Crystal structure analysis of molecular dynamics using synchrotron X-rays

CrystEngComm ◽  
2015 ◽  
Vol 17 (46) ◽  
pp. 8786-8795 ◽  
Author(s):  
Manabu Hoshino ◽  
Shin-ichi Adachi ◽  
Shin-ya Koshihara
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Structure Analysis ◽  
Crystal Structure Analysis ◽  
X Rays ◽  
X Ray ◽  
X Ray Crystallography

X-ray crystallography using synchrotron X-rays enables observation of molecular dynamics in a crystal.

Electron Donor-Acceptor Compounds. Synthesis and Structure of 5-(1,4-Benzoquinone-2-yl)-10,15,20-trialkylporphyrins

1998 ◽  
Vol 53 (9) ◽  
pp. 1021-1030 ◽  
Author(s):  
Steffen Runge ◽  
Mathias O. Senge
Keyword(s):  
Crystal Structure ◽  
Structure Analysis ◽  
Supramolecular Structure ◽  
Crystal Structure Analysis ◽  
Free Base ◽  
X Ray ◽  
X Ray Crystallography ◽  
New Methods ◽  
Polymeric Chains ◽  
Donor Acceptor

Abstract A series of 5-(benzoquinone)-10,15,20-trialkylporphyrins was synthesized via cross condensation of the respective aldehydes, 2,5-dimethoxybenzaldehyde and pyrrole followed by demethylation with BBr3 and oxidation with PbO2. This method worked reasonably well for compounds bearing the benzoquinone substituent and butyl, isopropyl, 1 -methylpropyl and 2-ethylpropyl residues (2a-d). The free base porphyrin quinones were converted into the zinc(II) complexes (3a-d) all of which showed remarkable stability for porphyrin quinones. The zinc(II) complex 3c bearing isopropyl residues was investigated by X-ray crystallography and showed a supramolecular structure consisting of polymeric chains facilitated by coordina­tion of a benzoquinone oxygen to a neighboring zinc(II) center. Attempts to synthesize a 5-(benzoquinone)-10,15,20-tris(terr-butylporphyrin) resulted in the formation of a yellow porphomethene (4), which could not be oxidized further. A crystal structure analysis of 4, the first for a free base porphomethene, shows an extremely twisted conformation with syn-orientation of the three tert-butyl groups. The results indicate that new methods will have to be developed for the synthesis of nonplanar porphyrin quinones.

scholarly journals Why crystal structure analysis works: a one-dimensional crystallography teaching tool

2015 ◽  
Vol 48 (3) ◽  
pp. 901-905 ◽  
Author(s):  
A. Alan Pinkerton
Keyword(s):  
Crystal Structure ◽  
Structure Analysis ◽  
Crystal Structure Analysis ◽  
Teaching Tool ◽  
One Dimensional ◽  
X Ray ◽  
X Ray Crystallography ◽  
Scientific Calculator ◽  
Hypothetical Structure

A teaching tool is proposed to help beginner students of crystallography understand how crystallographic calculations work. Examples of the most important methods taught in X-ray crystallography courses have been adapted to a one-dimensional hypothetical structure. All calculations can be carried out in class with a scientific calculator or by using a simple spreadsheet.

scholarly journals The refinement of atomic parameters by the technique known in X-ray crystallography as ‘the method of steepest descents’

1949 ◽  
Vol 197 (1050) ◽  
pp. 336-355 ◽  
Keyword(s):  
Crystal Structure ◽  
Structure Analysis ◽  
Relaxation Method ◽  
Crystal Structure Analysis ◽  
Actual Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Complete Discussion ◽  
General Configuration ◽  
Atomic Parameters

