Bimetallic clusters Pt6Au: geometric and electronic structures within density functional theory

Within density functional theory at the general gradient approximation for exchange and correlation (BPW91) and the relativistic 19-electron Los Alamos National Laboratory effective core pseudopotentials and basis sets (3s3p2d), the geometric and electronic structures of Pt(6)Au bimetallic clusters have been studied in detail in comparison with Pt(7). A total of 38 conformations for Pt(6)Au are located. The most stable conformation for Pt(6)Au is a sextet with an edge- and face-capped trigonal bipyramid, in which the Au atom caps an edge of the trigonal bipyramid. Pt(6)Au, in general, prefers a three-dimensional geometry and high spin electronic state with multireference character. The electronic impact of the doping of Au in Pt clusters on the overall chemical activity of the doped bimetallic cluster is not as significant as that of the doping of Pt in Au clusters; however, the doping of Au lowers the chemical activity, thus enhancing the chemoselectivity in the gas phase, of PtAu bimetallic clusters.     

Mechanism of ligand photodissociation in photoactivable [Ru(bpy)2L2]2+ complexes: a density functional theory study

A series of four photodissociable Ru polypyridyl complexes of general formula [Ru(bpy)2L2](2+), where bpy = 2,2'-bipyridine and L = 4-aminopyridine (1), pyridine (2), butylamine (3), and gamma-aminobutyric acid (4), was studied by density functional theory (DFT) and time-dependent density functional theory (TDDFT). DFT calculations (B3LYP/LanL2DZ) were able to predict and elucidate singlet and triplet excited-state properties of 1-4 and describe the photodissociation mechanism of one monodentate ligand. All derivatives display a Ru --> bpy metal-to-ligand charge transfer (MLCT) absorption band in the visible spectrum and a corresponding emitting triplet (3)MLCT state (Ru --> bpy). 1-4 have three singlet metal-centered (MC) states 0.4 eV above the major (1)MLCT states. The energy gap between the MC states and lower-energy MLCT states is significantly diminished by intersystem crossing and consequent triplet formation. Relaxed potential energy surface scans along the Ru-L stretching coordinate were performed on singlet and triplet excited states for all derivatives employing DFT and TDDFT. Excited-state evolution along the reaction coordinate allowed identification and characterization of the triplet state responsible for the photodissociation process in 1-4; moreover, calculation showed that no singlet state is able to cause dissociation of monodentate ligands. Two antibonding MC orbitals contribute to the (3)MC state responsible for the release of one of the two monodentate ligands in each complex. Comparison of theoretical triplet excited-state energy diagrams from TDDFT and unrestricted Kohn-Sham data reveals the experimental photodissociation yields as well as other structural and spectroscopic features.     

Towards rational syntheses of the elusive metallocarbohedrenes: density functional prescriptions for electronic and geometric structures

The metallocarbohedrenes are binary molecular clusters containing metal atoms linked by acetylenediide C(2) groups. Hundreds of these molecules have been generated, detected and reacted in the gas phase since the prototype, [Ti(8)(C(2))(6)], was reported in 1992, but none has yet been synthesised pure in bulk: the time gap between detection and preparation increasingly exceeds that of the fullerenes. We report here the results of density functional calculations of geometrical and electronic structure of more than 150 postulated metallocarbohedrenes, stabilised by terminal ligation, in order to recognise the more electronically favourable and less reactive targets. At least 38 metallocarbohedrenes have been identified as having a spin singlet ground state, with a relatively large (> 0.5 eV) energy gap between HOMO and LUMO, and an appropriate HOMO energy. In addition, a considerable number of electronically stable metallocarbohedrenes are predicted to have highly paramagnetic ground states, potentially useful in molecular magnetism. The geometrical principles for enclosing but unstrained coordination of metal sites by terminal ligands are outlined. Mechanisms for rational syntheses are considered in the context of reaction type and precursor selection, including issues of oxidation and reduction, and kinetic versus thermodynamic control. This leads to many diverse reactions suggested for the rational syntheses of metallocarbohedrenes. Some preliminary experimental results are presented.     

