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排序方式: 共有262条查询结果,搜索用时 11 毫秒
151.
Serdal Kirmizialtin Banu Sizirici Yildiz Ibrahim Yildiz 《Journal of Physical Organic Chemistry》2017,30(12)
Oxime chemistry has been proven to be a reliable bioconjugation method for biomedical applications. Because of its stable and bio‐orthogonal nature, a number of materials have been devised for in vitro and in vivo applications such as drug delivery, imaging, and biochemical assays. Polymers, synthetic molecules, nanoparticles, and biomolecules carrying alkoxyamine and aldehyde/ketone functional groups could be linked to each other through oxime bond, and a variety of modular platforms could be produced. Formation of oximes is catalyzed in acidic medium, and the proposed reaction mechanism follows classical imine formation pathways. Aniline has been found to accelerate the rate of oxime formation several orders of magnitude. In this computational study, we analyzed the proposed mechanism on model systems using DFT calculations including a solvation model. The energetics of the reaction steps in neutral and acidic conditions as well as in the presence of aniline was performed. Explicit water molecules were included in the calculations to study the energetics of solvent assisted proton transfer steps. 相似文献
152.
Dr. Ibrahim Yildiz 《Chemphyschem》2023,24(20):e202300431
D-Arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) is an amine oxidase which catalyzes the conversion of D-arginine into iminoarginine. It contains a non-covalent FAD cofactor that is involved in the oxidation mechanism. Based on substrate, solvent, and multiple kinetic isotope effects studies, a stepwise hydride transfer mechanism is proposed. It was shown that D-arginine binds to the active site of enzyme as α-amino group protonated, and it is deprotonated before a hydride ion is transferred from its α-C to FAD. Based on a mutagenesis study, it was concluded that a water molecule is the most likely catalytic base responsible from the deprotonation of α-amino group. In this study, we formulated computational models based on ONIOM method to elucidate the oxidation mechanism of D-arginine into iminoarginine using the crystal structure of enzyme complexed with iminoarginine. The calculations showed that Arg222, Arg305, Tyr249, Glu87, His 48, and two active site water molecules play key roles in binding and catalysis. Model systems showed that the deprotonation step occurs prior to hydride transfer step, and active site water molecule(s) may have participated in the deprotonation process. 相似文献
153.
Muge Yucel;Rabia Onbas;Ahu Arslan Yildiz;Umit Hakan Yildiz; 《Macromolecular bioscience》2024,24(4):2300402
This study describes the formation, size control, and penetration behavior of polymer nanodots (Pdots) consisting of single or few chain polythiophene-based conjugated polyelectrolytes (CPEs) via nanophase separation between good solvent and poor solvent of CPE. Though the chain singularity may be associated with dilution nanophase separation suggests that molecules of a good solvent create a thermodynamically driven solvation layer surrounding the CPEs and thereby separating the single chains even in their poor solvents. This statement is therefore corroborated with emission intensity/lifetime, particle size, and scattering intensity of polyelectrolyte in good and poor solvents. Regarding the augmented features, Pdots are implemented into cell imaging studies to understand the nuclear penetration and to differentiate the invasive characteristics of breast cancer cells. The python based red, green, blue (RGB) color analysis depicts that Pdots have more nuclear penetration ability in triple negative breast cancer cells due to the different nuclear morphology in shape and composition and Pdots have penetrated cell membrane as well as extracellular matrix in spheroid models. The current Pdot protocol and its utilization in cancer cell imaging are holding great promise for gene/drug delivery to target cancer cells by explicitly achieving the very first priority of nuclear intake. 相似文献
154.
Assoc. Prof. Dr. Cem B. Yildiz Dr. Kinga I. Leszczyńska Dr. Sandra González-Gallardo Dr. Michael Zimmer Prof. Dr. Akin Azizoglu Priv.-Doz. Dr. Till Biskup Prof. Dr. Christopher W. M. Kay Dr. Volker Huch Prof. Dr. Henry S. Rzepa Prof. Dr. David Scheschkewitz 《Angewandte Chemie (Weinheim an der Bergstrasse, Germany)》2020,132(35):15199-15204
155.
The structure of compound has also been examined cyrstallographically. It crystallizes in the monoclinic space group P21/c with a = 7.673(1), b = 16.251(2), c = 10.874(1) Å, β = 110.42(1)°, V = 1270.7(3) Å3, D x = 1.418 g cm?3, R 1 = 0.0349 and wR 2 = 0.0935 [I > 2σ(I)], respectively. The title compound has been synthesized from the reaction of isonicotinohydrazide with 2-hydroxy-3-methoxybenzaldehyde. It has been characterized by using elemental analysis, MS, IR, 1H NMR, 13C NMR and UV-Visible spectroscopic techniques. 相似文献
156.
