Dipolar C[triple-bond]N...C[triple-bond]N interactions in organic crystal structures: database analysis and calculation of interaction energies

2008 ◽  
Vol 64 (3) ◽  
pp. 393-396 ◽  
Author(s):  
Peter A. Wood ◽  
Simon J. Borwick ◽  
David J. Watkin ◽  
W. D. Samuel Motherwell ◽  
Frank H. Allen
Keyword(s):  
Crystal Structures ◽  
Triple Bond ◽  
Carbonyl Groups ◽  
Database Analysis ◽  
Nonbonded Interactions ◽  
Medium Strength ◽  
Analogous Manner ◽  
Structural Database ◽  
Cyano Groups ◽  
Intermolecular Perturbation Theory

The Cambridge Structural Database (CSD) has been used to study nonbonded interactions between dipolar cyano groups. The analysis shows that C[triple-bond]N...C[triple-bond]N interactions form in an analogous manner to those involving carbonyl groups, and with the same interaction motifs: a dominant antiparallel dimer (57.5%) together with smaller populations of perpendicular (19.4%) and sheared parallel (23.0%) motifs. Ab initio calculations using intermolecular perturbation theory (IMPT) show an attractive C[triple-bond]N...C[triple-bond]N interaction in the dominant antiparallel dimer, with E t = −20.0 kJ mol−1 at d(C...N) = 3.30 Å and with the motif having a shear angle close to 102°. The antiparallel C[triple-bond]N...C[triple-bond]N interaction is therefore slightly weaker than the analogous C=O...C=O dimer (−23.5 kJ mol−1), but both interactions have attractive energies similar to that of a medium-strength hydrogen bond and, where sterically favoured, they are important in the stabilization of extended crystal structures.

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.

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.

Three new [XC(O)NH]P(O)[N(CH2C6H5)2]2phosphoric triamides (X= CClF2, 3-F-C6H4and 3,5-F2-C6H3): a database analysis of tertiary N-atom geometry in compounds with a C(O)NHP(O)[N]2core

2012 ◽  
Vol 68 (10) ◽  
pp. o399-o404 ◽  
Author(s):  
Mehrdad Pourayoubi ◽  
Jerry P. Jasinski ◽  
Samad Shoghpour Bayraq ◽  
Hossein Eshghi ◽  
Amanda C. Keeley ◽  
...  
Keyword(s):  
Lone Electron Pair ◽  
Electron Pair ◽  
Bond Angle ◽  
Carbonyl Groups ◽  
Database Analysis ◽  
Acta Cryst ◽  
Phosphoric Triamide ◽  
Minimal Deviation ◽  
Structural Database ◽  
Phosphoric Triamides

In the phosphoric triamidesN,N,N′,N′-tetrabenzyl-N′′-(2-chloro-2,2-difluoroacetyl)phosphoric triamide, C30H29ClF2N3O2P, (I),N,N,N′,N′-tetrabenzyl-N′′-(3-fluorobenzoyl)phosphoric triamide, C35H33FN3O2P, (II), andN,N,N′,N′-tetrabenzyl-N′′-(3,5-difluorobenzoyl)phosphoric triamide, C35H32F2N3O2P, (III), the tertiary N atoms of the dibenzylamido groups havesp2character with minimal deviation from planarity. The sums of the three bond angles about the N atoms in (I)–(III) deviate by less than 8° from the planar value of 360°. The geometries of the tertiary N atoms in all phosphoric triamides with C(O)NHP(O)[N]2skeletons deposited in the Cambridge Structural Database [CSD; Allen (2002).Acta Cryst.B58, 380–388] have been examined and the bond-angle sums at the two tertiary N atoms (SUM1 and SUM2) and the parameter ΔSUM (= SUM1 − SUM2) considered. It was found that in compounds with a considerable ΔSUM value, the more pyramidal N atoms are usually oriented so that the corresponding lone electron pair isantiwith respect to the P=O group. In (I), (II) and (III), the phosphoryl and carbonyl groups, separated by an N atom, areantiwith respect to each other. In the C(O)NHP(O) fragment of (I)–(III), the P—N bond is longer and the O—P—N angle is contracted compared with the other two P—N bonds and the O—P—N angles in the molecules. These effects are also seen in analogous compounds deposited in the CSD. Compounds with [C(O)NH]P(O)[N]X(X≠ N), such as compounds with a [C(O)NH]P(O)[N][O] skeleton, have not been considered here. Also, compounds with a [C(O)NH]2P(O)[N] fragment have not been reported to date. In the crystal structures of all three title compounds, adjacent molecules are linkedviapairs of P=O...H—N hydrogen bonds, forming dimers withCisymmetry.