This paper is the first of a proposed set of three in which applications of the methods of ‘steepest descents’ are made to the problems of crystal structure analysis. The proposed programme is in three parts: (1) Working details of the method. (2) A discussion of the accuracy and convergence of the method. (3) Examples of the use of the method in actual structure determination. The present paper forms the first of this set and is complete in itself. A discussion of the normal methods of structure analysis results in a formulation of the problem as one of minimization, and leads naturally to the idea of optimum procedures for this purpose. Three techniques are derived from a unified presentation: ( a ) the ‘relaxation’ method, ( b ) the ‘least squares’ refinement, ( c ) the method of ‘steepest descents’. These are examined in detail and their virtues and defects noted. A complete discussion of the application of the steepest descent procedure to various types of structure analysis is given and techniques are derived for the cases of: refinement of a set of parameters already reasonably good; refinement of a structure where general configuration but not orientation is known; and refinement of structures given by electron densities on a lattice. Several variants of the process are given, in one of which only those planes of zero observed intensity being used; this gives a process which is independent of phase angle values and should be useful in the case of structures for which no chemical data is available.

scholarly journals Combined Use of Structure Analysis, Studies of Molecular Association in Solution, and Molecular Modelling to Understand the Different Propensities of Dihydroxybenzoic Acids to Form Solid Phases

Pharmaceutics ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 734
Author(s):  
Aija Trimdale ◽  
Anatoly Mishnev ◽  
Agris Bērziņš
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structure Analysis ◽  
Crystal Structure Analysis ◽  
Molecular Association ◽  
Hydroxyl Groups ◽  
Solid Phases ◽  
Solvent Molecules ◽  
Dynamics Simulations

The arrangement of hydroxyl groups in the benzene ring has a significant effect on the propensity of dihydroxybenzoic acids (diOHBAs) to form different solid phases when crystallized from solution. All six diOHBAs were categorized into distinctive groups according to the solid phases obtained when crystallized from selected solvents. A combined study using crystal structure and molecule electrostatic potential surface analysis, as well as an exploration of molecular association in solution using spectroscopic methods and molecular dynamics simulations were used to determine the possible mechanism of how the location of the phenolic hydroxyl groups affect the diversity of solid phases formed by the diOHBAs. The crystal structure analysis showed that classical carboxylic acid homodimers and ring-like hydrogen bond motifs consisting of six diOHBA molecules are prominently present in almost all analyzed crystal structures. Both experimental spectroscopic investigations and molecular dynamics simulations indicated that the extent of intramolecular bonding between carboxyl and hydroxyl groups in solution has the most significant impact on the solid phases formed by the diOHBAs. Additionally, the extent of hydrogen bonding with solvent molecules and the mean lifetime of solute–solvent associates formed by diOHBAs and 2-propanol were also investigated.

scholarly journals Preparative-scale HPLC Resolution of Metallacyclic η3-Allyltricarbonyliron Complexes and Determination of the Absolute Configuration by X-Ray Crystal Structure Analysis

1999 ◽  
Vol 23 (9) ◽  
pp. 578-579
Author(s):  
Rainer Schobert ◽  
Hermann Pfab ◽  
Jutta Böhmer ◽  
Frank Hampel ◽  
Andreas Werner
Keyword(s):  
Crystal Structure ◽  
Silica Gel ◽  
Structure Analysis ◽  
Absolute Configuration ◽  
Crystal Structure Analysis ◽  
Preparative Scale ◽  
X Ray ◽  
The Absolute

Racemates of (η3-allyl)tricarbonyliron lactone complex Fe(CO)3{η1:η3-C(O)XCH2CHCMeCH2} 1a (X = O) and (η3-allyl)tricarbonyliron lactam complex 2a (X = NMe) are resolved on a preparative scale by HPLC on cellulose tris(3,5-dimethylphenyl)carbamate/silica gel RP-8 and the absolute configuration of (-)-2a is determined by X-ray crystal structure analysis.

Second-Generation Inhibitors for the Metalloprotease Neprilysin Based on Bicyclic Heteroaromatic Scaffolds: Synthesis, Biological Activity, and X-Ray Crystal-Structure Analysis

2005 ◽  
Vol 88 (4) ◽  
pp. 731-750 ◽  
Author(s):  
Stefan Sahli ◽  
Brian Frank ◽  
W. Bernd Schweizer ◽  
François Diederich ◽  
Denise Blum-Kaelin ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Biological Activity ◽  
Structure Analysis ◽  
Second Generation ◽  
Crystal Structure Analysis ◽  
X Ray
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