Hydrogen bond competition between chemical groups: new methodology and the Cambridge Structural Database

2005 ◽  
Vol 220 (4) ◽  
Author(s):  
Lourdes Infantes ◽  
W. D. Sam Motherwell
Keyword(s):  
Hydrogen Bond ◽  
Intermolecular Hydrogen Bond ◽  
Intramolecular Hydrogen Bonding ◽  
Cambridge Structural Database ◽  
Strong Hydrogen Bond ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Interactions ◽  
Hydrogen Bond Networks ◽  
Structural Database ◽  
Chemical Groups

AbstractThe probabilities of formation of intermolecular hydrogen bond interactions between chemical groups have been studied using new methodology to extract information from the Cambridge Structural Database (CSD). Data for 41052 crystal structures containing at least one strong hydrogen bond donor have been analysed using the RPluto program, assigning 108 chemical group codes to atoms, and creating tables of hydrogen contacts for subsequent analysis using the Access relational database software. This has enabled the study of competition effects where there are specified limited numbers of chemical groups in a structure, which is often difficult with the standard CSD search program, ConQuest. There are sufficiently high numbers of certain combinations of groups to make significant observations of the preference of a given donor for choices of acceptor atoms. For example, COOH…COOH contacts are frequently disrupted by groups such as keto carbonyl, whereas CONH…CONH is very robust and is seldom disrupted. There are a surprising number of structures that do not present any intermolecular hydrogen bond interactions, often due to intramolecular hydrogen bonding taking preference. There is a tendency to use as many groups as possible to build intermolecular hydrogen bond networks. An estimate is made of the relative strengths of self-association interactions which are, in decreasing order, CONH, COOH, alcoholic OH and phenolic OH. The frequency of preferred contacts in some cases allows one to predict the most probable contacts for a given molecule with a specific combination and ratio of chemical groups.

scholarly journals Towards an understanding of the propensity for crystalline hydrate formation by molecular compounds

IUCrJ ◽  
2016 ◽  
Vol 3 (6) ◽  
pp. 430-439 ◽  
Author(s):  
Alankriti Bajpai ◽  
Hayley S. Scott ◽  
Tony Pham ◽  
Kai-Jie Chen ◽  
Brian Space ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Crystal Packing ◽  
Hydrate Formation ◽  
Crystalline Hydrate ◽  
Strong Hydrogen Bond ◽  
Hydrogen Bond Donor ◽  
Screening Experiments ◽  
Group Form ◽  
Structural Database ◽  
Molecular Compounds

Hydrates are technologically important and ubiquitous yet they remain a poorly understood and understudied class of molecular crystals. In this work, we attempt to rationalize propensity towards hydrate formation through crystallization studies of molecules that lack strong hydrogen-bond donor groups. A Cambridge Structural Database (CSD) survey indicates that the statistical occurrence of hydrates in 124 molecules that contain five- and six-memberedN-heterocyclic aromatic moieties is 18.5%. However, hydrate screening experiments on a library of 11N-heterocyclic aromatic compounds with at least two acceptor moieties and no competing hydrogen-bond donors or acceptors reveals that over 70% of this group form hydrates, suggesting that extrapolation from CSD statistics might, at least in some cases, be deceiving. Slurrying in water and exposure to humidity were found to be the most effective discovery methods. Electrostatic potential maps and/or analysis of the crystal packing in anhydrate structures was used to rationalize why certain molecules did not readily form hydrates.

Structure-directing weak phosphoryl XH...O=P (X = C, N) hydrogen bonds in cyclic oxazaphospholidines and oxazaphosphinanes

2008 ◽  
Vol 64 (2) ◽  
pp. 196-205 ◽  
Author(s):  
A. van der Lee ◽  
M. Rolland ◽  
X. Marat ◽  
D. Virieux ◽  
J.-N. Volle ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Functional Groups ◽  
Dft Calculation ◽  
Supramolecular Structures ◽  
Cambridge Structural Database ◽  
Phosphoryl Group ◽  
Hydrogen Bond Interactions ◽  
Structural Database

The structures of six cyclic oxazaphospholidines and three cyclic oxazaphosphinanes have been determined and their supramolecular structures have been compared. The molecules differ with respect to the functional groups attached to the central five- or six-membered rings, but have one phosphoryl group in common. The predominant feature in the supramolecular structures is the existence of relatively weak intermolecular phosphoryl XH...O=P (X = C, N) hydrogen bonds, creating in nearly all cases linear zigzag or double molecular chains. The molecular chains are in general linked to each other via very weak CH...π or usual hydrogen-bond interactions. A survey of the Cambridge Structural Database on similar XH...O=P interactions shows a very large flexibility of the XH...O angle, which is in agreement with the DFT calculation reported elsewhere. The strength of the XH...O=P interaction can therefore be considered as relatively weak to moderately strong, and is expected to play at least a role in the formation of secondary substructures.