Interaction geometries and energies of hydrogen bonds to C=O and C=S acceptors: a comparative study

2008 ◽  
Vol 64 (4) ◽  
pp. 491-496 ◽  
Author(s):  
Peter A. Wood ◽  
Elna Pidcock ◽  
Frank H. Allen
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Electron Delocalization ◽  
Interaction Energies ◽  
Thiourea Derivatives ◽  
Medium Strength ◽  
Geometrical Data ◽  
Structural Database ◽  
Intermolecular Perturbation Theory ◽  
Good Agreement

The occurrence, geometries and energies of hydrogen bonds from N—H and O—H donors to the S acceptors of thiourea derivatives, thioamides and thiones are compared with data for their O analogues – ureas, amides and ketones. Geometrical data derived from the Cambridge Structural Database indicate that hydrogen bonds to the C=S acceptors are much weaker than those to their C=O counterparts: van der Waals normalized hydrogen bonds to O are shorter than those to S by ∼ 0.25 Å. Further, the directionality of the approach of the hydrogen bond with respect to S, defined by the C=S...H angle, is in the range 102–109°, much lower than the analogous C=O...H angle which lies in the range 127–140°. Ab initio calculations using intermolecular perturbation theory show good agreement with the experimental results: the differences in hydrogen-bond directionality are closely reproduced, and the interaction energies of hydrogen bonds to S are consistently weaker than those to O, by ∼ 12 kJ mol−1, for each of the three compound classes. There are no CSD examples of hydrogen bonds to aliphatic thiones, (Csp 3)2C=S, consistent with the near-equality of the electronegativities of C and S. Thioureas and thioamides have electron-rich N substituents replacing the Csp 3 atoms. Electron delocalization involving C=S and the N lone pairs then induces a significant >Cδ+=Sδ− dipole, which enables the formation of the medium-strength C=S...H bonds observed in thioureas and thioamides.

Eight new crystal structures of 5-(hydroxymethyl)uracil, 5-carboxyuracil and 5-carboxy-2-thiouracil: insights into the hydrogen-bonded networks and the predominant conformations of the C5-bound residues

2016 ◽  
Vol 72 (5) ◽  
pp. 379-388
Author(s):  
Vanessa Kristina Seiler ◽  
Wilhelm Maximilian Hützler ◽  
Michael Bolte
Keyword(s):  
Hydrogen Bond ◽  
Dimethyl Sulfoxide ◽  
Crystal Structures ◽  
Carboxy Group ◽  
Pyrimidine Ring ◽  
Carbonyl Groups ◽  
Hydrogen Bonding Pattern ◽  
Crystallization Experiments ◽  
Structural Database ◽  
Cyclic Compounds

In order to examine the preferred hydrogen-bonding pattern of various uracil derivatives, namely 5-(hydroxymethyl)uracil, 5-carboxyuracil and 5-carboxy-2-thiouracil, and for a conformational study, crystallization experiments yielded eight different structures: 5-(hydroxymethyl)uracil, C5H6N2O3, (I), 5-carboxyuracil–N,N-dimethylformamide (1/1), C5H4N2O4·C3H7NO, (II), 5-carboxyuracil–dimethyl sulfoxide (1/1), C5H4N2O4·C2H6OS, (III), 5-carboxyuracil–N,N-dimethylacetamide (1/1), C5H4N2O4·C4H9NO, (IV), 5-carboxy-2-thiouracil–N,N-dimethylformamide (1/1), C5H4N2O3S·C3H7NO, (V), 5-carboxy-2-thiouracil–dimethyl sulfoxide (1/1), C5H4N2O3S·C2H6OS, (VI), 5-carboxy-2-thiouracil–1,4-dioxane (2/3), 2C5H4N2O3S·3C6H12O3, (VII), and 5-carboxy-2-thiouracil, C10H8N4O6S2, (VIII). While the six solvated structures,i.e.(II)–(VII), contain intramolecularS(6) O—H...O hydrogen-bond motifs between the carboxy and carbonyl groups, the usually favouredR22(8) pattern between two carboxy groups is formed in the solvent-free structure,i.e.(VIII). FurtherR22(8) hydrogen-bond motifs involving either two N—H...O or two N—H...S hydrogen bonds were observed in three crystal structures, namely (I), (IV) and (VIII). In all eight structures, the residue at the ring 5-position shows a coplanar arrangement with respect to the pyrimidine ring which is in agreement with a search of the Cambridge Structural Database for six-membered cyclic compounds containing a carboxy group. The search confirmed that coplanarity between the carboxy group and the cyclic residue is strongly favoured.

scholarly journals Isomorphous crystal structures of chlorodiacetylene and iododiacetylene derivatives: simultaneous hydrogen and halogen bonds on carbonyl

2017 ◽  
Vol 73 (8) ◽  
pp. 1175-1179 ◽  
Author(s):  
Pierre Baillargeon ◽  
Tarik Rahem ◽  
Édouard Caron-Duval ◽  
Jacob Tremblay ◽  
Cloé Fortin ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Carbonyl Group ◽  
Long Range ◽  
Triple Bond ◽  
Database Search ◽  
Two Dimensional ◽  
Halogen Bonds ◽  
Topochemical Polymerization ◽  
Structural Database ◽  
Van Der Waals Radii

