A parametric nonorthogonal tight-binding model (NTBM1) with the set of parameters for H–C–N–O systems is presented. This model compares well with widely used semi-empirical AM1 and PM3/PM7 models but contains less fitting parameters per atom. All NTBM1 parameters are derived based on a criterion of the best agreement between the calculated and experimental values of bond lengths, valence angles and binding energies for various H–C–N–O molecules. Results for more than 200 chemical compounds are reported. Parameters are currently available for hydrogen, carbon, nitrogen, oxygen atoms and corresponding interatomic interactions. The model has a good transferability and can be used for both relaxation of large molecular systems (e.g., high-molecular compounds or covalent cluster complexes) and long-timescale molecular dynamics simulation (e.g., modelling of thermal decomposition processes). The program package based on this model is available for download at no cost from http://ntbm.info. 相似文献
Thirteen X-ray crystal structures containing various non-covalent interactions such as halogen bonds, halogen–halogen contacts and hydrogen bonds (I?N, I?F, I?I, F?F, I?H and F?H) were considered and investigated using the DFT-D3 method (B97D/def2-QZVP). The interaction energies were calculated at MO62X/def2-QZVP and MP2/aug-cc-pvDZ level of theories. The higher interaction and dispersion energies (2nd crystal) of ?9.58 kcal mol?1 and ?7.10 kcal mol?1 observed for 1,4-di-iodotetrafluorobenzene bis [bis (2-phenylethyl) sulfoxide] structure indicates the most stable geometrical arrangement in the crystal packing. The electrostatic potential values calculated for all crystal structures have a positive σ-hole, which aids understanding of the nature of σ-hole bonds. The significance of the existence of halogen bonds in crystal packing environments was authenticated by replacing iodine atoms by bromine and chlorine atoms. Nucleus independent chemical shift analysis reported on the resonance contribution to the interaction energies of halogen bonds and halogen–halogen contacts. Hirshfeld surface analysis and topological analysis (atoms in molecules) were carried out to analyze the occurrence and strength of all non-covalent interactions. These analyses revealed that halogen bond interactions were more dominant than hydrogen bonding interactions in these crystal structures.
Graphical Abstract Molecluar structure of 1,4-Di-iodotetrafluorobenzene bis(thianthrene 5-oxide) moelcule and its corresponding molecular electrostatic potential map for the view of σ-hole.
This paper describes a [15N,1H]/[13C,1H]-TROSY experiment for the simultaneous acquisition of the heteronuclear chemical shift correlations of backbone amide 15N–1H groups, side chain 15N–1H2 groups and aromatic 13C–1H groups in otherwise highly deuterated proteins. The 15N–1H and 13C–1H correlations are extracted from two subspectra of the same data set, thus preventing possible spectral overlap of aromatic and amide protons in the 1H dimension. The side-chain 15N–1H2 groups, which are suppressed in conventional [15N,1H)-TROSY, are observed with high sensitivity in the 15N–1H subspectrum. [15N,1H]/[13C,1H]-TROSY was used as the heteronuclear correlation block in a 3D [1H,1H]-NOESY-[15N,1H]/[13C,1H]-TROSY experiment with the membrane protein OmpA reconstituted in detergent micelles of molecular weight 80000 Da, which enabled the detection of numerous NOEs between backbone amide protons and both aromatic protons and side chain 15N–1H2 groups. 相似文献
Several β-amidodehydroaminobutyric acid derivatives were prepared from N,C-diprotected β-bromodehydroaminobutyric acids and amides by a copper catalyzed C–N coupling reaction. The best reaction conditions include the use of a catalytic amount of CuI, N,N′-dimethylethylenediamine as ligand and K2CO3 as base in toluene at 110 °C. The stereochemistry of the products was determined using NOE difference experiments and the results obtained are in agreement with an E-stereochemistry. Thus, the stereochemistry is maintained in the case of the E-isomers of β-bromodehydroaminobutyric acid derivatives, but when the Z-isomers were used as substrates the reaction proceeds with inversion of configuration. The use of β-bromodehydrodipeptides as substrates was also tested. It was found that the reaction outcome depend on the stereochemistry of the β-bromodehydrodipeptide and on the nature of the first amino acid residue. The products isolated were the β-amidodehydrodipeptide derivatives and/or the corresponding dihydropyrazines. The same catalytic system (CuI/N,N′-dimethylethylene diamine) was used in the C–O coupling reactions between a tyrosine derivative and aryl bromides. The new O-aryltyrosine derivatives were isolated in moderate to good yields. The photophysical properties of two of these compounds were studied in four solvents of different polarity. The results show that these compounds after deprotection can be used as fluorescence markers. 相似文献
