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PubMed2002

The s-p bonded representatives of the prominent BaAl4 structure type: a case study on structural stability of polar intermetallic network structures.

This work presents a detailed, combined experimental and theoretical study on the structural stability of s-p bonded compounds with the BaAl4 structure type (space group I4/mmm, Z = 2) as part of a broad program to investigate the complex questions of structure formation and atomic arrangements in polar intermetallics. From ab initio calculations employing pseudopotentials and a plane wave basis set, we extracted optimized structural parameters, binding energies, and the electronic structure of the systems AeX(III)4, AeX(II)2X(IV)2, AeX(II)2X(III)2 (Ae = Ca, Sr, Ba; X(II) = Mg, Zn; X(III) = Al, Ga; X(IV) = Si, Ge). For all systems we found a pronounced pseudo-gap in the density of states separating network X42- bonding from antibonding electronic states that coincides with the Fermi level for an electron count of 14 electrons per formula unit, the optimum value for stable BaAl4-type polar intermetallics. However, the synthesis and structural characterization (from X-ray single crystal and powder diffraction data) of the new compounds AeZn2-Al2+, AeZn2-deltaGa2+delta (Ae = Ca, Sr, Ba; delta = 0-0.2) and AeMg0.9Al3.1, AeMg1.7Ga2.3 (Ae = Sr, Ba) manifested that electron deficiency is rather frequent for BaAl4-type polar intermetallics. The site preference for different "X" elements in the ternary systems was quantified by calculating "coloring energies", which, for some systems, was strongly dependent on the size of the electropositive Ae component. The Ae2+ cations decisively influence the nearest neighbor distances in the encapsulating polyanionic networks X4(2-) and the structures of these networks are surprisingly flexible to the size of the Ae component without changing the overall bonding picture. A monoclinically distorted variant of the BaAl4 structure occurs when the cations become too small for matching the size of encapsulating X4(2-) cages. An even larger size mismatch leads to the formation of the EuIn4 structure type.

Journal Article↗

PubMed2004

Prediction of solid solution formation in a family of diastereomeric salts. A molecular modeling study.

The possibility of solid solution behavior of diastereomeric salts, containing multiple resolving agents of the same family (Dutch Resolution), is predicted by molecular modeling. Super-cells containing different ratios of resolving agents in the diastereomeric salt are constructed and optimized, and their lattice energy is computed. The energy difference between these "simulated solid solutions" and the native structures is related in an understandable fashion to the probability of solid solution formation. This procedure is applied to a family of diastereomeric salts of ephedrine and cyclic phosphoric acids, for which the ternary diagrams have been determined experimentally at 25 degrees C in ethanol. Good agreement between experimental and computational results indicates that this relatively simple and fast method could predict the stable character of solid solution behavior in binary systems.

Journal Article↗

PubMed2004

Chemical evaluation of hypothetical uninodal zeolites.

Optimized structural parameters, framework energies relative to alpha-quartz, and volumes accessible to sorption have been calculated for the systematically enumerated hypothetical uninodal zeolitic structures (structures in which all tetrahedral sites are equivalent). The structures were treated as silica polymorphs, and their energies were minimized using the GULP program with the Sanders-Catlow silica potential. Results are given for 164 structures, which include all 21 known uninodal zeolites, two known minerals (tridymite and cristobalite), and 78 unknown zeolite topologies. Twenty-three hypothetical structures were identified as chemically feasible. Complete structural information is provided, and several structures are discussed in detail. The results will assist in the design of new synthetic routes and in the identification of newly synthesized materials.

Journal Article↗

PubMed2004

Synthesis and characterization of the non-Kekulé, singlet biradicaloid Ar'Ge(micro-NSiMe(3))(2)GeAr' (Ar' = 2,6-Dipp(2)C(6)H(3), Dipp = 2,6-i-Pr(2)C(6)H(3)).

