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QSAR analysis of the toxicity of aromatic compounds to Chlorella vulgaris in a novel short-term assay.

The use of alternative toxicity tests and computational prediction models is widely accepted to fill experimental data gaps and to prioritize chemicals for more expensive and time-consuming assessment. A novel short-term toxicity test using the alga Chlorella vulgaris was utilized in this study to produce acute aquatic toxicity data for 65 aromatic compounds. The compounds tested included phenols, anilines, nitrobenzenes, benzaldehydes and other poly-substituted benzenes. The toxicity data were employed in the development of quantitative structure-activity relationships (QSARs). Using multiple regression (MLR) and partial least squares (PLS) analyses, statistically significant, transparent and interpretable QSARs were developed using a small number of physicochemical descriptors. A two-descriptor model was developed using MLR (log(1/EC50)=0.73 log Kow-0.59 Elumo-1.91; n=65, r2=0.84, r2CV=0.82, s=0.43) and a four-descriptor model using PLS (log(1/EC50)=0.40 log Kow-0.23 Elumo+9.84 Amax+0.20 0chiv-5.40; n=65, r2=0.86, q2=0.84, RMSEE=0.40). The latter model was obtained by stepwise elimination of variables from a set of 102 calculated descriptors. Both models were validated successfully by simulating external prediction through the use of complementary subsets. The two factors, which were identified as being critical for the acute algal toxicity of this set of compounds were hydrophobicity and electrophilicity.

Chlorella↗

Chlorothalonil and its 4-hydroxy derivative in simple quartz sand soils: a comparison of sorption processes.

Quartz sandy soils from Simcoe, Ontario, Canada and North Carolina had sorption properties for chlorothalonil that were nearly the same. For labile surface sorption kinetics, the Simcoe soil gave a pseudo first-order rate constant of kS1 = (7.4 +/- 0.7) x 10(-2) days-1. At equilibrium, the labile surface sorption capacity theta c of Simcoe soil for chlorothalonil was 23.8 x 10(-6) (mol/g). The sorption properties of the 4-hydroxy derivative of chlorothalonil were different in two important respects. They were larger by an order of magnitude, and they were substantially different for the two soils. Sorption by the Simcoe soil was too fast for kinetics measurements by the on-line HPLC micro extraction method, but for the North Carolina soil kS1 = (1.15 +/- 0.01) days-1 was recorded. For the Simcoe and North Carolina soils, respectively, theta c > 200 (mumol/g) and theta c approximately 113 (mumol/g). Two conclusions can be drawn. First, the replacement of the Cl by OH on the 4 position of chlorothalonil makes the sorption effects much greater. Second, the stronger interactions are associated with a greater sensitivity to small differences in the chemical compositions of the soils. Subtle soil properties causing significant effects might include small amounts and physical structures of organic matter and metal oxides. This implies that, for predictive computer models, mechanism parameters will have to be correlated in two dimensions: chemical structure, and the composition and amounts of chemical materials in soils.

Adsorption↗

Peculiar antiaromatic inorganic molecules of tetrapnictogen in Na+Pn4- (Pn = P, As, Sb) and important consequences for hydrocarbons.

Although aromaticity has been observed in inorganic and all-metal species, the concept of antiaromaticity has not been extended beyond organic molecules. Here, we present theoretical and experimental evidence that the 6 -electron tetrapnictogen dianions in Na+Pn42- (Pn = P, As, Sb) undergo a transition from being aromatic to antiaromatic upon electron detachment, yielding the first inorganic antiaromatic Na+Pn4- molecules. Two types of antiaromatic structures were characterized, the conventional rectangular species and a new peculiar quasiplanar rhombus species. Aromaticity and antiaromaticity in the tetrapnictogen molecules were derived from molecular orbital analyses and verified by experimental photodetachment spectra of Na+Pn42-. On the basis of our findings for the tetrapnictogen clusters, we predicted computationally that the organic C4H4- anion also possesses two antiaromatic structures: rectangular and rhombus. Moreover, only the rhombus antiaromatic minimum was found for the radical NC3H4, thus extending the peculiar rhombus antiaromatic structure first uncovered in inorganic clusters into organic chemistry.

Journal Article↗

Arachno, nido, and closo aromatic isomers of the Li6B6H6 molecule.

