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51.
Electrostatic interactions in proteins can be probed experimentally through determination of residue-specific acidity constants. We describe here triple-resonance NMR techniques for direct determination of lysine and arginine side-chain protonation states in proteins. The experiments are based on detection of nonexchangeable protons over the full range of pH and temperature and therefore are well suited for pKa determination of individual amino acid side chains. The experiments follow the side-chain 15Nzeta (lysine) and 15Nepsilon or 13Czeta (arginine) chemical shift, which changes due to sizable changes in the heteronuclear electron distribution upon (de)protonation. Since heteronuclear chemical shifts are overwhelmed by the charge state of the amino acid side chain itself, these methods supersede 1H-based NMR in terms of accuracy, sensitivity, and selectivity. Moreover, the 15Nzeta and 15Nepsilon nuclei may be used to probe changes in the local electrostatic environment. Applications to three proteins are described: apo calmodulin, calbindin D9k, and FKBP12. For apo calmodulin, residue-specific pKa values of lysine side chains were determined to fall between 10.7 and 11.2 as a result of the high net negative charge on the protein surface. Ideal two-state titration behavior observed for all lysines indicates the absence of significant direct charge interactions between the basic residues. These results are compared with earlier studies based on chemical modification. 相似文献
52.
The determination of biurea: a novel method to discriminate between nitrofurazone and azodicarbonamide use in food products 总被引:2,自引:0,他引:2
Recently doubts have arisen on the usefulness of semicarbazide as marker residue for the illegal use of the antibiotic nitrofurazone (NFZ) in aquaculture and poultry production. Most notably azodicarbonamide (ADC) has been implicated as an alternative source of semicarbazide. ADC is used in some countries as a dough conditioner at concentrations up to 45 mg kg(-1). The use of ADC-treated flour or dough in coated or breaded food products may generate false non-compliant results in the analytical method for nitrofurazone metabolites, which is currently in use. During the dough preparation process ADC is largely reduced to biurea, which can be considered as an appropriate marker residue of ADC. Thus far no methods have been published for the determination of biurea in food commodities. Due to its polar nature it is very difficult to generate sufficient retention on conventional C18 HPLC columns. With a TSK amide HILIC type column good retention was obtained. A straightforward extraction-dilution protocol was developed. Using a mixture of dimethyl formamide and water biurea was nearly quantitatively extracted from a variety of fresh, coated and processed products. Mass spectrometric detection was performed with positive electrospray ionisation. The sensitivity and selectivity of the mass spectrometer for biurea was very good, allowing detection at concentrations as low as 10 microg kg(-1). However, in some extracts severe ion suppression effects was observed. To overcome the implications of ion suppression on the quantitative performance of the method an isotopically-labelled biurea internal standard was synthesized and incorporated in the method. The method developed can be used effectively in nitrofurazone analysis to eliminate the risk of false non-compliant results due to the presence of azodicarbonamide-treated components in the food product. 相似文献
53.
Mohammed Bakir Petrea C. Facey Ishmael Hassan Willem H. Mulder Roy B. Porter 《Acta Crystallographica. Section C, Structural Chemistry》2004,60(11):o798-o800
Mikanolide [systematic names: 1,10:2,3‐diepoxy‐6,8‐dihydroxy‐11‐vinylgermacr‐4‐ene 12,14‐di‐γ‐lactone and 7,10a‐dimethyl‐1a,1b,2a,6a,7,9a,10,10a‐octahydro‐4H‐6,3‐methenofuro[3,2‐c]bisoxireno[f,h]oxacycloundecin‐4,8(6H)‐dione], C15H14O6, derived from a variety of Mikania micrantha growing in Portland, Jamaica, contains a methylcyclodecane ring fused to an unsaturated planar α,γ‐lactone, an envelope‐type near‐planar vinyl‐β,γ‐lactone and two epoxide moieties. The crystal packing shows stacks of mikanolide molecules interlocked via a network of non‐classical C—H⋯O hydrogen bonds between the lactone units. 相似文献
54.