(Alpha-diimine)chromium complexes: molecular and electronic structures; a combined experimental and density functional theoretical study

Dark brown crystals of [Cr( (1)L) 2] ( 1) were obtained from the reaction of [Cr (III)(acac) 3] (acac (-) = 2,4-pentanedionate) with 2 equiv of 2-methyl-1,4-bis(2,6-dimethylphenyl)-1,4-diaza-1,3-butadiene ( (1)L) and 3 equiv of sodium in tetrahydrofuran (thf) under an Ar atmosphere. Complex 1 possesses an S = 1 ground state, which is attained via intramolecular antiferromagnetic coupling between a high-spin Cr (II) ion ( S Cr = 2) and two anionic alpha-diiminato(1-) ligand pi radicals ( (1)L (*)) (1-). The molecular structure of 1 exhibits a distorted tetrahedral, nearly square-planar geometry. The average C-N imine bond length at 1.346 A is characteristic for the pi radical anion ( (1)L (*)) (1-), and therefore, the electronic structure of 1 is best described as [Cr (II)( (1)L (*)) 2]. This has been confirmed by broken symmetry density functional theoretical calculations BS(4,2) (DFT) at the B3LYP level. The reaction of [Cr (III)(acac) 3] with 1 equiv of 2,3-dimethyl-1,4-bis(2,6-diisopropylphenyl)-1,4-diaza-1,3-butadiene ( (2)L) and 1 equiv of Na in thf under Ar yields red-brown crystals of [Cr (III)( (2)L (*))(acac) 2] ( 2) ( S = 1). The oxidation of 2 with 1 equiv of Fc(PF 6) (Fc (+) = ferrocenium) in CH 2Cl 2 affords crystals of [Cr (III)( (2)L (ox))(acac) 2](PF 6) ( 3) ( S = (3)/ 2). The crystal structure determinations of 2 and 3 revealed that 2 contains a neutral, octahedral Cr (III) species [Cr (III)( (2)L (*))(acac) 2], whereas in 3 the ligand is oxidized, yielding an octahedral monocation [Cr (III)( (2)L (ox))(acac) 2] (+). These electronic structures have been confirmed by DFT calculations.     

Correlation between the FeNO angle and d-p mixing in {FeNO}7 complexes

The great majority of low-spin {FeNO}(7) complexes exhibit FeNO angles of around 140-145°, whereas a small handful are characterized by linear FeNO units. Conspicuously absent are intermediate FeNO angles of 150-170°. Spurred by the recent observation of such an angle in a square-pyramidal {FeNO}(7) complex, we carried out a density functional theory survey of 12 additional, largely hypothetical complexes with porphyrin and corrole analogues as equatorial ligands. Our calculations predict several instances of intermediate FeNO angles. The calculations further indicate a strong, positive correlation (R(2) = 0.9) between the FeNO angle and metal p character in the Fe d(z(2))-based highest occupied molecular orbital.     

Unraveling the electronic structures of low-valent naphthalene and anthracene iron complexes: X-ray, spectroscopic, and density functional theory studies

