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Size-specific reactions of copper cluster ions with a methanol molecule.

Chemisorption of a methanol molecule onto a size-selected copper cluster ion, Cu(n)+ (n = 2-10), and subsequent reactions were investigated in a gas-beam geometry at a collision energy less than 2 eV in an apparatus based on a tandem-type mass spectrometer. Mass spectra of the product ions show that the following two reactions occur after chemisorption: dominant formation of Cu(n-1)+(H)(OH) (H(OH) formation) in the size range of 4-5 and that of Cu(n)O+ (demethanation) in the size range of 6-8 in addition to only chemisorption in the size range larger than 9. Absolute cross sections for the chemisorption, the H(OH) formation, and the demethanation processes were measured as functions of cluster size and collision energy. Optimized structures of bare copper cluster ions, reaction intermediates, and products were calculated by use of a hybrid method (B3LYP) consisting of the molecular orbital and the density functional methods. The origin of the size-dependent reactivity was explained as the structural change of cluster, two-dimensional to three-dimensional structures.

Journal Article↗

Methanol adsorption on the beta-Ga2O3 surface with oxygen vacancies: theoretical and experimental approach.

Methanol adsorption on beta-Ga2O3 surface has been studied by Fourier transform infrared spectroscopy (FTIR) and by means of density functional theory (DFT) cluster model calculations. Adsorption sites of tetrahedral and octahedral gallium ions with different numbers of oxygen vacancies have been compared. The electronic properties of the adsorbed molecules have been monitored by computing adsorption energies, optimized geometry parameters, overlap populations, atomic charges, and vibrational frequencies. The gallia-methanol interaction has different behaviors according to the local surface chemical composition. The calculations show that methanol can react in three different ways with the gallia surface giving rise to a nondissociative adsorption, a dissociative adsorption, and an oxidative decomposition. The surface without oxygen vacancies is very reactive and produces the methanol molecule decomposition. The molecule is nondissociatively adsorbed by means of a hydrogen bond between the alcoholic hydrogen atom and a surface oxygen atom and a bond between the alcoholic oxygen atom and a surface gallium atom. Two neighbor oxygen vacancies on tetrahedral gallium sites produce the dissociation of the methanol molecule and the formation of a bridge bond between two surface gallium atoms and the methoxy group.

Journal Article↗

Single crystals of L-O-serine phosphate X-irradiated at low temperatures: EPR, ENDOR, EIE, and DFT studies.

Single crystals of the phosphorylated amino acid L-O-serine phosphate were X-irradiated and studied at 10 K and at 77 K using EPR, ENDOR, and EIE techniques. Two radicals, R1(10 K) and R1(77 K), were detected and characterized as two different geometrical conformations of the protonated reduction product >CH-C(OH)(2). R1(10 K) is only observed after irradiation at 10 K, and upon heating to 40 K, R1(10 K) transforms rapidly and irreversibly into R1(77 K). The transition from R1(10 K) to R1(77 K) strongly increases the isotropic hyperfine coupling of the C-CH(beta) coupling (Delta = 32 MHz) and the major C-OH(beta) coupling (Delta = 47 MHz), in sharp contrast to the their much reduced anisotropic hyperfine couplings after the transition. An umbrella-like inversion of the carboxylic acid center, accompanied by minor geometrical adjustments, explains the changes of these observed isotropic and anisotropic couplings. DFT calculations were done on the reduced and protonated L-O-serine phosphate radical at the B3LYP/6-311+G(2df,p)//B3LYP/6-31+G(d) level of theory in order to support the experimental observations. Two different conformations of the anion radical, related by an inversion at the carboxylic center, could be found within the single molecule partial energy-optimization scheme. These two conformations reproduce the experimental hyperfine couplings from radicals R1(10 K) and R1(77 K). A third radical, radical R2, was observed experimentally at both 10 and 77 K and was shown to be due to the decarboxylated L-O-serine phosphate oxidation product, a conclusion fully supported from the DFT calculations. Upon thermal annealing from 77 to 295 K, radicals R1(77 K) and R2 disappeared and all three previously observed room-temperature radicals could be observed. No phosphate-centered radicals could be observed at any temperatures, indicating that the phosphate-ester bond break for one of the room-temperature radicals does not occur by dissociative electron capture at the phosphate group.

Alanine↗

A homology model for rat mu class glutathione S-transferase 4-4.