Reaction of Ar'GeGeAr' (1) with an excess of Me3SiN3 gives the non-Kekulé, biradicaloid Ar'Ge(mu-NSiMe3)2GeAr' (3, Ar' = 2,6-Dipp2C6H3, Dipp = 2,6-i-Pr2C6H3) which has a planar Ge2N2Si2 array and pyramidal geometry at the germaniums. DFT calculations for the model MeGe(mu-NSiH3)2GeMe indicate no Ge-Ge bonding and a singlet ground state. The calculated energy difference between the optimized singlet and triplet states is 17.51 kcal/mol.

Journal Article↗

PubMed1980

Quantitative structure-activity relationships by distance geometry: systematic analysis of dihydrofolate reductase inhibitors.

Extensions are presented for the distance geometry approach to rationalizing ligand binding data. These are algorithms to (i) detect when homologues are not binding with the same orientation in the binding site although they are chemically similar; (ii) deduce what the binding site's size and shape must be; and (iii) calculate the optimal set of interaction energies between parts of the site and parts of the ligand molecules. This improved methodology is tested on a set of 68 quinazoline inhibitors of S. faecium dihydrofolate reductase. Results are discussed and compared with the Hansch method of QSAR, and an improved inhibitor is predicted.

Binding Sites↗

PubMed2005

Solvation dynamics in aqueous anionic and cationic micelle solutions: sodium alkyl sulfate and alkyltrimethylammonium bromide.

Solvation dynamics of the fluorescence probe, coumarin 102, in anionic surfactant, sodium alkyl sulfate (C(n)H(2n+1)SO(4)Na; n = 8, 10, 12, and 14), and cationic surfactant, alkyltrimethylammonium bromide (C(n)H(2n+1)N(CH(3))(3)Br; n = 10, 12, 14, and 16), micelle solutions have been investigated by a picosecond streak camera system. The solvation dynamics in the time range of 10(-10)-10(-8) s is characterized by a biexponential function. The faster solvation time constants are about 110-160 ps for both anionic and cationic micelle solutions, and the slower solvation time constants for sodium alkyl sulfate and alkyltrimethylammonium bromide micelle solutions are about 1.2-2.6 ns and 450-740 ps, respectively. Both the faster and the slower solvation times become slower with longer alkyl chain surfactant micelles. The alkyl-chain-length dependence of the solvation dynamics in both sodium alkyl sulfate and alkyltrimethylammonium bromide micelles can be attributed to the variation of the micellar surface density of the polar headgroup by the change of the alkyl chain length. The slower solvation time constants of sodium alkyl sulfate micelle solutions are about 3.5 times slower than those of alkyltrimethylammonium bromide micelle solutions for the same alkyl-chain-length surfactants. The interaction energies of the geometry optimized mimic clusters (H(2)O-C(2)H(5)SO(4)(-) and H(2)O-C(2)H(5)N(CH(3))(3)(+)) have been estimated by the density functional theory calculations to understand the interaction strengths between water and alkyl sulfate and alkyltrimethylammonium headgroups. The difference of the slower solvation time constants between sodium alkyl sulfate and alkyltrimethylammonium bromide micelle solutions arises likely from their different specific interactions.

Anions↗

PubMed2003

A molecular understanding of complementary chromatic adaptation.

Photosynthetic activity and the composition of the photosynthetic apparatus are strongly regulated by environmental conditions. Some visually dramatic changes in pigmentation of cyanobacterial cells that occur during changing nutrient and light conditions reflect marked alterations in components of the major light-harvesting complex in these organisms, the phycobilisome. As noted well over 100 years ago, the pigment composition of some cyanobacteria is very sensitive to ambient wavelengths of light; this sensitivity reflects molecular changes in polypeptide constituents of the phycobilisome. The levels of different pigmented polypeptides or phycobiliproteins that become associated with the phycobilisome are adjusted to optimize absorption of excitation energy present in the environment. This process, called complementary chromatic adaptation, is controlled by a bilin-binding photoreceptor related to phytochrome of vascular plants; however, many other regulatory elements also play a role in chromatic adaptation. My perspectives and biases on the history and significance of this process are presented in this essay.

Journal Article↗

PubMed2004

Chemically feasible hypothetical crystalline networks.