Naphthalene and anthracene transition metalates are potent reagents, but their electronic structures have remained poorly explored. A study of four Cp*-substituted iron complexes (Cp* = pentamethylcyclopentadienyl) now gives rare insight into the bonding features of such species. The highly oxygen- and water-sensitive compounds [K(18-crown-6){Cp*Fe(η(4)-C(10)H(8))}] (K1), [K(18-crown-6){Cp*Fe(η(4)-C(14)H(10))}] (K2), [Cp*Fe(η(4)-C(10)H(8))] (1), and [Cp*Fe(η(4)-C(14)H(10))] (2) were synthesized and characterized by NMR, UV-vis, and (57)Fe M?ssbauer spectroscopy. The paramagnetic complexes 1 and 2 were additionally characterized by electron paramagnetic resonance (EPR) spectroscopy and magnetic susceptibility measurements. The molecular structures of complexes K1, K2, and 2 were determined by single-crystal X-ray crystallography. Cyclic voltammetry of 1 and 2 and spectroelectrochemical experiments revealed the redox properties of these complexes, which are reversibly reduced to the monoanions [Cp*Fe(η(4)-C(10)H(8))](-) (1(-)) and [Cp*Fe(η(4)-C(14)H(10))](-) (2(-)) and reversibly oxidized to the cations [Cp*Fe(η(6)-C(10)H(8))](+) (1(+)) and [Cp*Fe(η(6)-C(14)H(10))](+) (2(+)). Reduced orbital charges and spin densities of the naphthalene complexes 1(-/0/+) and the anthracene derivatives 2(-/0/+) were obtained by density functional theory (DFT) methods. Analysis of these data suggests that the electronic structures of the anions 1(-) and 2(-) are best represented by low-spin Fe(II) ions coordinated by anionic Cp* and dianionic naphthalene and anthracene ligands. The electronic structures of the neutral complexes 1 and 2 may be described by a superposition of two resonance configurations which, on the one hand, involve a low-spin Fe(I) ion coordinated by the neutral naphthalene or anthracene ligand L, and, on the other hand, a low-spin Fe(II) ion coordinated to a ligand radical L(?-). Our study thus reveals the redox noninnocent character of the naphthalene and anthracene ligands, which effectively stabilize the iron atoms in a low formal, but significantly higher spectroscopic oxidation state.     

Determination of structures, stabilities, and electronic properties for bimetallic cesium-doped gold clusters: a density functional theory study

The equilibrium geometric structures, stabilities, and electronic properties of bimetallic Au(n)Cs (n = 1-10) and pure gold Au(n) (n ≤ 11) clusters have been systematically investigated by using density functional theory with meta-generalized gradient approximation. The optimized geometries show that one Au atom capped on Au(n-1)Cs structures and Cs atom capped Au(n) structures for different sized Au(n)Cs (n = 1-10) clusters are two dominant growth patterns. Theoretical calculated results indicate that the most stable isomers have three-dimensional structures at n = 4 and 6-10. Averaged atomic binding energies, fragmentation energies, and second-order difference of energies exhibit a pronounced even-odd alternations phenomenon. The same even-odd alternations are found in the highest occupied-lowest unoccupied molecular orbital gaps, vertical ionization potential, vertical electron affinity, and hardnesses. In addition, it is found that the charge in corresponding Au(n)Cs clusters transfers from the Cs atom to the Au(n) host in the range of 0.851-1.036 electrons.     

Ring complexes of S-nitrosothiols with CU+: a density functional theory study

The density functional theory (DFT) method B3P86/6-311+G(2df,p) has been employed to investigate the complexes formed upon interaction of Cu(+) with nitrosylated cysteine (CysNO) and its decarboxylated (H(2)NCH(2)CH(2)SNO) and deaminated (HOOCCH(2)CH(2)SNO) derivatives. Optimized structures, relative enthalpies and relative free energies have been calculated and compared. In addition, the effects of binding an H(2)O molecule to the Cu(+) centre in the resulting complexes have also been considered. It is found that the most stable complexes are formed when Cu(+) coordinates to the S-nitrosothiol via S of the SNO group. This results in dramatic lengthenings of the SN bond with concomitant shortening of the NO bond. In contrast, when Cu(+) coordinates via the nitrogen of the SNO group, a shortening of the SN bond with lengthening of the NO bond is observed. These effects are tempered by the electron donating ability of other functional groups also coordinated with the Cu(+) centre in the complexes and on the coordination state of the Cu(+) ion.     

A density functional study on the electronic structures of TiN solid

The electronic structures of TiN bulk have been studied by using different theoretical formalisms, and the DFT method, especially the BLYP method can produce reasonable results. The band structure of TiN (001) surface is also investigated and two a type surface states are presented in our results. The state located at 2.9 eV below EF in angle resolved photoemis-sion in (ARPES) is well reproduced in this work, which consists essentially of 2pz orbital of surface N atom. Another surface state is associated with the bands originated from 3d orbital of surface Ti atom. Furthermore, the elastic constants of TiN are also calculated by using BLYP method.     