Glutathione S-transferases (GSTs) are an important class of phase II (de)toxifying enzymes, catalyzing the conjugation of glutathione (GSH) to electrophilic species. Recently, a number of cytosolic GSTs was crystallized. In the present study, molecular modeling techniques have been used to derive a three-dimensional homology model for rat GST 4-4 based upon the crystal structure of rat GST 3-3, both members of the mu class. GST 3-3 and GST 4-4 isoenzymes share a sequence homology of 88%. GST 4-4 distinguishes itself from GST 3-3 in being much more efficient and stereoselective in the nucleophilic addition of GSH to epoxides and alpha,beta-unsaturated ketones. GST 3-3, however, is much more efficient in catalyzing nucleophilic aromatic substitution reactions. In this study, several known substrates of GST 4-4 were selected and their GSH conjugates docked into the active site of GST 4-4. GSH conjugates of phenanthrene 9(S),10(R)-oxide and 4,5-diazaphenanthrene 9(S),10(R)-oxide were docked into the active site of both GST 3-3 and GST 4-4. From these homology modeling and docking data, the difference in stereoselectivity between GST 3-3 and GST 4-4 for the R- and S-configured carbons of the oxirane moiety could be rationalized. The data acquired from a recently derived small molecule model for GST 4-4 substrates were compared with the results of the present protein homology model of GST 4-4. The energy optimized positions of the conjugates in the protein model agreed very well with the original relative positions of the substrates within the substrate model, confirming the usefulness of small molecule models in the absence of structural protein data. The protein homology model, together with the substrate model, will be useful to further rationalize the substrate selectivity of GST 4-4, and to identify new potential GST 4-4 substrates.

Amino Acid Sequence↗

A three-dimensional protein model for human cytochrome P450 2D6 based on the crystal structures of P450 101, P450 102, and P450 108.

Cytochromes P450 (P450s) constitute a superfamily of phase I enzymes capable of oxidizing and reducing various substrates. P450 2D6 is a polymorphic enzyme, which is absent in 5-9% of the Caucasian population as a result of a recessive inheritance of gene mutations. This deficiency leads to impaired metabolism of a variety of drugs. All drugs metabolized by P450 2D6 contain a basic nitrogen atom, and a flat hydrophobic region coplanar to the oxidation site which is either 5 or 7 A away from the basic nitrogen atom. The aim of this study was to build a three-dimensional structure for the protein and more specifically for the active site of P450 2D6 in order to determine the amino acid residues possibly responsible for binding and/ or catalytic activity. Furthermore, the structural features of the active site can be implemented into the existing small molecule substrate model, thus enhancing its predictive value with respect to possible metabolism by P450 2D6. As no crystal structures are yet available for membrane-bound P450s (such as P450 2D6), the crystal structures of bacterial (soluble) P450 101 (P450cam), P450 102 (P450BM3), and P450 108 (P450terp) have been used to build a three-dimensional model for P450 2D6 with molecular modeling techniques. Several important P450 2D6 substrates were consecutively docked into the active site of the protein model. The energy optimized positions of the substrates in the protein agreed well with the original relative positions of the substrates within the substrate model. This confirms the usefulness of small molecule models in the absence of structural protein data. Furthermore, the derived protein model indicates new leads for experimental validation and extension of the substrate model.

Amino Acid Sequence↗

Controlled radiofrequency endotubal sterilization.

STUDY OBJECTIVE: A safe, effective, inexpensive method of transcervical tubal sterilization could have a major impact on women's health. In this study, we evaluated the efficacy of a new radiofrequency catheter prototype designed for endotubal sterilization using animal models. SETTING: Animal research laboratory. DESIGN: Prospective observational study. METHOD: The optimal energy delivery to create a complete circumferential transmural thermal lesion in the tube was determined in 114 in vitro acute studies using porcine and bovine fallopian tubes. A study was then initiated with eight mini-pigs. Thirty-four lesions were made in the fallopian tubes using computer-controlled power delivery. Three weeks later the animals were euthanized and evaluated. MEASUREMENTS AND MAIN RESULTS: A hydrosalpinx was evident in 8/11 of the tubes with separate proximal and distal cautery, implying occlusion at each of these sites. Complete occlusion of the tubes was seen at 12/22 sites evaluated by histology. Narrowing was seen in 9/22, and 1/22 was open. CONCLUSION: The endotubal cautery prototype creates a reproducible lesion, but did not always cause complete closure of the tube in this preliminary study. However, based on our results, we hypothesize that a radiofrequency catheter can be developed for minimally invasive transcervical sterilization.

Animals↗

Symbiosis insights through metagenomic analysis of a microbial consortium.

