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101.
表皮生长因子受体和抑制剂之间分子对接的研究 总被引:3,自引:0,他引:3
研究了表皮生长因子受体(EGFR)和4-苯胺喹唑啉类抑制剂之间的相互作用模式,表皮生长因子受体的三维结构通过同源蛋白模建的方法得到,而抑制剂和靶酶结合复合物结构则通过分子力学和分子动力学结合的方法计算得到。从模拟结果得到的抑制剂和靶酶之间的相互作用模式表明范德华相互作用、疏水相互作用以及氢键相互作用对抑制剂的活性都有重要的影响,抑制剂的苯胺部分位于活性口袋的底部,能够与受体残基的非极性侧链产生很强的范德华和疏水相互作用,抑制剂双环上的取代基团也能和活性口袋外部的部分残基形成一定的范德华和疏水性相互作用,而抑制剂喹唑啉环上的氮原子能和周围的残基形成较强的氢键相互作用,对抑制剂的活性有较大的影响,计算得到抑制剂和靶酶之间的非键相互作用能以及抑制剂和靶酶之间的相互作用信息能够很好地解释抑制剂活性和结构的关系,为全新抑制剂的设计提供了重要的结构信息。 相似文献
102.
Potential energy surfaces for rotations around two central CN bonds in N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF–dG) and its deacetylated derivative (AF–dG) were studied using Amber 95 molecular mechanics. Both of these adducts are known to be strong mutagens and carcinogens. New Amber 95 force field parameters were derived for the linkage connecting guanine and fluorene moieties in AAF–dG and AF–dG. For this purpose, we determined ab initio MP2/cc-pVDZ//B3-LYP/6-31G* and polarized continuum model Hartree–Fock/6-31G* potential energy surfaces of smaller model systems that included the N-methylimidazole–acetylaniline and N-methylimidazole–aniline adducts. The molecular mechanics parameters were adjusted to minimize differences between the gas-phase ab initio and molecular mechanics surfaces of these model systems. The resulting parameters were transferred to AF–dG and AAF–dG. The barrier for the rotation of the fluorene residue in AF–dG was found to be less than 2 kcal/mol. Such a small barrier renders the fluorene moiety freely rotatable at room temperature. In contrast, the fluorene rotation in AAF–dG is hindered by a significantly larger barrier of 10 kcal/mol. This barrier corresponds to conformations in which the fluorene and acetyl groups lie in the same plane, and is largely due to steric repulsion. Similarly, the coplanar arrangement of guanine and the bridging amino or acetyl groups is disfavored by 5–10 kcal/mol, with AAF–dG again being the more rigid of the two molecules. Energy minima for a rotation around a bond between guanine and the bridging nitrogen are found at ±80° in AAF–dG, and at 120° and –90° for AF–dG. Overall, the fluorene–dG linkages in AF–dG and AAF–dG adducts have significantly different equilibrium structures and torsional flexibilities. These differences may be contributing factors for the observed disparity in mutagenic effects of these adducts.Electronic Supplementary Material: Supplementary material is available in the online version of this article at Acknowledgements. This work was supported by the NSF REU grant no. CHE-0243825 to Loyola University Chicago. We thank to Tom Ellenberger and Shuchismita Dutta for providing us with their results prior to publication. 相似文献
103.
Dhanpat Rai Dean A. Moore Nancy J. Hess Kevin M. Rosso Linfeng Rao Steve M. Heald 《Journal of solution chemistry》2007,36(10):1261-1285
Chromium(III)-carbonate reactions are expected to be important in managing high-level radioactive wastes. Extensive studies
on the solubility of amorphous Cr(III) hydroxide solid in a wide range of pH (3–13) at two different fixed partial pressures
of CO2(g) (0.003 or 0.03 atm.), and as functions of K2CO3 concentrations (0.01 to 5.8 mol⋅kg−1) in the presence of 0.01 mol⋅dm−3 KOH and KHCO3 concentrations (0.001 to 0.826 mol⋅kg−1) at room temperature (22±2 °C) were carried out to obtain reliable thermodynamic data for important Cr(III)-carbonate reactions.
A combination of techniques (XRD, XANES, EXAFS, UV-Vis-NIR spectroscopy, thermodynamic analyses of solubility data, and quantum
mechanical calculations) was used to characterize the solid and aqueous species. The Pitzer ion-interaction approach was used
to interpret the solubility data. Only two aqueous species [Cr(OH)(CO3)22− and Cr(OH)4CO33−] are required to explain Cr(III)-carbonate reactions in a wide range of pH, CO2(g) partial pressures, and bicarbonate and carbonate concentrations. Calculations based on density functional theory support
the existence of these species. The log 10
K° values of reactions involving these species [{Cr(OH)3(am) + 2CO2(g)⇌Cr(OH)(CO3)22−+2H+} and {Cr(OH)3(am) + OH−+CO32−
⇌Cr(OH)4CO33−}] were found to be −(19.07±0.41) and −(4.19±0.19), respectively. No other data on any Cr(III)-carbonato complexes are available
for comparisons. 相似文献
104.