We describe here, adaptation of the HNN pulse sequence for multiple nuclei detection using two independent receivers by utilizing
the detectable 13Cα transverse magnetization which was otherwise dephased out in the conventional HNN experiment. It enables acquisition of 2D
13Cα–15N sequential correlations along with the standard 3D 15N–15N–1H correlations, which provides directionality to sequential walk in HNN, on one hand, and enhances the speed of backbone assignment,
on the other. We foresee that the implementation of dual direct detection opens up new avenues for a wide variety of modifications
that would further enhance the value and applications of the experiment, and enable derivation of hitherto impossible information. 相似文献
We present two time-shared experiments that enable the characterization of all nOes in 1H–13C-ILV methyl-labelled proteins that are otherwise uniformly deuterated and 15N enriched and possibly selectively protonated for distinct residue types. A 3D experiment simultaneously provides the spectra
of a 3D NOESY-HN-TROSY and of a 3D NOESY-HC-PEP-HSQC. Thus, nOes from any protons to methyl or amide protons are dispersed
with respect to 15N and 13C chemical shifts, respectively. The single 4D experiment presented here yields simultaneously the four 4D experiments HC-HSQC-NOESY-HC-PEP-HSQC,
HC-HSQC-NOESY-HN-TROSY, HN-HSQC-NOESY-HN-TROSY and HN-HSQC-NOESY-HC-PEP-HSQC. This allows for the unambiguous determination
of all nOes involving amide and methyl protons. The method was applied to a (1H,13C)-ILV−(1H)-FY-(U−2H,15N) sample of a 37 kDa di-domain of the E. coli enterobactin synthetase module EntF. 相似文献
Climate change has consequences for terrestrial functioning, but predictions of plant responses remain uncertain because of the gaps in the representation of nutrient cycles and C–N–P interactions in ecosystem models. Here, we review the processes that are included in ecosystem models, but focus on coupled C–N–P cycle models. We highlight important plant adjustments to climate change, elevated atmospheric CO2, and/or nutrient limitations that are currently not—or only partially—incorporated in ecosystem models by reviewing experimental studies and compiling data. Plant adjustments concern C:N:P stoichiometry, photosynthetic capacity, nutrient resorption rates, allocation patterns, symbiotic N2 fixation and root exudation (phosphatases, carboxylates) and the effect of root exudation on nutrient mobilization in the soil rhizosphere (P solubilization, biochemical mineralization of organic P and priming effect). We showed that several plant adjustments could be formulated and calibrated using existing experimental data in the literature. Finally, we proposed a roadmap for future research because improving ecosystem models necessitate specific data and collaborations between modelers and empiricists. 相似文献
1. An organism utilizing benzonitrile as sole carbon and nitrogen source was isolated by the enrichment-culture technique and identified as a Nocardia sp. of the rhodochrous group. 2. Respiration studies indicate that nitrile degradation proceeds through benzoic acid and catechol. 3. Cell-free extracts of benzonitrile-grown cells contain an enzyme that catalyses the conversion of benzonitrile directly into benzoic acid without intermediate formation of benzamide. 