We analyzed chemical bonding in low-lying isomers of the recently computationally predicted B(6)H(6)Li(6) molecule. According to our calculations the benzene-like B(6)H(6)Li(6) (D(2h), (1)A(1g)) arachno structure with the planar aromatic B(6)H(6)(6-) anion is the most stable one. A nido isomer with two aromatic B(6)H(6)(4-) (pentagonal pyramid) and Li(3)(+) (triangular) moieties, which can be considered as derived from the global minimum structure through a two-electron intramolecular transfer from B(6)H(6)(6-) to three Li(+) cations, was found to be 10.7 kcal/mol higher in energy. A closo isomer with three aromatic moieties (octahedral B(6)H(6)(2-) and two Li(3)(+)) was found to be 31.3 kcal/mol higher in energy than the global minimum. Another isomer with three aromatic moieties (two B(3)H(3)(2-) and Li(3)(+)) was found to be substantially higher in energy (74.4 kcal/mol). Thus, the intramolecular electron transfers from the highly charged B(6)H(6)(6-) anion to cations are not favorable for the B(6)H(6)Li(6) molecule, even when a formation of three-dimensional aromatic B(6)H(6)(2-) anion and two sigma-aromatic Li(3)(+) cations occurs in the closo isomer.

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Quantum chemical characterization of the bonding of N-heterocyclic carbenes to Cp2MI compounds [M = Ce(III), U(III)].

The binding of N-heterocyclic carbenes to Ce(III) and U(III) compounds is characterized by quantum chemical methods. Density functional methods are in qualitative agreement with experiment that binding to U(III) is more favorable than to Ce(III); after correcting for basis-set superposition error, quantitative agreement with experiment is achieved with a multireference second-order perturbation theory approach accounting for relativistic effects. The small computed (and observed) preference derives from a combination of several small effects, including differences in electronic binding energies, rovibrational partition functions, and solvation free energies. Prospects for ligand modification to improve the differentiation between lanthanides and actinides are discussed on the basis of computational predictions.

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Spin surface crossing in chromium-mediated olefin epoxidation with O(2).

[CpCr(mu-Cl)Cl](2) reacted with dioxygen (O(2)) to produce CpCr(O)Cl(2) (1), which has been structurally characterized. Although 1 oxidized PPh(3) and 1,4-cyclohexadiene catalytically, it did not epoxidize olefins. DFT calculations have been performed on the system to characterize the potential energy surface for the epoxidation of ethylene and, in particular, the consequences of the crossing from the doublet surface of the starting materials to the quartet surface of the product (i.e. a chromium(III) epoxide adduct). These calculations suggested that "spin-blocking" was not a significant problem and that the reaction of CpCr(O)Cl(2) (3) with ethylene should have a lower activation barrier. On the basis of this computational prediction, 3 was prepared; it was found to epoxidize olefins stoichiometrically.

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The surprising nitrogen-analogue chemistry of the methyltrioxorhenium-catalyzed olefin epoxidation.

Density functional theory calculations at the B3LYP level have been carried out to investigate the mechanism of the reaction of ethylene with [Re(O)2(O-NH)Me], a formal hydroxylamine derivative of the industrial epoxidation catalyst methyltrioxorhenium(VII) (MTO). A variety of reaction pathways has been considered, including the concerted heteroatom-transfer mechanism postulated by Sharpless and the stepwise mechanism via a five-membered "organometallacycle" postulated by Mimoun. Ethylene has been found not to coordinate directly at the metal. The calculations reveal similar activation free enthalpies for the concerted nitrene-transfer event (aziridination) and for the formation of an organometallic rhena-2,3-oxazolidine via [2+2] addition of ethylene across the Re-N bond of the metallaoxaziridine moiety. The fragmentation of the organometallacycle is faster than its formation and gives ethylideneazane rather than aziridine. An additional pathway has a lower activation free enthalpy and leads to a rhena-3,2-oxazolidine. The formation of this organometallacycle proceeds via an intermediate ring-opening product, [Re(O)2(eta1-O-NH)Me], which undergoes [3+2] cycloaddition across the C=C bond of ethylene. Analysis of its electronic structure reveals that the eta1 species should be considered a metalla-analogue nitrosonium ylide rather than a metalla-analogue imine oxide. Fragmentation of the rhena-3,2-oxazolidine liberates acetaldehyde. The discovery of favorable pathways leading to organometallacycles upon reaction of C=C bonds with [Re(O)2(O-NH)Me] stands in sharp contrast to the strong preference of the concerted mechanism in the olefin epoxidation with rhenium peroxo complexes. The calculations show the multiple mechanisms to be distinguishable by four different products, calling for further experimental studies. The successful search for the five-membered organometallacycles parallels the computational prediction of four-membered organometallacycles derived from d0 metal oxo complexes (Deubel, D. V.; Frenking, G. Acc. Chem. Res. 2003, 36, 645) and the indirect observation of metalla-2-oxetanes in recent gas-phase experiments (Chen, X.; Zhang, X.; Chen, P. Angew. Chem., Int. Ed. 2003, 42, 3798).