Symbioses between bacteria and eukaryotes are ubiquitous, yet our understanding of the interactions driving these associations is hampered by our inability to cultivate most host-associated microbes. Here we use a metagenomic approach to describe four co-occurring symbionts from the marine oligochaete Olavius algarvensis, a worm lacking a mouth, gut and nephridia. Shotgun sequencing and metabolic pathway reconstruction revealed that the symbionts are sulphur-oxidizing and sulphate-reducing bacteria, all of which are capable of carbon fixation, thus providing the host with multiple sources of nutrition. Molecular evidence for the uptake and recycling of worm waste products by the symbionts suggests how the worm could eliminate its excretory system, an adaptation unique among annelid worms. We propose a model that describes how the versatile metabolism within this symbiotic consortium provides the host with an optimal energy supply as it shuttles between the upper oxic and lower anoxic coastal sediments that it inhabits.

Animals↗

The telomeres of Streptomyces chromosomes contain conserved palindromic sequences with potential to form complex secondary structures.

The chromosomes of the gram-positive soil bacteria Streptomyces are linear DNA molecules, usually of about 8Mb, containing a centrally located origin of replication and covalently bound terminal proteins (which are presumably involved in the completion of replication of the telomeres). The ends of the chromosomes contain inverted repeats of variable lengths. The terminal segments of five Streptomyces chromosomes and plasmids were cloned and sequenced. The sequences showed a high degree of conservation in the first 166-168bp. Beyond the terminal homology, the sequences diverged and did not generally cross-hybridize. The homologous regions contained seven palindromes with a few nucleotide differences. Many of these differences occur in complementary pairs, such that the palindromicity is preserved. Energy-optimized modelling predicted that the 3' strand of the terminal palindromes can form extensive hairpin structures that are similar to the 3' ends of autonomous parvovirus genomes. Most of the putative hairpins have a GCGCAGC sequence at the loop, with the potential to form a stable single C-residue loop closed by a sheared G:A pairing. The similarity between the terminal structures of the Streptomyces replicons and the autonomous parvoviral genomes suggests that they may share some structural and/or replication features.

Base Sequence↗

Efficacy of low level laser therapy in reducing postoperative pain after endodontic surgery-- a randomized double blind clinical study.

The aim of the study was to evaluate the effect of low level laser application on postoperative pain after endodontic surgery in a double blind, randomized clinical study. Fifty-two healthy adults undergoing endodontic surgery were included into the study. Subsequently to suturing, 26 patients had the operation site treated with an 809 nm-GaAlAs-laser (oralaser voxx, Oralia GmbH, Konstanz, Germany) at a power output of 50 mW and an irradiation time of 150 s. Laser treatment was simulated in further 26 patients. Patients were instructed to evaluate their postoperative pain on 7 days after surgery by means of a visual analogue scale (VAS). The results revealed that the pain level in the laser group was lower than in the placebo group throughout the 7 day follow-up period. The differences, however, were significant only on the first postoperative day (Mann-Whitney U-test, p<0.05). Low level laser therapy can be beneficial for the reduction of postoperative pain. Its clinical efficiency and applicability with regard to endodontic surgery, however require further investigation. This is in particular true for the optimal energy dosage and the number of laser treatments needed after surgery.

Adult↗

Density-functional and electron correlated study of five linear birefringences--Kerr, Cotton-Mouton, Buckingham, Jones, and magnetoelectric--in gaseous benzene.

We present the results of an extended study of five birefringences--Kerr, Cotton-Mouton, Buckingham, Jones, and Magnetoelectric--on benzene in the gas phase. The relevant molecular quantities--first-order properties, linear, quadratic, and cubic response functions--are computed employing the density-functional theory (DFT) response theory, with a choice of functionals. In some cases, different functionals are employed for the wave-function computational step and for the subsequent analytical response calculation to determine the combination yielding at the same time the optimal energy and energy derivative results. Augmented correlation consistent basis sets of double and triple zeta quality are used. The DFT results are compared to those obtained at the Hartree-Fock level and in some cases within a coupled cluster singles and doubles electronic structure model. The study tries to assess the ability of the DFT response theory to describe a wide range of properties in a system of rather large size and high complexity. The relative strength of the five birefringences for plausible experimental conditions is determined and, when possible, comparison is made with the results of the measurements.

Journal Article↗

Exploration of NVE classical trajectories as a tool for molecular crystal structure prediction, with tests on ice polymorphs.