Our systematic enumeration of 4-connected crystalline networks (that is, networks in which each atom is connected to exactly four neighbours) used recent advances in tiling theory to evolve over 900 topologies. The results are relevant to the structures of zeolites and other silicates, aluminophosphates (AlPOs), oxides, nitrides, chalcogenides, halides, carbon networks, and even to polyhedral bubbles in foams. Given their importance as molecular sieves, ion exchangers, catalysts and catalyst supports, we have applied the results to microporous aluminosilicates and aluminophosphates (zeolites). Zeolite chemistry has to date produced 152 distinct types of structure. However, it was always clear that although many further structures can be synthesised, only a fraction of the mathematically generated networks would be chemically feasible (many are 'strained' frameworks requiring unrealistic bond lengths and bond angles), and that an effective 'filtering' process is needed to identify the most plausible frameworks. Here, we describe the use of computational chemistry methods to calculate optimized structural parameters, framework energies relative to alpha-quartz, volumes accessible to sorption, and X-ray diffraction patterns for systematically enumerated hypothetical 4-connected crystalline frameworks. Structures were treated as silica polymorphs with the empirical formula SiO(2), and their energies were minimized.

Crystallization↗

PubMed2006

Nano-jewellery: C5Au12--a gold-plated diamond at molecular level.

A mixed carbon-metal cluster is designed by combining the tetrahedral C(5) radical (with a central atom-the skeleton of the C(5)H(12) molecule) and the spherical Au(12) layer (the external atomic shell of the Au(13) cluster). The C(5)Au(12) cluster and its negative and positive ionic derivatives, C(5)Au(12)(+/-), are investigated ab initio (DFT) in terms of optimized structures and relative energies of a few spin-states, for the icosahedral-like and octahedral-like isomers. The cluster is predicted to be generally more stable in its octahedral shape (similar to C(5)H(12)) which prevails for the negative ion and may compete with the icosahedral shape for the neutral system and positive ion. Adiabatic ionization energies (AIE) and electron affinities (AEA) of C(5)Au(12), vertical electron-detachment (VDE) energies of C(5)Au(12)(-), and vertical ionization and electron-attachment energies (VIE, VEA) of C(5)Au(12) are calculated as well, and compared with those for the corresponding isomers of the Au(13) cluster. The AIE and VIE values are found to be close for the two systems, while the AEA and VDE values are significantly reduced for the radical-based species. A simple fragment-based model is proposed for the decomposition of the total interaction into carbon-gold and gold-gold components.

Journal Article↗

PubMed2005

First-principles study of the adsorption of cesium on Si(001)(2 x 1) surface.

First-principles calculations based on density functional theory-generalized gradient approximation method have been performed on cesium adsorption on Si(001)(2 x 1) surface. The optimized geometries and adsorption energies have been obtained and the preferred binding sites have been determined for the coverage (Theta) of one monolayer and half a monolayer. At Theta = 0.5 ML the most stable adsorption site is shown to be T3 site. At Theta = 1 ML two Cs atoms are adsorbed at HH and T3 sites, respectively. It was found that the saturation coverage of Cs for the Si(001)(2 x 1)-Cs surface is one monolayer instead of half a monolayer. This finding supports the majority of experimental observations but does not support recent coaxial impact collision ion scattering spectroscopy investigations [Surf. Sci. 531, L340 (2003)] and He(+) Rutherford backscattering spectroscopy studies [Phys. Rev. B 62, 4545 (2000)]. Mulliken charge and overlap population analysis showed that the Cs-Si bond is indeed ionic rather than polarized covalent as generally assumed for alkali metal (AM) on Si(001)(2 x 1) surface. Geometrical structure analysis seems to have limitations in determining the nature of AM-substrate bond. We also found that the silicon surface is metallic and semiconducting for the coverages of 0.5 and 1 ML, respectively.

Journal Article↗

PubMed2005

Global optimization of bimetallic cluster structures. I. Size-mismatched Ag-Cu, Ag-Ni, and Au-Cu systems.

