scholarly journals New developments in the BayMEM Suite

2014 ◽  
Vol 70 (a1) ◽  
pp. C103-C103
Author(s):  
Christian Hübschle ◽  
Sander van Smaalen
Keyword(s):  
Electrostatic Potential ◽  
Maximum Entropy Method ◽  
Dynamic Deformation ◽  
Entropy Method ◽  
Prior Density ◽  
New Developments ◽  
Deformation Density ◽  
File Formats ◽  
Modulated Structures ◽  
Dynamic Charge

The program suite BayMEM consists of the programs PRIOR, BayMEM and EDMA. It is intended to apply the Maximum Entropy Method (MEM) to ordinary and modulated structures[1]. The PRIOR program is intended to calculate the prior density for the MEM calculation, but it has been recently shown that it can be used to calculate the dynamic charge density from multipolar refinements[2] as well. As a new functionality it is now also possible to calculate the electrostatic potential from the dynamic deformation density by the method described by Steward and Spackman[3]. We will present a new MapConverter program which allows to convert electron density stored in different file formats into an other. It is also possible to rearrange and cut the density in such a way, that it is possible, to have clear view of one molecule, not obscured by its symmetry mates, in a molecular viewer like MoleCoolQt for example.

scholarly journals Nanoporous Structural Science Developed by the MEM/Rietveld Method

2014 ◽  
Vol 70 (a1) ◽  
pp. C1467-C1467
Author(s):  
Masaki Takata ◽  
Eiji Nishibori ◽  
Yoshiki Kubota ◽  
Hiroshi Tanaka
Keyword(s):  
Electrostatic Potential ◽  
Incomplete Data ◽  
Maximum Entropy Method ◽  
Rietveld Method ◽  
Entropy Method ◽  
Wide Spread ◽  
Noise Resistance ◽  
Data Set ◽  
Density Mapping ◽  
Metal Organic

Wide-spread functionalization research of Metal Organic Frameworks(MOFs) has brought rapid increase in variety of materials since the beginning of structural study in nanoporous of MOFs were made by SR(Synchrotron Radiation) powder diffraction using the MEM(Maximum Entropy Method)/Rietveld Method(Kitaura et al, 2002). The MEM/Rietveld method has successfully applied to refine the structural position of absorbed molecules and to investigate a bonding nature between the molecules and MOF's pore walls. Noise-resistance electron density mapping with incomplete data set was a key advantage of MEM to visualize unmodeled feature of molecules in nanoporous. Since then, the charge density studies by the MEM/Rietveld Method have uncovered various ordering structure of absorbed molecules into nanoporous more and more(Takata, 2008). Those findings ignited trends to design the nanoporous as the space to be functionalized. Recently, the MEM/Rietveld method has been further developed as the method to map an electrostatic potential and electric field(Tanaka 2006). This technique is making a progress in structural science of MOFs since the visualized electrostatic potential in the nanoporous ought to provide information of interplay between the molecule and the pore walls. The talk will present the recent progress and challenges of the MEM/Rietveld method to the structural science of the MOFs.

scholarly journals Topological properties of hydrogen bonds and covalent bonds from charge densities obtained by the maximum entropy method (MEM)

2009 ◽  
Vol 65 (5) ◽  
pp. 624-638 ◽  
Author(s):  
Jeanette Netzel ◽  
Sander van Smaalen
Keyword(s):  
Hydrogen Bonds ◽  
Maximum Entropy ◽  
Maximum Entropy Method ◽  
Dynamic Deformation ◽  
Entropy Method ◽  
Topological Properties ◽  
Covalent Bonds ◽  
Charge Densities

Charge densities have been determined by the Maximum Entropy Method (MEM) from the high-resolution, low-temperature (T ≃ 20 K) X-ray diffraction data of six different crystals of amino acids and peptides. A comparison of dynamic deformation densities of the MEM with static and dynamic deformation densities of multipole models shows that the MEM may lead to a better description of the electron density in hydrogen bonds in cases where the multipole model has been restricted to isotropic displacement parameters and low-order multipoles (l max = 1) for the H atoms. Topological properties at bond critical points (BCPs) are found to depend systematically on the bond length, but with different functions for covalent C—C, C—N and C—O bonds, and for hydrogen bonds together with covalent C—H and N—H bonds. Similar dependencies are known for AIM properties derived from static multipole densities. The ratio of potential and kinetic energy densities |V(BCP)|/G(BCP) is successfully used for a classification of hydrogen bonds according to their distance d(H...O) between the H atom and the acceptor atom. The classification based on MEM densities coincides with the usual classification of hydrogen bonds as strong, intermediate and weak [Jeffrey (1997). An Introduction to Hydrogen Bonding. Oxford University Press]. MEM and procrystal densities lead to similar values of the densities at the BCPs of hydrogen bonds, but differences are shown to prevail, such that it is found that only the true charge density, represented by MEM densities, the multipole model or some other method can lead to the correct characterization of chemical bonding. Our results do not confirm suggestions in the literature that the promolecule density might be sufficient for a characterization of hydrogen bonds.

