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.

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.

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.

Study of Hydrogen Bonding in Carboxylic Acids by the MNDO/M Method

1994 ◽  
Vol 59 (6) ◽  
pp. 1251-1260 ◽  
Author(s):  
Michal Bureš ◽  
Jaroslav Bezus
Keyword(s):  
Experimental Data ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Carboxylic Acids ◽  
Promising Method ◽  
Semiempirical Methods ◽  
Am1 Method ◽  
Bond Lengths ◽  
Pm3 Method

The semiempirical methods MNDO/M, AM1 and PM3 were applied to the study of hydrogen bonds in carboxylic acids. The calculated hydrogen bond lengths and enthalpies of dimerization were compared with experimental data. The AM1 method fails to properly describe systems with strong hydrogen bonds. The PM3 method predicts the hydrogen bond lengths correctly but underestimates systematically the enthalpies of dimerization. MNDO/M appears to be a promising method for the treatment of association of carboxylic acids.

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.

Extensive analysis of N—H...O hydrogen bonding in four classes of phosphorus compounds: a combined experimental and database study

2017 ◽  
Vol 73 (3) ◽  
pp. 287-297 ◽  
Author(s):  
Farahnaz Hamzehee ◽  
Mehrdad Pourayoubi ◽  
Marek Nečas ◽  
Duane Choquesillo-Lazarte
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Neutral Hydrogen ◽  
The Other ◽  
Phosphorus Compounds ◽  
Database Study ◽  
Extensive Analysis ◽  
Structural Database

The N—H...O hydrogen bond is the characteristic interaction in the crystal structures of N-benzyl-P-phenyl-N′-(p-tolyl)phosphonic diamide, C20H21N2OP or (C6H5)P(O)(NHCH2C6H5)(NHC6H4-p-CH3), (I), diphenylphosphinic 1-methylpropylamide, C16H20NOP or (C6H5)2P(O)[NHCH(CH3)(C2H5)], (II), (S)-1-phenylethylammonium N-[(S)-1-phenylethyl]phenylphosphonamidate, C8H12N+·C14H15NO2P− or [S-(C6H5)CH(CH3)NH3][(C6H5)P(O){S-NHCH(CH3)(C6H5)}(O)], (III), and (4-methylbenzyl)ammonium diphenylphosphinate, C8H12N+·C12H10O2P− or [4-CH3-C6H4CH2NH3][(C6H5)2P(O)(O)], (IV). This article focuses on the N—H...O hydrogen bonds by considering the structures of (I), (II), (III) and (IV), and reviewing their analogous compounds, including 43 (C)P(O)(N)2, 102 (C)2P(O)(N), 31 (C)P(O)(N)(O) and 96 (C)2P(O)(O) structures, deposited in the Cambridge Structural Database (CSD). For the structures with a (C)P(O)(N)2 segment, only neutral hydrogen bonds were found in the CSD. The other three classes of compounds included both neutral and `charge-assisted' hydrogen bonds, and the (C)2P(O)(O) structures were particularly noticeable for a high number of cation–anion compounds. The overall tendencies of N...O distances in neutral and cation–anion compounds were compared. The N—H...O hydrogen-bond angles were also analyzed for the four classes of phosphorus compounds.

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.

Accurate ab initio calculations of O–H⋯O and O–H⋯−O proton chemical shifts: towards elucidation of the nature of the hydrogen bond and prediction of hydrogen bond distances

2015 ◽  
Vol 13 (33) ◽  
pp. 8852-8868 ◽  
Author(s):  
Michael G. Siskos ◽  
Andreas G. Tzakos ◽  
Ioannis P. Gerothanassis
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Chemical Shifts ◽  
Bond Lengths ◽  
Sensitive Measure ◽  
Proton Chemical Shifts

Ab initio calculations of O–H⋯O and O–H⋯−O 1H chemical shifts provide accurate electronic description of hydrogen bonding and sensitive measure of hydrogen bond lengths.

Intermolecular N-H...O Hydrogen Bonding Assisted by Resonance. II. Self Assembly of Hydrogen-Bonded Secondary Enaminones in Supramolecular Catemers

1998 ◽  
Vol 54 (1) ◽  
pp. 50-65 ◽  
Author(s):  
V. Bertolasi ◽  
P. Gilli ◽  
V. Ferretti ◽  
G. Gilli
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Crystal Engineering ◽  
Self Assembly ◽  
Crystal Packing ◽  
Average Distance ◽  
Conjugated Systems ◽  
Structural Database ◽  
Bond Strengths ◽  
Chemical Groups

