Insights into the C–H⋯F–C hydrogen bond by Cambridge Structural Database analyses and computational studies

RSC Advances ◽  
2015 ◽  
Vol 5 (34) ◽  
pp. 26932-26940 ◽  
Author(s):  
Sagarika Dev ◽  
Sudeep Maheshwari ◽  
Angshuman Roy Choudhury
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Ab Initio ◽  
Gas Phase ◽  
Cambridge Structural Database ◽  
Computational Studies ◽  
Structural Database

C–H⋯F–C hydrogen bonding is analysed among fluorinated ethenes using ab initio calculations in the gas phase to understand the nature, strength and directionality of these interactions.

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.

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.

Hydrogen-Bond Acceptor and Donor Properties of Divalent Sulfur (Y-S-Z and R-S-H)

1997 ◽  
Vol 53 (4) ◽  
pp. 696-701 ◽  
Author(s):  
F. H. Allen ◽  
C. M. Bird ◽  
R. S. Rowland ◽  
P. R. Raithby
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Ab Initio ◽  
Bond Formation ◽  
Hydrogen Bond Acceptor ◽  
Similar Frequency ◽  
Alkyl Groups ◽  
Donor Ability ◽  
Structural Database ◽  
Divalent Sulfur

The hydrogen-bond acceptor ability of divalent sulfur in Y—S—Z systems, Y, Z= C, N, O or S, and the donor ability of thiol S—H have been studied using crystallographic data retrieved from the Cambridge Structural Database. Of 1811 Y—S—Z substructures that co-occur with N—H or O—H donors, only 86 (4.75%) form S...H—N,O bonds within S...H < 2.9 Å. In dialkylthioethers, the frequency of S...H bond formation is 6.24%, but drops below 3% when the alkyl groups are successively replaced by Csp 2 centres. This parallels an increasing \delta-positivity of S as calculated using ab initio methods. A similar frequency trend is observed for O...H—N,O bond formation by analogous oxyethers. Mean intermolecular >S...H distances for O—H [2.67 (3) Å] and N—H [2.75 (2) Å] donors (with H positions normalized to neutron values) are ca 0.25 Å longer than in C=S...H—N,O systems, indicative of very weak hydrogen bonding to >S. Intramolecular >S...H are slightly more frequent (8.56%), with S...H slightly shorter than for the intermolecular case. In contrast, 26 (70.3%) out of 37 S—H donors that co-occur with suitable acceptors form X...H—S bonds. The C=O...H—S system is predominant with a mean O...H distance of 2.34 (4) Å, considerably longer (weaker) than in C=O...H—O systems.

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.

Conformation and tautomerism of methoxy-substituted 4-phenyl-4-thiazoline-2-thiones: a combined crystallographic andab initioinvestigation

2016 ◽  
Vol 72 (5) ◽  
pp. 421-425 ◽  
Author(s):  
Monaem Balti ◽  
Bernadette Norberg ◽  
Mohamed Lotfi Efrit ◽  
Steve Lanners ◽  
Johan Wouters
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Solid State ◽  
Ab Initio ◽  
Gas Phase ◽  
Medicinal Chemistry ◽  
Crystal Packing ◽  
Lead Compound ◽  
Molecular Conformations ◽  
Pharmaceutical Compound

4-Phenyl-4-thiazoline-2-thiol is an active pharmaceutical compound, one of whose activities is as a human indolenamine dioxygenase inhibitor. It has been shown recently that in both the solid state and the gas phase, the thiazolinethione tautomer should be preferred. As part of both research on this lead compound and a medicinal chemistry program, a series of substituted arylthiazolinethiones have been synthesized. The molecular conformations and tautomerism of 4-(2-methoxyphenyl)-4-thiazoline-2-thione and 4-(4-methoxyphenyl)-4-thiazoline-2-thione, both C10H9NOS2, are reported and compared with the geometry deduced fromab initiocalculations [PBE/6-311G(d,p)]. Both the crystal structure analyses and the calculations establish the thione tautomer for the two substituted arylthiazolinethiones. In the crystal structure of the 2-methoxyphenyl regioisomer, the thiazolinethione unit was disordered over two conformations. Both isomers exhibit similar hydrogen-bond patterns [R22(8) motif] and form dimers. The crystal packing is further reinforced by short S...S interactions in the 2-methoxyphenyl isomer. The conformations of the two regioisomers correspond to stable geometries calculated from anab initioenergy-relaxed scan.

Ab initio study of tautomerism and hydrogen bonding of β-carbonylamine in the gas phase and in water solution

2000 ◽  
Vol 104 (3-4) ◽  
pp. 226-234 ◽  
Author(s):  
Giuseppe Buemi ◽  
Felice Zuccarello ◽  
Ponnambalam Venuvanalingam ◽  
Marimuthu Ramalingam
Keyword(s):  
Hydrogen Bonding ◽  
Ab Initio ◽  
Gas Phase ◽  
Water Solution ◽  
Ab Initio Study
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