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1.
Kamila B. Muchowska Dominic J. Pascoe Stefan Borsley Ivan V. Smolyar Ioulia K. Mati Catherine Adam Gary S. Nichol Kenneth B. Ling Scott L. Cockroft 《Angewandte Chemie (Weinheim an der Bergstrasse, Germany)》2020,132(34):14710-14716
Interactions between carbonyl groups are prevalent in protein structures. Earlier investigations identified dominant electrostatic dipolar interactions, while others implicated lone pair n→π* orbital delocalisation. Here these observations are reconciled. A combined experimental and computational approach confirmed the dominance of electrostatic interactions in a new series of synthetic molecular balances, while also highlighting the distance-dependent observation of inductive polarisation manifested by n→π* orbital delocalisation. Computational fiSAPT energy decomposition and natural bonding orbital analyses correlated with experimental data to reveal the contexts in which short-range inductive polarisation augment electrostatic dipolar interactions. Thus, we provide a framework for reconciling the context dependency of the dominance of electrostatic interactions and the occurrence of n→π* orbital delocalisation in C=O⋅⋅⋅C=O interactions. 相似文献
2.
Anna Peterson Mari-Liis Ludvig Jevgenija Martõnova Sandra Kaabel Paul Kerner Merle Uudsemaa 《Supramolecular chemistry》2020,32(5):313-319
ABSTRACT We demonstrate that Ullman fragment-coupling can be used to synthesise an oxacalix[4]arene monocarboxylic acid, which provides easy access to its water-soluble carboxylato derivatives. Crystallographic and computational data suggest that the new carboxyl-substituted oxacalix[4]arene adopts a 1,3-alternate conformation both in the solid-state and in methanol solution. Its water-soluble tetrabutylammonium derivate can detect the herbicide paraquat at neutral pH in aqueous media (K a = 111 ± 3 M–1) and in methanol (K a = 2020 ± 70 M–1). 相似文献
3.
The structure and rotational barrier for the mesityl-silicon bond of 2,2-dimesityl-1,1,1,3,3,3-hexamethyltrisilane have been investigated by 1H- and 13C-variable temperature nuclear magnetic resonance (NMR) as well as by density functional theory structural calculations. The calculations show that the lowest energy structure has C2 symmetry with nonequivalent ortho methyl groups, consistent with the crystal structure and solution NMR. The nonequivalent ortho methyl groups exchange through a Cs transition state with a calculated relative free energy of 11.0 kcal mol−1. The barrier for this rotation found by dynamic NMR is 13.4 ± 0.2 kcal mol−1 at 298 K. 相似文献
4.
《Physics letters. A》2019,383(22):2594-2603
In this work, we address the systematic biases and random errors stemming from finite step sizes encountered in diffusion simulations. We introduce the Effective Geometry Monte Carlo (EG-MC) simulation algorithm which modifies the geometry of the receiver. We motivate our approach in a 1D toy model and then apply our findings to a spherical absorbing receiver in a 3D unbounded environment. We show that with minimal computational cost the impulse response of this receiver can be precisely simulated using EG-MC. Afterwards, we demonstrate the accuracy of our simulations and give tight constraints on the single free parameter in EG-MC. Finally, we comment on the range of applicability of our results. While we present the EG-MC algorithm for the specific case of molecular diffusion, we believe that analogous methods with effective geometry manipulations can be utilized to approach a variety of problems in other branches of physics such as condensed matter physics and cosmological large scale structure simulations. 相似文献
5.
Enantiomeric Cyclic Peptides with Different Caco‐2 Permeability Suggest Carrier‐Mediated Transport 下载免费PDF全文
B. Sc. Eduard Puig Prof. Dr. Beat Ernst Prof. Dr. Horst Kessler 《Chemistry (Weinheim an der Bergstrasse, Germany)》2015,21(22):8023-8027
Recently, oral absorption of cyclic hexapeptides was improved by N‐methylation of their backbone amides. However, the number and position of N‐methylations or of solvent exposed NHs did not correlate to intestinal permeability, measured in a Caco‐2 model. In this study, we investigate enantiomeric pairs of three polar and two lipophilic peptides to demonstrate the participation of carrier‐mediated transporters. As expected, all the enantiomeric peptides exhibited identical lipophilicity (logD7.4) and passive transcellular permeability determined by the parallel artificial membrane permeability assay (PAMPA). However, the enantiomeric polar peptides exhibited different Caco‐2 permeability (Papp) in both directions a–b and b–a. The same trend was observed for one of the lipophilic peptide, whereas the second lipophilic enantiomer pair showed identical Caco‐2 permeability (within the errors). These findings provide the first evidence for the involvement of carrier‐mediated transport for peptides, especially for those of polar nature. 相似文献
6.
