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1.
The ring expansion reactions of unactivated alkynylcyclopropanes X‐C≡C‐C3H5 → X‐C=C4H5 (X = H, F, Cl, Me, OMe, NMe2, CMe3) were examined using the density functional theory calculations. All of the structures were completely optimized at the B3LYP/6‐311++G** level of theory. For clarify the effect of the cationic gold(I), we also added AuPH3+ as the catalyst into the system and the structures for Au were calculated at the B3LYP/LANL2DZ level of theory. The main finding of this work is that the singlet‐triplet splitting of X‐C≡C‐C3H5 play an important role in determining the kinetic and thermodynamic stability of the unactivated ring expansion reactions. When X‐C≡C‐C3H5 with a smaller singlet‐triplet splitting is utilized, the reaction has a smaller activation energy and a larger exothermicity.  相似文献   
2.
The effects of Debye plasma on the frequency‐dependent polarizabilities of Li and Na atoms are investigated using symplectic algorithm within the framework of the pseudostate summation technique. Dynamic dipole polarizabilities of Li (2s 2S) and Na(3s 2S) as functions of scaled number density of the plasma electrons for arbitrary plasma temperature are presented. Screening effects on the resonance frequencies are also presented. In free‐atomic cases, our calculated results are comparable with the reported theoretical and experimental predictions. © 2012 Wiley Periodicals, Inc.  相似文献   
3.
We study the deconvolution of the secondary ion mass spectrometry (SIMS) depth profiles of silicon and gallium arsenide structures with doped thin layers. Special attention is paid to allowance for the instrumental shift of experimental SIMS depth profiles. This effect is taken into account by using Hofmann's mixing‐roughness‐information depth model to determine the depth resolution function. The ill‐posed inverse problem is solved in the Fourier space using the Tikhonov regularization method. The proposed deconvolution algorithm has been tested on various simulated and real structures. It is shown that the algorithm can improve the SIMS depth profiling relevancy and depth resolution. The implemented shift allowance method avoids significant systematic errors of determination of the near‐surface delta‐doped layer position. Copyright © 2013 John Wiley & Sons, Ltd.  相似文献   
4.
The recent development of X‐ray Photoelectron Spectroscopy (XPS) instrumentation with spatial resolution down to several microns has advanced the capability of elemental and chemical state imaging. XPS imaging analysis has been applied in understanding the delamination problems of siloxane coatings on polymethyl‐methacrylate (PMMA) polymer. It was found that delamination occurred by interfacial failure, and the coating suffered complete delamination from a PMMA substrate. This example offered an opportunity for the investigation of X‐ray damage on polymers encountered in XPS imaging analysis. This paper also demonstrated how to construct a constrained peak model with the aid of chemical knowledge and supporting evidence of the sample. Monte Carlo error analysis was used to determine the validity of the peak fit models used. Copyright © 2013 John Wiley & Sons, Ltd.  相似文献   
5.
A detailed understanding of the adsorption of small molecules or macromolecules to a materials surface is of importance, for example, in the context of material and biomaterial research. Classical atomistic simulations in principle provide microscopic insight in the complex entropic and enthalpic interplay at the interface. However, an application of classical atomistic simulation techniques to such interface systems is a nontrivial problem, mostly because commonly used force fields cannot be straightforwardly applied, as they are usually developed to reproduce bulk properties of either solids or liquids but not the interfacial region between two phases. Therefore, a dual‐scale modeling approach has often been the method of choice in the past, in which the classical force field is parameterized such that quantum chemical information on near‐surface conformations and adsorption energies is reproduced by the classical force field. We will discuss in this review the current state‐of‐the‐art of quantum‐classical modeling of molecule–surface interactions and outline the major challenges in this field. In this context, we will, among other things, lay emphasis on discussing ways to obtain representable force fields and propose systematic and system‐independent strategies to optimize the quantum‐classical fitting procedure. © 2013 Wiley Periodicals, Inc.  相似文献   
6.