4. This nitrilase enzyme was purified by DEAE-cellulose chromatography and gel filtration on Sephadex G-100 in the presence and absence of substrate. The purity of the enzyme was confirmed by sodium dodecyl sulphate/polyacrylamide-gel electrophoresis and isoelectric focusing on polyacrylamide gel. 5. The enzyme shows a time-dependent substrate-activation process in which the substrate catalyses the association of inactive subunits of mol.wt. 45000 to form the polymeric 12-unit active enzyme of mol.wt. 560000. The time required for complete association is highly dependent on the concentration of the enzyme, temperature and pH. 6. The associated enzyme has a pH optimum of 8.0 and K(m) with benzonitrile as substrate of 4mm. The activation energy of the reaction as deduced from the Arrhenius plot is 51.8kJ/mol. 7. Enzyme activity is inhibited by thiol-specific reagents and several metal ions. 8. Studies with different substrates indicate that the nitrilase is specific for nitrile groups directly attached to the benzene ring. Various substituents in the ring are compatible with activity, though ortho-substitution, except by fluorine, renders the nitrile invulnerable to attack. 9. The environmental implications of these findings and the possible significance of the enzyme in the regulation of metabolism are discussed. 相似文献
Amyloid fibrils are present in the extracellular space of various tissues in neurodegenerative and protein misfolding diseases. Amyloid fibrils may be used in nanotechnology applications, because of their self-assembly properties and stability, if their growth and orientation can be controlled. Recently, we have shown that amyloid beta 25-35 (A beta 25-35) forms a highly oriented, K(+)-dependent network on mica. Here, we analyzed the properties of A beta 25-35_N27C, the cysteine residue of which may be used for subsequent chemical modifications. We find that A beta 25-35_N27C forms epitaxially growing fibrils on mica, which evolve into a trigonally oriented branched network. The binding is apparently more sensitive to cation concentration than that of the wild-type peptide. By nanomanipulating A beta 25-35_N27C fibrils with a gold-coated AFM tip, we show that the sulfhydryl of Cys27 is reactive and accessible from the solution. The oriented network of A beta 25-35_N27C fibrils can therefore be specifically labeled and may be used for constructing nanobiotechnological devices. 相似文献
Carbon isotopic composition of soils subjected to C3–C4 vegetation change can be used to estimate C turnover in bulk soil and in soil organic matter (SOM) pools with fast and intermediate
turnover rates. We hypothesized that the biological availability of SOM pools is inversely proportional to their thermal stability,
so that thermogravimetry can be used to separate SOM pools with contrasting turnover rates. Soil samples from a field plot
cultivated for 10.5 years with the perennial C4 plant Miscanthus×gigantheus were analyzed by thermogravimetry coupled with differential scanning calorimetry (DSC). Three SOM fractions were distinguished
according to the differential weight losses and exothermic or endothermic reactions measured by DSC. The δ13C and δ15N values of these three fractions obtained by gradual soil heating were measured by IRMS. The weight losses up to 190 °C mainly
reflected water evaporation because no significant C and N losses were detected and δ13C and δ15N values of the residual SOM remained unchanged. The δ13C values (−16.4‰) of SOM fraction decomposed between 190 and 390 °C (containing 79% of total soil C) were slightly closer
to that of the Miscanthus plant tissues (δ13C = −11.8‰) compared to the δ13C values (−16.8‰) of SOM fraction decomposed above 390 °C containing the residual 21% of SOM. Thus, the C turnover in the
thermally labile fraction was faster than that in thermally stable fractions, but the differences were not very strong. Therefore,
in this first study combining TG-DSC with isotopic analysis, we conclude that the thermal stability of SOM was not very strongly
related to biological availability of SOM fractions. In contrast to δ13C, the δ15N values strongly differed between SOM fractions, suggesting that N turnover in the soil was different from C turnover. More
detailed fractionation of SOM by thermal analysis with subsequent isotopic analysis may improve the resolution for δ13C. 相似文献
