Managing the computational chemistry big data problem: the ioChem-BD platform

We present the ioChem-BD platform ( www.iochem-bd.org ) as a multiheaded tool aimed to manage large volumes of quantum chemistry results from a diverse group of already common simulation packages. The platform has an extensible structure. The key modules managing the main tasks are to (i) upload of output files from common computational chemistry packages, (ii) extract meaningful data from the results, and (iii) generate output summaries in user-friendly formats. A heavy use of the Chemical Mark-up Language (CML) is made in the intermediate files used by ioChem-BD. From them and using XSL techniques, we manipulate and transform such chemical data sets to fulfill researchers' needs in the form of HTML5 reports, supporting information, and other research media.

Electronic properties of polyoxometalates: a DFT study of alpha/beta-[XM(12)O(40)](n-) relative stability (M=W, Mo and X a main group element)

Keggin heteropolyanions [XM(12)O(40)](n-) have various isomeric structures, alpha and beta being the most common. Conventionally, the alpha structure appears to be the most stable, but calculations carried out at the DFT level for X = P(V), Si(IV), Al(III), As(V), Ge(IV), and Ga(III) and M = W(VI) and Mo(VI) show that this stability depends on several factors, particularly on the nature of the heteroatom (X) and the total charge of the cluster. In this paper, we apply the clathrate model to the Keggin molecule to carry out a fragment-interaction study to elucidate when and why the traditional relative stability of various isomers can be inverted. The fully oxidized anions that have inverted the traditional stability trend in this series are [AlW(12)O(40)](5-) and [GaW(12)O(40)](5-), both of which contain a third-group heteroatom and an overall charge of -5. beta-isomers are always more easily reduced than alpha-isomers. This experimental observation suggests that reduction favors the stability of beta-isomers and one of the most important results of this study is that the alpha/beta inversion is achieved in most cases after the second reduction. The alpha- and beta-isomers may have different properties because the energy of the LUMO, a symmetry-adapted d(xy)-metal orbital, is different.

Rhodium/iridium-titanium azaheterometallocubanes

Treatment of [[Ti(eta5-C5Me5)(mu-NH)]3(mu3-N)] (1) with the diolefin complexes [[MCl(cod)]2] (M = Rh, Ir; cod = 1,5-cyclooctadiene) in toluene afforded the ionic complexes [M-(cod)(mu3-NH)3Ti3(eta5-C5Me5)3(mu3-N)]Cl [M = Rh (2), Ir (3)]. Reaction of complexes 2 and 3 with [Ag(BPh4)] in dichloromethane leads to anion metathesis and formation of the analogous ionic derivatives [M(cod)(mu3-NH)3Ti3-(eta5-C5Me5)3(mu3-N)][BPh4] [M = Rh (4), Ir (5)]. An X-ray crystal structure determination for 5 reveals a cube-type core [IrTi3N4] for the cationic fragment, in which 1 coordinates in a tripodal fashion to the iridium atom. Reaction of the diolefin complexes [[MCl(cod))2] (M = Rh, Ir) and [[RhCl(C2H4)2]2] with the lithium derivative [[Li(mu3-NH)2(mu3-N)-Ti3(eta5-C5Me5)3(mu3-N)]2] x C7H8 (6 C7H8) in toluene gave the neutral cube-type complexes [M(cod)(mu-NH)2(mu3-N)Ti3-(eta5-C5Me5)3(mu3-N)] [M = Rh (7), Ir (8)] and [Rh(C2H4)2(mu3-NH)2(mu3-N)Ti3(eta5-C5Me5)3(mu3-N)] (9), respectively. Density functional theory calculations have been carried out on the ionic and neutral azaheterometallocubane complexes to understand their electronic structures.

Electronic and magnetic properties of alpha-Keggin anions: A DFT study of [XM12O40](n-), (M = W, Mo; X = Al(III), Si(IV), P(V), Fe(III), Co(II), Co(III)) and [SiM11VO40](m- (M = Mo and W)

Calculations based on density functional theory (DFT) have been carried out to investigate the electronic and magnetic properties of the alpha-Keggin anions mentioned in the title. The atomic populations and the distribution of the electron density computed for the studied clusters support the hypothesis that an oxidized Keggin anion is an XO(4)(n-) clathrate inside a neutral M(12)O(36) cage. The energy gap between the band of occupied orbitals, formally delocalized over the oxo ligands, and the unoccupied d-metal orbitals, delocalized over the addenda, has been found to be independent of the central ion. However, substitution of a W or a Mo by V modifies the relative energy of the LUMO and then induces important changes in the redox properties of the cluster. In agreement with the most recent X-ray determination of [Co(III)W(12)O(40)](5-) and with the simplicity of the (183)W NMR and (17)O NMR spectra observed for this anion the calculations suggest that [Co(III)W(12)O(40)](5-) has a slightly distorted T(d ) geometry. For the parent cluster [CoW(12)O(40)](6-) the quadruplet corresponding to the anion encapsulating a Co(II) was found to be approximately 1 eV more stable than the species formed by a Co(III) and 1 e delocalized over the sphere of tungstens. The one-electron reduction of [Co(II)W(12)O(40)](6-) and [Fe(III)W(12)O(40)](5-) leads to the formation of the 1 e blue species [Co(II)W(12)O(40)](7-) and [Fe(III)W(12)O(40)](6-). The blue-iron cluster is considerably antiferromagnetic, and in full agreement with this behavior the low-spin state computed via a Broken Symmetry approach is 196 cm(-1) lower than the high-spin solution. In contrast, the cobalt blue anion has a low ferromagnetic coupling with an S-T energy gap of +20 cm(-1). This blue species is more stable than the alternative reduction product [Co(I)W(12)O(40)](7-) by more than 0.7 eV.

