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71.
Sałek P Høst S Thøgersen L Jørgensen P Manninen P Olsen J Jansík B Reine S Pawłowski F Tellgren E Helgaker T Coriani S 《The Journal of chemical physics》2007,126(11):114110
A linear-scaling implementation of Hartree-Fock and Kohn-Sham self-consistent field (SCF) theories is presented and illustrated with applications to molecules consisting of more than 1000 atoms. The diagonalization bottleneck of traditional SCF methods is avoided by carrying out a minimization of the Roothaan-Hall (RH) energy function and solving the Newton equations using the preconditioned conjugate-gradient (PCG) method. For rapid PCG convergence, the Lowdin orthogonal atomic orbital basis is used. The resulting linear-scaling trust-region Roothaan-Hall (LS-TRRH) method works by the introduction of a level-shift parameter in the RH Newton equations. A great advantage of the LS-TRRH method is that the optimal level shift can be determined at no extra cost, ensuring fast and robust convergence of both the SCF iterations and the level-shifted Newton equations. For density averaging, the authors use the trust-region density-subspace minimization (TRDSM) method, which, unlike the traditional direct inversion in the iterative subspace (DIIS) scheme, is firmly based on the principle of energy minimization. When combined with a linear-scaling evaluation of the Fock/Kohn-Sham matrix (including a boxed fitting of the electron density), LS-TRRH and TRDSM methods constitute the linear-scaling trust-region SCF (LS-TRSCF) method. The LS-TRSCF method compares favorably with the traditional SCF/DIIS scheme, converging smoothly and reliably in cases where the latter method fails. In one case where the LS-TRSCF method converges smoothly to a minimum, the SCF/DIIS method converges to a saddle point. 相似文献
72.
A series of intramolecularly hydrogen-bonded N-substituted 3-(piperidine, morpholine, N-methylpiperazine)thiopropionamides and some corresponding amides have been studied with special emphasis on hydrogen bonding. The compounds have been selected in order to vary and to minimize the N...N distance. Geometries, charge distributions, and chemical shifts of these compounds are obtained from DFT-type BP3LYP calculations. 1H and 13C 1D and 2D NMR experiments were performed to obtain H,H coupling constants, 13C chemical shifts assignments, and deuterium isotope effects on13C chemical shifts. Variable-temperature NMR studies and 2D exchange NMR spectra have been used to describe the rather complicated conformational behavior mainly governed by the ring flipping of the piperidine (morpholine) rings and intramolecular hydrogen bonding. Unusual long-range deuterium isotope effects on 13C chemical shifts are observed over as far as eight bonds away from the site of deuteriation. The isotope effects are related to the N...N distances, thus being related to the hydrogen bonding and polarization of the N-H bond. Arguments are presented showing that the deuterium isotope effects on 13C chemical shifts originate in electric field effects. 相似文献
73.
Propagator or Green's function methods are used to analyze the time-dependent Hartree–Fock model. The non-hermitian matrix problem for the time-dependent Hartree–Fock solution is reduced to a problem related only to hermitian matrices. Particular attention is given to the calculation of oscillator strength in different approximations. The connection between the stability of the Hartree–Fock solution and the solution of the time-dependent Hartree–Fock problem is demonstrated. The results of numerical calculations are given for aniline, azulene and pyridine. 相似文献
74.
We derive expressions for the first through fourth derivatives of the configuration-interaction (CI) electronic energy with respect to molecular deformation. By using unitary exponential parameterizations of the wavefunction's orbital and configuration amplitude response together with a power-series expansion of the geometry dependence of the hamiltonian, a computationally attractive expression for the CI energy derivatives is obtained. The use of so-called direct methods in evaluating the CI derivatives is discussed as are the relative efforts involved in using our CI-based energy-derivative expressions and those which we obtained earlier for derivatives of the multiconfigurational self-consistent-field energy. The power-series expansion of the geometry dependence of the hamiltonian that we have derived may be used for evaluating molecular-deformation derivatives for any approximate wavefunction constructed from a set of orthonormal orbitals. 相似文献
75.
76.
Photonic crystal fiber based evanescent-wave sensor for detection of biomolecules in aqueous solutions 总被引:5,自引:0,他引:5
Jensen JB Pedersen LH Hoiby PE Nielsen LB Hansen TP Folkenberg JR Riishede J Noordegraaf D Nielsen K Carlsen A Bjarklev A 《Optics letters》2004,29(17):1974-1976
We demonstrate highly efficient evanescent-wave detection of fluorophore-labeled biomolecules in aqueous solutions positioned in the air holes of the microstructured part of a photonic crystal fiber. The air-suspended silica structures located between three neighboring air holes in the cladding crystal guide light with a large fraction of the optical field penetrating into the sample even at wavelengths in the visible range. An effective interaction length of several centimeters is obtained when a sample volume of less than 1 microL is used. 相似文献
77.
Poul Olesen 《Physics letters. [Part B]》1977,66(4):370-372
Abstracting the decoupling theorem of Appelquist and Carazzone from perturbation theory we show that the Yang-Mills theory is infrared stable in the zero-instanton sector. We point out that our argument is not valid when instantons are present. 相似文献
78.
Ohne Zusammenfassung 相似文献
79.
Jensen SS Ariza X Nielsen P Vilarrasa J Kirpekar F 《Journal of mass spectrometry : JMS》2007,42(1):49-57
The collision-induced dissociation of adenosine, uridine and guanosine, and their corresponding nucleobases has been published previously.1-3 Here we report the collision-induced dissociation of cytidine and the elucidation of its fragmentation pathways using stable isotope-labeled cytidines, through a quadrupole ion trap for tandem mass spectrometry up to MS(4). Furthermore, we investigated the collision-induced dissociation of five cytidine derivatives: 3-methylcytidine, N(4)-methyl-2'-deoxycytidine, 5-methylcytidine, 2-thiocytidine and N(4)-acetylcytidine. The primary fragmentation pathway was the neutral loss of ribose. MS(3) on the retained nucleobase generally resulted in an intense signal from the elimination of ammonia, but also in fragment ions characteristic of the different cytosine derivatives. On the basis of the MS(n) data, fragmentation pathways and plausible mechanisms are suggested. 相似文献
80.
Nielsen P Christensen NK Dalskov JK 《Chemistry (Weinheim an der Bergstrasse, Germany)》2002,8(3):712-722
Alpha-LNA is presented as a stereoisomer of LNA (locked nucleic acid) with alpha-D-configuration. Three different approaches towards the thymine alpha-LNA monomer as well as the 5-methylcytosine alpha-LNA monomer are presented. Different alpha-LNA sequences have been synthesised and their hybridisation with complementary DNA and RNA has been evaluated by means of thermal stability experiments and circular dichroism spectroscopy. In a mixed pyrimidine sequence, alpha-LNA displays unprecedented parallel-stranded and selective RNA binding. Furthermore, a remarkable selectivity for hybridisation with RNA over DNA is indicated. 相似文献