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We estimated a high-resolution local gravity field model over the south pole of the Moon using data from the Gravity Recovery and Interior Laboratory's extended mission. Our solution consists of adjustments with respect to a global model expressed in spherical harmonics. The adjustments are expressed as gridded gravity anomalies with a resolution of 1/6° by 1/6° (equivalent to that of a degree and order 1080 model in spherical harmonics), covering a cap over the south pole with a radius of 40°. The gravity anomalies have been estimated from a short-arc analysis using only Ka-band range-rate (KBRR) data over the area of interest. We apply a neighbor-smoothing constraint to our solution. Our local model removes striping present in the global model; it reduces the misfit to the KBRR data and improves correlations with topography to higher degrees than current global models. Key Points We present a high-resolution gravity model of the south pole of the Moon Improved correlations with topography to higher degrees than global models Improved fits to the data and reduced striping that is present in global models

Lucina pectinata is a bivalve clam that is found in sulfide rich muds environments and lives in symbiosis with chemoautotrophic bacteria. Three different hemoglobins have been described in L. pectinata and in addition to their physiological role in the clam, are believed to be responsible for transportation hydrogen sulfide (H2S) and oxygen (O2) to a chemoautotrophic bacterial symbiont. Hemoglobin I (HbI) is a sulfide-reactive hemeprotein while Hemoglobin II (HbII) and Hemoglobin III (HbIII) are oxygen-reactive hemeproteins. Multiple sequence alignment analysis carried with L. pectinata hemoglobins and other mollusk globin sequences showed several conserved residues within this subfamily. Motif analysis using MEME also revealed a motif shared only between HbII and HbIII sequences. A phylogenetic tree was constructed the 19 molluscan globin sequences obtain after doing the CD-Hit clustering. The tree separated them into three main clusters, a cluster for the class of Pteriomorphia, another for Heteroconchi...

We produced gaseous hydrated clusters of sulfate and oxalate anions [SO 4 2– -(H 2 O) n and C 2 O 4 2– (H 2 O) n , where n = 4 to 40]. Photoelectron spectra of these clusters revealed that the solute dianions were in the center of the water cluster, (H 2 O) n . For small clusters, these spectra were characteristic of the respective solutes, but beyond the first solvation shell ( n ≈ 12), features in the spectra from the solutes were diminished and a new feature from ionization of water emerged, analogous to bulk aqueous solutions. For large clusters with dimensions greater than 1 nanometer, the solute photoemission features disappeared and the spectra were dominated by the ionization of water as the solvent coverage increased. A smooth transition from gas-phase clusters to behavior of electrolyte solutions was clearly revealed, and the large solvated clusters can be used as molecular models to investigate the photophysics and chemistry of aqueous electrolyte solutions.

In situ 13C NMR with both CAVERN and pulse−quench methods was used to understand the chemistry of acetone on the silico-aluminophosphate catalyst HSAPO-34. The isotropic shift of [2-13C]acetone shows that most of the acid sites on this catalyst are weaker than those on aluminosilicate zeolites, but a minority site was resolved with a shift higher than that on zeolite HZSM-5. At elevated temperatures, acetone dimerized to diacetone alcohol and dehydrated to mesityl oxide. Mesityl oxide cracked in the presence of water to acetic acid and isobutylene. Trimerization of butenes formed a significant amount of a persistent carbenium ion with unusual spectroscopic properties, and this is proposed to be the heptamethylcyclopentenyl cation, the first observation of a persistent carbenium ion on a SAPO catalyst. Chemical shift calculations at the GIAO-MP2 level revealed a discrepancy for one signal of the proposed cation but ruled out an alternative assignment. Methylaromatic formation coincided with cyclopentenyl c...

The effects of electron correlation are often of little importance in theoretical 1H NMR chemical shift calculations. Indeed, the differences between uncorrelated and correlated values are typically ca. 0.2 ppm or less for organic compounds. Here we demonstrate a very important case where this assumption breaks down; protons involved in strong hydrogen bonds. We found that the isotropic shifts calculated with the gauge-including atomic orbital (GIAO) approach at the RHF level overestimate the corresponding MP2 values by well over 1 ppm and commonly by 2 ppm. This is true for minimum energy geometries as well as for the transition states for proton transfer. In contrast, electron correlation effects are an order of magnitude smaller for the non-hydrogen-bonding protons in the structures we studied. The systems treated theoretically were FHF-, N2H7+, H3O2-, the enol of 2,4-pentanedione, the monoanion of cis-maleic acid, and the monoanion of dimethylmalonic acid. Geometries were calculated at either the MP2/...

Molecular dynamics (MD) simulation of the rat class 3 aldehyde dehydrogenase (ALDH) with nicotinamide dinucleotide (NAD) cofactors and explicit water molecules are reported. Our results demonstrate that MD simulation using the latest methodologies can maintain the crystal structure of the enzyme, as well as closely reproduce the short timescale dynamics of the enzyme. Furthermore, the examination of the distance between the nucleophilic Cys-243 and the NAD cofactor reveal important fluctuations that could be linked to ALDH catalysis. Finally, our quantum mechanical model of benzaldehyde in the active site of ALDH demonstrates that the enzyme requires only minor conformational changes to be poised for nucleophilic attack on the substrate.

