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.

Graph-set and packing analysis of hydrogen-bonded networks in polyamide structures in the Cambridge Structural Database

2000 ◽  
Vol 56 (5) ◽  
pp. 857-871 ◽  
Author(s):  
W. D. Samuel Motherwell ◽  
Gregory P. Shields ◽  
Frank H. Allen
Keyword(s):  
Crystal Packing ◽  
Three Dimensional ◽  
Cambridge Structural Database ◽  
Dimensional Network ◽  
Hydrogen Bond Networks ◽  
Structural Database ◽  
Graph Set ◽  
Graph Set Analysis ◽  
Packing Analysis ◽  
Hydrogen Bonded

The hydrogen-bond networks and crystal packing of 81 unique secondary di- and polyamides in the Cambridge Structural Database are investigated. Graph-set analysis, as implemented in the RPluto program, is used to classify network motifs. These have been rationalized in terms of the relative dispositions of the amide groups. Peptide and retropeptides exhibit significant conformational flexibility, which permits alternative hydrogen-bonding patterns. In peptides, dihedral angles of −ψ ≃ φ ≃ 105° allow an antiparallel ladder arrangement, containing rings of either the same or alternating sizes. For retropeptides, and diamides with an odd number of CH2 spacers, this conformation leads to a parallel ladder with rings of equal size. If φ approaches −60° and ψ 180°, ladders adopt a helical twist, and if the conformation is distorted further, a three-dimensional network is usually adopted. Diamides with aromatic or an even number of CH2 spacers generally form either antiparallel ladders or sheets, although some exhibit both polymorphs. Symmetry relationships within and between hydrogen-bonded chains, ladders and sheets in the crystal packing have also been analysed. Polyamides form considerably more complex networks, although many of the structural motifs present in the diamides occur as components of these networks.

Two single-enantiomer amidophosphoesters: a database study on the chirality of (O)2P(O)(N)-based structures

2019 ◽  
Vol 75 (1) ◽  
pp. 77-84 ◽  
Author(s):  
Fahimeh Sabbaghi ◽  
Mehrdad Pourayoubi ◽  
Marek Nečas ◽  
Krishnan Damodaran
Keyword(s):  
Hydrogen Bond ◽  
Nmr Spectra ◽  
Chemical Shifts ◽  
Coupling Constants ◽  
Two Dimensional ◽  
One Dimensional ◽  
Space Groups ◽  
Structural Database ◽  
Graph Set ◽  
Hydrogen Bonded

The crystal structures of two single-enantiomer amidophosphoesters with an (O)2P(O)(N) skeleton, i.e. diphenyl [(R)-(+)-α-methylbenzylamido]phosphate, (I), and diphenyl [(S)-(−)-α-methylbenzylamido]phosphate, (II), both C20H20NO3P, are reported. In both structures, chiral one-dimensional hydrogen-bonded architectures, along [010], are mediated by N—H...OP interactions. The statistically identical assemblies include the noncentrosymmetric graph-set motif C(4) and the compounds crystallize in the chiral space group P21. As a result of synergistic co-operation from C—H...O interactions, a two-dimensional superstructure is built including a noncentrosymmetric R 4 4(22) hydrogen-bonded motif. A Cambridge Structural Database survey was performed on (O)2P(O)(N)-based structures in order to review the frequency of space groups observed in this family of compounds; the hydrogen-bond motifs in structures with chiral space groups and the types of groups inducing chirality are discussed. The 2,3 JX –P (X = H or C) coupling constants from the NMR spectra of (I) and (II) have been studied. In each compound, the two diastereotopic C6H5O groups are different, which is reflected in the different chemical shifts and some coupling constants.

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.

scholarly journals Crystal structure of 3,6,6-trimethyl-4-oxo-1-(pyridin-2-yl)-4,5,6,7-tetrahydro-1H-indazol-7-aminium chloride and its monohydrate

2017 ◽  
Vol 73 (12) ◽  
pp. 1931-1936
Author(s):  
Anatoly Mishnev ◽  
Alvis Mengots ◽  
Māris Turks
Keyword(s):  
Hydrogen Bond ◽  
Amino Group ◽  
X Ray Diffraction ◽  
X Ray ◽  
Partially Saturated ◽  
Protonated Amino Group ◽  
Saturated Ring ◽  
Hydrate Crystal ◽  
Graph Set ◽  
Graph Sets

The title compounds, C15H19N4O+·Cl−and C15H19N4O+·Cl−·H2O, obtained in attempts to synthesize metal complexes using tetrahydroindazole as a ligand, were characterized by NMR, IR and X-ray diffraction techniques. The partially saturated ring in the tetrahydroindazole core adopts a sofa conformation. An intramolecular N—H...N hydrogen bond formed by the protonated amino group and the N atom of the pyridyl substituent is found in the first structure. In the hydrochloride, the organic moieties are linked by two N—H...Cl−hydrogen bonds, forming aC(4) graph-set. In the hydrate crystal, a Cl−anion and a water molecule assemble the moieties into infinite bands showing hydrogen-bond patterns with graph setsC(6),R64(12) andR42(8). Organic moieties form π–π stacked supramolecular structures running along thebaxis in both structures.

Supramolecular Alcohol–Amine Crystals and Their Hydrogen-Bond Patterns

1998 ◽  
Vol 54 (5) ◽  
pp. 695-704 ◽  
Author(s):  
J. H. Loehlin ◽  
K. J. Franz ◽  
L. Gist ◽  
R. H. Moore
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Three Dimensional ◽  
Covalently Bonded ◽  
Hydrogen Bond Networks ◽  
Amine Groups ◽  
Graph Set ◽  
Hydrogen Bond Patterns ◽  
Graph Sets

An analysis of the structures of five new cocrystals with saturated hydrogen bonding between amines and alcohols is presented. These five are all cocrystals with p-phenylenediamine (PDA) and a mono- or diol. The cocrystals are p-phenylenediamine–phenol (1/2) [PDA·2 phenol, (I)], p-phenylenediamine–p-phenylphenol (1/2) [PDA·2 p-phenylphenol (II)], p-phenylenediamine–2,6-dihydroxynaphthalene (1/1) [PDA·2,6-dihydroxynaphthalene (III)], p-phenylenediamine–1,6-hexanediol (1/1) [PDA·1,6-hexanediol (IV)] and p-phenylenediamine–p-chlorophenol (1/2) [PDA·2 p-chlorophenol (V)]. These crystals have two distinctly different supramolecular hydrogen-bond patterns, when considering only the hydroxyl and amine groups. There are, in addition, variations in the ways covalently bonded crosslinks connect these hydrogen-bond networks. The graph sets of the hydrogen-bond networks of these and other published saturated amine–alcohol crystals are compared and suggestions made on how to present the graph-set descriptions, especially those involving infinite two- and three-dimensional networks of intersecting chains which are characteristic of most of these materials.

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