Five pseudopolymorphs of 6-amino-2-thiouracil: absence of N—H...S hydrogen bonds

2012 ◽  
Vol 69 (1) ◽  
pp. 93-100 ◽  
Author(s):  
Wilhelm Maximilian Hützler ◽  
Michael Bolte
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Cambridge Structural Database ◽  
Hydrogen Bonding Pattern ◽  
Crystallization Experiments ◽  
Structural Database ◽  
Thiouracil Derivatives

In order to study the preferred hydrogen-bonding pattern of 6-amino-2-thiouracil, C4H5N3OS, (I), crystallization experiments yielded five different pseudopolymorphs of (I), namely the dimethylformamide disolvate, C4H5N3OS·2C3H7NO, (Ia), the dimethylacetamide monosolvate, C4H5N3OS·C4H9NO, (Ib), the dimethylacetamide sesquisolvate, C4H5N3OS·1.5C4H9NO, (Ic), and two different 1-methylpyrrolidin-2-one sesquisolvates, C4H5N3OS·1.5C5H9NO, (Id) and (Ie). All structures containR21(6) N—H...O hydrogen-bond motifs. In the latter four structures, additionalR22(8) N—H...O hydrogen-bond motifs are present stabilizing homodimers of (I). No type of hydrogen bond other than N—H...O is observed. According to a search of the Cambridge Structural Database, most 2-thiouracil derivatives form homodimers stabilized by anR22(8) hydrogen-bonding pattern, with (i) only N—H...O, (ii) only N—H...S or (iii) alternating pairs of N—H...O and N—H...S hydrogen bonds.

Understanding distortions of inorganic substructures in chloridobismuthates(III)

2021 ◽  
Vol 77 (5) ◽  
Author(s):  
Maciej Bujak
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Inorganic Anions ◽  
Cambridge Structural Database ◽  
Molar Ratio ◽  
Organic Cations ◽  
Hybrid Crystals ◽  
Structural Database ◽  
Distortion Parameters

The molar ratio variations of organic and inorganic reactants of chloridobismuthates(III) with N,N-dimethylethane-1,2-diammonium, [(CH3)2NH(CH2)2NH3]2+, and N,N,N′,N′-tetramethylguanidinium, [NH2C{N(CH3)2}2]+, cations lead to the formation of four different products, namely, tris(N,N-dimethylethane-1,2-diammonium) bis[hexachloridobismuthate(III)], [(CH3)2NH(CH2)2NH3]3[BiCl6]2 (1), catena-poly[N,N-dimethylethane-1,2-diammonium [[tetrachloridobismuthate(III)]-μ-chlorido]], {[(CH3)2NH(CH2)2NH3][BiCl5]} n (2), tris(N,N,N′,N′-tetramethylguanidinium) tri-μ-chlorido-bis[trichloridobismuthate(III)], [NH2C{N(CH3)2}2]3[Bi2Cl9] (3), and catena-poly[N,N,N′,N′-tetramethylguanidinium [[dichloridobismuthate(III)]-di-μ-chlorido]], {[NH2C{N(CH3)2}2][BiCl4]} n (4). The hybrid crystals 1–4, containing relatively large but different organic cations, are composed of four distinct anionic substructures. They are built up from isolated [BiCl6]3− octahedra in 1, from face-sharing bioctahedral [Bi2Cl9]3− units in 3, from polymeric corner-sharing {[BiCl5]2−} n chains in 2 and from edge-sharing {[BiCl4]−} n chains in 4. The distortions shown by the single [BiCl6]3− polyhedra in 1–4 are associated with intrinsic interactions within the anionic substructures and the organic...inorganic substructures interactions, namely, N/C—H...Cl hydrogen bonds. The first factor is the stronger, which is evident in comparison of the experimentally determined geometrical and calculated distortion parameters for the isolated octahedron in 1 to the more complex inorganic substructures in 2–4. The formation of N—H...Cl hydrogen bonds, in terms of their number and strength, is favoured for 1 and 3 containing relatively easily accessed hydrogen-bond acceptors of isolated [BiCl6]3− and [Bi2Cl9]3− units. The studies of the deviations from regularity of the [BiCl6]3− octahedra within inorganic substructures were supported by a survey of the Cambridge Structural Database, which confirmed the role played by different factors in the variations in geometry of the inorganic anions.