Site-directed mutagenesis was performed in class 3 aldehyde dehydrogenase (ALDH) on both strictly conserved, non-glycine residues, Glu-333 and Phe-335. Both lie in Motif 8 and are indicated to be of central catalytic importance from their positions in the tertiary structure. In addition, a highly conserved residue at the end of Motif 8, Pro-337, and Asp-247, which interacts with the main chain of Motif 8, were also mutated. All substitutions were conservative. Kinetic values clearly show that Glu-333 and Phe-335 are crucial to efficient catalysis, along with Asp-247. Pro-337 appears to have a different role, most likely relating to folding.

Despite its ubiquity in nature, SO42− as an isolated dianion has never been detected because of its electronic instability as a result of the two negative charges. This study shows how the first few waters solvate and stabilize an isolated SO42−, molecule-by-molecule, using photodetachment spectroscopy and theoretical calculations. We find that the minimum number of water required to stabilize a free SO42− is three. The first four waters bind tightly to SO42−, each forming two H-bonds with SO42− without inter-water H-bonding. The charges of the dianion are stabilized sufficiently that additional waters form only single H-bonds with SO42− and that inter-water H-bonding is observed starting at n=5.

The measurement of the type and number of acid sites on sulfated zirconia catalysts using the 31P NMR spectrum of adsorbed P(CH3)3 has been vexed by spectral assignment controversies. Using a combination of NMR experiments and theoretical methods, including chemical shift calculations at the GIAO-MP2 level, we show that a previously observed 31P resonance at +27 ppm is due to P(CH3)4+, formed in a reaction that consumes a Bronsted site. The coproduct of this reaction, PH(CH3)2, is protonated on the surface to yield a 31P resonance in the region expected for P(CH3)3 on a Lewis site. Further complications result from a signal due to OP(CH3)3, formed by oxidizing sites on the surface, complexed to unidentified acid sites. As an alternative, we show that carefully designed 15N experiments using the less reactive and less basic probe pyridine-15N provide more easily interpreted measurements of Bronsted and Lewis sites on sulfated zirconias of diverse composition, preparation, and treatment. Quantitative studie...

The geometries and binding enthalpies of M+(benzene) complexes (M = Li, Na, K, Rb, and Cs) were obtained from large basis set second-order perturbation theory and coupled cluster theory calculations. The best ΔH298 estimates (in kcal/mol) are Li+(benzene) = −36.8 ± 0.2 (theory) vs −37.9 and −39.3 ± 3.2 (expt), Na+(benzene) = −24.7 ± 0.3 (theory) vs −28.0 ± 1.5 and −22.5 ± 1.5 (expt), K+(benzene) = −20.1 ± 0.4 (theory) vs −19.2 and −17.1 ± 0.9 (expt), Rb+(benzene) = −16.4 ± 0.2 (theory) vs −16.4 ± 0.9 (expt), and Cs+(benzene) = −12.5 ± 0.2 (theory) vs −15.1 ± 1.1 (expt). The present findings include small corrections for core/valence correlation effects and lead to binding enthalpies uniformly larger than those of previous theoretical studies.

Calixarenes are used as molecular scaffolds for the preparation of novel receptors for cations, anions, and neutral molecules. Although widely studied, the nature of the host−guest interactions within these molecules remains obscure. We present a combined density-functional theory and second-order perturbation theory study of the complexation of the alkali cations Na+ and Cs+ with tetramethoxycalix[4]arene. The results show that the host−guest interactions of this simple system are much more complex than previously thought and suggest new approaches for the design of selective cation receptors.

Photoelectron spectra of the three isomers of the benzene dicarboxylate dianion (o-, m-, and p-BDC2−) were measured in the gas phase at five photon energies. Detachment features from the carboxylate groups and the π electrons of the ring were clearly observed and distinguished. The electron binding energies were found to increase from the very small value of ∼0.2 eV in o-BDC2− to about 1.0 eV in p-BDC2−, due to the reduced Coulomb repulsion as the two excess charges become farther apart. We found that the repulsive Coulomb barrier (RCB) for detaching electrons from the carboxylates decreases from o-BDC2− to p-BDC2−. However, the RCB for detaching the ring π electrons was found to be significantly higher and remain constant for the three isomers. This distinct anisotropy in the RCB involving different detachment channels is related to the different intramolecular Coulomb repulsions experienced by electrons localized on the carboxylates and the ring. Theoretical calculations were performed to obtain the equ...

In situ 13C NMR measurements on samples prepared using a pulse-quench catalytic reactor show that the 1,3-dimethylcyclopentenyl carbenium ion (1) is an intermediate in the synthesis of toluene from ethylene on zeolite catalyst HZSM-5. Cation 1 forms in less than 0.5 s when ethylene is pulsed onto the catalyst bed at 623 K, and its presence obviates the kinetic induction period for conversion of a subsequent pulse of dimethyl ether, or methanol, into olefins (MTO chemistry). The kinetic induction period returns when the interval between pulses is many times the half-life of 1 in the catalyst bed. Density functional theory calculations (B3LYP/ 6-311G**) on a cluster model of the zeolite confirm that 1 is stable in the zeolite as a free cation and suggest why the alternative framework alkoxy is not observed. A π complex of the neutral cyclic diene is only 2.2 kcal/mol higher in energy than that of the ion pair. Theoretical (GIAO-MP2/tzp) 13C isotropic shifts of isolated 1 are in good agreement with the exper...