Trapping of an activated HF molecule inside a double four-ring unit: a quantum chemical model of the microporous fluorinated gallium phosphate ULM-18

The penetration of a proton into the prenucleation building unit of a microporous gallophosphate and its interaction with an encapsulated fluorine anion have been investigated by means of DFT calculations. The inorganic part of the fluorinated gallophosphate ULM-18 has been modeled by a neutral, double four-ring (D4R) unit of formula [(GaOH)4(HPO4)4-H2O] encapsulating the fluorine ion. Assuming the cage to be rigid and to retain throughout the calculations the geometry determined from X-ray diffraction (XRD), the position of F(-) has been optimized, either as an isolated guest species or in the presence of an incoming proton. In agreement with the XRD structure, the fluorine atom has been shown to occupy in both cases a nonsymmetric position in the cage, being attached to three gallium atoms out of four. The distribution of the molecular electrostatic potential inside and outside the (F(-))@[(GaOH)4(HPO4)4-H2O] system has provided indications concerning the pathways that could be used by an incoming proton to penetrate the D4R unit and to approach the fluorine anion. The migration of a proton from an external site of fixation to the interior of the D4R unit has been found possible through two faces out of six. In both cases, the process has been found exothermic by approximately 0.17 eV and the energy barrier was estimated to approximately 0.8 eV. Inside the gallophosphate cage, the proton first adopts a position typical of a strong F...H...O bond made possible through an important shift of the fluorine anion away from the tripod of bonded gallium atoms. Then, the F(-)...H(+) system can easily evolve back and forth on a flat potential curve between one of the F...H...O bonded conformations and a situation characterized by the cleavage of the H...O link and the formation of a moderately activated F-H molecule, with the fluorine still attached to three gallium atoms.

Ammonolysis of mono(pentamethylcyclopentadienyl) titanium(IV) derivatives

Ammonolyses of mono(pentamethylcyclopentadienyl) titanium(IV) derivatives [Ti(eta5-C5Me5)X3] (X = NMe2, Me, Cl) have been carried out in solution to give polynuclear nitrido complexes. Reaction of the tris(dimethylamido) derivative [Ti(eta5-C5Me5)(NMe2)3] with excess of ammonia at 80-100 degrees C gives the cubane complex [[Ti(eta5-C5Me5)]4(mu3-N)4] (1). Treatment of the trimethyl derivative [Ti(eta5-C5Me5)Me3] with NH3 at room temperature leads to the trinuclear imido-nitrido complex [[Ti(eta/5-CsMes)(mu-NH)]3(mu3-N)] (2) via the intermediate [[Ti(eta5-C5Me5)Me]2(mu-NH)2] (3). The analogous reaction of [Ti(eta5-C5Me5)Me3] with 2,4,6-trimethylaniline (ArNH2) gives the dinuclear imido complex [[Ti(eta5-C5Me5)Me])2(mu-NAr)2] (4) which reacts with ammonia to afford [[Ti(eta5-C5Me5)(NH2)]2(mu-NAr)2] (5). Complex 2 has been used, by treatments with the tris(dimethylamido) derivatives [Ti(eta5-C5H5-nRn)(NMe2)3], as precursor of the cubane nitrido systems [[Ti4(eta5-C5Me5)3(eta5-C5H5-nRn)](mu3-N)4] [R = Me n = 5 (1), R = H n = 0 (6), R = SiMe3 n = 1 (7), R = Me n = 1 (8)] via dimethylamine elimination. Reaction of [Ti(eta5-C5Me5)Cl3] or [Ti(eta5-C5Me5)(NMe2)Cl2] with excess of ammonia at room temperature gives the dinuclear complex [[Ti2(eta5-C5Me5)2Cl3(NH3)](mu-N)] (9) where an intramolecular hydrogen bonding and a nonlineal nitrido ligand bridge the "Ti(eta5-C5Me5)Cl(NH3)" and "Ti(eta5-C5Me5)Cl2" moieties. The molecular structures of [[Ti(eta5-C5Me5)Me]2 (mu-NAr)2] (4) and [[Ti2(eta5-C5Me5)2Cl3(NH3)](mu-N)] (9) have been determined by X-ray crystallographic studies. Density functional theory calculations also have been conducted on complex 9 to confirm the existence of an intramolecular N-H...Cl hydrogen bond and to evaluate different aspects of its molecular disposition.

Construction of Heterometallic Cubanes

Incorporation of M(CO)(3) fragments by trinuclear Ti complexes [{Ti(3)Cp<![IGNORE[$\curr {\brol{{\stern}}{3}}$]]>(µ(3)-CR)}(µ-O)(3)] and [{Ti(3)Cp<![IGNORE[$\curr {\brol{{\stern}}{3}}$]]>(µ(3)-N)}(µ-NH)(3)] (Cp*=eta(5)-C(5)Me(5)) leads to the formation of an unprecedented class of heterometallic clusters with cubane structure [e.g., Eq. (a)]. Density functional calculations on these complexes indicate the existence of electron delocalization in the Ti(3)M cores (M=Cr, Mo, W).

Influence of the chromatographic capacity factor (log k') as an index of lipophilicity in the antibacterial activity of a series of 6-fluoroquinolones. Relationship between physico-chemical and structural properties and their hydrophobicity

The aim of this study was to establish the influence of lipophilicity on the antibacterial activity (log 1/MIC50) of 22 fluoroquinolones and to assess the influence of their electronic, steric and topological properties on their hydrophobicity. The lipophilicity of the compounds, expressed as the chromatographic capacity factor (log k'), was determined by ion-pair reversed-phase HPLC. On the basis of the mathematical models developed, an attempt was made to confirm the mechanism of interaction of the quinolones with DNA-gyrase proposed previously.