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Structure and magnetism of VnBz(n+1) sandwich clusters.

Results on structural, energetic, electronic, and magnetic properties of linear sandwich VnBzn+1 clusters obtained using high-accuracy density functional computations are presented and analyzed. Energetically close-lying configurations and states of different spin-multiplicities are identified. The computed characteristics are in good agreement with the available experimental data. The computations predict that the most stable forms of the clusters in the size range n >/= 4 are chiral. This feature, combined with the magnetism of these systems, makes them of potential importance as building blocks of nanosystems with coupled optical and magnetic functionalities.

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Resonance Raman spectroscopy of the neutral radical Trp306 in DNA photolyase.

The resonance Raman spectrum of the tryptophan neutral radical in a protein, Escherichia coli photolyase, is reported for the first time. The data compare very well to a solution study and computational predictions, and tentative assignments are made for the observed vibrations. This important new result demonstrates the potential of time-resolved resonance Raman spectroscopy as a powerful tool to investigate these radicals in protein electron-transfer processes and in enzymatic reactions in real time.

Deoxyribodipyrimidine Photo-Lyase↗

An anion-dependent switch in selectivity results from a change of C-H activation mechanism in the reaction of an imidazolium salt with IrH5(PPh3)2.

Changing the counteranion along the series Br, BF4, PF6, SbF6 in their ion-paired 2-pyridylmethyl imidazolium salts causes the kinetic reaction products with IrH5(PPh3)2 to switch from chelating N-heterocyclic carbenes (NHCs) having normal C2 (N path) to abnormal C5 binding (AN path). Computational work (DFT) suggests that the AN path involves C-H oxidative addition to Ir(III) to give Ir(V) with little anion dependence. The N path, in contrast, goes by heterolytic C-H activation with proton transfer to the adjacent hydride. The proton that is transferred is accompanied by the counteranion in an anion-coupled proton transfer, leading to an anion dependence of the N path, and therefore of the N/AN selectivity. The N path goes via Ir(III), not Ir(V), because the normal NHC is a much less strong donor ligand than the abnormal NHC. PGSE NMR experiments support the formation of ion-pair in both the reactants and the products. 19F,1H-HOESY NMR experiments indicate an ion-pair structure for the products that is consistent with the computational prediction (ONIOM(B3PW91/UFF)).

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Two-stage method for protein-ligand docking.

A two-stage method for the computational prediction of the structure of protein-ligand complexes is proposed. Given an experimentally determined structure of the protein, in the first stage a large number of plausible ligand conformations is generated using the fast docking algorithm FlexX. In the second stage these conformations are minimized and reranked using a method based on a classical force field. The two-stage method is tested for 10 different protein-ligand complexes. For 9 of them experimentally determined structures are known. It turns out that the two-stage method strongly improves the predictive power as compared to that of the fast docking stage alone. The tenth case is a bona fide prediction of a complex of thrombin with a new inhibitor for which no experimentally determined structure is available so far.

Algorithms↗

Novel pathways for oxygen insertion into unactivated C-H bonds by dioxiranes. Transition structures for stepwise routes via radical pairs and comparison with the concerted pathway.

