Cage doping of Ti, Zr, and Hf-based 13-atom nanoclusters: two sides of the same coin.

Transition metal nanoclusters can exhibit unique and tunable properties which result not only from their chemical composition but also from their atomic packing and quantized electronic structures. Here, we introduce a promising family of bimetallic TM@Ti12, TM@Zr12, and TM@Hf12 nanoclusters with icosahedral geometry, where TM represents an atom from groups 3 to 12. Density functional theory calculations show that their stability can be explained with familiar concepts of metal cluster electronic and atomic shell structures. The magnetic properties of these quasispherical clusters are entirely consistent with superatom electronic shells and Hund's rules, and can be tuned by the choice of the TM dopant. The computed cluster atomization energies were analyzed in terms of the elements' cohesive energy, Ecoh, and contributions from geometric distortion, Edis, surface energy, Es, and ionic bonding, Ei. Some clusters have anomalous stability relative to Ecoh + Edis + Es + Ei. We attribute this to superatomic character associated with a favorable atomic and electronic shell structure. This raises the possibility of designing stable superatoms and materials with tailored electronic and magnetic properties.

Fundamental Determinants of the Accuracy of Equilibrium Constants for Affinity Complexes.

The equilibrium constant of a chemical reaction is arguably the key thermodynamic parameter in chemistry; we naturally expect that equilibrium constants are determined accurately. The majority of equilibrium constants determined today are those of binding reactions that form affinity complexes, such as protein-protein, protein-DNA, and protein-small molecule. There is growing awareness that the determination of equilibrium constants for highly stable affinity complexes may be very inaccurate. However, fundamental (i.e., method-independent) determinants of accuracy are poorly understood. Here, we present a study that explicitly shows what the accuracy of equilibrium constants of affinity complexes depends on. This study reveals the critical importance of the choice of concentration of interacting components and creates a theoretical foundation for improving the accuracy of the equilibrium constants. The predicted influence of concentrations on accuracy was confirmed experimentally. The results of this fundamental study provide instructive guidance for experimentalists independently on the method they use.

Predicted Reversal in N-Methylazepine/N-Methyl-7-azanorcaradiene Equilibrium Upon Formation of Their N-Oxides.

Density functional calculations and up to five different basis sets have been applied to the exploration of the structural, enthalpy and free energy changes upon conversion of the azepine to the corresponding N-oxide. Although it is well known that azepines are typically much more stable than their 7-azanorcaradiene valence isomers, the stabilities are reversed for the corresponding N-oxides. Structural, thermochemical as well as nucleus-independent chemical shift (NICS) criteria are employed to probe the potential aromaticity, antiaromaticity and nonaromaticity of N-methylazepine, its 7-azanorcaradiene valence isomer. For the sake of comparison, analogous studies are performed on N-methylpyrrole and its N-oxide.

Batch-to-batch variation in domestic paints: Insights into the newly commercialized recycled paints.

A few recent studies attempted to evaluate the differentiation of paints at a production batch level and reported results depending largely on the paint type. The discrimination from production batches is much more random than brands and/or models levels and subject to many unknowns, which suggests that a particular production batch can suddenly present a substantially different composition than the one produced right before or right after it. To add to this existing complexity, most of the paint companies now propose a range of recycled paints among their products. These recycled paints are composed of wastes collected by recycling plants, sorted by their color and binder type (i.e. latex, alkyds), and mixed together in large tanks to form the basis material for future formulations. Quality controls on these recycled batches are voluntarily less precise, and a higher variation is expected in esthetic and chemical properties of the paint. In this project, we collaborated with a North American paint producer that gave us access to its samples, paint formulations recipes, and a summary of the quality controls and corrections they performed on each production batches. The whole study was conducted blindfold and a final verification was made with the manufacturer to evaluate the accuracy of the results. The data set comprised two models of regular paints and two models of recycled paint. Five different production batches were collected per model for a total of 20 samples analyzed by Microscopy, Infrared spectroscopy, Raman spectroscopy, and Pyrolysis GC/MS.

Evaluation of flunixin meglumine pour-on administration on prostaglandin E2 concentration in inflammatory exudate after induction of inflammation in cattle.

The effect of flunixin transdermal pour-on solution (Finadyne® Transdermal; MSD Animal Health) on prostaglandin E2 (PGE2) synthesis in bovine inflammatory exudate was evaluated in a tissue cage model of acute inflammation. Twelve calves were randomly allocated to two-treatment groups over two sequences. Three weeks prior to the first period, sterile hollow perforated polyethylene balls were surgically embedded in the subcutis at four distinct sites in each animal. On the first day of each period, an aseptic inflammation was induced by injecting 0.5mL of a 2% carrageenan solution into the lumen of each tissue cage. Treatment with either flunixin transdermal or negative control (NaCl) immediately followed. 0.5mL of exudate was collected prior to challenge, and at 2, 4, 8, 12, 24, 36 and 48h after challenge. Exudate PGE2 concentrations were analyzed using ultra-high pressure liquid chromatography coupled with tandem mass spectrometry method. Mean PGE2 concentrations were consistently lower in calves treated with flunixin transdermal than those measured in calves treated with negative control, indicating an inhibitory activity on cyclooxygenase. Inhibition was the highest at 8h after treatment, and differences with the negative control were significant at +8, 24, 36 and 48h. The flunixin transdermal formulation was effective in reducing PGE2 concentrations in bovine exudate following an induced inflammation. Its anti-inflammatory action started in the first hours after treatment and lasted up to 48h.

