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81.
Talhout R Villa A Mark AE Engberts JB 《Journal of the American Chemical Society》2003,125(35):10570-10579
The binding of a series of p-alkylbenzamidinium chloride inhibitors to the serine proteinase trypsin over a range of temperatures has been studied using isothermal titration (micro)calorimetry and molecular dynamics simulation techniques. The inhibitors have small structural variations at the para position of the benzamidinium ion. They show small differences in relative binding affinity but large compensating differences in enthalpy and entropy. Binding affinity decreases with increased branching at the first carbon but increases with increasing the length of a linear alkyl substituent, suggesting that steric hindrance and hydrophobic interactions play dominant roles in binding. Structural analysis showed that the backbone of the enzyme was unaffected by the change of the para substituent. In addition, binding does not correlate strongly with octanol/water partition data. To further characterize this system, the change in the heat capacity on binding, the change in solvent-accessible surface area on binding, the effect of inhibitor binding on the hydration of the active site, the pK(a) of His57, and interactions within the catalytic triad have been investigated. Although the changes in inhibitor structure are small, it is demonstrated that simple concepts such as steric hindrance, hydrophobicity, and buried surface area are insufficient to explain the binding data. Other factors, such as access to the binding site and the cost of dehydration of the active site, are of equal or greater importance. 相似文献
82.
The binding of a set of 10 triphenoxypyridine derivatives to two serine proteases, factor Xa and trypsin, has been used to analyze factors related to sampling and convergence in free energy calculations based on molecular dynamics simulation techniques. The inhibitors investigated were initially proposed as part of the Critical Assessment of Techniques for Free Energy Evaluation (CATFEE) project for which no experimental results nor any assessment of the predictions submitted by various groups have ever been published. The inhibitors studied represent a severe challenge for explicit free energy calculations. The mutations from one compound to another involve up to 19 atoms, the creation and annihilation of net charge and several alternate binding modes. Nevertheless, we demonstrate that it is possible to obtain highly converged results (+/- 5-10 kJ/mol) even for such complex multi-atom mutations by simulating on a nanosecond time scale. This is achieved by using soft-core potentials to facilitate the creation and deletion of atoms and by a careful choice of mutation pathway. The results show that given modest computational resources, explicit free energy calculations can be successfully applied to realistic problems in drug design. 相似文献
83.
A fundamental parameters approach that incorporates data on scattered radiation is shown to be a useful tool for the determination of trace elements in light matrices. For thick, transparent samples, a computer program is developed that uses differetial intensity equations adjusted for decreasing geometric efficiency. Various organic and biological reference materials are analysed to assess the reliability of the procedure. A nested design for analysis of variance shows that major errors can originate from the deconvolution process and sample inhomogeneities in many cases. For loose powders, great care must be exercised to avoid errors caused by scatter from the sample cups. The program is also useful for alloys. 相似文献
84.
Alessandra Forni Julieta Gradinaru 《Acta Crystallographica. Section C, Structural Chemistry》2002,58(6):o342-o344
The structure of the title S‐alkylated isothiosemicarbazide, C12H15N3OS, was determined by single‐crystal diffractometry and compared with the structures of other compounds containing the S‐alkylthiosemicarbazide moiety. Such structures cluster into two groups, according to the different orientation of the –SR group with respect to the hydrazine N atom of the thiosemicarbazide. The cis arrangement is preferred by most molecules in the solid state, in spite of the possibility of intramolecular N—H?N interactions in the opposite orientation. 相似文献
85.
Irene Bravo-Osuna Christine Vauthier Alessandra Farabollini Gioconda Millotti Gilles Ponchel 《Journal of nanoparticle research》2008,10(8):1293-1301
Surface modified nanoparticles composed of poly(isobutylcyanoacrylate) (PIBCA) cores surrounded by a chitosan and thiolated
chitosan gel layer were prepared and characterized in previous works. The presence of such biopolymers on the nanoparticle
surface conferred those nanosystems interesting characteristics that might partially overcome the gastrointestinal enzymatic
barrier, improving the oral administration of pharmacologically active peptides. In the present work, the antiprotease behaviour
of this family of core–shell nanoparticles was in vitro tested against two model metallopeptidases present in the gastrointestinal
tract (GIT): Carboxypeptidase A -CP A- (luminal protease) and Leucine Aminopeptidase M -LAP M- (membrane protease). As previous
step, the zinc-binding capacity of these nanoparticles was evaluated. Interestingly, an improvement of both the zinc-binding
capacity and the antiprotease effect of chitosan was observed when the biopolymers (chitosan and thiolated chitosan) were
used as coating component of the core–shell nanoparticles, in comparison with their behaviour in solution, thanks to the different
biopolymer chains rearrangement. The presence of amino, hydroxyl and thiol groups on the nanoparticle surface promoted zinc
binding and hence the inhibition of the metallopeptidases analysed. On the contrary, the occurrence of a cross-linked structure
in the gel layer surrounding the PIBCA cores of thiolated formulations, due to the formation of interchain and intrachain
disulphide bonds, partially limited the inhibition of the proteases. The low accessibility of cations to the active groups
of the cross-linked polymeric shell was postulated as a possible explanation of this behaviour. Results obtained in this work
make this family of surface-modified nanocarriers promising candidates for the successfull administration of pharmacologically
active peptides and proteins by the oral route. 相似文献
86.