Electronic structures and reactivities of iodinating agents in the gas phase and in solutions: A density functional study

The electronic and spatial structures of a broad spectrum of neutral compounds with X-Hal (X = N, O, Cl; Hal = Cl, Br, I) bonds and their protonated forms and of different electronic states of triiodide cation, I₃ ⁺, were determined from density functional B3LYP/6 311G* quantum chemical calculations. The effects of the structure of these compounds on the parameters of electrophilic reactivity were revealed and the thermochemical characteristics of homolytic and heterolytic X-Hal bond dissociation and of iodine transfer in hydroxyl-containing solvents were calculated. Due to low homolytic bond dissociation energies of X-I, the formation of molecular iodine and triiodide cation I₃ ⁺ becomes thermodynamically favorable and the cation should act as iodinating agent alternative to acylhypoiodites and N-iodoimides. The solvation effects of MeOH and CH₂Cl₂ on the X-Hal bond homolysis and heterolysis were determined using the PCM model. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1280–1288, August, 2006.     

CuCl3]- and [CuCl4]2- hydrates in concentrated aqueous solution: a density functional theory and ab initio study

In this work, structures and thermodynamic properties of [CuCl(3)](-) and [CuCl(4)](2-) hydrates in aqueous solution were investigated using density functional theory and ab initio methods. Contact ion pair (CIP) and solvent-shared ion pair (SSIP) structures were both taken into account. Our calculations suggest that [CuCl(3)(H(2)O)(n)](-) clusters might favor a four-coordinated CIP structure with a water molecule coordinating with the copper atom in the equatorial position for n = 3 and 4 in aqueous solution, whereas the four-coordinated SSIP structure with one chloride atom dissociated becomes more stable as n increases to 5. For the [CuCl(4)](2-) cluster, the four-coordinated tetrahedron structure is more stable than the square-planar one, whereas for [CuCl(4)(H(2)O)(n)](2-) (n ≥ 1) clusters, it seems that four-coordinated SSIP structures are slightly more favorable than CIP structures. Our calculations suggest that Cu(2+) perhaps prefers a coordination number of 4 in CuCl(2) aqueous solution with high Cl(-) concentrations. In addition, natural bond orbital (NBO) calculations suggest that there is obvious charge transfer (CT) between copper and chloride atoms in [CuCl(x)](2-x) (x = 1-4) clusters. However, compared with that in the [CuCl(2)](0) cluster, the CT between the copper and chloride atoms in [CuCl(3)](-) and [CuCl(4)](2-) clusters becomes negligible as the number of attached redundant Cl(-) ions increases. This implies that the coordination ability of Cl(-) is greatly weakened for [CuCl(3)](-) and [CuCl(4)](2-) clusters. Electronic absorption spectra of these different hydrates were obtained using long-range-corrected time-dependent density functional theory. The calculated electronic transition bands of the four-coordinated CIP conformer of [CuCl(3)(H(2)O)(n)](-) for n = 3 and 4 are coincident with the absorption of [CuCl(3)](-)(aq) species (～284 and 384 nm) resolved from UV spectra obtained in CuCl(2) (ca. 10(-4) mol·kg(-1)) + LiCl (>10 mol·kg(-1)) solutions, whereas the calculated bands of [CuCl(3)(H(2)O)(n)](-) in their most stable configurations are not when n = 0 - 2 or n > 4, which means that the species [CuCl(3)](-)(aq) exists in those CuCl(2) aqueous solutions in which the water activity is neither too low nor too high. The calculated bands of [CuCl(4)(H(2)O)(n)](2-) clusters correspond to the absorption spectra (～270 and 370 nm) derived from UV measurements only when n = 0, which suggests that [CuCl(4)](2-)(aq) species probably exist in environments in which the water activity is quite low.     