Optimizing molecular properties using a relative index of thermodynamic stability and global optimization techniques.

We devised a global optimization (GO) strategy for optimizing molecular properties with respect to both geometry and chemical composition. A relative index of thermodynamic stability (RITS) is introduced to allow meaningful energy comparisons between different chemical species. We use the RITS by itself, or in combination with another calculated property, to create an objective function F to be minimized. Including the RITS in the definition of F ensures that the solutions have some degree of thermodynamic stability. We illustrate how the GO strategy works with three test applications, with F calculated in the framework of Kohn-Sham Density Functional Theory (KS-DFT) with the Perdew-Burke-Ernzerhof exchange-correlation. First, we searched the composition and configuration space of CmHnNpOq (m = 0-4, n = 0-10, p = 0-2, q = 0-2, and 2 ≤ m + n + p + q ≤ 12) for stable molecules. The GO discovered familiar molecules like N2, CO2, acetic acid, acetonitrile, ethane, and many others, after a small number (5000) of KS-DFT energy evaluations. Second, we carried out a GO of the geometry of CumSnn (+) (m = 1, 2 and n = 9-12). A single GO run produced the same low-energy structures found in an earlier study where each CumSnn (+) species had been optimized separately. Finally, we searched bimetallic clusters AmBn (3 ≤ m + n ≤ 6, A,B= Li, Na, Al, Cu, Ag, In, Sn, Pb) for species and configurations having a low RITS and large highest occupied Molecular Orbital (MO) to lowest unoccupied MO energy gap (Eg). We found seven bimetallic clusters with Eg > 1.5 eV.

Photochemical generation of 9H-fluorenyl radicals.

A series of 9-substituted fluorenols and 9,9'-disubstituted-9,9'-bifluorenyls were irradiated to give products derived from fluorenyl radicals. Product distribution was solvent dependent. A TEMPO adduct was isolated from the photoexcitation of 9-fluorenol. An unusual unsymmetrical 3,9'-bifluorenyl was observed from the photolysis of 9-trifluoromethylfluorenol and 9,9'-di(trifluoromethyl)-9,9'-bifluorenyl in more polar or hydrogen-bonding solvents. The electronic nature of 9-substituted fluorenyl radicals was probed using theoretical calculations showing the dipolar character of species with electron-deficient groups. These constitute the first examples of "doubly destabilized" radicals.

Automated fit of high-dimensional potential energy surfaces using cluster analysis and interpolation over descriptors of chemical environment.

We present a method for fitting high-dimensional potential energy surfaces that is almost fully automated, can be applied to systems with various chemical compositions, and involves no particular choice of function form. We tested it on four systems: Ag20, Sn6Pb6, Si10, and Li8. The cost for energy evaluation is smaller than the cost of a density functional theory (DFT) energy evaluation by a factor of 1500 for Li8, and 60,000 for Ag20. We achieved intermediate accuracy (errors of 0.4 to 0.8 eV on atomization energies, or, 1% to 3% on cohesive energies) with rather small datasets (between 240 and 1400 configurations). We demonstrate that this accuracy is sufficient to correctly screen the configurations with lowest DFT energy, making this function potentially very useful in a hybrid global optimization strategy. We show that, as expected, the accuracy of the function improves with an increase in the size of the fitting dataset.

Density functional theory and global optimization study of Sn(m)Pb(n) clusters (7 ≤ m + n ≤ 12, 0 ≤ m/(m + n) ≤ 1).

The global minima of the neutral binary Sn(m)Pb(n) atomic clusters, 7 ≤ m + n ≤ 12, of all the possible stoichiometric ratios have been found using tabu search in descriptor space and density functional theory. The effects of spin-orbit coupling on optimized geometries and energies are important. All of the binary clusters form substitution alloys. Apart from the 11-atom case, the pure clusters of the same size have the same ground state geometry. The relative energies of the isomers of a cluster depend on, in order of decreasing importance: the overall geometry; the specific sites occupied by the two atom types; and the degree of segregation. The total cohesive energy difference between the lowest energy homotops is typically on the order of 0.02 eV. The mixing/segregation trends are found to be very different depending on the size of the basis set. Calculations generally overestimate the dipole moments. The trends in calculated dipole moments agree with experiment for the lead-rich clusters, and to a lesser degree, the tin-rich clusters.

Bimetallic cages.

We report the results of density functional theory for 39 clusters A(x)B(y) (x + y = 10 or 12) where A and B are metals from group 1, 2, 11, 12, 13, or 14 of the periodic table. The chemical compositions were chosen to satisfy an electronic shell closing criterion. We performed an unbiased search for the global minimum (GM) by taboo search in descriptor space in each case. Eight of the 39 putative GM are cages even though none of the clusters contains gold, a metal with a well known propensity to form cages. These cages are large enough to accommodate a dopant atom with an atomic radius varying between 0.7 Å and 1.2 Å. The chemical compositions most likely to produce cages have an element of group 11 alloyed with an element of group 2, 12, or 13.