We present a combined photoelectron spectroscopic and theoretical study of SO4- and HSO4- and their corresponding neutral species in the gas phase. We measured very high electron affinities for SO4 and HSO4, which are 5.10(0.10) and 4.75(0.10) eV, respectively. Theoretical calculations of the neutral and anionic species using both density functional and ab initio molecular orbital theory confirm the high electron affinities of the two species. The theoretically predicted vertical and adiabatic detachment energies are in good agreement with the experimental measurements. We find that both SO4- and SO4 have C2v symmetry, whereas both HSO4- and HSO4 have Cs symmetry. We predict significant geometry changes between the equilibrium geometries of the anion species and the neutral species for both systems that are consistent with the broad nature of the measured photoelectron spectra.

The authors present optimized geometries and binding energies for alkali metal cation complexes with anisole (methoxybenzene). Results are obtained for Li{sup +} through Cs{sup +} at the RHF/6-311G* and MP2/6-311+G* levels of theory, with K{sup +}, Rb{sup +}, and Cs{sup +} represented by relativistic ECPs and associated valence basis sets. RHF/6-311G{sup {minus}} frequencies are used to verify that the optimized geometries are minima and to calculate binding enthalpies. The effects of basis set superposition error (BSSE) are estimated at both the RHF and MP2 levels. The alkali metals bind to anisole in two ways, either predominantly through interactions with the aromatic ring or with the ether oxygen. For binding to the ring, BSSE-corrected MP2/6-311+G* binding enthalpies (in kcal/mol) of {minus}38.1 (Li{sup +}), {minus}23.6 (Na{sup +}), {minus}18.3 (K{sup +}), {minus}15.4 (Rb{sup +}), and {minus}13.6 (Cs{sup +}) were obtained. The average distances (in {angstrom}) between the ring carbons and the cations are 2.33 (Li{sup +}), 2.79 (Na{sup +}), 3.20 (K{sup +}), 3.44 (Rb{sup +}), and 3.70 (Cs{sup +}). For binding to the ether oxygen, the BSSE-corrected MP2/6-311+G* binding enthalpies (in kcal/mol) are {minus}37.6 (Li{sup +}), {minus}25.2 (Na{sup +}), {minus}19.4 (K{sup +}), {minus}16.4 (Rb{sup +}), and {minus}14.3 (Cs{sup +}). The distances (in {angstrom})more » between the ether oxygen and the cations are 1.82 (Li{sup +}), 2.24 (Na{sup +}), 2.62 (K{sup +}), 2.87 (Rb{sup +}), and 3.10 (Cs{sup +}). Although the differences in binding energy between the two sites are small, the cations generally prefer to bind to the oxygen.« less

The cardiac sarcolemmal Na+/Ca2+exchanger plays a primary role in Ca2+efflux and is important in regulating intracellular Ca2+and beat-to-beat contractility. Of the three Na+/Ca2+exchanger genes cloned (NCX1, NCX2, and NCX3), only NCX1 is expressed in cardiac myocytes. NCX1 has alternative promoters for heart, kidney, and brain tissue-specific transcripts. Analysis of the cardiac NCX1 promoter (at −336 bp) identified a cardiac-specific minimum promoter (at −137) and two GATA sites (at −75 and −145). In this study, gel shift and supershift analyses identified GATA-4 in primary neonatal cardiac myocytes. Site-directed mutagenesis of the GATA-4 site at −75 abolishes binding and reduces activity of the minimum and full-length promoters by >90 and ∼60%, respectively. Mutation of the GATA site at −145 reduces activity of the full-length promoter by ∼30%. Mutation of an E-box at −175 does not alter promoter activity.

The reflectance of highly reduced ${\mathrm{SrTiO}}_{3\ensuremath{-}x}$ has been studied in samples where the carrier concentration---or oxygen-vacancy density --- varies from about ${10}^{18}$ to ${10}^{21} {\mathrm{cm}}^{\ensuremath{-}3}.$ Several phonon modes are strongly influenced by oxygen-vacancy density. Oxygen reduction induces a mid-infrared band whose oscillator strength scales with carrier density. In highly reduced samples, a weakly localized plasmon mode develops.

The authors present a combined experimental and theoretical investigation of alkali metal sulfate ion pairs and their doubly charged dimers in the gas phase: Na{sup +}SO{sub 4}{sup 2{minus}}, K{sup +}SO{sub 4}{sup 2{minus}}, (NaSO{sub 4}){sub 2}{sup 2{minus}}, (KSO{sub 4}){sub 2}{sup 2{minus}}, and NaK(SO{sub 4}){sub 2}{sup 2{minus}}. They produced these anions using an electrospray technique and measured their photoelectron spectra at three photon energies, 355, 266, and 193 nm. The photoelectron spectra of each anion exhibit two detachment features, which approximately correspond to detachment from the HOMO and HOMO-1 of the SO{sub 4}{sup 2{minus}} group perturbed by the cations. The electron binding energies of the dimer dianions are lower than those of the monomers because of the strong electron-electron repulsion in the dianions. The authors also observed the repulsive Coulomb barriers in the dianions and their effects on the photodetachment spectra. They used density functional theory and ab initio molecular orbital theory to obtain the geometric and electronic structure of the ion pairs. The calculated electron binding energies and orbital energy separations are in reasonable agreement with the experimental values. The authors found that the MSO{sub 4}{sup {minus}} ion pairs have C{sub 3v} symmetry with a C{sub 2v} structure slightly higher inmore » energy. In the dimer dianions the two alkali metal cations bridge the two SO{sub 4}{sup 2{minus}} groups.« less

