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151.
苯并三氮唑及其羧酸酯衍生物对铜缓蚀机理的分子动力学模拟研究 总被引:1,自引:0,他引:1
用分子动力学(MD)方法, 模拟计算了5种铜缓蚀剂[苯并三氮唑(BTA)、苯并三氮唑-5-羧酸甲酯(MBTC)、苯并三氮唑-5-羧酸丁酯(BBTC)、苯并三氮唑-5-羧酸己酯(HBTC)、苯并三氮唑-5-羧酸辛酯(OBTC)]与Cu2O晶体的相互作用. 结果发现, 中性条件下缓蚀剂分子与Cu2O晶体的结合能均大于酸性条件下的数值, 但两种条件下结合能的大小排序均为OBTC>HBTC>BBTC>MBTC>BTA. 对体系各种相互作用以及对关联函数g(r)的分析表明, 体系结合能主要由库仑作用提供, Cu2O晶体中的Cu原子与缓蚀剂分子中的N原子之间形成了配位键. 在与Cu2O(001)晶面结合过程中, BTA及其衍生物分子发生了扭曲变形, 但形变能远小于体系的非键相互作用能. 相似文献
152.
Julliane Diniz Yoneda Magaly Giro Albuquerque Ktia Zaccur Leal Peter R. Seidl Ralph A. Wheeler Scott E. Boesch Ricardo Bicca de Alencastro Maria Cecília B.V. de Souza Vitor F. Ferreira 《Journal of Molecular Structure》2006,778(1-3):97-103
Conformational analysis of nucleosides may have direct applications to the structure–activity relationship (SAR) studies and in the design of new drug candidates. Although conformational analysis may be accessed in many different ways, in this work it was performed using molecular dynamics (MD) simulation in order to study the dynamic behavior of a nucleoside derivative of 1,4-dihydro-4-oxoquinoline-3-carboxylic acid, synthesized by our group as a potential antiviral agent. The MD simulation was carried out during 10 ns in vacuum and in a box of water at two different temperatures (i.e., 300 and 600 K) using the AMBER force field. The in vacuum MD simulation results are in agreement with the crystallographic structure and with the DFT calculations of the nucleoside, revealing the anti conformer as the more stable one. The simulation in water, however, shows that both conformers may exist at 300 K, the temperature of the in vivo and in vitro assays, revealing that both the syn and anti conformers should be considered in a MD simulation study of the inhibitor–enzyme complex. Simulations are also in agreement with the NOE experiment, which shows that the anti conformer is the preferential one in DMSO-d6 solution at 298 K. 相似文献
153.
A global optimization strategy, based upon application of a genetic algorithm (GA), is demonstrated as an approach for determining the structures of molecules possessing significant conformational flexibility directly from gas-phase electron diffraction data. In contrast to the common approach to molecular structure determination, based on trial-and-error assessment of structures available from quantum chemical calculations, the GA approach described here does not require expensive quantum mechanical calculations or manual searching of the potential energy surface of the sample molecule, relying instead upon simple comparison between the experimental and calculated diffraction pattern derived from a proposed trial molecular structure. Structures as complex as all-trans retinal and p-coumaric acid, both important chromophores in photosensing processes, may be determined by this approach. In the examples presented here, we find that the GA approach can determine the correct conformation of a flexible molecule described by 11 independent torsion angles. We also demonstrate applications to samples comprising a mixture of two distinct molecular conformations. With these results we conclude that applications of this approach are very promising in elucidating the structures of large molecules directly from electron diffraction data. 相似文献
154.
Several methodologies were employed to calculate the Gibbs standard free energy of binding for a collection of protein-ligand complexes, where the ligand is a peptide and the protein is representative for various protein families. Almost 40 protein-ligand complexes were employed for a continuum approach, which considers the protein and the peptide at the atomic level, but includes solvent as a polarizable continuum. Five protein-ligand complexes were employed for an all-atom approach that relies on a combination of the double decoupling method with thermodynamic integration and molecular dynamics. These affinities were also computed by means of the linear interaction energy method. Although it generally proved rather difficult to predict the absolute free energies correctly, for some protein families the experimental ranking order was correctly reproduced by the continuum and all-atom approach. Considerable attention has also been given to correctly analyze the affinities of charged peptides, where it is required to judge the effect of one or more ions that are being decoupled in an all-atom approach to preserve electroneutrality. The various methods are further judged upon their merits. 相似文献
155.