Couplings between electronic transitions in a subsystem formulation of time-dependent density functional theory

A subsystem formulation of time-dependent density functional theory (TDDFT) within the frozen-density embedding (FDE) framework and its practical implementation are presented, based on the formal TDDFT generalization of the FDE approach by Casida and Wesolowski [Int. J. Quantum Chem. 96, 577 (2004)]. It is shown how couplings between electronic transitions on different subsystems can be seamlessly incorporated into the formalism to overcome some of the shortcomings of the approximate TDDFT-FDE approach in use so far, which was only applicable for local subsystem excitations. In contrast to that, the approach presented here allows to include couplings between excitations on different subsystems, which become very important in aggregates composed of several similar chromophores, e.g., in biological or biomimetic light-harvesting systems. A connection to Forster- and Dexter-type excitation energy coupling expressions is established. A hybrid approach is presented and tested, in which excitation energy couplings are selectively included between different chromophore fragments, but neglected for inactive parts of the environment. It is furthermore demonstrated that the coupled TDDFT-FDE approach can cure the inability of the uncoupled FDE approach to describe induced circular dichroism in dimeric chromophores, a feature known as a "couplet," which is also related to couplings between (nearly) degenerate electronic transitions.     

Assignment of molecular structures to the electrochemical reduction products of diiron compounds related to [Fe-Fe] hydrogenase: a combined experimental and density functional theory study

The reduction chemistry of (mu-bridge)[Fe(CO)3]2 [bridge = propane-1,3-dithiolate (1) and ethane-1,2-dithiolate (2)] is punctuated by the formation of distinct products, resulting in a marked difference in CO inhibition of electrocatalytic proton reduction. The products formed following reduction of 2 have been examined by a range of electrochemical, spectroelectrochemical, and spectroscopic approaches. Density functional theory has allowed assessment of the relative energies of the structures proposed for the reduction products and agreement between the calculated spectra (IR and NMR) and bond distances with the experimental spectra and EXAFS-derived structural parameters. For 1 and 2, one-electron reduction is accompanied by dimerization, but the structure, stability, and reaction with CO of the dimer is different in the two cases, and this is responsible for the different CO inhibition response for electrocatalytic proton reduction. Calculations of the alternate structures of the two-electron, one-proton reduced forms of 2 show that the isomers with terminally bound hydrides are unlikely to play a significant role in the chemistry of these species. The hydride-transfer chemistry of the 1B species is more reasonably attributed to a hydride-bridged form. The combination of experimental and computational results provides a solid foundation for the interpretation of the reduction chemistry of dithiolate-bridged diiron compounds, and this will underpin translation of the diiron subsite of the [FeFe] hydrogenase H cluster into an abiological context.     

The relationship between formate adsorption energy and electronic properties: A first principles density functional theory study

First principles density functional theory calculations have been performed for the chemisorption of formate adsorption on some metal surfaces. For the most stable adsorption site of short-bridge, the calculated formate adsorption energy follows the order of Au(110) < Ag(110) < Cu(110) < Pd(110) < Pt(110) < Ni(110) < Rh(110) < Fe(100) < Mo(100), and a clear linear correlation exists between the adsorption energy and the corresponding heat of formation of metal oxides. Moreover, it has been found that the fo...     

Paramagnetic NMR spectroscopy and density functional calculations in the analysis of the geometric and electronic structures of iron-sulfur proteins

