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991.
Naïm M Bhat S Rankin KN Dennis S Chowdhury SF Siddiqi I Drabik P Sulea T Bayly CI Jakalian A Purisima EO 《Journal of chemical information and modeling》2007,47(1):122-133
We present a binding free energy function that consists of force field terms supplemented by solvation terms. We used this function to calibrate the solvation model along with the binding interaction terms in a self-consistent manner. The motivation for this approach was that the solute dielectric-constant dependence of calculated hydration gas-to-water transfer free energies is markedly different from that of binding free energies (J. Comput. Chem. 2003, 24, 954). Hence, we sought to calibrate directly the solvation terms in the context of a binding calculation. The five parameters of the model were systematically scanned to best reproduce the absolute binding free energies for a set of 99 protein-ligand complexes. We obtained a mean unsigned error of 1.29 kcal/mol for the predicted absolute binding affinity in a parameter space that was fairly shallow near the optimum. The lowest errors were obtained with solute dielectric values of Din = 20 or higher and scaling of the intermolecular van der Waals interaction energy by factors ranging from 0.03 to 0.15. The high apparent Din and strong van der Waals scaling may reflect the anticorrelation of the change in solvated potential energy and configurational entropy, that is, enthalpy-entropy compensation in ligand binding (Biophys. J. 2004, 87, 3035-3049). Five variations of preparing the protein-ligand data set were explored in order to examine the effect of energy refinement and the presence of bound water on the calculated results. We find that retaining water in the final protein structure used for calculating the binding free energy is not necessary to obtain good results; that is the continuum solvation model is sufficient. Virtual screening enrichment studies on estrogen receptor and thymidine kinase showed a good ability of the binding free energy function to recover true hits in a collection of decoys. 相似文献
992.
We present the first model-independent comparison of recent measurements of the entropy and of the critical temperature of a unitary Fermi gas, performed by Luo et al., with the most complete results currently available from finite temperature Monte Carlo calculations. The measurement of the critical temperature in a cold fermionic atomic cloud is consistent with a value T(c) = 0.23(2)epsilon(F) in the bulk, as predicted by the present authors in their Monte Carlo calculations. 相似文献
993.
We propose and demonstrate a method for measuring the spectral density matrix of a single photon pulse. The method is based on registering Hong-Ou-Mandel interference between a photon to be measured and a pair of attenuated and suitably delayed laser pulses described by a known spectral amplitude. The density matrix is retrieved from a two-dimensional interferogram of coincidence counts. The method has been implemented for a type-I down-conversion source, pumped by ultrashort laser pulses. The experimental results agree well with a theoretical model which takes into account the temporal as well as spatial effects in the source. 相似文献
994.
Piotr Kot 《Czechoslovak Mathematical Journal》2007,57(1):29-47
We solve the Dirichlet problem for line integrals of holomorphic functions in the unit ball
For a function u which is lower semi-continuous on
we give necessary and sufficient conditions in order that there exists a holomorphic function f ∈
such that
. 相似文献
995.
Influence of the Homopolar Dihydrogen Bonding CH⋅⋅⋅HC on Coordination Geometry: Experimental and Theoretical Studies 下载免费PDF全文
Dr. Damir A. Safin Dr. Maria G. Babashkina Dr. Koen Robeyns Dr. Mariusz P. Mitoraj Dr. Piotr Kubisiak Prof. Yann Garcia 《Chemistry (Weinheim an der Bergstrasse, Germany)》2015,21(46):16679-16687
The reaction of the N‐thiophosphorylated thiourea (HOCH2)(Me)2CNHC(S)NHP(S)(OiPr)2 (HL), deprotonated by the thiophosphorylamide group, with NiCl2 leads to green needles of the pseudotetrahedral complex [Ni(L‐1,5‐S,S′)2] ? 0.5 (n‐C6H14) or pale green blocks of the trans square‐planar complex trans‐[Ni(L‐1,5‐S,S′)2]. The former complex is stabilized by homopolar dihydrogen C?H???H?C interactions formed by n‐hexane solvent molecules with the [Ni(L‐1,5‐S,S′)2] unit. Furthermore, the dispersion‐dominated C?H??? H?C interactions are, together with other noncovalent interactions (C?H???N, C?H???Ni, C?H???S), responsible for pseudotetrahedral coordination around the NiII center in [Ni(L ‐1,5‐S,S′)2] ? 0.5 (n‐C6H14). 相似文献
996.
