The interstitial bond is realized by the two bond orbitals a_1g, t_1u, and, additional, by three t_1u orbitals of the 5 p(I) band. The Zr-Zr bonds are week. The cluster CZr₆I ₁₈ ^4– is held together by strong C-Zr and Zr-I bonds.

     

Multiisotopic modeling of fragmentation ion patterns in mass spectra of organometallic and coordination compounds

Investigation of hardly interpretable complex patterns can lead to an explanation of details of fragmentation and, therefore, the identification of ion clusters can be a significant procedure of mass spectra interpretation. The modeling presented remains a simple tool for mass spectra interpretation and determination of parameters of complex cluster components. Good adjustment of model to experimental data suggests that such components must be considered in the pattern interpretation; approach results in the model fits within a 1% precision for the cluster of two or more components. Applications of the Multiisotopic Modeling of Fragmentation Ion Patterns (MMFIP method) are presented for bis(dibutyldithiophosphate)‐zinc(II)‐[(C₄H₉O)₂PS₂]₂Zn, 1′,1‴‐dibenzylbiferrocene‐C₃₄H₃₀Fe₂ and 1,1′,2,2′,3,3′‐hexachloroferrocene‐C₁₀H₄Cl₆Fe as examples. It seems that the isotopic cluster modeling based on the least squares method can be a helpful aid for determination of the complex pattern components. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 354–365, 2001     

SP3-Hybridization Feature of Ag4 Superatom in Superatomic Molecules

Analogous to atoms, superatoms can be used as building blocks to compose molecules and materials. To demonstrate this idea, the possibility of using tetrahedral Ag₄ cluster to form a series of superatomic molecules Ag₄X₄ (X=H, Li, Na, K, Cu, Ag, Au and F, Cl, Br) is discussed. Based on the super valence bond model, a tetrahedral Ag₄ cluster can be viewed as a 4-electron superatom, which can mimic a sp³ hybridization C atom. By comparison of the representative superatomic molecules Ag₄X₄ (X=Au, Cl) with the corresponding simple molecules CX₄ (X=H, Cl), the similarities in terms of chemical bonding patterns and molecular orbitals (MOs) are conspicuous. Energy calculations predict that the Ag₄ superatom can bind with all the involved ligands. Furthermore, the stabilities of superatomic molecules are enhanced by the large gaps of the highest occupied molecular orbital and the lowest unoccupied molecular orbital (HOMO-LUMO gaps) and high aromaticity. Our studies may find applications in assembling materials with superatoms.     

Computer simulation of molecular complexes H3O+(H2O) n under conditions of thermal fluctuations: II. Work of formation and structure

The free energy, entropy, and work of formation of H₃O⁺(H₂O)_n clusters (n=1–27) in water vapor (300 K) were calculated by the Monte Carlo method. Binary correlation functions were calculated. The calculations are based on the nonpair interaction model presented in the previous publication. The hydration shell of the ion is thermally stable in the size range under study. Nonpair interactions exert an essential effect on the structure of the cluster. Fitting the cluster behavior to its experimental thermodynamic characteristics shows that the excess charge of the ion is spatially delocalized at room temperature, and the role of hydrogen bonds is strengthened on this background. Clusters formed on electric charges have such a fundamental characteristic as transition size. The transition size is independent of vapor pressure and demarcates two qualitatively different mechanisms of holding molecules in a cluster. A change in the holding mode is reflected on the mechanism of vapor nucleation.Translated from Zhurnal Obshchei Khimii, Vol. 74, No. 10, 2004, pp. 1585–1592.Original Russian Text Copyright © 2004 by Shevkunov.For communication I, see [1].This revised version was published online in April 2005 with a corrected cover date.     

Structure and Reactivity of an Asymmetric Synthetic Mimic of Nitrogenase Cofactor

The Mo nitrogenase catalyzes the ambient reduction of N₂ to NH₃ at its M‐cluster site. A complex metallocofactor with a core composition of [MoFe₇S₉C], the M‐cluster, can be extracted from the protein scaffold and used to facilitate the catalytic reduction of CN^?, CO, and CO₂ into hydrocarbons in the isolated state. Herein, we report the synthesis, structure, and reactivity of an asymmetric M‐cluster analogue with a core composition of [MoFe₅S₉]. This analogue, referred to as the Mo‐cluster, is the first synthetic example of an M‐cluster mimic with Fe and Mo positioned at opposite ends of the cluster. Moreover, the ability of the Mo‐cluster to reduce C₁ substrates to hydrocarbons suggests the feasibility of developing nitrogenase‐based biomimetic approaches to recycle C₁ waste into fuel products.     