We present optimized geometries and binding energies for alkali-metal cation complexes with benzene. Results are obtained for Li+ through Cs+ at the RHF/6-311G* and MP2/6-311+G* levels of theory with K+, Rb+, and Cs+ represented by relativistic ECPs and associated valence basis sets. RHF/6-311G* frequencies are used to verify the optimized geometries are minima and used to calculate binding enthalpies. The effects of basis-set superposition error (BSSE) are estimated at both the RHF and MP2 levels. We obtain BSSE-corrected MP2/6-311+G* binding enthalpies (in kcal/mol) of 35.0 (Li+), 21.0 (Na+), 16.0 (K+), 13.3 (Rb+), and 11.6 (Cs+). The distances (A) between the center of the benzene ring and the cation are 1.865 (Li+), 2.426 (Na+), 2.894 (K+), 3.165 (Rb+), and 3.414 (Cs+). Additional single-point CCSD(T)/6-311+G*//MP2/6-311+G* and CCSD(T)/6-311+G(2d,2p)//MP2/6-311+G* calculations indicate that the MP2/6-311+G* results are well converged with regard the extent of electron correlation, whereas small change...

In a previous study (Wang, L. S., Nicholas, J. B., Dupuis, M., Wu, H., and Colson, S. D., 1997, Phys. Rev. Lett., 78, 4450) of small silicon oxide clusters with stochiometry Si3Oy(y = 1-6), it was found that the molecule Si3O2 and its anion required special theoretical attention. This is due to a particular electronic structure feature of the neutral cluster: the s,p hybrid atomic orbitals of the two bonded silicon atoms give rise to a low lying empty π molecular orbital. As a result the ground state of Si3O2 has a triplet spin, and a state of singlet spin is a low lying excited electronic state at about 0.5 eV above the triplet state. Ab initio molecular orbital calculations show that photoelectron detachment proceeds from the 2B1 state of the anion to the 3B1 ground state of the neutral cluster. Detachment via the 1A1 state of the neutral cluster lies in the shoulder of the detachment via the triplet state.

Extraction experiments show that 2-benzylphenol is an efficient and selective extractant for cesium. The structures of cesium and potassium 2-benzylphenolate were determined. Both structures also contain 2-benzylphenol, which ligates the cation, through its phenolic oxygen atom and the benzyl ring. The phenolate oxygen atom does not directly contact the cation in either structure, but is a hydrogen-bond acceptor to the 2-benzylphenol ligands, forming a supramolecular assembly. For comparison to the bound ligands, the structure of 2-benzylphenol was also determined. Molecular mechanics and ab initio molecular orbital theory are used to rationalize several aspects of Cs/Na selectivity.

We calculated the chemical shift tensors for acetone and 12 complexes of acetone with Bronsted and Lewis acids. Each complex was optimized at the MP2/6-311+G* or B3LYP/DZVP2 level of theory. Chemical shift tensors were calculated with the gauge including atomic orbital (GIAO) approach at the RHF and MP2 levels of theory. We discovered a strong correlation between the MP2 and RHF 13C isotropic shifts of the carbonyl carbon in the complexes studied. Linear regression indicates that the MP2 isotropic shifts can be predicted by δMP2 = [1.12 (±0.04)]δRHF − 42.1 (±10.5) ppm (R2 = 0.9974). We were thus able to study two systems that are currently intractable at the GIAO-MP2 level. One is the complex of acetone with a large model of a zeolite, (H3SiO)3SiOHAl(OSiH3)3. The RHF shift of the carbonyl carbon of acetone on the zeolite model (238.4 ppm) is in poor agreement with the experimental (223 ppm) value. However, the MP2 result predicted by the linear correlation (224.0 ppm) is in much closer agreement. We were ...

Multiply charged anions, though ubiquitous in nature, have been difficult to produce and study in the gas phase. Photoelectron spectroscopy has been combined with an electrospray ion source to probe the repulsive Coulomb barriers, excess electron binding, and intramolecular electron-electron interactions in a series of dicarboxylate dianions, ${}^{\ensuremath{-}}{\mathrm{O}}_{2}\mathrm{C}({\mathrm{CH}}_{2}{)}_{n}{\mathrm{CO}}_{2}^{\ensuremath{-}}$ $(n\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}3--10)$. These experiments provide quantitative information about the repulsive Coulomb barriers and how the excess electron binding energy and the barrier height depend on the intramolecular Coulomb repulsion.

We present a combined density functional theory, gauge-including atomic orbital (GIAO), in situ 13C MAS NMR, and in situ infrared study of acetylene adsorption on nano-sized MgO powder. Geometries were optimized using the hybrid B3LYP exchange-correlation functional and triple-ζ basis sets. By utilizing models of the surface ranging in size from Mg4O4 to Mg8O8, we optimized geometries for a variety of surface-bound species on corner and edges sites. No stable dissociation products on the flat, (100)-like surface of an Mg12O12 cluster could be obtained theoretically, in agreement with a previous ultrahigh vacuum surface science experiment. We also present GIAO-restricted Hartree−Fock predictions of the 13C chemical shifts of all species and their vibrational frequencies. The agreement between theory and experiment is outstanding. Both the theoretical and experimental results strongly support the formation of an acetylide on the MgO surface, while an alternative vinylidene species is not present. A minority...

