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Molecular dynamics was used to study the hydration of superoxide (O). The Helmholtz free energy of hydration of O was estimated by the thermodynamic integration method. The diffusion of O and the water structure around O were also studied. Two water models were used in the calculations and the results were compared to experiments. 相似文献
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An experimental study of the thermal decomposition of a β‐hydroxy alkene, 3‐methyl‐3‐buten‐1‐ol, in m‐xylene solution, has been carried out at five different temperatures in the range of 513.15–563.15 K. The temperature dependence of the rate constants for the decomposition of this compound in the corresponding Arrhenius equation is given by ln k (s?1) = (25.65 ± 1.52) ? (17,944 ± 814) (kJ·mol?1)·T?1. A computational study has been carried out at the M05–2X/6–31+G(d,p) level of theory to calculate the rate constants and the activation parameters by the classical transition state theory. There is a good agreement between the experimental and calculated rate constants and activation Gibbs energies. The bonding characteristics of reactant, transition state, and products have been investigated by the natural bond orbital analysis, which provides the natural atomic charges and the Wiberg bond indices. Based on the results obtained, the mechanism proposed is a one‐step process proceeding through a six‐membered cyclic transition state, being a concerted and slightly asynchronous process. The results have been compared with those obtained previously by us (Struct Chem 2013, 24, 1811–1816) for the thermal decomposition of 3‐buten‐1‐ol, in m‐xylene solution. We can conclude that in the compound studied in this work, 3‐methyl‐3‐buten‐1‐ol, the effect of substitution at position 3 by a weakly activating CH3 group is the stabilization of the transition state formed in the reaction and therefore a small increase in the rate of thermal decomposition. 相似文献
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Abstract Due to the wide use of polymers in medicine, researchers are required to solve a very important problem–to understand the interaction between materials of nonphysiological origin and the surrounding biological liquids, and tissues, particularly blood. 相似文献
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Michael K. Gilson J. Andrew McCammon Jeffry D. Madura 《Journal of computational chemistry》1995,16(9):1081-1095
The accuracy and simplicity of the Poisson-Boltzmann electrostatics model has led to the suggestion that it might offer an efficient solvent model for use in molecular mechanics calculations on biomolecules. We report a successful merger of the Poisson-Boltzmann and molecular dynamics approaches, with illustrative calculations on the small solutes dichloroethane and alanine dipeptide. The algorithm is implemented within the program UHBD. Computational efficiency is achieved by the use of rather coarse finite difference grids to solve the Poisson-Boltzmann equation. Nonetheless, the conformational distributions generated by the new method agree well with reference distributions obtained as Boltzmann distributions from energies computed with fine finite difference grids. The conformational distributions also agree well with the results of experimental measurements and conformational analyses using more detailed solvent models. We project that when multigrid methods are used to solve the finite difference problem and the algorithm is implemented on a vector supercomputer, the computation of solvent electrostatic forces for a protein of modest size will add only about 0.1 s computer time per simulation step relative to a vacuum calculation. © 1995 by John Wiley & Sons, Inc. 相似文献
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Many recent advances in Poisson-Boltzmann and generalized Born implicit solvent models have used atom-centered polynomial or Gaussian functions to define the boundary separating low and high dielectric regions. In contrast to the Lee and Richards molecular surface, atom-centered surfaces result in interatomic crevices and buried pockets of high dielectric which are too small for a solvent molecule to occupy. We show that these interstitial high dielectric regions are of significant magnitude in globular proteins, that they artificially increase solvation energies, and that they distort the free energy surface of nonbonded interactions. These results suggest that implicit solvent dielectric functions must exclude interstitial high dielectric regions in order to yield physically meaningful results. 相似文献
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We report the first measurements of fine Ni particles from61Ni Mössbauer spectroscopy. The average hyperfine field of the 10 nm particles at 4.2K is measured to be 7.7(4) T, compared to the measured value for Ni foil of 7.5(3) T. Application of an external field of 6 T to the fine particles causes a reduction of the hyperfine splitting to 1.5(6) T, a consequence of the negative hyperfine field at Ni nuclei. These results are discussed in terms of fine particle effects. 相似文献