Intramolecular Electronic Energy Transfer in a Supersonic Jet Expansion

Intramolecular electronic energy transfer (intra-EET) was investigated in an isolated bichromophoric naphthalene (N) and anthracene (A) 1:1 molecular cluster. Investigation of the spectroscopic properties of these chromophores, separately and loosely bound in a van der Waals complex, helps to understand the dependence of the EET rate on the initially excited vibronic level and on the cluster's interchromophoric orientation. Measurement of fluorescence excitation spectra of anthracene, at different anthracene pressures shows bands that can be assigned to dimers of anthracene. From measurement of the anthracene excitation spectrum at increasing naphthalene pressures one can identify other spectral features, characterized by different spectral shifts from excitations of the bare molecule. Some transitions are probably due to a 13.5 cm^?1 progression associated with an interchromophore cluster bond. Pressure dependence of fluorescence intensity gives evidence for 1:1 cluster composition, and for a slow intra-EET rate that is associated with an unfavoured orientation of the two chromophores in one of the two possible conformers of the A-N cluster, as supported by a calculation of the cluster geometry and by comparison with a recent study of intra-EET in the A-(CH₂)_n-N bichromophoric molecules.     

Isotope substitution effects on spin dynamics of the molecular nanomagnet Fe8 cluster studied by NMR

We have carried out ¹H NMR at T=1.5 K in both ⁵⁷Fe-enriched Fe8 cluster and non-enriched Fe8 cluster to investigate isotope substitution effects on magnetic properties. The field dependence of 1/T₁ can be fitted well by using a simple model in terms of the thermal fluctuations of the total spin S=10 of the cluster originating from the spin–phonon interactions. The absence of a difference of the magnetic field dependence of 1/T₁ between the two systems indicates that the spin–phonon coupling constant is not affected by the change of mass of the isotopes in the Fe8 cluster.     

Reactivity of [Ge9{Si(SiMe3)3}3]− Towards Transition‐Metal M2+ Cations: Coordination and Redox Chemistry

Recently the metalloid cluster compound [Ge₉Hyp₃]^? ( 1 ; Hyp=Si(SiMe₃)₃) was oxidatively coupled by an iron(II) salt to give the largest metalloid Group 14 cluster [Ge₁₈Hyp₆]. Such redox chemistry is also possible with different transition metal (TM) salts TM²⁺ (TM=Fe, Co, Ni) to give the TM⁺ complexes [Fe(dppe)₂][Ge₉Hyp₃] ( 3 ; dppe=1,2‐bis(diphenylphosphino)ethane), [Co(dppe)₂][Ge₉Hyp₃] ( 4 ), [Ni(dppe)(Ge₉Hyp₃)] ( 5 ) and [Ni(dppe)₂(Ge₉Hyp₃)]⁺ ( 6 ). Such a redox reaction does not proceed for Mn, for which a salt metathesis gives the first open shell [Hyp₃Ge₉‐M‐Ge₉Hyp₃] cluster ( 2 ; M=Mn). The bonding of the transition metal atom to 1 is also possible for Ni (e.g., compound 6 ), in which one or even two nickel atoms can bind to 1 . In contrast to this in case of the Fe and Co compounds 3 and 4 , respectively, the transition‐metal atom is not bound to the Ge₉ core of 1 . The synthesis and the experimentally determined structures of 2 – 6 are presented. Additionally the bonding within 2 – 6 is analyzed and discussed with the aid of EPR measurements and quantum chemical calculations.     

The effect of constraints on the initial steps of adsorption of nitrogen atoms on the silicon surface as modeled by the cluster [Si9H12 + N]

The effect of constraints on the initial steps of the incorporation of nitrogen on silicon has been assessed by calculations with the [Si₉H₁₂ + N] model cluster using density functional theory with the hybrid functional B3LYP, and two basis sets that differ significantly in size. The relative stability of the various stationary points is dependent on the type of constraints imposed on the cluster. Constrained calculations have predicted the structure with the nitrogen symmetrically bonded to the dimer silicons as the global minimum, however, if no constraint is imposed and the whole cluster is optimized, as done in this work, a structure with the nitrogen inserted between the dimer and the first layer and bonded to three silicon atoms is predicted to be the most stable one by about 17 kcal/mol by either the doublet or quartet route. The whole process is very exothermic and reaction barriers in the intermediate steps are easily overcome. Calculations with the smaller basis do not essentially change the major conclusion about the relative stability of the various stationary points. The most stable structure and frequency calculations are consistent with a planar NSi₃ moiety and its asymmetrical stretching frequency.     