Microarrays are becoming a ubiquitous tool of research in life sciences. However, the working principles of microarray-based methodologies are often misunderstood or apparently ignored by the researchers who actually perform and interpret experiments. This in turn seems to lead to a common over-expectation regarding the explanatory and/or knowledge-generating power of microarray analyses. In this note we intend to explain basic principles of five (5) major groups of analytical techniques used in studies of microarray data and their interpretation: the principal component analysis (PCA), the independent component analysis (ICA), the t-test, the analysis of variance (ANOVA), and self organizing maps (SOM). We discuss answers to selected practical questions related to the analysis of microarray data. We also take a closer look at the experimental setup and the rules, which have to be observed in order to exploit microarrays efficiently. Finally, we discuss in detail the scope and limitations of microarray-based methods. We emphasize the fact that no amount of statistical analysis can compensate for (or replace) a well thought through experimental setup. We conclude that microarrays are indeed useful tools in life sciences but by no means should they be expected to generate complete answers to complex biological questions. We argue that even well posed questions, formulated within a microarray-specific terminology, cannot be completely answered with the use of microarray analyses alone. 相似文献
87.
Thieuleux C Quadrelli EA Basset JM Döbler J Sauer J 《Chemical communications (Cambridge, England)》2004,(15):1729-1731
The silica-supported Zr(iv) dihydride [(triple bond)SiO)2ZrH2] reacts quickly and completely with methane to yield [(triple bond)SiO)2ZrMe2] through the intermediate [(triple bond)SiO)2ZrHMe], while its monohydride analogue [(triple bond)SiO)3ZrH] yields the monomethylated product [(triple bond)SiO)3ZrMe] slowly and incompletely. 相似文献
88.
The oxidation chemistry of 17beta-estradiol (1) is of central relevance to the nongenomic effects of estrogens and offers valuable prospects in the search for novel steroidal scaffolds of academic and industrial interest. Herein, we report the results of a detailed investigation into the nature of the oligomer products formed by phenolic oxidation of 1. Of the oxidants tested, the peroxidase/H2O2 system proved to be the most effective in inducing conversion of 1 to a complex mixture of oligomer species. Repeated chromatographic fractionation followed by extensive 2D NMR and mass spectrometric analysis allowed identification of a series of phenolic coupling products comprising, besides the C2-symmetric dimers 2 and 3, a 2,4' dimer (4), two O-linked dimers (5, 6), and the novel trimers 7-9. All 4-linked biphenyl-type oligomers, i.e., 3 and 7-9, occurred as couples of atropoisomers, reflecting steric hindrance at biphenyl linkages. For all atropoisomers, absolute configuration was established by the exciton chirality method and the interconversion energy was determined by dynamic NMR. These results provide the first systematic inventory of oxidative coupling products of 1 and lay the foundation for future studies aimed to develop novel estrogen derivatives based on oligomeric scaffolds. 相似文献
89.
Galzerano G Sani E Toncelli A Della Valle G Taccheo S Tonelli M Laporta P 《Optics letters》2004,29(7):715-717
Continuous-wave laser action at approximately 2 microm is demonstrated in a Tm-Ho:KYF4 single crystal at room temperature. Crystal growth, spectroscopic measurements, and laser results are presented. An output power in excess of 250 mW is obtained with a tuning range of 99 nm, the largest ever published, to our knowledge, for Tm-Ho in any crystalline host. 相似文献
90.
The electron charge distribution in a strongly twisted push-pull ethylene [PPE, 3-(1,3-diisopropyl-2-imidazolidinylidene)-2,4-pentanedione] has been determined by low temperature (T = 21 K) single-crystal X-ray diffraction analysis. The derived electronic properties are consistent with a zwitterionic molecule, as indicated by a charge transfer of 0.82(16) e from the push to the pull moieties and a charge polarization of 0.29(7) e on the olefinic bond. A dipole moment of 12(3) D has been determined, which compares well with ab initio theoretical results in terms of both modulus and orientation. The second moments, which have also been obtained with good precision, characterize PPE as a highly quadrupolar molecule. The special electronic features of the molecule confer particular topological properties to the electron density distribution, as evidenced by comparison with "standard" organic molecules. The crystallographic asymmetric unit of the present system includes one water molecule, which is hydrogen bonded to PPE. Its topological properties have also been investigated, together with an analysis of the hydrogen bonds involved. 相似文献