Following an initial Communication [Buch et al., J. Chem. Phys. 123, 051108 (2005)], a new molecular-dynamics-based approach is explored to search for candidate crystal structures of molecular solids corresponding to minima of the enthalpy. The approach is based on the observation of phase transitions in an artificial periodic system with a small unit cell and relies on the existence of an optimal energy range for observing freezing to low-lying minima in the course of classical trajectories. Tests are carried out for O structures of nine H2O-ice polymorphs. NVE trajectories for a range of preimposed box shapes display freezing to the different crystal polymorphs whenever the box dimensions approximate roughly the appropriate unit cell; the exception is ice II for which freezing requires unit cell dimensions close to the correct ones. In an alternate version of the algorithm, an initial box shape is picked at random and subsequently readjusted at short trajectory intervals by enthalpy minimization. Tests reveal the existence of ice forms which are "difficult" and "easy" to locate in this way. The former include ice IV, which is also difficult to crystallize experimentally from the liquid, and ice II, which does not interface with the liquid in the phase diagram. On the other hand, the latter crystal search procedure located successfully the remaining seven ice polymorphs, including ice V, which corresponds to the most complicated structure of all ice phases, with a monoclinic cell of 28 molecules.

Journal Article↗

Adsorption geometry and core excitation spectra of three phenylpropene isomers on Cu(111).

Theoretical C 1s near edge x-ray absorption fine structure (NEXAFS) spectra for the C(9)H(10) isomers trans-methylstyrene, alpha-methylstyrene, and allylbenzene in gas phase and adsorbed at Cu(111) surfaces have been obtained from density functional theory calculations where adsorbate geometries were determined by corresponding total energy optimizations. The three species show characteristic differences in widths and peak shapes of the lowest C 1s-->pi(*) transitions which are explained by different coupling of the pi-electron system of the C(6) ring with that of the side chain in the molecules as well as by the existence of nonequivalent carbon centers. The adsorbed molecules bind only weakly with the substrate which makes the use of theoretical NEXAFS spectra of the oriented free molecules meaningful for an interpretation of experimental angle-resolved NEXAFS spectra of the adsorbate systems obtained in this work. However, a detailed quantitative account of relative peak intensities requires theoretical angle-resolved NEXAFS spectra of the complete adsorbate systems which have been evaluated within the surface cluster approach. The comparison with experiment yields almost perfect agreement and confirms the reliability of the calculated equilibrium geometries of the adsorbates. This can help to explain observed differences in the catalytic epoxidation of the three molecules on Cu(111) based on purely geometric considerations.

Journal Article↗

Coupling the folding of homologous proteins.

The empirical observation that homologous proteins fold to similar structures is used to enhance the capabilities of an ab initio algorithm to predict protein conformations. A penalty function that forces homologous proteins to look alike is added to the potential and is employed in the coupled energy optimization of several homologous proteins. Significant improvement in the quality of the computed structures (as compared with the computational folding of a single protein) is demonstrated and discussed.

Amino Acid Sequence↗

The evolution of endothermy and its diversity in mammals and birds.

Many elements of mammalian and avian thermoregulatory mechanisms are present in reptiles, and the changes involved in the transition to endothermy are more quantitative than qualitative. Drawing on our experience with reptiles and echidnas, we comment on that transition and on current theories about how it occurred. The theories divide into two categories, depending on whether selection pressures operated directly or indirectly on mechanisms producing heat. Both categories of theories focus on explaining the evolution of homeothermic endothermy but ignore heterothermy. However, noting that hibernation and torpor are almost certainly plesiomorphic (=ancestral, primitive), and that heterothermy is very common among endotherms, we propose that homeothermic endothermy evolved via heterothermy, with the earliest protoendotherms being facultatively endothermic and retaining their ectothermic capacity for "constitutional eurythermy." Thus, unlike current models for the evolution of endothermy that assume that hibernation and torpor are specialisations arising from homeothermic ancestry, and therefore irrelevant, we consider that they are central. We note the sophistication of thermoregulatory behavior and control in reptiles, including precise control over conductance, and argue that brooding endothermy seen in some otherwise ectothermic Boidae suggests an incipient capacity for facultative endothermy in reptiles. We suggest that the earliest insulation in protoendotherms may have been internal, arising from redistribution of the fat bodies that are typical of reptiles. We note that short-beaked echidnas provide a useful living model of what an (advanced) protoendotherm may have been like. Echidnas have the advantages of endothermy, including the capacity for homeothermic endothermy during incubation, but are very relaxed in their thermoregulatory precision and minimise energetic costs by using ectothermy facultatively when entering short- or long-term torpor. They also have a substantial layer of internal dorsal insulation. We favor theories about the evolution of endothermy that invoke direct selection for the benefits conferred by warmth, such as expanding daily activity into the night, higher capacities for sustained activity, higher digestion rates, climatic range expansion, and, not unrelated, control over incubation temperature and the benefits for parental care. We present an indicative, stepwise schema in which observed patterns of body temperature are a consequence of selection pressures, the underlying mechanisms, and energy optimization, and in which homeothermy results when it is energetically desirable rather than as the logical endpoint.