A genetic algorithm approach is applied to the optimization of the potential energy of a wide range of binary metallic nanoclusters, Ag-Cu, Ag-Ni, Au-Cu, Ag-Pd, Ag-Au, and Pd-Pt, modeled by a semiempirical potential. The aim of this work is to single out the driving forces that make different structural motifs the most favorable at different sizes and chemical compositions. Paper I is devoted to the analysis of size-mismatched systems, namely, Ag-Cu, Ag-Ni, and Au-Cu clusters. In Ag-Cu and Ag-Ni clusters, the large size mismatch and the tendency of Ag to segregate at the surface of Cu and Ni lead to the location of core-shell polyicosahedral minimum structures. Particularly stable polyicosahedral clusters are located at size N = 34 (at the composition with 27 Ag atoms) and N = 38 (at the composition with 32 and 30 Ag atoms). In Ag-Ni clusters, Ag32Ni13 is also shown to be a good energetic configuration. For Au-Cu clusters, these core-shell polyicosahedra are less common, because size mismatch is not reinforced by a strong tendency to segregation of Au at the surface of Cu, and Au atoms are not well accommodated upon the strained polyicosahedral surface.

Journal Article↗

PubMed2006

The water exchange process of tetraaquaplatinum(II): density-functional theory and ab initio computational study.

The water exchange process of square planar tetraaquaplatinum(II) was computationally investigated at the Hartree-Fock, density-functional theory (B3LYP, PW91PW91, and mPW1PW91) and the second-order Moller-Plesset perturbation theory of levels of calculation. The stationary points on the gas phase and on the reaction field potential-energy surface were fully optimized and characterized. The self-consistent reaction field (SCRF) methods were also applied on the same system. The structures and energetic processes of all the species involved were investigated. The kinetic and thermodynamic properties for the gas phase and SCRF model data were compared with the available experimental data. The rate constants in MP2 level of theory and B3LYP isodensity polarized continuum model reaction field are in good agreement with the experimental data.

Journal Article↗

PubMed2005

Diet during pregnancy, neonatal outcomes and later health.

Renewed interest in nutrition during pregnancy has been generated by the hypothesis that adult disease has origins in early life. Animal experiments clearly show that altering maternal diet before and during pregnancy can induce permanent changes in the offspring's birth size, adult health and lifespan. Among women living in Western societies, cigarette smoking is the most important factor known to reduce fetal growth, followed by low pre-pregnancy weight and low gestational weight gain. Obesity is also associated with pregnancy complications and adverse neonatal outcomes, so inadequate or excessive energy intake is not optimal for the developing fetus. Against a history of inconsistent results, several recent studies suggest that in Western settings the balance of macronutrients in a woman's diet can influence newborn size. Effects appear to be modest, but this relationship may not encapsulate the full significance for health of the child, as there is emerging evidence of associations with long-term metabolic functioning that are independent of birth size. Consequences of inadequate maternal nutrition, for the offspring, may depend on timing during gestation, reflecting critical windows for fetal development. Where women are not malnourished, changing a woman's nutritional plane during pregnancy may be detrimental to the unborn baby, and systematic reviews of the literature on dietary supplementation during pregnancy indicate few benefits and possible risks. In view of this, improved diet before pregnancy deserves greater attention.

Animals↗

PubMed1995

Overtraining: consequences and prevention.

Overtraining refers to prolonged fatigue and reduced performance despite increased training. Its roots include muscle damage, cytokine actions, the acute phase response, improper nutrition, mood disturbances, and diverse consequences of stress hormone responses. The clinical features are varied, non-specific, anecdotal and legion. No single test is diagnostic. The best treatment is prevention, which means (1) balancing training and rest, (2) monitoring mood, fatigue, symptoms and performance, (3) reducing distress and (4) ensuring optimal nutrition, especially total energy and carbohydrate intake.

Affect↗

PubMed1996

Hyperactivity: is candy causal?