Tissue transglutaminase (tTgase) catalyzes the posttranslational modification of proteins by forming Ca2(+)-dependent intermolecular epsilon (gamma-glutamyl) lysine crosslinks; however, its physiological function is unclear despite increasing evidence for its involvement in the extracellular environment. To define where the enzyme is active and characterizes targets of crosslinking we have modulated tTgase expression in stably transformed Swiss 3T3 cell lines, generated by transfecting tTgase cDNA under the control of a tetracycline-regulated inducible promoter. Induced expression of tTgase enabled the detection of two pools of transglutaminase antigen, one intracellular and the other extracellular, which has a cellular distribution comparable to fibronectin. Incubation of cells with the fluorescent tTgase substrate fluorescein cadaverine indicated incorporation only in the extracellular matrix of healthy cells even though the amine was freely permeable to cells. Incorporation paralleled the deposition of fibronectin during fibril assembly when monitored by immunofluorescence. Fibronectin polymerization was confirmed by Western blotting. Cell surface-related tTgase was further demonstrated by preincubation of cells with tTgase antibody which led to inhibition of activity and cell attachment. Activation of the intracellular tTgase by increasing cytosolic Ca2+ using ionomycin resulted in cell death accompanied by extensive crosslinking in the cytoplasm, nucleus, and cell substratum contacts of induced cells. These dead cells were not typical of those undergoing apoptosis or necrosis since they remained adherent, preserved their microtubule network, and showed little DNA fragmentation. Modulation of expression of tTgase has indicated a possible physiological function for the enzyme in cell attachment, the crosslinking of fibronectin during fibril assembly, and the maintenance of cellular integrity in a novel form of cell death.

Substantial controversy surrounds the role of the isopropyl cation in the reactions of propene on acidic zeolites. Here we report new experimental and theoretical results that together provide a more detailed description of the chemistry of propene on zeolite solid acids. At cryogenic temperatures, propene is weakly bound to the Bronsted site as a π complex. Density functional theory (DFT) calculations indicate the binding energy of the π complex is only 2.6 kcal/mol, with essentially no charge transfer between the acid site and the alkene. At higher temperature, propene reacts with the acid site to form a framework-bound isopropoxyl. DFT predicts this isopropoxyl has a charge of +0.44|e|, far less than the unit positive charge of a free carbenium ion. Assignment of π complex and framework bound species is supported by the excellent agreement between experimental and theoretical 13C chemical shifts. NMR experiments indicate propene does not undergo complete label scrambling on zeolite HZSM-5, demonstrating that the isopropyl cation does not exist on this catalyst (under these conditions). In contrast, complete label scrambling does occur for isopropyl bromide on true superacids such as SbF5 and AlBr3.

Solid state NMR, calorimetry, and density functional theory (DFT) all provide a consistent interpretation of the acidity of the solid acid catalyst (SG)nAlCl2, which is prepared by reacting aluminum chloride with conditioned silica gel. These studies firmly establish that the acid sites are Bronsted in nature and that their strength is significantly greater than those in zeolites. Proton NMR results, including experiments exploiting 1H−27Al dipolar couplings, demonstrate that the Bronsted acid sites have an isotropic 1H chemical shift of 5.7 ppm and a concentration of 0.58 mmol/g. The strongest sites on this solid acid, present at 0.03 mmol/g, have −ΔHav values of 52 kcal/mol for reaction with pyridine. A value of 44 kcal/mol is maintained for incremental addition of pyridine up to 0.1 mmol/g. In comparison, −ΔHav for the strongest sites in zeolite HZSM-5 is only 42 kcal/mol. 15N magic angle spinning (MAS) NMR studies of adsorbed pyridine and 31P MAS NMR of trimethylphosphine confirm the Bronsted nature o...

Intermolecular proton transfer in the gas phase is usually strongly disfavoured because the charged products are highly unstable. It is promoted in aqueous solution, however, because the high dielectric constant (e = 78.3) of water allows efficient stabilization of the corresponding cations and anions. Zeolites—microporous catalysts used in petroleum refining and the synthesis of chemical feedstocks—provide another medium for proton-transfer reactions1,2,3, because their anionic aluminosilicate frameworks are highly acidic. The low dielectric constant of zeolites (e ≈ 1.6; ref. 3) suggests, however, that such processes in the zeolite channels should involve concerted action rather than strong charge separation, and thus resemble gas-phase reactions. Here we demonstrate that solution-like proton-transfer behaviour can be induced in zeolites. We find that the co-injection of nitromethane into a catalytic flow reactor clearly enhances the conversion of methanol, isopropanol and acetone over the zeolite catalyst HZSM-5. Conservation of nitromethane during the course of reaction and its effects on the reactant–zeolite interaction complex seen by solid-state NMR indicate that nitromethane behaves in a manner similar to polar solvents: it promotes proton transfer by stabilizing ion-pair structures. These findings suggest that rationally selected solvents might provide a simple means to increase the efficiency of these industrially important catalysts.