The crystal structures of 15 compounds containing the 2-en-3-amino-1-one heterodienic system and forming intermolecular N—H...O hydrogen bonds assisted by resonance (RAHB) are reported: (1) 3-phenylamino-2-cyclohexen-1-one; (2) 3-(4-methoxyphenylamino)-2-cyclohexen-1-one; (3) 3-(4-chlorophenylamino)-2-cyclohexen-1-one; (4) 3-(4-methoxyphenylamino)-2-methyl-2-cyclohexen-1-one; (5) 3-(4-methoxyphenylamino)-5-methyl-2-cyclohexen-1-one; (6) 3-isopropylamino-5,5-dimethyl-2-cyclohexen-1-one; (7) 3-phenylamino-5,5-dimethyl-2-cyclohexen-1-one; (8) 3-(3-methoxyphenylamino)-5,5-dimethyl-2-cyclohexen-1-one; (9) N,N-3-aza-pentane-1,5-bis[1-(3-oxo-5,5-dimethyl-1-cyclohexenyl)]; (10) 3-phenylamino-6,6-dimethyl-2-cyclohexen-1-one; (11) 3-(2-methoxyphenylamino)-6,6-dimethyl-2-cyclohexen-1-one; (12) 3-(3-chlorophenylamino)-6,6-dimethyl-2-cyclohexen-1-one; (13) 3-(4-chlorophenylamino)-6,6-dimethyl-2-cyclohexen-1-one; (14) 1-(4-chlorophenyl)-4-(4-chlorophenylamino)-6-methyl-2-pyridone; (15) 3-(4-chlorophenylamino)-5-phenyl-2-cyclopenten-1,4-dione. All compounds form intermolecular N—H...O=C hydrogen bonds assisted by resonance connecting the heteroconjugated enaminonic groups in infinite chains. Chain morphologies are analyzed to find out crystal engineering rules able to predict and interpret the crystal packing. Simple secondary enaminones [i.e. (1)–(13) together with a number of structures retrieved from the Cambridge Structural Database] are found to form hydrogen bonds having π-delocalizations, as characterized by a C=O bond-length average of 1.239 ± 0.004 Å, and hydrogen-bond strengths, represented by the N...O average distance of 2.86 ± 0.05 Å, very similar to those previously found for amides. Enaminones, however, can be easily substituted by chemical groups able to influence both π-conjugations and N...O hydrogen-bond distances. Some substituted enaminones, retrieved from the literature, display, in fact, N...O hydrogen-bond distances as short as 2.627 Å and large π-delocalizations with C=O double-bond distances as long as 1.285 Å. These effects appear to be associated with (a) the presence of further π-conjugated systems involving the C=O and NH groups of the enaminone moiety or (b) the transformation of the enaminone carbonyl group in an amidic function.

Newrac-XP(O)(OC6H5)(NHC6H4-p-CH3) [X= N(CH3)(cyclo-C6H11) and NH(C3H5)] andrac-(C6H5CH2NH)P(O)(OC6H5)(NH-cyclo-C6H11) mixed-amide phosphinates

2013 ◽  
Vol 69 (10) ◽  
pp. 1181-1185 ◽  
Author(s):  
Mehrdad Pourayoubi ◽  
Fatemeh Karimi Ahmadabad ◽  
Hossein Eshtiagh-Hosseini ◽  
Monika Kučeráková ◽  
Václav Eigner ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Bond Lengths ◽  
Hydrogen Bonding Interactions ◽  
Chlorine Compound ◽  
First Time

The mixed-amide phosphinates,rac-phenyl (N-methylcyclohexylamido)(p-tolylamido)phosphinate, C20H27N2O2P, (I), andrac-phenyl (allylamido)(p-tolylamido)phosphinate, C16H19N2O2P, (II), were synthesized from the racemic phosphorus–chlorine compound (R,S)-(Cl)P(O)(OC6H5)(NHC6H4-p-CH3). Furthermore, the phosphorus–chlorine compound ClP(O)(OC6H5)(NH-cyclo-C6H11) was synthesized for the first time and used for the synthesis ofrac-phenyl (benzylamido)(cyclohexylamido)phosphinate, C19H25N2O2P, (III). The strategies for the synthesis of racemic mixed-amide phosphinates are discussed. The P atom in each compound is in a distorted tetrahedral (N1)P(=O)(O)(N2) environment. In (I) and (II), thep-tolylamido substituent makes a longer P—N bond than those involving theN-methylcyclohexylamido and allylamido substituents. In (III), the differences between the P—N bond lengths involving the cyclohexylamido and benzylamido substituents are not significant. In all three structures, the phosphoryl O atom takes part with the N—H unit in hydrogen-bonding interactions,viz.an N—H...O=P hydrogen bond for (I) and (N—H)(N—H)...O=P hydrogen bonds for (II) and (III), building linear arrangements along [001] for (I) and along [010] for (III), and a ladder arrangement along [100] for (II).

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