Adverse behavioral responses to ingestion of any kind of candy have been reported repeatedly in the lay press. Parents and teachers alike attribute excessive motor activity and other disruptive behaviors to candy consumption. However, anecdotal observations of this kind need to be tested scientifically before conclusions can be drawn, and criteria for interpreting diet behavior studies must be rigorous. Ingredients in nonchocolate candy (sugar, artificial food colors), components in chocolate candy (sugar, artificial food colors in coatings, caffeine), and chocolate itself have been investigated for any adverse effects on behavior. Feingold theorized that food additives (artificial colors and flavors) and natural salicylates caused hyperactivity in children and elimination of these components would result in dramatic improvement in behavior. Numerous double-blind studies of the Feingold hypothesis have led to the rejection of the idea that this elimination diet has any benefit beyond the normal placebo effect. Although sugar is widely believed by the public to cause hyperactive behavior, this has not been scientifically substantiated. Twelve double-blind, placebo-controlled studies of sugar challenges failed to provide any evidence that sugar ingestion leads to untoward behavior in children with Attention-Deficit Hyperactivity Disorder or in normal children. Likewise, none of the studies testing candy or chocolate found any negative effect of these foods on behavior. For children with behavioral problems, diet-oriented treatment does not appear to be appropriate. Rather, clinicians treating these children recommend a multidisciplinary approach. The goal of diet treatment is to ensure a balanced diet with adequate energy and nutrients for optimal growth.

Attention Deficit Disorder with Hyperactivity↗

PubMed2006

Berberine potently inhibits protein tyrosine phosphatase 1B: investigation by docking simulation and experimental validation.

Berberine was investigated as an inhibitor of human protein tyrosine phosphatase 1B (h-PTP 1B) in an attempt to explain its anti-hyperglycemic activitiy. The investigation included simulated docking experiments to fit berberine within the binding pocket of h-PTP 1B. Berberine was found to readily fit within the binding pocket of h-PTP 1B in a low energy orientation characterized with optimal electrostatic attractive interactions bridging the isoquinolinium positively charged nitrogen atom of berberine and the negatively charged acidic residue of ASP 48 of h-PTP 1B. Experimentally, berberine was found to potently competitively inhibit recombinant h-PTP 1B in vitro (Ki value = 91.3 nM). Our findings strongly suggest that h-PTP 1B inhibition is at least one of the reasons for the reported anti-hyperglycemic activities of berberine.

Berberine↗

PubMed2000

Accuracy of gamma probes in localizing radioactivity: in-vitro assessment and clinical implications.

BACKGROUND: Radioguided surgery (RGS) uses gamma probes to localize radioactive targets. We examined the in-vitro localizing properties of commercially available gamma probes for three common RGS radioisotopes: technetium-99m (99mTc), indium-111 (111In), and iodine-125 (125I). METHODS: The linear and angular localizing properties of five gamma probes were assessed. Radioactive counts in air were obtained at multiple energy threshold settings for each radioisotope. The full width half maximum (FWHM) and angular half maximum (AHM) were calculated to determine localizing accuracy. RESULTS: The FWHM of the five probes ranged from 1.2 to 3.4 cm for 99mTc, 1.8 to 2.7 cm for 111In and 1.6 to 2.8 cm for 125I. AHM of the probes ranged from 20 to 49 degrees for 99mTc, 14 to 35 degrees for 111In, and 18 to 47 degrees for 125I. The ranking of probe accuracy depended on the radioisotope studied. Absolute count rates varied with energy threshold settings for each probe and radioisotope. Probes required individualized energy threshold settings for optimal performance. CONCLUSIONS: The five probes varied in their characteristics for localizing the three radioisotopes. Each probe has particular detection characteristics that may change with different radioisotopes. Differences in radioisotope detection may explain intraoperative variation in localization during lymphatic mapping and sentinel lymph node dissection (LM/SL). Surgeons should be aware of probe performance characteristics before intraoperative use.

Gamma Rays↗

PubMed1991

Denervation of the gastric acid-producing zone by a gastric wall laser seromyotomy.

The application of various surgical laser devices offers the possibility for significant simplification of the technique of the selective denervation of a gastric acid-producing zone proposed by Tylor as the gastric wall seromyotomy. The application of laser technique results in decreased operative time, a wide range of surgical practice, less operative bleeding, and more reliable denervation. Operations performed in 38 patients provide a basis for recommending optimal parameters of laser energy for the gastric wall incision and reveal the advantages and disadvantages of different irradiation sources. Early results of of the operation are not worse than after the proximal selective vagotomy.

Duodenal Ulcer↗