Experimental charge density and electrostatic potential in nicotinamide

1999 ◽  
Vol 55 (1) ◽  
pp. 78-84 ◽  
Author(s):  
Yoshihisa Miwa ◽  
Takashi Mizuno ◽  
Kazunori Tsuchida ◽  
Tooru Taga ◽  
Yutaka Iwata
Keyword(s):  
Electrostatic Potential ◽  
Pyridine Ring ◽  
Electron Distribution ◽  
Maximum Entropy Method ◽  
Molecular Conformation ◽  
Entropy Method ◽  
Ring Plane ◽  
X Ray ◽  
Experimental Charge Density ◽  
Potential Peak

The accurate crystal structure of nicotinamide, 3-pyridinecarboxamide, was determined from X-ray and neutron diffraction experiments: C6H6N2O, Mr = 122.13, monoclinic, P21/c, Z = 4. The electron distribution at 150 K was determined by the maximum entropy method and the electrostatic potential in the crystal was calculated by Fourier convolution of the electron distribution. The electrostatic properties of the nicotinamide molecule depend on the molecular conformation. The asymmetric electrostatic potential field observed above and below the pyridine-ring plane is related to the rotation of the carboxamide group with respect to the pyridine plane. The positive potential peak at the C4 atom of the pyridine ring extends to the C=O-group side of the plane. The asymmetry of the potential on the C4 atom is consistent with the stereospecificity of hydride transfer in NAD+/NADH oxidoreduction.

Incommensurate modulations made visible by the Maximum Entropy Method in superspace

2004 ◽  
Vol 219 (11) ◽  
Author(s):  
Lukás Palatinus ◽  
Sander van Smaalen
Keyword(s):  
Missing Data ◽  
Maximum Entropy ◽  
Electron Density ◽  
Maximum Entropy Method ◽  
Entropy Method ◽  
Basic Principles ◽  
Layer Compound ◽  
Modulated Structures ◽  
Structure Solution ◽  
Superspace Formalism

AbstractThis paper presents the application of the Maximum Entropy Method (MEM) to structure solution of incommensurately modulated structures within the superspace formalism. The basic principles of the MEM are outlined, and its generalization toward superspace is discussed. Possible problems in MEM reconstructions and their solutions are summarized. They include series-termination errors in the reconstructed electron density, the effect of insufficient constraints, and the effect of missing data. The use of the MEM in superspace is illustrated by three examples: the structure of the misfit-layer compound (LaS)

Enhanced Information Recovery in 2D On-and Off-Resonance Nutation NQR using the Maximum Entropy Method

1996 ◽  
Vol 51 (5-6) ◽  
pp. 337-347 ◽  
Author(s):  
Mariusz Maćkowiak ◽  
Piotr Kątowski
Keyword(s):  
Maximum Entropy ◽  
Maximum Entropy Method ◽  
Theoretical Description ◽  
Entropy Method ◽  
Zero Field ◽  
Resonance Effects ◽  
Information Recovery ◽  
Truncation Errors ◽  
Enhanced Resolution ◽  
2D Data

Abstract Two-dimensional zero-field nutation NQR spectroscopy has been used to determine the full quadrupolar tensor of spin - 3/2 nuclei in serveral molecular crystals containing the 3 5 Cl and 7 5 As nuclei. The problems of reconstructing 2D-nutation NQR spectra using conventional methods and the advantages of using implementation of the maximum entropy method (MEM) are analyzed. It is shown that the replacement of conventional Fourier transform by an alternative data processing by MEM in 2D NQR spectroscopy leads to sensitivity improvement, reduction of instrumental artefacts and truncation errors, shortened data acquisition times and suppression of noise, while at the same time increasing the resolution. The effects of off-resonance irradiation in nutation experiments are demonstrated both experimentally and theoretically. It is shown that off-resonance nutation spectroscopy is a useful extension of the conventional on-resonance experiments, thus facilitating the determination of asymmetry parameters in multiple spectrum. The theoretical description of the off-resonance effects in 2D nutation NQR spectroscopy is given, and general exact formulas for the asymmetry parameter are obtained. In off-resonance conditions, the resolution of the nutation NQR spectrum decreases with the spectrometer offset. However, an enhanced resolution can be achieved by using the maximum entropy method in 2D-data reconstruction.

Estimating the distribution of primary reflection coefficients

Geophysics ◽  
2003 ◽  
Vol 68 (4) ◽  
pp. 1417-1422 ◽  
Author(s):  
Danilo R. Velis
Keyword(s):  
Maximum Entropy ◽  
Maximum Entropy Method ◽  
Entropy Method ◽  
Reflection Coefficients ◽  
Log Data ◽  
Neuquen Basin ◽  
Neuquén Basin ◽  
Skewness And Kurtosis

The distribution of primary reflection coefficients can be estimated by means of the maximum entropy method, giving rise to smooth nonparametric functions which are consistent with the data. Instead of using classical moments (e.g. skewness and kurtosis) to constraint the maximization, nonconventional sample statistics help to improve the quality of the estimates. Results using real log data from various wells located in the Neuquen Basin (Argentina) show the effectiveness of the method to estimate both robust and consistent distributions that may be used to simulate realistic sequences.

ISLAND-SIZE DISTRIBUTIONS OF Ag ON Pd(111)

1996 ◽  
Vol 03 (03) ◽  
pp. 1393-1402 ◽  
Author(s):  
R. FISCHER ◽  
TH. FAUSTER ◽  
W. VON DER LINDEN ◽  
V. DOSE
Keyword(s):  
Maximum Entropy Method ◽  
Entropy Method ◽  
Bayesian Probability ◽  
Magic Numbers ◽  
Size Distributions ◽  
Island Size ◽  
Two Phase ◽  
Two Photon ◽  
Small Clusters ◽  
Image State

Island-size distributions of submonolayer Ag films on Pd(111) adsorbed at 90 K and after annealing of the film are recovered from two-photon photoemission spectra of the first image state. The inversion of the ill-conditioned problem with the maximum-entropy method reveals magic numbers in the island-size distributions. Hypothesis testing within the framework of Bayesian probability theory indicates a critical nucleus size i=1. After annealing of the film large islands coexist with small clusters in a two-phase state.

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