Di-μ-2-sulfonatobenzoato-bis[aqua(1,10-phenanthroline)copper(II)] trihydrate

2006 ◽  
Vol 62 (4) ◽  
pp. m875-m877
Author(s):  
Wei-Bing Zhang ◽  
Shuang-Di Ruan ◽  
Shu-Juan Zhu ◽  
Hong-Ping Xiao ◽  
Sai-Ya Ye
Keyword(s):  
Hydrogen Bond ◽  
Network Structure ◽  
Title Compound ◽  
Intermolecular Hydrogen Bond ◽  
Two Dimensional ◽  
Bridging Ligands ◽  
Pyramidal Geometry ◽  
Hydrogen Bond Interactions ◽  
Dimensional Network ◽  
Square Pyramidal Geometry

In the title compound, [Cu2(C7H4O5S)2(C12H8N2)2(H2O)2]·3H2O, each copper(II) atom is coordinated by two N atoms from one 1,10-phenanthroline molecule, two carboxylate O atoms from two 2-sulfonatobenzoato dianions and one aqua O atom in a distorted square pyramidal geometry. The 2-sulfonatobenzoato dianions function as μ2-bridging ligands in the formation of a dinuclear complex. Intermolecular hydrogen-bond interactions link the dinuclear units into a two-dimensional network structure.

Synthesis of ReItricarbonyl complexes with various sulfur- and oxygen-donating ligands: crystal structures of two ReIdinuclear structures bridged by S atoms

2018 ◽  
Vol 74 (10) ◽  
pp. 1116-1122
Author(s):  
Pheello I. Nkoe ◽  
Hendrik G. Visser ◽  
Chantel Swart ◽  
Alice Brink ◽  
Marietjie Schutte-Smith
Keyword(s):  
Hydrogen Bond ◽  
Intermolecular Hydrogen Bond ◽  
Synthesis And Characterization ◽  
X Ray Diffraction ◽  
Metal Centre ◽  
Pyridine Ligand ◽  
X Ray ◽  
Hydrogen Bond Interactions ◽  
Mononuclear Complexes

The synthesis and characterization of two dinuclear complexes, namelyfac-hexacarbonyl-1κ3C,2κ3C-(pyridine-1κN)[μ-2,2′-sulfanediyldi(ethanethiolato)-1κ2S1,S3:2κ3S1,S2,S3]dirhenium(I), [Re2(C4H8S3)(C5H5N)(CO)6], (1), and tetraethylammoniumfac-tris(μ-2-methoxybenzenethiolato-κ2S:S)bis[tricarbonylrhenium(I)], (C8H20N)[Re2(C7H7OS)3(CO)6], (2), together with two mononuclear complexes, namely (2,2′-bithiophene-5-carboxylic acid-κ2S,S′)bromidotricarbonylrhenium(I), (3), and bromidotricarbonyl(methyl benzo[b]thiophene-2-carboxylate-κ2O,S)rhenium(I), (4), are reported. Crystals of (1) and (2) were characterized by X-ray diffraction. The crystal structure of (1) revealed two Re—S—Re bridges. The thioether S atom only bonds to one of the ReImetal centres, while the geometry of the second ReImetal centre is completed by a pyridine ligand. The structure of (2) is characterized by three S-atom bridges and an Re...Re nonbonding distance of 3.4879 (5) Å, which is shorter than the distance found for (1) [3.7996 (6)/3.7963 (6) Å], but still clearly a nonbonding distance. Complex (1) is stabilized by six intermolecular hydrogen-bond interactions and an O...O interaction, while (2) is stabilized by two intermolecular hydrogen-bond interactions and two O...π interactions.

Intermolecular hydrogen bond interactions in N-carboxymethyl chitosan and nH2O: DFT and NBO studies

2020 ◽  
Author(s):  
Beti Safitri ◽  
Dwi Hudiyanti ◽  
Marlyn Dian Laksitorini ◽  
Nurwarrohman Andre Sasongko ◽  
Parsaoran Siahaan
Keyword(s):  
Hydrogen Bond ◽  
Intermolecular Hydrogen Bond ◽  
Carboxymethyl Chitosan ◽  
Hydrogen Bond Interactions
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