Density functional theory guided Monte Carlo simulations: application to melting of Na13.

We present a density functional theory (DFT) based Monte Carlo simulation method in which a simple energy function gets fitted on-the-fly to DFT energies and gradients. The fitness of the energy function gets tested periodically using the classical importance function technique [R. Iftimie, D. Salahub, D. Wei, and J. Schofield, J. Chem. Phys. 113, 4852 (2000)]. The function is updated to fit the DFT energies and gradients of the most recent structures visited whenever it fails to achieve a preset accuracy. In this way, we effectively break down the problem of fitting the entire potential energy surface (PES) into many easier problems, which are to fit small local regions of the PES. We used the scaled Morse potential empirical function to guide a DFT Monte Carlo simulation of Na(13) at various temperatures. The use of empirical function guide produced a computational speed-up of about 7 in our test system without affecting the quality of the results.

catena-Poly[[[cis-aqua-dibromido-cobalt(II)]-µ-(pyrazine-2-carb-oxy-lic acid)-κN,O:N] monohydrate].

The title compound, {[CoBr(2)(C(5)H(4)N(2)O(2))(H(2)O)]·H(2)O}(n), is a one-dimensional coordination polymer which crystallizes as a monohydrate. The asymmetric unit contains one Co(II) atom in a distorted octa-hedral geometry, forming a chain parallel to [010] with the pyrazine carb-oxy-lic acid ligands coordinating on one side in a bidentate fashion through one N and one O atom, and in a monodentate fashion through a N atom, with N atoms trans, and with both ligands lying in the same plane. The bromide atoms are cis to each other, while a water mol-ecule occupies the final octa-hedral coordination site. The chains are linked together though an O-H⋯Br hydrogen bonding network, and are further stabilized by an O-H⋯Br and O-H⋯O hydrogen-bonding framework with the solvent water mol-ecule.

Using swarm intelligence for finding transition states and reaction paths.

We describe an algorithm that explores potential energy surfaces (PES) and finds approximate reaction paths and transition states. A few (≈6) evolving atomic configurations ("climbers") start near a local minimum M1 of the PES. The climbers seek a shallow ascent, low energy, path toward a saddle point S12, cross over to another valley of the PES, and climb down to a new minimum M2 that was not known beforehand. Climbers use both energy and energy derivatives to make individual decisions, and they use relative fitness to make team-based decisions. In sufficiently long runs, they keep exploring and may go through a sequence M1-S12-M2-S23-M3 ... of minima and saddle points without revisiting any of the critical points. We report results on eight small test systems that highlight advantages and disadvantages of the method. We also investigated the PES of Li(8), Al(7)(+), Ag(7), and Ag(2)NH(3) to illustrate potential applications of this new method.

Synthesis of cyclobutane nucleosides.

2-(6-Chloropurinyl)-3-benzoyloxymethylcyclobutanone can be prepared by reaction of 6-chloropurine with 3-benzoyloxymethyl-2-bromocyclobutanone. The N-alkylation gave both N-9 and N-7 regioisomers. Both regioisomers upon hydride reduction followed by aminolysis gave the corresponding adenine nucleoside analogues. However, the N-7 series led to the hypoxanthine analogues as byproducts.

Self-consistent charge equilibration method and its application to Au13Na(n) (n = 1,10) clusters.

We modified the charge equilibration method (QEq) of Rappe et al. by including the third and fourth order terms in the series expansion for the energy of charged atoms. This leads to a self-consistent scheme for obtaining charges and total energy in a molecule. We combined the modified QEq with a scaled morse potential (SMP) to get a new potential, SMP/QEq. The SMP/QEq method allows to do realistic geometry optimizations and calculate reliable charge distributions and ionization energies. The performance of SMP/QEq was fully tested by comparing to high level theories and experiments. We established a connection between first-principles DFT and SMP/QEq which gives insight into SMP/QEq and suggests ways to improve it.

Trends in Energies and Geometric Structures of Neutral and Charged Aluminum Clusters.

The minimum energy geometric structures of Aln, A[Formula: see text] , and A[Formula: see text] (4 ≤ n ≤ 15) are predicted from the results of "Tabu Search" (TS) global optimizations performed directly on the BPW91/LANL2DZ potential energy surface. In 24 of the 36 cases investigated, the TS delivered a lower energy structure than previously reported, in one case (A[Formula: see text] ) it failed to find the global minimum, and in the remaining 11 cases TS confirmed previous structures. All clusters (with 4 ≤ n ≤ 15) have the lowest spin state as their ground state except Al4 (triplet), A[Formula: see text] (quartet), A[Formula: see text] (triplet), and maybe A[Formula: see text] (singlet and triplet are degenerate). The 20-electron A[Formula: see text] and 40-electron A[Formula: see text] clusters are relatively stable compared to other clusters, on several criteria; to a lesser degree, Al7, Al12, and A[Formula: see text] are also stable.