Brath U Akke M Yang D Kay LE Mulder FA 《Journal of the American Chemical Society》2006,128(17):5718-5727
Transverse relaxation dispersion NMR spectroscopy can provide atom-specific information about time scales, populations, and the extent of structural reorganization in proteins under equilibrium conditions. A method is described that uses side-chain methyl groups as local reporters for conformational transitions taking place in the microsecond regime. The experiment measures carbon nuclear spin relaxation rates in the presence of continuous wave off-resonance irradiation, in proteins uniformly enriched with 13C, and partially randomly labeled with 2H. The method was applied to human FK-506 binding protein (FKBP12), which uses a common surface for binding substrates in its dual role as both an immunophilin and folding assistant. Conformational dynamics on a time scale of approximately 130 micros were detected for methyl groups located in the substrate binding pocket, demonstrating its plasticity in the absence of substrate. The spatial arrangement of affected side-chain atoms suggests that substrate recognition involves the rapid relative movement of the subdomain comprising residues Ala81-Thr96 and that the observed dynamics play an important role in facilitating the interaction of this protein with its many partners, including calcineurin. 相似文献
55.
Alexey V. Lyulin J. Li Tim Mulder Bart Vorselaars M.A.J. Michels 《Macromolecular Symposia》2006,237(1):108-118
Summary: In order to have better insight into the polymer specifics of the dynamic glass transition molecular dynamics (MD) computer simulations of three glass-formers have been carried out: low-molecular-weight isopropylbenzene (iPB), brittle atactic polystyrene (PS) and tough bisphenol A polycarbonate (PC). Simulation of the uniaxial deformation of these mechanically different types of amorphous polymers shows that the mechanical experimental data could be realistically reproduced. Now the objective is to study the local orientational mobility in the non-deformed isotropic state and to find the possible connection of the segmental dynamics with the different bulk mechanical properties. Local orientational mobility has been studied via Legendre polynomials of the second order and CONTIN analysis. Insight into local orientational dynamics on a range of length- and time scales is acquired. The fast transient ballistic process describing the very initial part of the relaxation has been observed for all temperatures. For all three simulated materials the slowing down of cage escape (α-relaxation) follows mode-coupling theory above Tg, with non-universal, material-specific exponents. Below Tg universal activated segmental motion has been found. At high temperature the α process is merged with the β process. The β process which corresponds to the motions within cage continues below Tg and can be described by an activation law. 相似文献
56.
Brownlee Alexander E. I. Epitropakis Michael G. Mulder Jeroen Paelinck Marc Burke Edmund K. 《Journal of Heuristics》2022,28(4):509-538
Journal of Heuristics - Industrial software often has many parameters that critically impact performance. Frequently, these are left in a sub-optimal configuration for a given application because... 相似文献
57.
Octahedral 38-, 44- and 48-electron systems are closed-shells and could be stable. The latter two systems have a high energy and dissociate via a non-symmetric path. (NH)6 in a chair conformation should be stable. 相似文献
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60.
Schimmel HG Kearley GJ Nijkamp MG Visser CT de Jong KP Mulder FM 《Chemistry (Weinheim an der Bergstrasse, Germany)》2003,9(19):4764-4770
Single-walled carbon nanotubes (SWNT) were reported to have record high hydrogen storage capacities at room temperature, indicating an interaction between hydrogen and carbon matrix that is stronger than known before. Here we present a study of the interaction of hydrogen with activated charcoal, carbon nanofibers, and SWNT that disproves these earlier reports. The hydrogen storage capacity of these materials correlates with the surface area of the material, the activated charcoal having the largest. The SWNT appear to have a relatively low accessible surface area due to bundling of the tubes; the hydrogen does not enter the voids between the tubes in the bundles. Pressure-temperature curves were used to estimate the interaction potential, which was found to be 580+/-60 K. Hydrogen gas was adsorbed in amounts up to 2 wt % only at low temperatures. Molecular rotations observed with neutron scattering indicate that molecular hydrogen is present, and no significant difference was found between the hydrogen molecules adsorbed in the different investigated materials. Results from density functional calculations show molecular hydrogen bonding to an aromatic C[bond]C that is present in the materials investigated. The claims of high storage capacities of SWNT related to their characteristic morphology are unjustified. 相似文献