Although several methods for determining erythrocyte lifespan are used in research studies that involve mice, all involve the alteration of RBC to allow for its tracking over time, which may affect overall RBC survival. The aims of this study were to determine 1) whether sex affects RBC survival; 2) whether RBC survival differs between the biotin method and an alternative method that uses GFP; and 3) whether repeat exposure of mice to biotin results in an antibiotin antibody response or decreased RBC survival. The results suggest no difference in the RBC half-life between male and female C57BL/6 mice (22.9 ± 1.2 and 22.4 ± 0.9 d, respectively). In addition, RBC half-life did not differ between the biotin- and GFP-based methods (20.5 ± 2.1 d and 22.7 ± 2.1 d, respectively). Finally, retransfusion of mice 90 d after an initial transfusion with biotin-labeled RBC did not induce detectable antibiotin antibodies nor alter the half-life of transfused biotin-labeled RBC (initial transfusion, 22.0 ± 1.2 d; subsequent transfusion, 23.4 ± 1.4 d, respectively).Abbreviations: T1/2, half-lifeRBC lifespan and senescence are important parameters used both clinically and in research studies of hereditary disorders of erythrocyte metabolism, transfusion medicine, and sepsis.8,21,27,32,35 Labeling RBC with a biotinylating reagent is a common method used to determine their circulating lifespan. Other methods involve using radioactive isotopes, such as 51Cr and 59Fe.7,20 Biotinylating reagents are preferred for various research applications with humans,8,23,24 and are used in a variety of animal models.1,25,33,34,37 Once biotin attaches to RBC surface proteins, streptavidin (a protein derived from Streptomyces avidinii) that is labeled with a fluorescent dye is used to form a strong and rapid complex with biotin, thereby allowing for its detection through flow cytometry. Blood samples analyzed sequentially over a period of weeks will show a linear decline in biotin–streptavidin signal as labeled cells age and are cleared from the circulation through the reticuloendothelial system.The characteristics of an ideal label for performing RBC survival studies include: 1) stable presence on or within the cell throughout its normal lifespan; 2) specificity for RBC; 3) inertness, such that the cell does not become prone to accelerated destruction; 4) nonrecycling (that is, the label does not reenter the circulation and bind to new cells after destruction of the labeled RBC); and 5) easy and accurate measurement by using available assays. Radioactive isotopes and other labels fulfill several of these criteria, but their limitations include elution from RBC as well as safety concerns.7,22 In contrast, biotin poses little to no risk of accumulation or toxicity. The sulfo- N-hydroxysuccinimide–biotin ester used for RBC tracking studies in humans and animals can be administered directly or through the transfusion of biotinylated RBC. Although it is generally accepted that biotinylation of RBC does not affect their function, antibodies to biotin have been demonstrated in some human studies, posing the question of whether repeated administration of biotin ester or biotinylated RBC could interfere with subsequent results within the same subject.4,20 Repeat transfusions of biotinylated RBC to mice have not been described in the literature. One aim of this study was to determine whether exposure to biotinylated RBC induces an antibiotin antibody response in mice. Furthermore, we tested whether the survival of biotinylated RBC changed after repeat exposure.Recently GFP-expressing RBC have been used to track the posttransfusion survival and recovery of stored RBC administered to nonGFP-expressing recipient mice.9,12,36 The C57BL/6-Tg(UBC–GFP)30Scha/J mouse strain is characterized by GFP expression under the control of a human ubiquitin C promoter. All tissues of these mice express GFP, including blood.26 GFP expression appears to be consistent throughout life and does not otherwise alter the normal structure, physiology, or function of RBC. In addition, GFP is unaffected by ambient light contamination or degradation, drawbacks that are associated with fluorescent dyes.15 In addition, GFP allows for the separation of cell populations through flow cytometry.9,11 Many qualities of GFP suggest that it may serve as a useful surrogate marker in place of other labeling techniques in mice. Therefore, we sought to evaluate the utility of UBC–GFP transgenic mice as an alternative to labeling RBC with biotin esters. Our aim for this work was to determine the survival of RBC in wild-type C57BL/6 mice and in the UBC–GFP strain and to compare methods for determining RBC half-life (T1/2). 相似文献