A DFT Investigation of Surface‐Enhanced Raman Scattering of Adenine and 2′‐Deoxyadenosine 5′‐Monophosphate on Ag20 Nanoclusters

We present a detailed analysis of the surface‐enhanced Raman scattering (SERS) of adenine and 2′‐deoxyadenosine 5′‐monophosphate (dAMP) adsorbed on an Ag₂₀ cluster by using density functional theory. Calculated Raman spectra show that spectral features of all complexes depend greatly on adsorption sites of adenine and dAMP. The complexes consisting of adenine adsorbed on the Ag₂₀ cluster through N3 reproduce the measured SERS spectra in silver colloids, and thus demonstrated that adenine interacts with the silver surface via N3. We also investigate the SERS spectrum of adenine at the junction between two Ag₂₀ clusters and demonstrate that adenine can bind to the clusters through N3 and the external amino group, while dAMP can be adsorbed on the cluster in an end‐on orientation with the ribose and phosphate groups near to or away from the silver cluster. In contrast to the adenine–Ag₂₀ complexes, the dAMP–Ag₂₀ complexes produce new and strong bands in the low‐ or high‐wavenumber region of the Raman spectra, due to vibrations of the ribose and phosphate groups. Furthermore, the spectrum of dAMP bound to the Ag₂₀ cluster via N7 approaches the experimental SERS spectra on silver colloids.     

How to find an optimum cluster size through topological site properties: MoSxmodel clusters

Computational investigations in catalysis frequently use model clusters to represent realistically the catalyst and its reaction sites. Detailed knowledge of the molecular charge, thus electronic density, of a cluster would then allow physical and chemical insights of properties and can provide a procedure to establish their optimum size for catalyst studies. For this purpose, an approach is suggested to study model clusters based on the distributed multipole analysis (DMA) of molecular charge properties. After full density functional theory (DFT) geometry optimization of each cluster, DMA computed from the converged DFT one‐electron density matrix allowed the partition of the corresponding cluster charge distribution into monopole, dipole, and quadrupole moments on the atomic sites. The procedure was applied to MoS₂ model clusters Mo₁₀S₁₈, Mo₁₂S₂₆, Mo₁₆S₃₂, Mo₂₃S₄₈, and Mo₂₇S₅₄. This analysis provided detailed features of the charge distribution of each cluster, focused on the 101 0 (Mo or metallic edge) and 1 010 (sulfur edge) active planes. Properties of the Mo₂₇S₅₄ cluster, including the formation of HDS active surfaces, were extensively discussed. The effect of cluster size on the site charge distribution properties of both planes was evaluated. The results showed that the Mo₁₆S₃₂ cluster can adequately model both active planes of real size Mo₂₇S₅₄. These results can guide future computational studies of MoS₂ catalytic processes. Furthermore, this approach is of general applicability. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

The effect of conjugated spacer on novel carbazole derivatives for dye‐sensitized solar cells: Density functional theory/time‐dependent density functional theory study

The ground‐state structure and frontier molecular orbital of D‐π‐A organic dyes, CFT1A, CFT2A, and CFT1PA were theoretically investigated using density functional theory (DFT) on B3LYP functional with 6‐31G(d,p) basis set. The vertical excitation energies and absorption spectra were obtained using time‐dependent DFT (TD‐DFT). The adsorptions of these dyes on TiO₂ anatase (101) were carried out by using a 38[TiO₂] cluster model using Perdew–Burke–Ernzerhof functional with the double numerical basis set with polarization (DNP). The results showed that the introduction of thiophene–thiophene unit (T–T) as conjugated spacer in CFT2A could affect the performance of intramolecular charge transfer significantly due to the inter‐ring torsion of T–T being decreased compared with phenylene–phenylene (P–P) spacer of CFP2A in the researhcers' previous report. It was also found that increasing the number of π‐conjugated unit gradually enhanced charge separation between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of these dyes, leading to a high‐efficiency photocurrent generation. The HOMO–LUMO energy gaps were calculated to be 2.51, 2.37, and 2.50 eV for CFT1A, CFT2A, and CFT1PA respectively. Moreover, the calculated adsorption energies of these dyes on TiO₂ cluster were ～14 kcal/mol, implying that these dyes strongly bind to TiO₂ surface. Furthermore, the electronic HOMO and LUMO shapes of all dye–TiO₂ complexes exhibited injection mechanism of electron via intermolecular charge‐transfer transition. © 2012 Wiley Periodicals, Inc.