scholarly journals Hydrogen Bonds of C=S, C=Se and C=Te with C-H in Small-Organic Molecule Compounds Derived from the Cambridge Structural Database (CSD)

2022 ◽  
Vol 11 (01) ◽  
pp. 1-22
Author(s):  
Dikima D. Bibelayi ◽  
Albert S. Lundemba ◽  
Philippe V. Tsalu ◽  
Pitchouna I. Kilunga ◽  
Jules M. Tshishimbi ◽  
...  
2021 ◽  
Vol 10 (04) ◽  
pp. 57-69
Author(s):  
Albert S. Lundemba ◽  
Dikima D. Bibelayi ◽  
Philippe V. Tsalu ◽  
Peter A. Wood ◽  
Jason Cole ◽  
...  

Author(s):  
Wilhelm Maximilian Hützler ◽  
Michael Bolte

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.


Author(s):  
Maciej Bujak

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.


IUCrData ◽  
2018 ◽  
Vol 3 (2) ◽  
Author(s):  
Alexandre Pocinho ◽  
Sonia Mallet-Ladeira ◽  
Christelle Hureau ◽  
Emmanuel Gras

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.


2012 ◽  
Vol 68 (4) ◽  
pp. o164-o169 ◽  
Author(s):  
Mehrdad Pourayoubi ◽  
Atekeh Tarahhomi ◽  
Fatemeh Karimi Ahmadabad ◽  
Karla Fejfarová ◽  
Arie van der Lee ◽  
...  

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.


Author(s):  
Dikima Bibelayi ◽  
Albert S. Lundemba ◽  
Frank H. Allen ◽  
Peter T. A. Galek ◽  
Juliette Pradon ◽  
...  

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.


Author(s):  
Peter T. A. Galek ◽  
James A. Chisholm ◽  
Elna Pidcock ◽  
Peter A. Wood

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.


2013 ◽  
Vol 69 (2) ◽  
pp. 184-194
Author(s):  
Mehrdad Pourayoubi ◽  
Maryam Toghraee ◽  
Vladimir Divjakovic ◽  
Arie van der Lee ◽  
Teresa Mancilla Percino ◽  
...  

Crystals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 460 ◽  
Author(s):  
Sławomir J. Grabowski

The BF4− anion is characterised by weak Lewis base properties; it is usually classified as a “non-coordinating anion”. The searches through the Cambridge Structural Database (CSD) were performed and it was found that the BF4− anion often occurs in crystal structures and it is involved in numerous intermolecular interactions; hydrogen bonds are the majority of them. The hydrogen bonds involving the BF4− anion as a proton acceptor are closer to linearity with the increase of the strength of interaction that is in line with the tendency known for other hydrogen bonds. However, even for short contacts between the proton and the Lewis base centre, slight deviations from linearity occur. The MP2/aug-cc-pVTZ calculations on the BF4−…HCN complex and on the BF4−…(HCN)4 cluster were also carried out to characterise corresponding C-H…F hydrogen bonds; such interactions often occur in crystal structures.


1996 ◽  
Vol 52 (4) ◽  
pp. 734-745 ◽  
Author(s):  
F. H. Allen ◽  
J. P. M. Lommerse ◽  
V. J. Hoy ◽  
J. A. K. Howard ◽  
G. R. Desiraju

Crystallographic results, retrieved from the Cambridge Structural Database, show that the C--H protons of cyclopropane, aziridine and oxirane form C—H...O (particularly C—H...O—C) hydrogen bonds. The frequency of formation and geometrical characteristics of these bonds indicate a bond-strength ordering: Csp 1—H...O > C(ring)—H...O ≃ Csp 2—H...O > Csp 3—H...O, which is in excellent agreement with the well known ethylenic properties of C(ring)—H and with residual δ+ charges calculated for these systems. There is some evidence to suggest that C=C—H in cyclopropene, known to be a highly acidic H, forms stronger hydrogen bonds than C—H in saturated three-membered rings. Crystallographic data have also been used to provide geometrical evidence for the formation of O,N—H...π(ring) bonding to three-membered rings, proposed on the basis of spectroscopic data [Joris, Schleyer & Gleiter (1968). J. Am. Chem. Soc. 90, 327–336]. The two modes of H...π(ring) binding suggested there, viz. `edge-on' approach of H to a ring C—C bond and `face-on' approach towards the ring centroid, are found to be dominant in crystallographic observations of this novel hydrogen bond.


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