L-selectin is a protein with potential importance for numerous diseases and clinical disorders. In this paper, we present a new aptamer-based luminescent assay developed to detect L-selectin. The sensing system working principle is based on Förster Resonance Energy Transfer (FRET) from a donor terbium complex (TbC) to an acceptor cyanine dye (Cy5). In the present approach, the biotinylated aptamer is combined with Cy5-labelled streptavidin (Cy5-Strep) to yield an aptamer-based acceptor construct (Apta-Cy5-Strep), while L-selectin is conjugated using luminescent TbC. Upon aptamer binding to the TbC-labelled L-selectin (L-selectin-TbC), permanent donor-acceptor proximity is established which allows for radiationless energy transfer to occur. However, when unlabelled L-selectin is added, it competes with the L-selectin-TbC and the FRET signal decreases as the L-selectin concentration increases. FRET from the TbC to Cy5 was observed with time-gated time-resolved luminescence spectroscopy. A significant change in the corrected luminescence signal was observed in the dynamic range of 10–500 ng/mL L-selectin, the concentration range relevant for accelerated cognitive decline of Alzheimer's disease, with a limit of detection (LOD) equal to 10 ng/mL. The aptasensor-based assay is homogeneous and can be realized within one hour. Therefore, this method has the potential to become an alternative to tedious heterogeneous analytical methods, e.g. based on enzyme-linked immunosorbent assay (ELISA). 相似文献
997.
998.
An Allosteric Receptor by Simultaneous “Casting” and “Molding” in a Dynamic Combinatorial Library 下载免费PDF全文
Dr. Jianwei Li Piotr Nowak Prof. Dr. Sijbren Otto 《Angewandte Chemie (International ed. in English)》2015,54(3):833-837
Allosteric synthetic receptors are difficult to access by design. Herein we report a dynamic combinatorial strategy towards such systems based on the simultaneous use of two different templates. Through a process of simultaneous casting (the assembly of a library member around a template) and molding (the assembly of a library member inside the binding pocket of a template), a Russian‐doll‐like termolecular complex was obtained with remarkable selectivity. Analysis of the stepwise formation of the complex indicates that binding of the two partners by the central macrocycle exhibits significant positive cooperativity. Such allosteric systems represent hubs that may have considerable potential in systems chemistry. 相似文献
999.
Localized Template‐Driven Functionalization of Nanoparticles by Dynamic Combinatorial Chemistry 下载免费PDF全文
Piotr Nowak Dr. Vittorio Saggiomo Dr. Fatemeh Salehian Mathieu Colomb‐Delsuc Dr. Yang Han Prof. Dr. Sijbren Otto 《Angewandte Chemie (International ed. in English)》2015,54(14):4192-4197
We have developed a method for the localized functionalization of gold nanoparticles using imine‐based dynamic combinatorial chemistry. By using DNA templates, amines were grafted on the aldehyde‐functionalized nanoparticles only if and where the nanoparticles interacted with the template molecules. Functionalization of the nanoparticles was controlled solely by the DNA template; only amines capable of interacting with DNA were bound to the surface. Interestingly, even though our libraries contained only a handful of simple amines, the DNA sequence influenced their attachment to the surface. Our method opens up new opportunities for the synthesis of multivalent, nanoparticle‐based receptors for biomacromolecules. 相似文献
1000.
Dr. Qing Li Prof. Xiaodong Wen Prof. Gang Wu Dr. Hoon T. Chung Dr. Rui Gao Dr. Piotr Zelenay 《Angewandte Chemie (International ed. in English)》2015,54(26):7524-7528
Dimethyl ether (DME) has been considered as a promising alternative fuel for direct‐feed fuel cells but lack of an efficient DME oxidation electrocatalyst has remained the challenge for the commercialization of the direct DME fuel cell. The commonly studied binary PtRu catalyst shows much lower activity in DME than methanol oxidation. In this work, guided by density functional theory (DFT) calculation, a ternary carbon‐supported PtRuPd catalyst was designed and synthesized for DME electrooxidation. DFT calculations indicated that Pd in the ternary PtRuPd catalyst is capable of significantly decreasing the activation energy of the C? O and C? H bond scission during the oxidation process. As evidenced by both electrochemical measurements in an aqueous electrolyte and polymer‐electrolyte fuel cell testing, the ternary catalyst shows much higher activity (two‐fold enhancement at 0.5 V in fuel cells) than the state‐of‐the‐art binary Pt50Ru50/C catalyst (HiSPEC 12100). 相似文献