Ray tracing is one of the computer graphics techniques used to render high quality images. Unfortunately, the ray tracing of complex scenes can require large amounts of CPU time, making the technique impractical for everyday use. Since the ray tracing calculations that determine the values of individual pixels are independent, this appears to be an easy problem to parallelize, and parallel algorithms have been proposed. However, pixel computation times can vary significantly, and naive attempts at parallelization give poor speedup due to the load imbalance between the processors. The key to achieving high parallel efficiency is to ensure that the computational load is evenly balanced. In this paper, we propose two new load balancing schemes and evaluate their performance for ray tracing on parallel processors. We term the new methods 'local distributed control' (LDC) and 'global distributed control' (GDC). Our new strategies are complementary: GDC performs forms well for high computational complexity images and LDC works well for low computational complexity images. >

We have studied the classification of the environment of residues within protein structures. Eisenberg's original idea created environmental categories to discriminate between similar residues [Bowie et al., Science (1991), 253, 164-170]. These environments grouped residues based upon their buried surface area, polarity of the surrounding environment, and secondary structure element in which the residue is found. However, Eisenberg's original categories led to incomplete discrimination between residues that only partially substitute for each other. We have expanded on Eisenberg's original idea of environmental categories, by both considering additional contacts in the calculation of the solvent-accessible molecular surface area and by subdividing the environmental plot into regions based upon its theoretical features. Our alternative surface area calculations were used in conjunction with the polarity of the environment of the residue to define a new set of environmental categories. These new categories were able to discriminate between residues such as threonine, valine, and aspartic acid while reflecting the propensity of these residues to substitute for each other.

We studied the structure and bonding of a series of silicon oxide clusters, ${\mathrm{Si}}_{3}{\mathrm{O}}_{y}$ $(y\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}1--6)$, using anion photoelectron spectroscopy and ab initio calculations. For $y\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}1--3$ the clusters represent the sequential oxidation of ${\mathrm{Si}}_{3}$, and provide structural models for the oxidation of silicon surfaces. For $y\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}4--6$, the clusters contain a central Si in a tetrahedral bonding environment, suggesting the onset of the bulklike structure. Evidence is presented that suggests the ${\mathrm{Si}}_{3}{\mathrm{O}}_{4}$ cluster $({D}_{2d})$ may provide a structural model for oxygen-deficient defect sites in bulk ${\mathrm{SiO}}_{2}$ materials.

We report the principal components of the 13C chemical shift tensors for seven acylium ions, determined by both slow speed magic angle spinning (MAS) nuclear magnetic resonance (NMR) and theoretical methods. Experimentally, the acylium ions were prepared either by direct reaction of the parent acyl halides with metal halide powders, including frozen antimony pentafluoride, or by the reaction of alkyl halides with carbon monoxide on aluminum chloride (AlCl3). The generalization of our recent observation of the acetylium ion on AlCl3 to other cations is direct proof of free acylium ion intermediates in Friedel−Crafts acylation reactions. 13C CP MAS NMR spectra of the acylium ions were acquired at temperatures ranging from 83 to 298 K, and the principal components of the 13C chemical shift tensors were extracted by fitting the side band intensities of the MAS spectra. With the exception of the chloroacetylium ion, the acylium ions studied have isotropic 13C1 chemical shifts of 154 ± 1 ppm, but clear variatio...

In this paper we present an ab initio periodic Hartree−Fock study of the electronic structure zeolite NaCaA. A model system of composition Ca8Na8Si24Al24O96 is produced, with F43c symmetry and strict alternate ordering of silicon and aluminum. The positions of the Na and Ca cations were optimized using the RHF/STO-3G level of theory. Properties of the crystal, such as the partial charges and bond populations, the electrostatic potential, and the electric field within the zeolite cage, were calculated at the more accurate RHF/6-21G* level of theory. Results indicate that the cations are situated slightly above the 6-ring units, in agreement with recent experimental X-ray crystallographic studies. The calculated RHF/6-21G* field of the zeolite is negligible in the center of both the α- and β-cage, but rises quickly close to the cation centers.

We have implemented exhaustive genetic sequence alignment codes on a variety of high performance computers. In this article, we compare and contrast the implementation issues encountered on different high performance computer architecture and the approaches used to overcome these problems. In addition, we discuss advanced sequence alignment techniques, including context sensitive and multiple sequence alignments.

