A Cambridge Structural Database analysis of the C–H⋯Cl interaction: C–H⋯Cl− and C–H⋯Cl–M often behave as hydrogen bonds but C–H⋯Cl–C is generally a van der Waals interaction

CrystEngComm ◽  
2001 ◽  
Vol 3 (27) ◽  
pp. 114-119 ◽  
Author(s):  
Praveen K. Thallapally ◽  
Ashwini Nangia
Keyword(s):  
Hydrogen Bonds ◽  
Van Der Waals ◽  
Van Der Waals Interaction ◽  
Cambridge Structural Database ◽  
Database Analysis ◽  
Structural Database

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.

Three new phosphoric triamides with a [C(O)NH]P(O)[N(C)(C)]2skeleton: a database analysis of C—N—C and P—N—C bond angles

2014 ◽  
Vol 70 (10) ◽  
pp. 998-1002 ◽  
Author(s):  
Mehrdad Pourayoubi ◽  
Atekeh Tarahhomi ◽  
Arnold L. Rheingold ◽  
James A. Golen
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
The Other ◽  
Database Analysis ◽  
Acta Cryst ◽  
Bond Angles ◽  
Cyclic Amide ◽  
Phosphoric Triamide ◽  
Structural Database ◽  
Phosphoric Triamides

InN,N,N′,N′-tetraethyl-N′′-(4-fluorobenzoyl)phosphoric triamide, C15H25FN3O2P, (I), andN-(2,6-difluorobenzoyl)-N′,N′′-bis(4-methylpiperidin-1-yl)phosphoric triamide, C19H28F2N3O2P, (II), the C—N—C angle at each tertiary N atom is significantly smaller than the two P—N—C angles. For the other new structure,N,N′-dicyclohexyl-N′′-(2-fluorobenzoyl)-N,N′-dimethylphosphoric triamide, C21H33FN3O2P, (III), one C—N—C angle [117.08 (12)°] has a greater value than the related P—N—C angle [115.59 (9)°] at the same N atom. Furthermore, for most of the analogous structures with a [C(=O)NH]P(=O)[N(C)(C)]2skeleton deposited in the Cambridge Structural Database [CSD; Allen (2002).Acta Cryst.B58, 380–388], the C—N—C angle is significantly smaller than the two P—N—C angles; exceptions were found for four structures with theN-methylcyclohexylamide substituent, similar to (III), one structure with the seven-membered cyclic amide azepan-1-yl substituent and one structure with anN-methylbenzylamide substituent. The asymmetric units of (I), (II) and (III) contain one molecule, and in the crystal structures, adjacent molecules are linkedviapairs of N—H...O=P hydrogen bonds to form dimers.

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.

Crystal structures of four δ-keto esters and a Cambridge Structural Database analysis of cyano–halogen interactions

2015 ◽  
Vol 71 (10) ◽  
pp. 921-928 ◽  
Author(s):  
Kulsoom Kamal ◽  
Hardesh K. Maurya ◽  
Atul Gupta ◽  
Prema G. Vasudev
Keyword(s):  
Crystal Structures ◽  
Crystal Packing ◽  
Noncovalent Interactions ◽  
Halogen Bonding ◽  
Cambridge Structural Database ◽  
Database Analysis ◽  
Molecular Conformations ◽  
Keto Esters ◽  
Organic Molecular Crystals ◽  
Structural Database