O1s core‐electron binding energies (CEBE) of the atomic oxygens on different Ag surfaces were investigated by the symmetry adapted cluster‐configuration interaction (SAC‐CI) method combined with the dipped adcluster model, in which the electron exchange between bulk metal and adsorbate is taken into account properly. Electrophilic and nucleophilic oxygens (Oelec and Onuc) that might be important for olefin epoxidation in a low‐oxygen coverage condition were focused here. We consider the O1s CEBE as a key property to distinguish the surface oxygen states, and series of calculation was carried out by the Hartree–Fock, Density functional theory, and SAC/SAC‐CI methods. The experimental information and our SAC/SAC‐CI results indicate that Oelec is the atomic oxygen adsorbed on the fcc site of Ag(111) and that Onuc is the one on the reconstructed added‐row site of Ag(110) and that one‐ and two‐electron transfers occur, respectively, to the Oelec and Onuc adclusters from the silver surface. © 2013 Wiley Periodicals, Inc.  相似文献   
7.
Coarse‐grained protein structure models offer increased efficiency in structural modeling, but these must be coupled with fast and accurate methods to revert to a full‐atom structure. Here, we present a novel algorithm to reconstruct mainchain models from C traces. This has been parameterized by fitting Gaussian mixture models (GMMs) to short backbone fragments centered on idealized peptide bonds. The method we have developed is statistically significantly more accurate than several competing methods, both in terms of RMSD values and dihedral angle differences. The method produced Ramachandran dihedral angle distributions that are closer to that observed in real proteins and better Phaser molecular replacement log‐likelihood gains. Amino acid residue sidechain reconstruction accuracy using SCWRL4 was found to be statistically significantly correlated to backbone reconstruction accuracy. Finally, the PD2 method was found to produce significantly lower energy full‐atom models using Rosetta which has implications for multiscale protein modeling using coarse‐grained models. A webserver and C++ source code is freely available for noncommercial use from: http://www.sbg.bio.ic.ac.uk/phyre2/PD2_ca2main/ . © 2013 Wiley Periodicals, Inc.  相似文献   
8.
Water is an important component in living systems and deserves better understanding in chemistry and biology. However, due to the difficulty of investigating the water functions in protein structures, it is usually ignored in computational modeling, especially in the field of computer‐aided drug design. Here, using the potential of mean forces (PMFs) approach, we constructed a water PMF (wPMF) based on 3946 non‐redundant high resolution crystal structures. The extracted wPMF potential was first used to investigate the structure pattern of water and analyze the residue hydrophilicity. Then, the relationship between wPMF score and the B factor value of crystal waters was studied. It was found that wPMF agrees well with some previously reported experimental observations. In addition, the wPMF score was also tested in parallel with 3D‐RISM to measure the ability of retrieving experimentally observed waters, and showed comparable performance but with much less computational cost. In the end, we proposed a grid‐based clustering scheme together with a distance weighted wPMF score to further extend wPMF to predict the potential hydration sites of protein structure. From the test, this approach can predict the hydration site at the accuracy about 80% when the calculated score lower than ?4.0. It also allows the assessment of whether or not a given water molecule should be targeted for displacement in ligand design. Overall, the wPMF presented here provides an optional solution to many water related computational modeling problems, some of which can be highly valuable as part of a rational drug design strategy. © 2012 Wiley Periodicals, Inc.  相似文献   
9.
We investigate the influence of vibronic coupling on a molecular dimer strongly coupled to a single cavity mode. In the framework of the Holstein-Tavis-Cummings model, the energy structure of the molecular dimer is analyzed by numerical exact diagonalization and perturbation theory. Under numerical exact diagonalization, we find that the degeneracy of lower polaritons vanishes in the presence of vibronic coupling. Under the second-order degenerate perturbation theory, the degeneracy breaking of lower polaritons can be associated with asymmetric indirect interactions mediated by the upper polaritons and the dark states. The consistency of the two approaches confirms the robustness of our simulations, indicating that the vibration-induced symmetry breaking should be experimentally observed.  相似文献   
10.
Discrete choice models are widely used for understanding how customers choose between a variety of substitutable goods. We investigate the relationship between two well studied choice models, the Nested Logit (NL) model and the Markov choice model. Both models generalize the classic Multinomial Logit model and admit tractable algorithms for assortment optimization. Previous evidence indicates that the NL model may be well approximated by, or be a special case of, the Markov model. We establish that the Nested Logit model, in general, cannot be represented by a Markov model. Further, we show that there exists a family of instances of the NL model where the choice probabilities cannot be approximated to within a constant error by any Markov choice model.  相似文献   
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