The oxygen insertion into C-H bonds (of methane, isobutane, and acetone) by dioxiranes (parent dioxirane and dimethyldioxirane) to give alcohols was studied with the DFT theory, using both restricted and unrestricted B3LYP methods, and 6-31G(d) and 6-311+G(d,p) basis sets to evaluate the feasibility of stepwise mechanisms and their competition with the concerted counterpart. Confirming previous results by other authors, we have located, with the RB3LYP method, concerted TSs in which the oxygen bound to be inserted interacts very strongly with the hydrogen atom and very weakly with the carbon atom of the C-H bond. These TSs nicely explain all the experimental observations (e.g., configuration retention at the chiral centers), but all of them exhibit an RHF --> UHF wave function instability that preclude considering them as genuine transition structures. We also were able to characterize, with UB3LYP methods, two alternative two-step processes that can lead to final products (alcohol + carbonyl compound) via singlet radical pair intermediates. For the first step of both processes we located genuine diradicaloid TSs, namely, TSs rad,coll and TSs rad,perp, that have stable wave functions. In TSs rad,coll the alkane C-H bond tends to be collinear with the breaking O(1)- - -O(2) bond while in TSs rad,perp the alkane C-H bond is almost perpendicular to the O(1)- - -O(2) bond. The first step, of both processes, can represent an example of a "molecule induced homolysis" reaction: collision between alkane and dioxirane brings about the homolytic cleavage of the dioxirane O-O bond and the hydrogen abstraction follows afterward to produce the diradicaloid TS that then falls down to a singlet radical pair. This hypothesis was fully confirmed by IRC analysis in the case of TSs rad,coll. The possible pathways that lead from the intermediate radical pair to final products are discussed as well as the hypothesis that the radical collinear TSs may collapse directly to products in a "one-step nonconcerted" process. However, diradical mechanisms cannot explain the experimental data as satisfactorily as the concerted pathway does. As for computational predictions about competition of diradical vs concerted mechanisms, they strongly depend (i) on the alkane C-H type, (ii) on whether gas phase or solution is considered, and (iii) on the basis set used for calculations. In short, the concerted TS benefits, with respect to the corresponding diradicaloid TSs, of alkyl substitution at the C-H center, solvation effects, and basis set extension. Actually, in the case of DMD reactions with methane and acetone, the diradicaloid TSs are always (both in gas phase and in solution and with both the basis sets used) strongly favored over their concerted counterpart. In the case of DMD reaction with isobutane tertiary C-H bond the large favor for the diradicaloid TSs over the concerted TS, predicted in gas phase by the B3LYP/6-31G(d) method, progressively decreases as a result of basis set extension and introduction of solvent effects: the higher theory level [B3LYP/6-311+G(d,p)] suggests that in acetone solution TS conc has almost the same energy as TS rad,perp while TS rad,coll resides only 2 kcal/mol higher.

Journal Article↗

Stereomutations of two-bladed propeller derivatives: ortho-substituted diaryl ethylene and diaryl ketone.

Stereochemical analysis, supported by ab initio computations, predicts the existence of three possible stable helical conformers for o,o'-diisopropyl-1,1'-diphenylethylene (1) and o,o'-diisopropylbenzophenone (2). At low temperature the NMR spectra of 1 showed distinct sets of signals for these conformers, thus allowing the measurement of the three barriers involved in the related stereomutation processes to be obtained (DeltaG=6.45, 4.65, and < or =4.0 kcal mol(-1)). The NMR spectra also indicate that the asymmetric conformer (C1 point group) is the most stable one in solution, as anticipated by calculations. X-ray diffraction confirmed that this structure is that adopted in the crystalline state. On the other hand, o,o'-diisopropylbenzophenone (2) is predicted by calculations to exist essentially as a C2-type conformer, a result that was confirmed by the low-temperature NMR spectra. The interconversion barrier for the enantiomeric forms of this conformer was also measured (DeltaG=6.3(5) kcal mol(-1)).

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Ring opening of 2,5-didehydrothiophene: matrix photochemistry of C4H2S isomers.

Irradiation (lambda > 254 nm) of matrix-isolated 2,5-diiodothiophene (10) gives rise to IR bands assigned to ethynylthioketene (6). Diethynyl sulfide (3), which would form in the process of retro-Bergman cyclization of the incipient 2,5-didehydrothiophene (4), is not detected. Under the same irradiation conditions, matrix-isolated diethynyl sulfide (3) rearranges to thioketene 6 and butatrienethione (5), the global minimum on C4H2S potential energy surface. The photochemical formation of thioketene 6 from either diyl 4 or sulfide 3 may be interpreted in line with a recent computational prediction on the thermal ring opening of diyl 4, which favors C-S bond cleavage, leading to 6, over C-C bond cleavage, leading to 3. Photolysis of matrix-isolated 3,4-thiophenedicarboxylic acid anhydride (11) enables the observation of the photoequilibration of three low-energy C4H2S isomers, butatrienethione (5), ethynylthioketene (6), and butadiynylthiol (7), via apparent [1,3]-hydrogen shifts.