The revived interest in halogen bonding as a tool in pharmaceutical cocrystals and drug design has indicated that cyano–halogen interactions could play an important role. The crystal structures of four closely related δ-keto esters, which differ only in the substitution at a single C atom (by H, OMe, Cl and Br), are compared, namely ethyl 2-cyano-5-oxo-5-phenyl-3-(piperidin-1-yl)pent-2-enoate, C19H22N2O3, (1), ethyl 2-cyano-5-(4-methoxyphenyl)-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C20H24N2O4, (2), ethyl 5-(4-chlorophenyl)-2-cyano-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C19H21ClN2O3, (3), and the previously published ethyl 5-(4-bromophenyl)-2-cyano-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C19H21BrN2O3, (4) [Maurya, Vasudev & Gupta (2013).RSC Adv.3, 12955–12962]. The molecular conformations are very similar, while there are differences in the molecular assemblies. Intermolecular C—H...O hydrogen bonds are found to be the primary interactions in the crystal packing and are present in all four structures. The halogenated derivatives have additional aromatic–aromatic interactions and cyano–halogen interactions, further stabilizing the molecular packing. A database analysis of cyano–halogen interactions using the Cambridge Structural Database [CSD; Groom & Allen (2014).Angew. Chem. Int. Ed.53, 662–671] revealed that about 13% of the organic molecular crystals containing both cyano and halogen groups have cyano–halogen interactions in their packing. Three geometric parameters for the C—X...N[triple-bond]C interaction (X = F, Cl, Br or I),viz.the N...Xdistance and the C—X...N and C—N...Xangles, were analysed. The results indicate that all the short cyano–halogen contacts in the CSD can be classified as halogen bonds, which are directional noncovalent interactions.

scholarly journals N,N′-Bis(4-bromophenyl)-N,N′-dimethylurea

IUCrData ◽  
2018 ◽  
Vol 3 (2) ◽  
Author(s):  
Alexandre Pocinho ◽  
Sonia Mallet-Ladeira ◽  
Christelle Hureau ◽  
Emmanuel Gras
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Cambridge Structural Database ◽  
Halogen Bonds ◽  
Aromatic Rings ◽  
Compound C ◽  
Structural Database

The structure of the title compound, C15H14Br2N2O, at 180 K has monoclinic (P21/n) symmetry. It was obtained unexpectedly from the decomposition of the parent 4-bromo-N-tert-butoxycarbonyl-N-methyl-aniline. It exhibits an `endo' conformation with angles between the two aromatic rings slightly lower than the average values found for similar compounds on the Cambridge Structural Database. In the crystal, C—H...O hydrogen bonds and short Br...Br halogen bonds [3.444 (1) Å] are observed.

The shortest chalcogen...halogen contacts in molecular crystals

2019 ◽  
Vol 75 (5) ◽  
pp. 865-869 ◽  
Author(s):  
Michał Kaźmierczak ◽  
Andrzej Katrusiak
Keyword(s):  
Interatomic Distance ◽  
Main Type ◽  
Van Der Waals ◽  
Molecular Crystals ◽  
Structural Models ◽  
Covalent Bond ◽  
Cambridge Structural Database ◽  
Molecular Arrangement ◽  
Structural Database ◽  
Van Der Waals Radii

The survey of the shortest contacts in structures deposited in the Cambridge Structural Database shows that chalcogen...halogen, halogen...halogen and chalcogen...chalcogen interactions can compete as cohesion forces in molecular crystals. The smallest parameter δ (defined as the interatomic distance minus the sum of relevant van der Waals radii) for Ch...X contacts between chalcogens (Ch: S, Se) and halogens (X: F, Cl, Br, I) is present only in 0.86% out of 30 766 deposited structures containing these atoms. Thus, in less than 1% of these structures can the Ch...X forces be considered as the main type of cohesion forces responsible for the molecular arrangement. Among the 263 structures with the shortest Ch...X contact, there are four crystals where no contacts shorter than the sums of van der Waals radii are present (so-called loose crystals). The smallest δ criterion has been used for distinguishing between the bonding (covalent bond) and non-bonding contacts and for validating the structural models of crystals.

