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小木虫论坛-学术科研互动平台 » 计算模拟区 » 量子化学 » Gaussian » 【求助】直接导入晶体结构的数据来进行单点计算的文献
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tiechong

金虫 (著名写手)

[交流] 【求助】直接导入晶体结构的数据来进行单点计算的文献

哪位虫子看到过直接导出晶体结构来单点计算得到电子密度或者轨道的文献？
晶体结构和气相优化的结构无法统一，只关心固相下的性质, 所以打算放弃优化的结构，直接将晶体结构导入高斯来计算电子密度和轨道，用来解释固相下的结构，不知道这样做有意义不？有谁看到过这样的文献吗，没有进行优化或者放弃优化的结构直接使用晶体结构来解释固相下的性质？
太远的（比如上个世纪的)就不要了

[ Last edited by tiechong on 2009-9-25 at 10:38 ]
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yalefield

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tiechong(金币+1,VIP+0):跑题了，我问的不是这个阿 9-25 10:42
电荷密度分布专题

Peter Luger Fast electron density methods in the life sciences—a routine application in the future?
Org. Biomol. Chem., 2007, 5, 2529–2540

Birger Dittrich, Tibor Koritsnszky, and Peter Luger A Simple Approach to Nonspherical Electron Densities by Using Invarioms. Angew. Chem. Int. Ed. 2004, 43, 2718-2721

陈小明，引文：

（1）Guang Wu, Anatoliy Volkov, PhilipCoppens. X-ray charge density study of p-amino-p'-nitrobiphenyl at 20K using a CCD area detector and synchrotron radiation: a very large dipole moment enhancement in the solid state. Journal of Synchrotron Radiation. 1999. 6(5):1007-1015

（2）Anatoliy Volkov, Yuriy Abramov, Philip Coppens* and Carlo Gatti. On the origin of topological differences between experimental and theoretical crystal charge densities. Acta Cryst. (2000). A56(4):332-339

计算方法：

一、最大熵法（Maximum Entropy）

DOUGLAS M. COLLINS. Electron density images from imperfect data by iterative entropy maximization
Nature. 1982, 298:49-51

WENDO WEI. Application of the Maximum Entropy Method to Electron Density Determination
J. Appl. Cryst. (1985). 18, 442-445

Abstract: The principle of maximum entropy is adopted to derive a procedure for obtaining the electron density distribution in crystals from incomplete X-ray diffraction data. This method was applied to cementite and the result proved to be better than the conventional Fourier inversion in resolution as well as in the absence of ripples. The potential advantages of this method are: (1) the amount of subjective judgment imposed on unavailable data is significantly limited, and (2) the result of this method is consistent with the known information and maximally noncommittal with regard to the unknowns. It is shown that the method is especially well suited to the problem of the determination of a high-resolution electron density map from insufficient experimental data.

M. Sakata and M. Sato
Accurate structure analysis by the maximum-entropy method
Acta Cryst. (1990). A46, 263-270

S. Kumazawa, Y. Kubota, M. Takata, M. Sakata and Y. Ishibashi
MEED: a program package for electron-density-distribution calculation by the maximum-entropy method
J. Appl. Cryst. (1993). 26, 453-457

摘要？

C. J. Gilmore
Maximum Entropy and Bayesian Statistics in Crystallography: a Review of Practical Applications
Acta Cryst. (1996). A52:561-589

摘要？

Janusz Waliszewski and Ludwik Dobrzyńsk
On the Application of Maximum Entropy Method to the Electron Density Distribution and Phaseless Problem
J. Phys. Soc. Jpn. 70 (2001) pp. 148-154

摘要？

Janusz Waliszewski and Ludwik Dobrzyńsk
On the Application of Maximum Entropy Method to the Electron Density Distribution and Phaseless Problem
J. Phys. Soc. Jpn. 2001. 70(1):148-154

Abstract: The application of Maximum Entropy Method to the electron density reconstruction in the case of phaseless problem in both centro- and non-centrosymmetric structures is described. The use of specially constructed priors is suggested for a simultaneous refinement of the electron density distribution and phases of the observed structure factors. On an example of GaN data it is shown that a non-uniform prior may be a necessity for arriving at proper reconstruction of the charge density distributions. MEM can be also very sensitive to the positional parameters as demonstrated on the case of FeSi. The use of non-uniform prior helps also to understand the origin of covalent bonding, which is demonstrated on the Si case, for which obtained charge density distribution is in excellent agreement with theoretical predictions.

L. DOBRZYN′ SKI and J. WALISZEWSKI
Error Maps in Charge and Momentum Density Studies by the Maximum Entropy Methods
Journal of the Physical Society of Japan. 2003. 72(9):2203–2212

Abstract: The uncertainty of the electron charge and momentum densities reconstructed by the maximum entropy method is analyzed. The paper discusses various sources of uncertainties and errors that can appear in the reconstructions. In particular, it is shown that small features seen on the maps have to be treated with caution and analysis of their statistical significance must be particularly well done.