Jane E. G. Lipson Scott T. Milner 《Journal of polymer science. Part A, Polymer chemistry》2006,44(24):3528-3545
Recent differential scanning calorimetry (DSC) results on polystyrene–solvent mixtures show two distinct glass transitions whose positions and widths vary with composition. Parallel work on the dynamic response in polymer blends has focused on how segmental mobilities are controlled by local composition variations within a “cooperative volume” containing the segment. Such variations arise from both chain connectivity and composition fluctuations. We account for both using a lattice model for polymer–solvent mixtures that yields the composition distribution around polymer and solvent segments. Insights from our lattice model lead us to simplified calculations of the mean and variance of local composition, both in good agreement with lattice results. Applying our model to compute DSC traces leads to an estimate of the cooperative volume, since a larger cooperative volume both reduces the biasing effect of connectivity, and narrows the composition distribution. Comparing our results to data, we are able to account for the composition-dependent broadening with a cooperative length scale of about 2.5 nm. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 3528–3545, 2006 相似文献
105.
G. Benfatto C. Marchioro E. Presutti M. Pulvirenti 《Journal of statistical physics》1980,22(3):349-362
We consider an anharmonic crystal described by variablesS
x
,x
d
,S
x
, with one-body interaction ¦S
x
¦
and nearest neighbor (n.n.) two body interaction ¦S
x
–S
y
¦. We prove that, for
d
bounded, , where
is the correlation function for the free boundary condition Gibbs state in ,>0 and are suitable constants independent of and . This generalizes previous results obtained in the case.Research partially supported by Consiglio Nazionale delle Ricerche. 相似文献
106.
Julie A. Braatz Michael B. Bass Rick L. Ornstein 《Journal of computer-aided molecular design》1994,8(5):607-622
Summary P450SU1 and P450SU2 are herbicide-inducible bacterial cytochrome P450 enzymes from Streptomyces griseolus. They have two of the highest sequence identities to camphor hydroxylase (P450cam from Pseudomonas putida), the cytochrome P450 with the first known crystal structure. We have built several models of these two proteins to investigate the variability in the structures that can occur from using different modeling protocols. We looked at variability due to alignment methods, backbone loop conformations and refinement methods. We have constructed two models for each protein using two alignment algorithms, and then an additional model using an identical alignment but different loop conformations for both buried and surface loops. The alignments used to build the models were created using the Needleman-Wunsch method, adapted for multiple sequences, and a manual method that utilized both a dotmatrix search matrix and the Needleman-Wunsch method. After constructing the initial models, several energy minimization methods were used to explore the variability in the final models caused by the choice of minimization techniques. Features of cytochrome P450cam and the cytochrome P450 superfamily, such as the ferredoxin binding site, the heme binding site and the substrate binding site were used to evaluate the validity of the models. Although the final structures were very similar between the models with different alignments, active-site residues were found to be dependent on the conformations of buried loops and early stages of energy minimization. We show which regions of the active site are the most dependent on the particular methods used, and which parts of the structures seem to be independent of the methods. 相似文献
107.
108.
A large succinic acid (HOOC(CH2)2COOH) matrix containing 7 × 7 × 7 unit cells with guest oligonucleotide AGCAGCT was modeled with molecular dynamics simulation
for infrared matrix-assisted laser desorption ionization. We simulated the laser heating of the succinic acid (this data is
still missing from the literature) with λ=2.94 μm infrared laser pulses and compared it to ultraviolet excitation. We did
this in order to elucidate the cluster formation of succinic acid in the gas phase in itself and around the analyte. At this
wavelength, the laser energy is coupled into the matrix through the OH vibrations of the carboxyl groups. The most pronounced
difference we observed at 1,500 K simulation is that infrared heating generates about 10–15 more succinic acid molecules bound
to the analyte in noncovalent complex form than the ultraviolet mode, which generates about 2 molecules thus bound. We report
energy redistribution within the matrix between the host and guest species as well as other dynamical properties. The parameter
and topology data for succinic acid that we used are reported and ready for use in CHARMM computer code environment for simulation.
Revised: 12 October 2001 / Accepted: 27 February 2002 / Published online: 13 June 2002 相似文献
109.
Yoshida T Sakakibara K Asami M Chen KH Lii JH Allinger NL 《Journal of computational chemistry》2003,24(3):319-327
The MM3 force field has been extended to deal with the lithium amide molecules that are widely used as efficient catalysts for stereoselective asymmetric synthesis. The MM3 force field parameters have been determined on the basis of the ab initio MP2/6-31G* and/or DFT (B3LYP/6-31G*, B3-PW91/6-31G*) geometry optimization calculations. To evaluate the electronic interactions specific to the lithium amides derived from the diamine molecules properly, the Lewis bonding potential term for the interaction between the lithium atom and the nonbonded adjacent electronegative atom such as nitrogen was introduced into the MM3 force field. The bond dipoles were evaluated correctly from the electronic charges on the atoms calculated by fitting to the electrostatic potential at points selected. The MM3 results on the molecular structures, conformational energies, and vibrational spectra show good agreement with those from the quantum mechanical calculations. 相似文献
110.
O. V. Shishkin A. S. Polyakova S. N. Desenko D. V. Orlov S. V. Lindeman Yu. T. Struchkov 《Russian Chemical Bulletin》1995,44(3):470-474
The equilibrium geometry and inversion barriers of 5,6-dihydropyrimidine, 6,7-dihydroazolopyrimidines with node nitrogen atoms and their alkyl (Me, Et, Pri, But) and phenyl derivatives were calculated using a molecular mechanics approach. Annelation with azole cycles and the introduction of substituents have a slight effect on the equilibrium conformation of the dihydrocycle (distorted sofa). Alkyl substutuents at saturated carbons have an essentially equatorial orientation in 5,6-dihydropyridimine derivatives and are axial in the annelated analogs. On the other hand, the equatorial conformers are more stable in phenyl derivatives of dihydroazolopyrimidines. Factors determining the relative stability of conformers were analyzed.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 487–491, March, 1995. 相似文献