Case Study on the Interpretation of Crystal Structures Inducing Preferential Enrichment Based on the Graph Set Analysis of Hydrogen Bond Motifs

2015 ◽  
Vol 15 (6) ◽  
pp. 3052-3062 ◽  
Author(s):  
Sekai Iwama ◽  
Hiroki Takahashi ◽  
Hirohito Tsue ◽  
Rui Tamura
Keyword(s):  
Hydrogen Bond ◽  
Crystal Structures ◽  
Graph Set ◽  
Graph Set Analysis

Hydrogen bonding in enantiomeric versus racemic mono-carboxylic acids; a case study of 2-phenoxypropionic acid

2003 ◽  
Vol 59 (1) ◽  
pp. 132-140 ◽  
Author(s):  
Henning Osholm Sørensen ◽  
Sine Larsen
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Carboxylic Acids ◽  
Crystal Packing ◽  
Cyclic Dimer ◽  
Optically Pure ◽  
Pure Enantiomer ◽  
Hydrogen Bonded

The structural and thermodynamic backgrounds for the crystallization behaviour of racemates have been investigated using 2-phenoxypropionic acid (PPA) as an example. The racemate of PPA behaves normally and forms a racemic compound that has a higher melting point and is denser than the enantiomer. Low-temperature crystal structures of the pure enantiomer, the enantiomer cocrystallized with n-alkanes and the racemic acid showed that hydrogen-bonded dimers that form over crystallographic symmetry elements exist in all but the structure of the pure enantiomer. A database search for optically pure chiral mono-carboxylic acids revealed that the hydrogen-bonded cyclic dimer is the most prevalent hydrogen-bond motif in chiral mono-carboxylic acids. The conformation of PPA depends on the hydrogen-bond motif; the antiplanar conformation relative to the ether group is associated with a catemer hydrogen-bonding motif, whereas the more abundant synplanar conformation is found in crystals that contain cyclic dimers. Other intermolecular interactions that involve the substituent of the carboxylic group were identified in the crystals that contain the cyclic dimer. This result shows how important the nature of the substituent is for the crystal packing. The differences in crystal packing have been related to differences in melting enthalpy and entropy between the racemic and enantiomeric acids. In a comparison with the equivalent 2-(4-chlorophenoxy)-propionic acids, the differences between the crystal structures of the chloro and the unsubstituted acid have been identified and related to thermodynamic data.

scholarly journals Crystal structures and hydrogen bond analysis of five amino acid conjugates of terephthalic and benzene-1,2,3-tricarboxylic acids

CrystEngComm ◽  
2014 ◽  
Vol 16 (35) ◽  
pp. 8243-8251 ◽  
Author(s):  
Anirban Karmakar ◽  
Clive L. Oliver ◽  
Ana E. Platero-Prats ◽  
Elina Laurila ◽  
Lars Öhrström
Keyword(s):  
Hydrogen Bond ◽  
Amino Acid ◽  
Crystal Structures ◽  
Hirshfeld Surface ◽  
Water Molecules ◽  
Narrow Channels ◽  
Amino Acid Conjugates ◽  
Graph Set ◽  
Hydrogen Bond Analysis ◽  
Hydrogen Bonded

This amino acid derived (red&blue) π-stacked (green) hydrogen bonded (striped) dimer forms a pcu-net with water molecules in the narrow channels. Four related molecules are also presented and all were subjected to graph set and Hirshfeld surface analyses.

The formation of paracetamol (acetaminophen) adducts with hydrogen-bond acceptors

2002 ◽  
Vol 58 (6) ◽  
pp. 1057-1066 ◽  
Author(s):  
Iain D. H. Oswald ◽  
David R. Allan ◽  
Pamela A. McGregor ◽  
W. D. Samuel Motherwell ◽  
Simon Parsons ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Crystal Structures ◽  
Systematic Study ◽  
Guest Molecule ◽  
Guest Molecules ◽  
Oh Groups ◽  
Stacking Interaction ◽  
Hydrogen Bond Interactions ◽  
Π Stacking Interaction ◽  
Graph Set

The crystal structures of five hemiadducts of paracetamol with 1,4-dioxane, N-methylmorpholine, morpholine, N,N-dimethylpiperazine and piperazine and a related 1:1 adduct of paracetamol with 4,4′-bipyridine are described. All structures are characterized by the formation of chains of paracetamol molecules, which are linked via either OH...O=C interactions [C(9) chains in graph-set notation] or NH...O=C interactions [C(4) chains], depending on the presence or absence of substituent groups on the guest molecule. In all cases except for the morpholine and bipyridine adducts these chains are connected by hydrogen-bond interactions with the guest molecules, which reside on crystallographic inversion centres. In the bipyridine adduct this linkage also involves a π-stacking interaction; in the morpholine adduct it is formed between the OH groups of two opposed paracetamol molecules. Most adducts (that with 4,4′-bipyridine is an exception) decompose on heating to give monoclinic paracetamol. This is the first systematic study of a series of co-crystals containing paracetamol.