156.
Complex permittivity spectra in the frequency range 0.95v (GHz)89 for acetonitrile and its solutions of LiBr, NaI, NaClO4, and Bu4NBr at 25°C show one Debye equation for the neat solvent whereas the superposition of a Debye process for the solute and a Cole-Cole distribution for the solvent is necessary to account for the dielectric relaxation behavior of the solutions. The reorientation of bulk acetonitrile is diffusive and only weakly coupled to viscosity. The number of solvent molecules irrotationally bound to the electrolyte is in good agreement with conventional solvation numbers for all electrolytes, when kinetic depolarization is assumed to be negligible. The solute relaxation process is dominated by the formation kinetics and reorientation of contact ion pairs. There is evidence for solvent-shared ion pairs in dilute NaClO4 solutions. 相似文献
157.
I NQR and spectroscopic investigation of impurity-doped and mixed lithium iodate Li1−xHxIO3 crystals
A. Barabash T. Gavrilko K. Eshimov J. Baran H. Ratajczak 《Journal of Molecular Structure》2004,708(1-3):113-116
The 127I NQR, IR absorption and Raman spectra of impurity-doped and mixed lithium iodate Li1−xHxIO3 crystals grown from water solutions with different LiIO3/HIO3 ratios were investigated depending on the content of the impurity hydrogen x. The NQR results suggested that, at small concentration of doping iodic acid x<0.22, the lattice dynamics of the crystal grown from water solution changes significantly though the crystal retains hexagonal symmetry. Spectroscopic studies are compatible with average hexagonal symmetry of the grown doped crystals. From the results of Raman studies at room temperature and 100 K, the concentration range of hydrogen dopant 0.22<x<0.36 was found where disordered solid solution crystals Li1−xHxIO3 are formed. 相似文献
158.
Tatiana Murakhtina Jasper Heuft Evert Jan Meijer Daniel Sebastiani 《Chemphyschem》2006,7(12):2578-2584
A combined experimental and ab initio study is presented of the 1H NMR chemical shift distribution of aqueous hydrogen chloride solution as a function of acid concentration, based on Car-Parrinello molecular dynamics simulations and fully periodic NMR chemical-shift calculations. The agreement of computed and experimental spectra is very good. From first-principles calculations, we can show that the individual contributions of Eigen and Zundel ions, regular water molecules, and the chlorine solvation shell to the NMR line are very distinct and almost independent of the acid concentration. From the computed instantaneous NMR distributions, it is further possible to characterize the average variation in hydrogen-bond strength of the different complexes. 相似文献
159.
Ciminelli C Granucci G Persico M 《Chemistry (Weinheim an der Bergstrasse, Germany)》2004,10(9):2327-2341
We have simulated the photoisomerization dynamics of azobenzene, taking into account internal conversion and geometrical relaxation processes, by means of a semiclassical surface hopping approach. Both n-->pi* and pi-->pi* excitations and both cis-->trans and trans-->cis conversions have been considered. We show that in all cases the torsion around the N==N double bond is the preferred mechanism. The quantum yields measured are correctly reproduced and the observed differences are explained as a result of the competition between the inertia of the torsional motion and the premature deactivation of the excited state. Recent time-resolved spectroscopic experiments are interpreted in the light of the simulated dynamics. 相似文献
160.
Energized molecules are the essential actors in chemical transformations in solution. As the rearrangement of bonds requires a movement of nuclei, vibrational energy is often the driving force for a reaction. Vibrational energy can be redistributed within the "hot" molecule, or relaxation can occur when molecules interact. Both processes govern the rates, pathways, and quantum yields of chemical transformations in solution. Unfortunately, energy transfer and the breaking, formation, and rearrangement of bonds take place on ultrafast timescales. This Review highlights experimental approaches for the direct, ultrafast measurement of photoinduced femtochemistry and energy flow in solution. In the first part of this Review, we summarize recent experiments on intra- and intermolecular energy transfer. The second part discusses photoinduced decomposition of large organic peroxides, which are used as initiators in free radical polymerization. The mechanisms and timescales of their decarboxylation determine the initial steps of polymerization and the microstructure of the polymer product. 相似文献