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991.
Xin Feng Kelin Xia Zhan Chen Yiying Tong Guo‐Wei Wei 《Journal of computational chemistry》2013,34(24):2100-2120
Geometric modeling of biomolecules plays an essential role in the conceptualization of biolmolecular structure, function, dynamics, and transport. Qualitatively, geometric modeling offers a basis for molecular visualization, which is crucial for the understanding of molecular structure and interactions. Quantitatively, geometric modeling bridges the gap between molecular information, such as that from X‐ray, NMR, and cryo‐electron microscopy, and theoretical/mathematical models, such as molecular dynamics, the Poisson–Boltzmann equation, and the Nernst–Planck equation. In this work, we present a family of variational multiscale geometric models for macromolecular systems. Our models are able to combine multiresolution geometric modeling with multiscale electrostatic modeling in a unified variational framework. We discuss a suite of techniques for molecular surface generation, molecular surface meshing, molecular volumetric meshing, and the estimation of Hadwiger's functionals. Emphasis is given to the multiresolution representations of biomolecules and the associated multiscale electrostatic analyses as well as multiresolution curvature characterizations. The resulting fine resolution representations of a biomolecular system enable the detailed analysis of solvent–solute interaction, and ion channel dynamics, whereas our coarse resolution representations highlight the compatibility of protein‐ligand bindings and possibility of protein–protein interactions. © 2013 Wiley Periodicals, Inc. 相似文献
992.
The conditions of formation of strong two‐center one‐electron bonds in neutral compounds are discussed. Both molecular orbital and valence bond analyses show that good candidates are adducts of radicals .AR3 (A=C, Si, Ge) of low ionization energy (IE) with boranes BX3 of high electron affinity (EA). This is confirmed by ab initio calculations. The bond energy of adducts of B(CF3)3 with various radicals ranges from 18 kcal mol?1 for .CH3 to approximately 40 kcal mol?1 for Me3Si., and a clear correlation with IE–EA difference is found. This allows one to expect B(CF3)3, among other fluoroboranes, to be an efficient radical scavenger. 相似文献
993.
Latifa Latrous Jeanine Tortajada Violette Haldys Emmanuelle Léon Catarina Correia Jean‐Yves Salpin 《Journal of mass spectrometry : JMS》2013,48(7):795-806
Gas‐phase interactions of organotins with glycine have been studied by combining mass spectrometry experiments and quantum calculations. Positive‐ion electrospray spectra show that the interaction of di‐ and tri‐organotins with glycine results in the formation of [(R)2Sn(Gly)‐H]+and [(R)3Sn(Gly)]+ ions, respectively. Di‐organotin complexes appear much more reactive than those involving tri‐organotins. (MS/MS) spectra of the [(R)3Sn(Gly)]+ ions are indeed simple and only show elimination of intact glycine, generating the [(R)3Sn]+ carbocation. On the other hand, MS/MS spectra of [(R)2Sn(Gly)‐H]+complexes are characterized by numerous fragmentation processes. Six of them, associated with elimination of H2O, CO, H2O + CO and formation of [(R)2SnOH]+ (?57 u),[(R)2SnNH2]+( ?58 u) and [(R)2SnH]+ (?73 u), are systematically observed. Use of labeled glycines notably concludes that the hydrogen atoms eliminated in water and H2O + CO are labile hydrogens. A similar conclusion can be made for hydrogens of [(R2)SnOH]+and [(R2)SnNH2]+ions. Interestingly, formation [(R)2SnH]+ ions is characterized by a migration of one the α hydrogen of glycine onto the metallic center. Finally, several dissociation routes are observed and are characteristic of a given organic substituent. Calculations indicated that the interaction between organotins and glycine is mostly electrostatic. For [(R)2Sn(Gly)‐H]+complexes, a preferable bidentate interaction of the type η2‐O,NH2 is observed, similar to that encountered for other metal ions. [(R)3Sn]+ ions strongly stabilize the zwitterionic form of glycine, which is practically degenerate with respect to neutral glycine. In addition, the interconversion between both forms is almost barrierless. Suitable mechanisms are proposed in order to account for the most relevant fragmentation processes. Copyright © 2013 John Wiley & Sons, Ltd. 相似文献
994.