Paramagnetic NMR spectroscopy has been underutilized in the study of metalloproteins. One difficulty of the technique is that paramagnetic relaxation broadens signals from nuclei near paramagnetic centers. In systems with low electronic relaxation rates, this makes such signals difficult to observe or impossible to assign by traditional methods. We show how the challenges of detecting and assigning signals from nuclei near the metal center can be overcome through the combination of uniform and selective 2H, 13C, and 15N isotopic labeling with NMR experiments that utilize direct one-dimensional (2H, 13C, and 15N) and two-dimensional (13C-X) detection. We have developed methods for calculating NMR chemical shifts and relaxation rates by density functional theory (DFT) approaches. We use the correspondence between experimental NMR parameters and those calculated from structural models of iron-sulfur clusters derived from X-ray crystallography to validate the computational approach and to investigate how structural differences are manifested in these values. We have applied this strategy to three iron-sulfur proteins: Clostridium pasteurianum rubredoxin, Anabaena [2Fe-2S] ferredoxin, and human [2Fe-2S] ferredoxin. Provided that an accurate structural model of the iron-sulfur cluster and surrounding residues is available from diffraction data, our results show that DFT calculations can return NMR observables with excellent accuracy. This suggests that it might be possible to use calculations to refine structures or to generate structural models of active sites when crystal structures are unavailable. The approach has yielded insights into the electronic structures of these iron-sulfur proteins. In rubredoxin, the results show that substantial unpaired electron spin is delocalized across NH...S hydrogen bonds and that the reduction potential can be changed by 77 mV simply by altering the strength of one of these hydrogen bonds. In reduced [2Fe-2S] ferredoxins, hyperfine shift data have provided quantitative information on the degree of valence trapping. The approach described here for iron-sulfur proteins offers new avenues for detailed studies of these and other metalloprotein systems.     

Mechanism of oxidative shuttling for [2]rotaxane in a Stoddart-Heath molecular switch: density functional theory study with continuum-solvation model

The central component of the programmable molecular switch demonstrated recently by Stoddart and Heath is [2]rotaxane, which consists of a cyclobis-(paraquat-p-phenylene) ring-shaped shuttle [(CBPQT(4+))(PF(6)(-))(4)] encircling a finger and moving between two stations on the finger: tetrathiafulvalene (TTF) and 1,5-dioxynaphthalene (DNP). We report here a quantum mechanics (QM) study of the mechanism by which movement of the ring (and in turn the on-off switching) is controlled by the oxidation-reduction process. We use B3LYP density functional theory to describe how oxidation of the [2]rotaxane components (in using Poisson-Boltzmann continuum-solvation theory for acetonitrile solution) induces the motions associated with switching (translation of the ring). These calculations support the proposal that oxidation occurs on TTF, leading to repulsion between two positive charge centers (TTF(2+) and CBPQT(4+)) that drives the CBPQT(4+) ring from the TTF(2+) station toward the neutral DNP station. The theory also supports the experimental observation that the first and second oxidation potentials are nearly the same (separated by 0.09 eV in the QM). This excellent agreement between the QM and experiment suggests that QM can be useful in designing new systems.     

Electronic structure and bonding of {Fe(PhNO2)}6 complexes: a density functional theory study

Reduction of nitro-aromatic compounds (NACs) proceeds through intermediates with a partial electron transfer into the nitro group from a reducing agent. To estimate the extent of such a transfer and, therefore, the activity of various model ferrous-containing reductants toward NAC degradation, the unrestricted density functional theory (DFT) in the basis of paired L?wdin-Amos-Hall orbitals has been applied to complexes of nitrobenzene (NB) and model Fe(II) hydroxides including cationic [FeOH]+, then neutral Fe(OH)2, and finally anionic [Fe(OH)3]-. Electron transfer is considered to be a process of unpairing electrons (without the change of total spin projection Sz) that reveals itself in a substantial spin contamination of the unrestricted solution. The unrestricted orbitals are transformed into localized paired orbitals to determine the orbital channels for a particular electron-transfer state and the weights of idealized charge-transfer and covalent electron structures. This approach allows insight into the electronic structure and bonding of the {Fe(PhNO2)}6 unit (according to Enemark and Feltham notation) to be gained using model nitrobenzene complexes. The electronic structure of this unit can be expressed in terms of pi-type covalent bonding [Fe+2(d6, S = 2) - PhNO2(S = 0)] or charge-transfer configuration [Fe+3(d5, S = 5/2) - {PhNO2}- ((pi*)1, S = 1/2)].