Two newXP(O)[NHC(CH3)3]2phosphoramidates, withX= (CH3)2N and [(CH3)3CNH]2P(O)(O)

2012 ◽  
Vol 68 (4) ◽  
pp. o164-o169 ◽  
Author(s):  
Mehrdad Pourayoubi ◽  
Atekeh Tarahhomi ◽  
Fatemeh Karimi Ahmadabad ◽  
Karla Fejfarová ◽  
Arie van der Lee ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Cambridge Structural Database ◽  
Asymmetric Unit ◽  
Structural Database ◽  
Independent Molecules ◽  
Hydrogen Bond Patterns

InN,N′-di-tert-butyl-N′′,N′′-dimethylphosphoric triamide, C10H26N3OP, (I), andN,N′,N′′,N′′′-tetra-tert-butoxybis(phosphonic diamide), C16H40N4O3P2, (II), the extended structures are mediated by P(O)...(H—N)2interactions. The asymmetric unit of (I) consists of six independent molecules which aggregate through P(O)...(H—N)2hydrogen bonds, givingR21(6) loops and forming two independent chains parallel to theaaxis. Of the 12 independenttert-butyl groups, five are disordered over two different positions with occupancies ranging from 1 \over 6 to 5 \over 6. In the structure of (II), the asymmetric unit contains one molecule. P(O)...(H—N)2hydrogen bonds giveS(6) andR22(8) rings, and the molecules form extended chains parallel to thecaxis. The structures of (I) and (II), along with similar structures having (N)P(O)(NH)2and (NH)2P(O)(O)P(O)(NH)2skeletons extracted from the Cambridge Structural Database, are used to compare hydrogen-bond patterns in these families of phosphoramidates. The strengths of P(O)[...H—N]x(x= 1, 2 or 3) hydrogen bonds are also analysed, using these compounds and previously reported structures with (N)2P(O)(NH) and P(O)(NH)3fragments.

Hydrogen bonding at C=Se acceptors in selenoureas, selenoamides and selones

2016 ◽  
Vol 72 (3) ◽  
pp. 317-325 ◽  
Author(s):  
Dikima Bibelayi ◽  
Albert S. Lundemba ◽  
Frank H. Allen ◽  
Peter T. A. Galek ◽  
Juliette Pradon ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Ab Initio ◽  
Crystal Engineering ◽  
Cambridge Structural Database ◽  
Bond Lengths ◽  
Partial Charges ◽  
Structural Database

In recent years there has been considerable interest in chalcogen and hydrogen bonding involving Se atoms, but a general understanding of their nature and behaviour has yet to emerge. In the present work, the hydrogen-bonding ability and nature of Se atoms in selenourea derivatives, selenoamides and selones has been explored using analysis of the Cambridge Structural Database andab initiocalculations. In the CSD there are 70 C=Se structures forming hydrogen bonds, all of them selenourea derivatives or selenoamides. Analysis of intramolecular geometries andab initiopartial charges show that this bonding stems from resonance-induced Cδ+=Seδ−dipoles, much like hydrogen bonding to C=S acceptors. C=Se acceptors are in many respects similar to C=S acceptors, with similar vdW-normalized hydrogen-bond lengths and calculated interaction strengths. The similarity between the C=S and C=Se acceptors for hydrogen bonding should inform and guide the use of C=Se in crystal engineering.

Hydrogen-bond coordination in organic crystal structures: statistics, predictions and applications

2014 ◽  
Vol 70 (1) ◽  
pp. 91-105 ◽  
Author(s):  
Peter T. A. Galek ◽  
James A. Chisholm ◽  
Elna Pidcock ◽  
Peter A. Wood
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Structural Stability ◽  
Statistical Models ◽  
Cambridge Structural Database ◽  
Acceptor Atom ◽  
Coordination Behaviour ◽  
Structural Database

Statistical models to predict the number of hydrogen bonds that might be formed by any donor or acceptor atom in a crystal structure have been derived using organic structures in the Cambridge Structural Database. This hydrogen-bond coordination behaviour has been uniquely defined for more than 70 unique atom types, and has led to the development of a methodology to construct hypothetical hydrogen-bond arrangements. Comparing the constructed hydrogen-bond arrangements with known crystal structures shows promise in the assessment of structural stability, and some initial examples of industrially relevant polymorphs, co-crystals and hydrates are described.

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