Dr. Stefano Elli Dr. Eduardo Stancanelli Dr. Zhangjie Wang Dr. Maurice Petitou Prof. Jian Liu Dr. Marco Guerrini 《Chemistry (Weinheim an der Bergstrasse, Germany)》2020,26(51):11814-11818
Heparin binds to and activates antithrombin (AT) through a specific pentasaccharide sequence, in which a trisaccharide subsite, containing glucuronic acid (GlcA), has been considered as the initiator in the recognition of the polysaccharide by the protein. Recently it was suggested that sulfated iduronic acid (IdoA2S) could replace this “canonical” GlcA. Indeed, a heparin octasaccharidic sequence obtained by chemoenzymatic synthesis, in which GlcA is replaced with IdoA2S, has been found to similarly bind to and activate antithrombin. By using saturation-transfer-difference (STD) NMR, NOEs, transferred NOEs (tr-NOEs) NMR and molecular dynamics, we show that, upon binding to AT, this IdoA2S unit develops comparable interactions with AT as GlcA. Interestingly, two IdoA2S units, both present in a 1C4-2S0 equilibrium in the unbound saccharide, shift to full 2S0 and full 1C4 upon binding to antithrombin, providing the best illustration of the critical role of iduronic acid conformational flexibility in biological systems. 相似文献
7.
Yerko Torres-Nova 《Journal of Pure and Applied Algebra》2021,225(1):106465
Let be integers. A generalized Fermat curve of type is a compact Riemann surface S that admits a subgroup of conformal automorphisms isomorphic to , such that the quotient surface is biholomorphic to the Riemann sphere and has branch points, each one of order k. There exists a good algebraic model for these objects, which makes them easier to study. Using tools from algebraic topology and integration theory on Riemann surfaces, we find a set of generators for the first homology group of a generalized Fermat curve. Finally, with this information, we find a set of generators for the period lattice of the associated Jacobian variety. 相似文献
8.
Dr. Vadim B. Krylov Dr. Alexey G. Gerbst Dmitry A. Argunov Dr. Andrey S. Dmitrenok Prof. Dr. Alexander S. Shashkov Prof. Dr. Zbigniew Kaczynski Prof. Dr. Johannes Huebner Prof. Dr. Otto Holst Prof. Dr. Nikolay E. Nifantiev 《Chemistry (Weinheim an der Bergstrasse, Germany)》2015,21(4):1749-1754
Enterococcus faecalis is one of most important nosocomial and often multi‐antibiotic resistant pathogens responsible for infections that are difficult to treat. Previously, a cell‐wall polysaccharide termed diheteroglycan (DHG) was isolated and characterized as a promising vaccine candidate. However, the configuration of its lactic acid (LA) residue attached to the galactofuranoside unit was not assessed, although it influences conformation of DHG chain in terms of biological recognition and immune evasion. This study proves the R configuration of the LA residue by means of chemical analysis, investigation of intramolecular NMR nuclear Overhauser effects and molecular dynamics simulations of native DHG and corresponding R and S models, which were obtained by using pyranoside‐into‐furanoside rearrangement. As alternative treatment and prevention strategies for E. faecalis are desperately needed, this discovery may offer the prospect of a synthetic vaccine to actively immunize patients at risk. 相似文献
9.
10.
Relative amino acid residue solvent accessibility values allow the quantitative comparison of atomic solvent-accessible surface areas in different residue types and physical environments in proteins and in protein structural alignments. Geometry-optimised tri-peptide structures in extended solvent-exposed reference conformations have been obtained for 43 amino acid residue types at a high level of quantum chemical theory. Significant increases in side-chain solvent accessibility, offset by reductions in main-chain atom solvent exposure, were observed for standard residue types in partially geometry-optimised structures when compared to non-minimised models built from identical sets of proper dihedral angles abstracted from the literature. Optimisation of proper dihedral angles led most notably to marked increases of up to 54% in proline main-chain atom solvent accessibility compared to literature values. Similar effects were observed for fully-optimised tri-peptides in implicit solvent. The relief of internal strain energy was associated with systematic variation in N, Cα and Cβ atom solvent accessibility across all standard residue types. The results underline the importance of optimisation of ‘hard’ degrees of freedom (bond lengths and valence bond angles) and improper dihedral angle values from force field or other context-independent reference values, and impact on the use of standardised fixed internal co-ordinate geometry in sampling approaches to the determination of absolute values of protein amino acid residue solvent accessibility. Quantum chemical methods provide a useful and accurate alternative to molecular mechanics methods to perform energy minimisation of peptides containing non-standard (chemically modified) amino acid residues frequently present in experimental protein structure data sets, for which force field parameters may not be available. Reference tri-peptide atomic co-ordinate sets including hydrogen atoms are made freely available. 相似文献