二、多极修正（Multipole Refinement）

1、初始文献

N. K. Hansen and P. Coppens
Testing aspherical atom refinements on small-molecule data sets
Acta Cryst. (1978). A34, 909-921

提出了multipolar pseudo-atom model

Abstract: X-ray data on silicon, tetracyanoethylene, p-nitropyridine N-oxide and ammonium thiocyanate are refined with a generalized aspherical-atom formalism as introduced by Stewart, but modified to have a spherical valence more similar to the unperturbed HF valence shell. Several types of radial dependences of the multipole functions are tested and criteria are developed for judging the adequacy of the aspherical-atom refinement. The aspherical-atom model leads to a significant decrease in the least-squares error function, a reduction of features in the residual map, and an improvement in thermal parameters when comparison is made with the neutron results or when the rigid-bond postulate proposed by Hirshfeld is applied. Positional parameters are often improved except in the case of terminal atoms for which discrepancies, attributed to correlation between dipole-population and positional parameters, are sometimes observed. Deformation maps based on the aspherical-atom least-squares parameters contain less noise than X -- N maps and benefit from inclusion of calculated values of weak structure amplitudes in the summation. In the cases studied, deformation maps including terms beyond the experimental resolution do not yield additional information.

2、关于MoPro程序

http://www.crystallography.fr/emqc/mopro.html

MoPro is a cristallographic least square refinement package allowing structural or charge density studies of cristal stuctures of variable sizes, ranging from small molecules to biological macromolecules.

It implements spherical and non spherical, multipolar model of atomic electron density, the latter being necessary to take into account the deformation of electron density arising from interatomic interactions, which becomes visible and quantifiable at subatomic resolution.

Its complementary program VMoPro allows the computation of derived properties based on the multipolar formalism, as molecular electrostatic potential, topological properties or intermolecular interaction énergies.

MoPro and VMoPro are interfaced with the experimental multipolar database, which groups the multipolar parameters necessary to describe the charge density of common protein chemical groups. hence, the transfer of these parameters allows to compute derived electrostatic properties of biological macromolecules obtained at atomic resolution only.

MoPro的程序，引用文献：

Guillot, B., Viry, L., Guillot, R., Lecomte, C., and Jelsch, C.
Refinement of proteins at subatomic resolution with MOPRO
J. Appl. Crystallogr. 2001. 34(2):214–223

Abstract: Crystallography at subatomic resolution permits the observation and measurement of the non-spherical character of the atomic electron density. Charge density studies are being performed on molecules of increasing size. The MOPRO least-squares refinement software has thus been developed, by extensive modifications of the program MOLLY, for protein and supramolecular chemistry applications. The computation times are long because of the large number of reflections and the complexity of the multipolar model of the atomic electron density; the structure factor and derivative calculations have thus been parallelized. Stereochemical and dynamical restraints as well as the conjugate gradient algorithm have been implemented. A large number of the normal matrix off-diagonal terms turn out to be very small and the block diagonal approximation is thus particularly efficient in the case of large structures at very high resolution.

C. Jelsch, B. Guillot, A. Lagoutte and C. Lecomte
Advances in protein and small-molecule charge-density refinement methods using MoPro
J. Appl. Cryst. (2005). 38(1):38-54

Abstract: With an increasing number of biological macromolecule structures solved at ultra-high resolution and with the advances of supramolecular chemistry, it becomes necessary to extend to large systems experimental charge-density study methods that are usually applied to small molecules. The latest developments in the refinement program MoPro (Molecular Properties), dedicated to the charge-density refinement at (sub)atomic resolution of structures ranging from small molecules to biological macromolecules, are presented. MoPro uses the Hansen & Coppens [Acta Cryst. (1978), A34, 909-921] multipolar pseudo-atom model for the electron-density refinement. Alternative methods are also proposed, such as modelling bonding and lone-pair electron density by virtual spherical atoms. For proteins at atomic resolution, a charge-density database developed in the laboratory enables the transfer of multipolar parameters. The program allows complex refinement strategies to be written and has numerous restraints, constraints and analysis tools for use in the structure and electron-density analysis. New kappa and multipolar parameter restraints/constraints are also implemented and discussed. Furthermore, constraints on the electron density, such as local symmetry and atom equivalence, are easily defined. Some examples of applications, from small molecules to large unit cells (including the enzyme aldose reductase), are given in order to guide the MoPro user and to show the large field of applicability of this code.

实例：

R. Guillot, N. Muzet, S. Dahaoui, C. Lecomte and C. Jelsch
Experimental and theoretical charge density of DL-alanyl-methionine
Acta Cryst. 2001. B57(4):567-578

Abstract: X-ray diffraction data up to d = 0.50 Å resolution have been collected at 100 K for a DL-alanyl-methionine single crystal using a CCD area detector. Multipolar crystallographic refinement was carried out and the electron density of the molecule has been analyzed. The deformation electron density around the S atom reveals two lone pairs with an sp3 hybridization and agrees with the results of density functional theory calculations. The topological properties of the covalent bonds and of the hydrogen bonds have been investigated. Two weak polar intramolecular interactions of the type C5 (pentagonal cyclic structure) have unfavorable geometrical parameters for hydrogen bonds and are devoid of critical points. The two electron lone pairs of the carbonyl oxygen appear asymmetric in the experimental deformation density. This could be attributed to the different strength of the hydrogen bond and intramolecular polar interaction involving the carbonyl oxygen. In the ab-initio-derived deformation maps, the asymmetry of the electron doublets is reproduced only very partially.

[ Last edited by yalefield on 2009-9-25 at 10:19 ]
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