995.
996.
Ab initio molecular orbital theory and density functional theory have been used to study nine isomers of N7 ionic clusters with low spin at the HF/6-31G*, MP2/6-31G*, B3LYP/6-31G*, and B3LYP/6-311(+)G* levels of theory. All stationary
points are examined with harmonic vibrational frequency analyses. Four N7
+ isomers and five N7
− isomers are determined to be local minima or very close to the minima on their potential-energy hypersurfaces, respectively.
For N7
+ and N7
−, the energetically low lying isomers are open-chain structures (C
2
v
and C
2
v
or C2). The results are very similar to those of other known odd-number nitrogen ions, such as N5
+, N9
+, and N9
−, for which the open-chain structures are also the global minima. This research suggests that the N7 ionic clusters are likely to be stable and to be potential high-energy-density materials if they could be synthesized.
Received: 16 July 2001 / Accepted: 8 October 2001 / Published online: 21 January 2002 相似文献
997.
Sławomir J. Grabowski 《Monatshefte für Chemie / Chemical Monthly》2002,133(11):1373-1380
Summary. The topological parameters derived from the Bader theory such as the electron density and its Laplacian at the ring critical point (RCP) are analysed here as possible measures of the H-bond stength for intramolecular H-bonds.
The parameters of RCP correlate well with the other properties of intramolecular H-bonds which are known as good measures
of the H-bond strength. The calculations were performed on two samples of compounds with intramolecular H-bonds: the derivatives
of malonaldehyde and the derivatives of o-hydroxybenzaldehyde. MP2 and HF calculations were carried out using a 6-311++G** basis set.
E-mail: slagra@krysia.uni.lodz.pl
Received February 18, 2002; accepted (revised) May 27, 2002 相似文献
998.
应用从头算分子轨道法分别在RHF/6-31G**和UHF/6-31G**水平上对3腔┤┓肿拥幕?S0)和三重激发态(T1)单键旋转异构反应机理进行了研究,优化出反应物和产物在S0态和T1态的4种平衡态和过渡态的几何构型,通过振动分析得到的虚频和计算的内禀反应坐标对过渡态进行了确认,并得到了零点能,根据基态和激发态反应途径分析了光反应机理。计算结果表明,基态和激发态的3腔┤┓肿拥ゼ旃狗从ξ焕萁系停嘏湃菀追⑸永砺凵涎橹ち斯夥从κ笛橹屑钢忠旃固宓拇嬖凇? 相似文献
999.
Teobald Kupka Roman Wrzalik Gra
yna Pasterna Karol Pasterny 《Journal of Molecular Structure》2002,616(1-3):17-32
The results of extended MO calculations using density functional theory (DFT) approximation supported by experimental Raman, 1H and 13C NMR studies on thiophene are reported. Raman spectra of liquid thiophene were re-examined and the performance of a hybrid B3PW91 density functional was compared with the ab initio restricted Hartree–Fock (RHF) method. With the basis sets of the 6-311++G** quality, the DFT calculated bond lengths, dipole moments and harmonic vibrations were predicted in a very good agreement with available experimental data.
Additionally, the results on thiophene were extended by calculations on 3-methylthiophene and selenophene. In this case, a significant change in geometry and charge distribution in thiophene ring due to a methyl group substituent or replacement of sulphur by selene atom was observed.
A linear correlation between the predicted harmonic vibrational frequencies (scaled using SQM method) and experimental ones for thiophene, selenophene and 3-methylthiophene was shown. The theoretically calculated spectra have satisfactorily reproduced the available experimental spectra for thiophene and selenophene. 相似文献
1000.
Recently, Gill and Chien introduced a new radial quadrature for multiexponential integrands (MultiExp grid) to deal with the radial part of the numerical integration. In this article, the MultiExp grid is studied and used to integrate the charge density. The MultiExp grid, along with an optimal pruning scheme, performed very well both in terms of accuracy and efficiency compared to other radial mappings commonly used in Density Functional Theory. 相似文献