The crystal structures of tert-butyl (5-chloropenta-2,4-diyn-1-yl)carbamate, C10H12ClNO2 (II), and tert-butyl (5-iodopenta-2,4-diyn-1-yl)carbamate, C10H12INO2 (IV), are isomorphous to previously reported structures and accordingly their molecular and supramolecular structures are similar. In the crystals of (II) and (IV), molecules are linked into very similar two-dimensional wall organizations with antiparallel carbamate groups involved in a combination of hydrogen and halogen bonds (bifurcated N—H...O=C and C[triple-bond]C—X...O=C interactions on the same carbonyl group). There is no long-range parallel stacking of diynes, so the topochemical polymerization of diacetylene is prevented. A Cambridge Structural Database search revealed that C[triple-bond]C—X...O=C contacts shorter than the sum of the van der Waals radii are scarce (only one structure for the C[triple-bond]C—Cl...O=C interaction and 13 structures for the similar C[triple-bond]C—I...O=C interaction).

Undecacarbonyl(pyridine-κN)-tetrahedro-tetrairidium(4Ir—Ir)

2006 ◽  
Vol 62 (4) ◽  
pp. m838-m840 ◽  
Author(s):  
Alvaro J. Pardey ◽  
Manoa A. Moreno ◽  
Matthias Lutz ◽  
Matti Haukka ◽  
Reinaldo Atencio
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Triple Bond ◽  
Crystal Packing ◽  
Pyridine Molecule ◽  
Carbonyl Groups ◽  
Carbonyl Ligands

The title compound, [Ir4(C5H5N)(CO)11], shows a tetrahedral Ir4 core in which each Ir atom is linked to three other Ir atoms and three terminal carbonyl groups, except for one Ir atom, which carries two carbonyl ligands and one N-coordinated pyridine molecule. An intricate set of C—H...π hydrogen bonds stabilizes the crystal packing, where the π-systems are those of the C[triple-bond]O bonds of the carbonyl ligands.

scholarly journals π-Hole Tetrel Bonds—Lewis Acid Properties of Metallylenes

Crystals ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 112
Author(s):  
Sławomir J. Grabowski
Keyword(s):  
Quantum Theory ◽  
Crystal Structures ◽  
Lewis Acid ◽  
Natural Bond Orbital ◽  
Database Search ◽  
Lewis Base ◽  
Atoms In Molecules ◽  
Acid Properties ◽  
Structural Database ◽  
Tetrel Bonds

The MP2/aug-cc-pVTZ calculations were performed on the dihalometallylenes to indicate their Lewis acid and Lewis base sites. The results of the Cambridge Structural Database search show corresponding and related crystal structures where the tetrel center often possesses the configuration of a trigonal bipyramid or octahedron. The calculations were also carried out on dimers of dichlorogermylene and dibromogermylene and on complexes of these germylenes with one and two 1,4-dioxide molecules. The Ge⋯Cl, Ge⋯Br, and Ge⋯O interactions are analyzed. The Ge⋯O interactions in the above mentioned germylene complexes may be classified as the π-hole tetrel bonds. The MP2 calculations are supported by the results of the Quantum Theory of Atoms in Molecules (QTAIM) and the Natural Bond Orbital (NBO) approaches.

scholarly journals Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals

2020 ◽  
Vol 48 (15) ◽  
pp. 8302-8319
Author(s):  
Małgorzata Katarzyna Cabaj ◽  
Paulina Maria Dominiak
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Small Molecule ◽  
Base Pair ◽  
Base Pairs ◽  
Standard Pattern ◽  
Planar Structures ◽  
Structural Database ◽  
Derivatives Of

Abstract We used the high resolution and accuracy of the Cambridge Structural Database (CSD) to provide detailed information regarding base pairing interactions of selected nucleobases. We searched for base pairs in which nucleobases interact with each other through two or more hydrogen bonds and form more or less planar structures. The investigated compounds were either free forms or derivatives of adenine, guanine, hypoxanthine, thymine, uracil and cytosine. We divided our findings into categories including types of pairs, protonation patterns and whether they are formed by free bases or substituted ones. We found base pair types that are exclusive to small molecule crystal structures, some that can be found only in RNA containing crystal structures and many that are native to both environments. With a few exceptions, nucleobase protonation generally followed a standard pattern governed by pKa values. The lengths of hydrogen bonds did not depend on whether the nucleobases forming a base pair were charged or not. The reasons why particular nucleobases formed base pairs in a certain way varied significantly.

Stacking interactions of resonance-assisted hydrogen-bridged rings and C6-aromatic rings

2020 ◽  
Vol 22 (24) ◽  
pp. 13721-13728 ◽  
Author(s):  
Jelena P. Blagojević Filipović ◽  
Michael B. Hall ◽  
Snežana D. Zarić
Keyword(s):  
Crystal Structures ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Cambridge Structural Database ◽  
Stacking Interactions ◽  
Aromatic Rings ◽  
Structural Database

Stacking interactions between six-membered resonance-assisted hydrogen-bridged (RAHB) rings and C6-aromatic rings have been studied by analyzing crystal structures in the Cambridge Structural Database and performing quantum chemical calculations.

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