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Vinyltrimethylsilane (VTMS) as a probe of chemical reactivity of a TiCN diffusion barrier-covered silicon surface.

This paper presents the first molecular level investigation of chemical reactivity of a surface of an amorphous diffusion barrier film deposited on a Si(100)-2 x 1 single crystal. Vinyltrimethylsilane (VTMS) is chosen as a probe molecule because of its chemical properties and because of its role as a ligand in a common copper deposition precursor, hexafluoroacetylacetonato-copper-vinyltrimethylsilane, (hfac)Cu(VTMS). The surface chemistry of vinyltrimethylsilane on titanium carbonitride-covered Si(100)-2 x 1 has been investigated using multiple internal reflection Fourier transform infrared spectroscopy (MIR-FTIR), Auger electron spectroscopy (AES), thermal desorption mass spectrometry, and computational analysis. On a film with nominal surface stoichiometry TiC(x)N(y) (x approximately y approximately 1) preannealed to 800 K, VTMS adsorbs molecularly at cryogenic temperatures even at submonolayer coverages; the major pathway for its temperature-programmed evolution is desorption. Adsorption at room temperature leads to chemisorption via a double-bond attachment. A set of computational models was designed to investigate the possible adsorption sites for a VTMS molecule on a TiCN-covered Si(100)-2 x 1 surface. A comparison of the computational predictions for a variety of possible adsorption sites with the results of thermal desorption and infrared measurements suggests that approximately 90% of the adsorbed VTMS is chemisorbed along the Ti-C bond while approximately 10% is chemisorbed on a Ti corner atom, the minority site of the surface. The Ti-N bond is not participating in the chemisorption process.

Journal Article↗

Conformers and photochemistry of propyl nitrites: a matrix isolation study.

The infrared spectra of both constitutional isomers (n and i) of propyl nitrite have been recorded in an Ar matrix. Conformational analysis and assignments of the vibrational transitions have been carried out on the basis of quantum chemical calculations. Assignment of spectral lines to different conformers was also aided experimentally, by utilizing the different rate of photodecomposition of the conformers, as well as by employing conformational cooling using a supersonic jet as the inlet source for matrix deposition. The rate of photodecomposition is primarily determined by the steric alignment of the nitrite group, whereas jet cooling affects mainly the conformation of the alkyl tail. On the basis of these experimental observations and computational predictions two to three conformers of isopropyl nitrite and eight conformers of n-propyl nitrite were identified. After broadband ultraviolet-visible (UV-vis) photolysis of isopropyl nitrite in the matrix, HNO, acetone, HNO.acetone complex, acetaldehyde, and nitrosomethane were identified as the main products. Furthermore, in a small amount, NO and possibly the isopropoxy radical were also present in the matrix. Photolysis of n-propyl nitrite yielded HNO, propanal, and their 1:1 complex as the main products together with a small amount of NO and cis-1-nitrosopropanol.

Journal Article↗

Experimental and computational growth morphology of two polymorphs of a yellow isoxazolone dye.

We report on the crystal structures and the experimentally found and the computationally predicted growth morphologies of two polymorphs of a yellow isoxazolone dye. The stable polymorph I has a blocklike habit, and the metastable polymorph II grows as fine needles, nucleating only by heterogeneous or contact nucleation. The habits of both polymorphs depend on the supersaturation during growth. The experimental observations are compared with predictions of the attachment energy model and kinetic Monte Carlo lattice simulations in which the growth is modeled as an "atomistic process", governed by surface energetics. These Monte Carlo simulations correctly predict the shape and the dependence on supersaturation of the crystal morphology for both polymorphs: for polymorph I, a strong dependence on supersaturation is found from the simulations. For polymorph II, the order of morphological importance is reproduced correctly, as well as the needlelike morphology.

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A theoretical prediction of potentially observable lithium compounds with planar tetracoordinate carbons.

Several potentially experimentally accessible lithiated heterocyclic and heteroatom compounds with planar tetracoordinate carbons (ptC) have been predicted computationally. These utilize the strong electron-donating ability and the bridging proclivity of lithium to achieve the ptC preferences. As the p orbitals on the central carbons are only partially occupied, their electronic structures are similar to those of the related carbenes, e.g. imidazole-2-ylidene, rather than to the other ptC compounds such as dilithiocyclopropane.

Journal Article↗