Adaptation, Physiological↗

A controlled comparison of three very-low-calorie diets: effects on weight, body composition, and symptoms.

To determine the optimal energy intake of very-low-calorie diets (VLCDs), 76 obese women were randomly assigned, in a double-blind fashion, to one of three liquid-formula diets: 1758 kJ/d (420 kcal/d), 2763 kJ/d (660 kcal/d), or 3349 kJ/d (800 kcal/d). Weight, body composition, symptoms, mood, and acceptability of the diet were assessed throughout the 6-mo study. There were no significant differences in weight losses or changes in body composition among the three dietary conditions at the end of treatment, nor were there significant differences among conditions in acceptability of the diet, symptoms, or mood. These results suggest that there is no clinical advantage to using VLCDs that provide less than 3349 kJ/d (800 kcal/d).

Adult↗

A simple point score system for predicting the efficacy of external rectilinear biphasic cardioversion for persistent atrial fibrillation.

AIMS: To develop a simple point score system that can accurately predict the optimal energy of initial rectilinear biphasic (RLB) waveform shock for cardioversion (DC) of persistent atrial fibrillation (AF). METHODS AND RESULTS: Data from 302 consecutive patients with AF who underwent a step-up protocol of sequential shocks of 50 J-from 1 up to 2 J/kg-200 J of RLB waveform DC were prospectively examined. Using a logistic regression model, three variables independently predicted the need for 2 J/kg shocks: AF duration > 7 months, previous DC, and increased left atrial (LA) diameter > 4.5 cm. A simplified point score system (REBICAF score) that spans from 0 to 4 was developed. The score gives two points for AF duration > 7 months and one point for previous DC or LA diameter > 4.5 cm. The area under the receiver operator curve (ROC) of the proposed score for predicting the need for 2 J/kg shock was 0.84. There was a progressive increase in the need for 1 J/kg, 2 J/kg, and 200 J as the point score increased (P < 0.001, chi2 test for trend). More than 90% cumulative success rate was achieved in the low- (0-1), intermediate- (2), and high-REBICAF (3-4) score subgroups with 1 J/kg, 2 J/kg, and 200 J RLB shocks, respectively. CONCLUSION: A simple point score system is useful in prediction of successful initial RLB energy for DC of AF.

Adult↗

Role of macrophage tissue infiltration in metabolic diseases.

PURPOSE OF REVIEW: White adipose tissue is necessary for optimal energy homeostasis and the excessive development of fat mass is clearly associated with the metabolic syndrome. The fact that adipocytes secrete a number of specific factors or 'adipokines' has forced a reassessment of the involvement of adipose tissue in a wide range of physiological and pathophysiological processes. Obesity has recently been described as a 'low-grade' inflammatory condition, a state proposed to represent a common determinator in the genesis of obesity-associated pathologies, i.e. diabetes and atherosclerosis. RECENT FINDINGS: Recent reports of an increase in the number of macrophages that infiltrate the fat mass in obese individuals led to the suggestion that adipose tissue itself is a source and site of inflammation. SUMMARY: This review summarizes recent data on the characterization of the macrophage population in fat tissue. Their origin, fate and activation will be considered. The potential involvement of adipose tissue macrophages in the development of insulin resistance and vascular pathologies, as well as in the control of adipose tissue growth and metabolism, will be examined.

Adipocytes↗

Femtosecond electron diffraction: 'making the molecular movie'.

Femtosecond electron diffraction (FED) has the potential to directly observe transition state processes. The relevant motions for this barrier-crossing event occur on the hundred femtosecond time-scale. Recent advances in the development of high-flux electron pulse sources with the required time resolution and sensitivity to capture barrier-crossing processes are described in the context of attaining atomic level details of such structural dynamics-seeing chemical events as they occur. Initial work focused on the ordered-to-disordered phase transition of Al under strong driving conditions for which melting takes on nm or molecular scale dimensions. This work has been extended to Au, which clearly shows a separation in time-scales for lattice heating and melting. It also demonstrates that superheated face-centred cubic (FCC) metals melt through thermal mechanisms involving homogeneous nucleation to propagate the disordering process. A new concept exploiting electron-electron correlation is introduced for pulse characterization and determination of t=0 to within 100fs as well as for spatial manipulation of the electron beam. Laser-based methods are shown to provide further improvements in time resolution with respect to pulse characterization, absolute t=0 determination, and the potential for electron acceleration to energies optimal for time-resolved diffraction.

Journal Article↗