Objective: Estimated glomerular filtration rate (eGFR), a measure of kidney function, is heritable, suggesting that genes influence renal function. Genes that influence eGFR have been identified through genome-wide association studies. However, family-based linkage approaches may identify loci that explain a larger proportion of the heritability. This study used genome-wide linkage and association scans to identify quantitative trait loci (QTL) that influence eGFR. Methods: Genome-wide linkage and sparse association scans of eGFR were performed in families ascertained by probands with advanced diabetic nephropathy (DN) from the multi-ethnic Family Investigation of Nephropathy and Diabetes (FIND) study. This study included 954 African Americans (AA), 781 American Indians (AI), 614 European Americans (EA) and 1,611 Mexican Americans (MA). A total of 3,960 FIND participants were genotyped for 6,000 single nucleotide polymorphisms (SNPs) using the Illumina Linkage IVb panel. GFR was estimated by the Modification of Diet in Renal Disease (MDRD) formula. Results: The non-parametric linkage analysis, accounting for the effects of diabetes duration and BMI, identified the strongest evidence for linkage of eGFR on chromosome 20q11 (log of the odds [LOD] = 3.34; P = 4.4×10-5) in MA and chromosome 15q12 (LOD = 2.84; P = 1.5×10-4) in EA. In all subjects, the strongest linkage signal for eGFR was detected on chromosome 10p12 (P = 5.5×10-4) at 44 cM near marker rs1339048. A subsequent association scan in both ancestry-specific groups and the entire population identified several SNPs significantly associated with eGFR across the genome. Conclusion: The present study describes the localization of QTL influencing eGFR on 20q11 in MA, 15q21 in EA and 10p12 in the combined ethnic groups participating in the FIND study. Identification of causal genes/variants influencing eGFR, within these linkage and association loci, will open new avenues for functional analyses and development of novel diagnostic markers for DN. © 2013 Thameem et al.

Background. Tubulo-interstitial nephropathy (TIN) is a common cause of chronic kidney disease (CKD). Consumption of an adenine-containing diet causes the accumulation of 2,8-dihydroxyadenine in the renal tubules triggering intense chronic TIN and progressive CKD in rats. CKD in this model is associated with, and largely driven by, oxidative stress and inflammation. Oxidative stress and inflammation in rats with spontaneous focal segmental glomerulosclerosis and rats with CKD induced by 5/6 nephrectomy are associated with an impaired activation of nuclear factor-erythroid-2-related factor 2 (Nrf2) which is the master regulator of genes encoding many antioxidant and detoxifying enzymes. The effect of TIN on the Nrf2 pathway and its key target genes is unknown and was investigated here. Methods. Sprague-Dawley rats were randomized to control and adenine-treated (rat chow-containing 0.7% adenine for 2 weeks) groups and followed up for 4 weeks. Results. The adenine-treated animals exhibited marked azotemia, impaired urinary concentrating capacity, intense tubular and glomerular damage, interstitial inflammation and fibrosis. This was associated with an increased expression of NAD(P)H oxidase, cyclooxygenase-2 and 12-lipoxygenase, and activation of NF-κB, the master regulator of pro-inflammatory cytokines and chemokines. Oxidative stress and inflammation in the kidneys of adenine-treated animals was accompanied by an impaired activation of Nrf2 and down-regulation of its target gene products including, catalase, heme oxygenase-1 and glutamate-cysteine ligase. Conclusions. Chronic TIN is associated with impaired Nrf2 activity which contributes to the pathogenesis of oxidative stress and inflammation and amplifies their damaging effects on the kidney. © The Author 2012.

Purpose of review Persons with chronic kidney disease (CKD) exhibit a disproportionate burden of elevated blood pressure (BP) with a high prevalence of premature end-stage renal disease and cardiovascular events. Recent findings Results of recent randomized controlled clinical trials suggest that most patients with reduced estimated glomerular filtration rate (eGFR) and hypertension experience optimal clinical outcomes when SBP is less than 140 mmHg and DBP is less than 90 mmHg. The benefit of additional lowering of SBP to less than 130 mmHg and DBP to less than 80 mmHg remains controversial, and appears to be of most benefit to the subset of CKD patients with proteinuria (>300 mg/day). The combination of a diuretic and an angiotensin receptor blocker (ARB) or angiotensin-converting enzyme inhibitor (ACEI) has demonstrated particular promise in patients with reduced eGFR and proteinuria. Summary A practical approach in clinical practice for the treatment of elevated BP in persons with CKD is to achieve a BP less than 140/90 mmHg with a combination of diuretic and an ARB or ACEI. Consideration for a lower BP goal and other therapeutic and nontherapeutic interventions can be made based on the cause of CKD, presence of proteinuria, or other coexisting medical conditions.

This paper describes the design of a patient-specific, radiotherapy quality assurance target that can be used to verify a treatment plan by measurement of actual dosage. Staring from a patient's (segmented) MR images, a physical model containing insertable cartridges for holding dosimeters is printed in 3D. Dosimeters can be located at specific locations of interest (e.g., tumor, nerve bundles, urethra). The model (dosimeter insert) can be placed into a pelvis 'shell' and subject to a specified treatment plan. A design for the dosimeter insert can be efficiently fabricated using rapid prototyping techniques.

This paper describes the development of a procedure to generate patient-specific, three-dimensional (3D) solid models of prostates (and related anatomy) from magnetic resonance (MR) images. The 3D models are rendered in STL file format which can be physically printed or visualized on a holographic display system. An example is presented in which a 3D model is printed following this procedure.

Silica sodalite is an ideal model system to establish base-line computer requirements of ab initio periodic Hartree-Fock (PHF) calculations of zeolites. In this article, the authors investigate the effect of various basis sets on the structural and electronic properties of bulk silica sodalite. They also study the interaction of He, Ne, and Ar with the sodalite cage. This work shows that basis-set superposition errors (BSSE) in calculations using STO-3G and 6-21G(*) basis sets are as large as the interaction energies, leading to poor confidence in the results. To cure this problem, the authors present high-quality basis sets for si, O, He, Ne, and Ar, optimized for use with PHF methods, and demonstrate that the new basis set greatly reduces BSSE. The theoretical barriers for transfer of the rare gases between sodalite cages are 5.6, 13.2, and 62.1 kcal/mol for He, Ne, and Ar. 27 refs., 6 figs., 8 tabs.

