The flexible alignment of molecular structures using simulated annealing with weighted Lagrangian multipliers

2010 ◽  
Vol 32 (2) ◽  
pp. 210-217 ◽  
Author(s):  
John W. Raymond ◽  
Daniel D. Holsworth ◽  
Mehran Jalaie
Keyword(s):  
Simulated Annealing ◽  
Molecular Structures ◽  
Lagrangian Multipliers ◽  
Flexible Alignment

Molecular Design of Solvents for Extractive Distillation

2011 ◽  
Vol 233-235 ◽  
pp. 2938-2944
Author(s):  
Jing Song ◽  
Tao Qi ◽  
Jing Kui Qu ◽  
Xue Gang Zhang ◽  
Wei Feng Shen
Keyword(s):  
Simulated Annealing ◽  
Environmental Performance ◽  
Simulated Annealing Algorithm ◽  
Molecular Design ◽  
Extractive Distillation ◽  
Molecular Structures ◽  
Separation Performance ◽  
Transition Strategies ◽  
Annealing Algorithm ◽  
Group Contribution Methods

This paper presents an optimization technology for the molecular design of environmentally friendly solvents for extractive distillation. The approach based on the concept of group contribution methods (GCM). To decrease the complexity and random of design problem, a set of functional groups are pre-selected based on the modified UNIFAC method. Combination of groups can produce different molecule, once the molecule is generated, the properties are evaluated to determine if it satisfy the criteria. The criteria include separation performance and environmental performance. Simulated annealing algorithm is used to search feasible molecular structures. The molecule transition strategies and parameters of algorithm are described detailedly. Finally, the method is demonstrated with two examples, and the design results show that the proposed technology is a valid technology to design the desirable solvents.

Solution of organic crystal structures from powder diffraction by combining simulated annealing and direct methods

2003 ◽  
Vol 36 (2) ◽  
pp. 230-238 ◽  
Author(s):  
Angela Altomare ◽  
Rocco Caliandro ◽  
Carmelo Giacovazzo ◽  
Anna Grazia Giuseppina Moliterni ◽  
Rosanna Rizzi
Keyword(s):  
Monte Carlo ◽  
Simulated Annealing ◽  
Electron Density ◽  
Powder Diffraction ◽  
Direct Methods ◽  
Molecular Geometry ◽  
Molecular Structures ◽  
Chemical Information ◽  
Density Map ◽  
Electron Density Map

Theab initiocrystal structure solution from powder diffraction data can be attemptedviadirect methods. If heavy atoms are present, they are usually correctly located; then some crystal chemical information can be exploited to complete the partial structure model. Organic structures are more resistant to direct methods; as an alternative, their molecular geometry is used as prior information for Monte Carlo methods. In this paper, a new procedure is described which combines the information contained in the electron density map provided by direct methods with a Monte Carlo method which uses simulated annealing as a minimization algorithm. A figure of merit has been designed based on the agreement between the experimental and calculated profiles, and on the positions of the peaks in the electron density map. The procedure is completely automatic and has been included inEXPO; its performance has been validated and tested for a set of known molecular structures.

scholarly journals Application of simulated annealing approach for structure solution of molecular crystals from X-ray laboratory powder data

2001 ◽  
Vol 216 (1) ◽  
Author(s):  
S. G. Zhukov ◽  
V. V. Chernyshev ◽  
E. V. Babaev ◽  
E. J. Sonneveld ◽  
H. Schenk
Keyword(s):  
Simulated Annealing ◽  
Molecular Crystals ◽  
Molecular Structures ◽  
X Ray ◽  
Structure Solution

AbstractSimulated annealing approach was successfully applied to solve three unknown molecular structures from X-ray laboratory powder data using

Crystal structure and diffraction data for a polymorph of voglibose (C10H21NO7)

2010 ◽  
Vol 25 (S1) ◽  
pp. S28-S30
Author(s):  
G. Q. Zhang ◽  
G. L. Lv
Keyword(s):  
Crystal Structure ◽  
Simulated Annealing ◽  
Rigid Body ◽  
Rietveld Refinement ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Molecular Structures ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Crystal And Molecular Structures

X-ray powder diffraction data of voglibose are reported, and its crystal and molecular structures were determined by simulated annealing and rigid-body Rietveld refinement methods. Voglibose was found to be crystallized in triclinic symmetry with space group P-1. The lattice parameters were determined to be a=6.1974(6) Å, b=6.9918(5) Å, c=7.3955(9) Å, α=70.8628(3), β=103.5312(4), γ=94.3867(5)°, V=294.2(2) Å3, and ρcal=1.495 g/cm3. The crystal structure contains isolated C10H21NO7 molecular.

DASH: a program for crystal structure determination from powder diffraction data

2006 ◽  
Vol 39 (6) ◽  
pp. 910-915 ◽  
Author(s):  
William I. F. David ◽  
Kenneth Shankland ◽  
Jacco van de Streek ◽  
Elna Pidcock ◽  
W. D. Samuel Motherwell ◽  
...  
Keyword(s):  
Simulated Annealing ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Global Minimum ◽  
Molecular Structures ◽  
Powder Diffraction Data ◽  
Peak Fitting ◽  
Structure Factors ◽  
Integrated Intensities ◽  
User Friendly

DASHis a user-friendly graphical-user-interface-driven computer program for solving crystal structures from X-ray powder diffraction data, optimized for molecular structures. Algorithms for multiple peak fitting, unit-cell indexing and space-group determination are included as part of the program. Molecular models can be read in a number of formats and automatically converted to Z-matrices in which flexible torsion angles are automatically identified. Simulated annealing is used to search for the global minimum in the space that describes the agreement between observed and calculated structure factors. The simulated annealing process is very fast, which in part is due to the use of correlated integrated intensities rather than the full powder pattern. Automatic minimization of the structures obtained by simulated annealing and automatic overlay of solutions assist in assessing the reproducibility of the best solution, and therefore in determining the likelihood that the global minimum has been obtained.

Electron Microscopy in Molecular Biology

1967 ◽  
Vol 25 ◽  
pp. 2-3
Author(s):  
Cecil E. Hall
Keyword(s):  
Electron Microscopy ◽  
Molecular Biology ◽  
Noise Level ◽  
Molecular Structures ◽  
Material Structure ◽  
The Arts ◽  
Shadow Casting ◽  
Electron Image ◽  
High Degree ◽  
Very High

The visualization of organic macromolecules such as proteins, nucleic acids, viruses and virus components has reached its high degree of effectiveness owing to refinements and reliability of instruments and to the invention of methods for enhancing the structure of these materials within the electron image. The latter techniques have been most important because what can be seen depends upon the molecular and atomic character of the object as modified which is rarely evident in the pristine material. Structure may thus be displayed by the arts of positive and negative staining, shadow casting, replication and other techniques. Enhancement of contrast, which delineates bounds of isolated macromolecules has been effected progressively over the years as illustrated in Figs. 1, 2, 3 and 4 by these methods. We now look to the future wondering what other visions are waiting to be seen. The instrument designers will need to exact from the arts of fabrication the performance that theory has prescribed as well as methods for phase and interference contrast with explorations of the potentialities of very high and very low voltages. Chemistry must play an increasingly important part in future progress by providing specific stain molecules of high visibility, substrates of vanishing “noise” level and means for preservation of molecular structures that usually exist in a solvated condition.

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