Anto PL Panicker CY Varghese HT Philip D Temiz-Arpaci O Tekiner-Gulbas B Yildiz I 《Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy》2007,67(3-4):744-749
FT-Raman and FT-IR spectra of 5-methyl-2-(p-fluorophenyl)benzoxazole were recorded and analysed. The vibrational frequencies of the compound have been computed using the Hartree-Fock/6-31G* basis and compared with the experimental values. 相似文献
157.
Hydrophobically modified and thermally reversible neutral and ionic copolymer hydrogels were prepared from N‐isopropylacrylamide (NIPAAm), vinyl terminated poly (dimethylsiloxane) (VTPDMS) and itaconic acid (IA) by free radical solution polymerization, and their properties such as swelling ratio and compression modulus were studied at the 25°C. The incorporation of VTPDMS as a hydrophobic macrocrosslinker into the structures of neutral NIPAAm hydrogels increased their mechanical strength around 10 times than those of the ones crosslinked with conventional tetra functional monomer, i.e., N,N′‐methylene bisacrylamide (BIS). Compression modulus decreased with an increase in IA content for ionic samples and increased with increasing molecular weight and content of VTPDMS for neutral samples. It was assumed that in the first case, electrostatic repulsive forces resulting from the ionized carboxyl groups of IA were responsible for decreasing mechanical strength, while in the second case, hydrophobic interactions between dimethylsiloxane units of VTPDMS chains enhanced the compression moduli. According to the results presented in this work, it can be said that the right balance of hydrophobic and hydrophilic constituents and adjustment of the number of ionized groups, as well as crosslinking degree, change the structure and physical properties of NIPPAAm hydrogels. 相似文献
158.
We describe the detection of specific, conserved DNA sequences of herpes simplex virus (HSV) type 1 by means of a novel, high sensitivity acoustic biosensor. Repeated assays on planar and polymeric carboxylic acid- and biotin-presenting surface chemistries enabled statistical comparison of assay specificity and sensitivity and evaluation of assay Z-factor scores. Using a three minute hybridisation with NeutrAvidin capture for signal enhancement, it was possible to detect HSV viral nucleic acids at 5.2 x 10(-11) M concentration. 相似文献
159.
Tekiner-Gulbas B Temiz-Arpaci O Oksuzoglu E Eroglu H Yildiz I Diril N Aki-Sener E Yalcin I 《SAR and QSAR in environmental research》2007,18(3-4):251-263
Previously synthesized 2,5-disubstituted benzoxazole and benzimidazole derivatives, were tested for their genotoxic activity in the Bacillus subtilis rec- assay. The results revealed that 5-methyl-2-(p-aminobenzyl)benzoxazole exhibited the highest genotoxic response, which was comparable to 4-nitroquinoline 1-oxide (4-NQO), the reference agent of classical positive mutagen. Among the other tested compounds, four showed a genotoxic activity. A QSAR study revealed that structural parameters IY(C(2)H(4)) and IY(CH(2)O), indicating the bridge elements between the phenyl moiety and the fused ring system at position 2 and the quantum chemical parameter (DeltaE ), showing the difference between HOMO and LUMO energies, were found significant for enhancing the genotoxic activity in these compounds. In addition, the substituent effects on positions R and R(1) were found important for the activity as well as holding a substituent possessing a maximum length with a minimum width property on position R(1) like alkyl groups. On the other hand, substituting position R with an electron donating group instead of electron withdrawing group increased the genotoxic activity. 相似文献
160.
Nima Tofighi Murat Ozbulut James J. Feng Mehmet Yildiz 《Theoretical and Computational Fluid Dynamics》2016,30(5):469-483
Manipulation of the Rayleigh-Taylor instability using an external electric field has been the subject of many studies. However, most of these studies are focused on early stages of the evolution. In this work, the long-term evolution of the instability is investigated, focusing on the forces acting on the interface between the two fluids. To this end, numerical simulations are carried out at various electric permittivity and conductivity ratios as well as electric field intensities using Smoothed Particle Hydrodynamics method. The electric field is applied in parallel to gravity to maintain unstable evolution. The results show that increasing top-to-bottom permittivity ratio increases the rising velocity of the bubble while hindering the spike descent. The opposite trend is observed for increasing top-to-bottom conductivity ratio. These effects are amplified at larger electric field intensities, resulting in narrower structures as the response to the excitation is non-uniform along the interface. 相似文献