Random RNA libraries, consisting of > 10(13) unique sequences, contain molecules capable of specifically binding small molecule and protein ligands by noncovalent interaction. Successive steps of affinity purification and amplification allow the propagation and eventual isolation of specific binding molecules, called aptamers. Although protein- and small-molecule-binding aptamers have been characterized previously, selection of RNA aptamers capable of binding nucleic acids has previously yielded only molecules capable of Watson-Crick base pairing to the nucleic acid ligand used for selection. On the other hand, it is known from studies on catalytic and other RNAs that both inter- and intramolecular RNA-RNA interaction can occur by non-Watson-Crick means. We have therefore incorporated a strategy to obviate the possibility of Watson-Crick interaction into a selection scheme for the isolation of RNA-recognizing aptamers. The aptamers so isolated do not show extensive Watson-Crick complementarity with the RNA ligand used for the selection, thereby validating the selection strategy. Curiously, all of the aptamers characterized contain several oligo-G stretches bounded by U residues. This sequence motif, which occurs as DNA in telomeres (chromosome ends) may therefore be a general RNA-RNA interaction motif. An additional sequence motif is apparently superimposed on this background structure.

We present a study of transition state optimization with the divide‐and‐conquer (DC) density functional theory (DFT) method, using the addition of HF to trans‐2‐butene as an example. We present relative energies and geometries for each state in the reaction. We show that the DC method gives results that agree well with those obtained by conventional Kohn–Sham DFT methods, using the same exchange‐correlation functional and basis set.

A pairwise additive potential energy expression for the water/MgO interaction was obtained by fitting the parameters to ab initio electronic structure energy data, computed using correlation-corrected periodic Hartree−Fock (PHF) theory, at selected adsorbate/surface geometries. This potential energy expression was used in molecular dynamics and Monte Carlo simulations to elucidate the water/MgO interaction. Energy minimization reveals a nearly planar adsorbate/surface equilibrium geometry (−15° from the surface plane with the hydrogens pointing toward the surface oxygens) for an isolated water on perfect MgO (001), with a binding energy of 17.5 kcal/mol; subsequent PHF calculations on this system confirmed that this is a potential minimum. Rate constants for desorption (kdsorb), intersite hopping (khop), intrasite rotation (krot), and intrasite flipping (kflip) were estimated for an isolated water on the surface using simple transition state theory. The computed rates (at T = 300 K) are kdsorb = 1.1 × 105...

The proton and water affinities of the Li+ cation are predicted from ab initio molecular orbital theory using Gaussian 90 and Gaussian 92. These calculations were undertaken in order to understand the role that the hydrated Li+ cation has in controlling acidity within the clay interlayers. Proton affinities for hydrated Li(OH) complexes increase with increasing degree of hydration but level off above two waters. This results in the highest acidity for the Li+ complex with fewer than two waters of hydration. Acidity is controlled by the effective charge on the Li+ cation. Stabilization of the charge by associated water molecules contributes to the reduced acidity at higher hydration numbers. Implication of a tight, inner sphere coordination complex is suggested from the calculations. The calculations imply that acidity in Li+ clays is relatively independent of the degree of hydration. Comparison with experimentally-derived hydration data for smectite clays reveals that sufficient water exists within the cl...

Both basic science and clinical studies support the concept that vitamin D deficiency is involved in the pathogenesis of cardiovascular and renal diseases through its association with diabetes, obesity, and hypertension. Understanding the underlying mechanisms may provide a rationale for advocating adequate intake of vitamin D and calcium in all populations, thereby preventing many chronic diseases. This review explores the effect of vitamin D deficiency in the development of cardiovascular and renal diseases, and the role of vitamin D supplementation on cardiovascular outcomes. In addition, it highlights the importance of vitamin D intake for the prevention of adverse long-term health consequences, and in ways to facilitate the management of cardiovascular disease. This is particularly true for African American and postmenopausal women, who are at added risk for cardiovascular disease. We suggest that the negative cardiovascular effects of low vitamin D in postmenopausal women could be improved by a combined treatment of vitamin D and sex steroids acting through endothelium-dependent and/or -independent mechanisms, resulting in the generation of nitric oxide and calcitonin gene-related peptide (CGRP).

We studied the structure of disiloxane (H3Si–O–SiH3), silanol (H3Si–OH), and the silanol anion (H3Si–O−) with ab initio molecular orbital theory and the correlation consistent polarized basis sets of Dunning and co‐workers. We present results for the correlation consistent polarized valence double zeta (cc‐pVDZ), triple zeta (cc‐pVTZ), and quadruple zeta [cc‐pVQZ(‐g)] basis sets. Optimized geometries and energies are given at both the restricted Hartree–Fock (RHF) level and with the inclusion of electron correlation by second order Mo/ller–Plesset perturbation theory (MP2). The correlation consistent basis sets provide a systematic expansion of the orbital basis set, with each set of additional functions adding a similar contribution to the correlation energy. We find that the calculated molecular properties show exponential convergence with increasing basis set size. These calculations answer long‐standing questions regarding the structure and barrier to linearization of disiloxane. Results at the highes...