Graph-set analysis of hydrogen-bond patterns: some mathematical concepts

1999 ◽  
Vol 55 (6) ◽  
pp. 1030-1043 ◽  
Author(s):  
J. Grell ◽  
J. Bernstein ◽  
G. Tinhofer
Keyword(s):  
Hydrogen Bond ◽  
Iminodiacetic Acid ◽  
Mathematical Tool ◽  
Mathematical Concepts ◽  
Structural Database ◽  
Graph Set ◽  
Pattern Forming ◽  
Definition Of ◽  
Graph Sets ◽  
Graph Set Analysis

To provide a foundation for further theoretical and software development of the application of graph sets to patterns of hydrogen bonding and other intermolecular interactions a number of mathematical concepts and tools are defined, developed and demonstrated. Following a review of the basic definitions and uses of graph sets, the directional properties of hydrogen bonds are now included in the treatment. The concepts of a constructor graph and covalent distance matrix have been developed to aid in the generation of a qualitative descriptor for the straightforward, consistent and ultimately automatic (with appropriate software) definition of patterns. An additional mathematical tool, the arrowed T-labeling, has been developed to deal with situations in which pattern-forming moieties are located on crystallographic special positions. To demonstrate the utility and various features of these concepts they are applied in detail to two particular structures, polymorphic iminodiacetic acid [N-(carboxymethyl)glycine] and trans-tetraamminedinitrocobalt(III) acetate. To facilitate the application and use of graph sets many of these developments have already been incorporated into the software of the Cambridge Structural Database, as described in the accompanying paper.

scholarly journals Graph-set analysis of hydrogen-bond patterns: some mathematical concepts. Erratum

2000 ◽  
Vol 56 (1) ◽  
pp. 166-166 ◽  
Author(s):  
J. Grell ◽  
J. Bernstein ◽  
G. Tinhofer
Keyword(s):  
Hydrogen Bond ◽  
Mathematical Concepts ◽  
Acta Cryst ◽  
Graph Set ◽  
Hydrogen Bond Patterns ◽  
Graph Set Analysis

Owing to a serious printing error, this article [Grell et al. (1999). Acta Cryst. B55, 1030–1043] was printed incorrectly. Pages 1029–1044 have thus been reprinted and included as a loose insert with this issue of the journal.

The typical crystal structures of a few representative α-aryl-α-hydroxyphosphonates

2019 ◽  
Vol 75 (3) ◽  
pp. 283-293 ◽  
Author(s):  
Zita Rádai ◽  
Nóra Zsuzsa Kiss ◽  
Mátyás Czugler ◽  
Konstantin Karaghiosoff ◽  
György Keglevich
Keyword(s):  
Hydrogen Bond ◽  
Solid State ◽  
Crystal Structures ◽  
Weak Interactions ◽  
Aryl Group ◽  
Dialkyl Phosphites ◽  
The Pudovik Reaction ◽  
Graph Set ◽  
Graph Sets ◽  
Primary Graph

The crystal structures of seven α-aryl-α-hydroxyphosphonates synthesized by the Pudovik reaction of substituted benzaldehydes and dialkyl phosphites, namely dimethyl [(hydroxy)(phenyl)methyl]phosphonate, C9H13O4P, dimethyl [(3,4-dimethoxyphenyl)(hydroxy)methyl]phosphonate, C11H17O6P, dimethyl (1-hydroxy-1-phenylethyl)phosphonate, C10H15O4P, dimethyl [1-hydroxy-1-(4-nitrophenyl)ethyl]phosphonate, C10H14NO6P, dibenzyl [hydroxy(2-nitrophenyl)methyl]phosphonate, C21H20NO6P, dibenzyl [(3-chlorophenyl)(hydroxy)methyl]phosphonate, C21H20ClO4P, and dibenzyl [hydroxy(4-methylphenyl)methyl]phosphonate, C22H23O4P, were studied to gain a better understanding of the organization in this type of molecule in the solid state. The crystals obtained for this series of compounds show a balance between C—OH...O=P chain-linked packing and the dimeric types of hydrogen-bond bridges of intermolecular pairs of such functions. The description is based on primary graph-set descriptors. Using graph-set descriptors one level deeper (i.e. secondary graph sets of the C—H...O type) revealed a similarity in the graph-set descriptors, suggesting a fine interplay of substituent- and shape-dependent effects on strong–weak interactions. It seems that the formation of chains or dimers is governed not only by the presence of a tertiary Cα atom, but also by the nature and crowding of the ortho substituents of the α-aryl group.

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