Intramolecular resonance assisted N–H•••O=C hydrogen bond and weak noncovalent interactions in two asymmetrically substituted geminal amido-esters: Crystal structures and quantum chemical exploration

The 1:1 and 2:1 cocrystals of isophthalic acid and 2,1,3-benzoselenadiazole have been successfully synthesized and resolved; the noncovalent interactions in the crystal structures have been studied in detail by quantum chemical calculations. In both of the crystal structures, isophthalic acid and 2,1,3-benzoselenadiazole are bound together by a cyclic supramolecular heterosynthon assembled by an O–H···N hydrogen bond and a N–Se···O chalcogen bond. The crystal structures of the 1:1 and 2:1 cocrystals of isophthalic acid and 2,1,3-benzoselenadiazole and the crystal structure of pure isophthalic acid are very similar, which indicates that the [COOH]···[Se−N] cyclic heterosynthon can be an effective alternative to the strong [COOH]2 cyclic homosynthon. The quantum theory of atoms in molecules further recognizes the existence of the hydrogen bond and chalcogen bond. The results of quantum chemical calculations show that the strengths of the π···π stacking interactions in the 1:1 cocrystals of isophthalic acid and 2,1,3-benzoselenadiazole are almost the same as those in the 2:1 cocrystals of isophthalic acid and 2,1,3-benzoselenadiazole, and the strengths of the [COOH]···[Se−N] cyclic heterosynthons (about 9.00 kcal/mol) are less than the strengths of the much stronger [COOH]2 cyclic homosynthons (14.00 kcal/mol). These calculated results are in good agreement with those experimentally observed, demonstrating that, although not as strong as the [COOH]2 cyclic homosynthon, the [COOH]···[Se−N] cyclic heterosynthon can also play a key role in the crystal growth and design.

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Noncovalent Interactions between 1,3,5-Trifluoro-2,4,6-triiodobenzene and a Series of 1,10-Phenanthroline Derivatives: A Combined Theoretical and Experimental Study

Crystals ◽

10.3390/cryst9030140 ◽

2019 ◽

Vol 9 (3) ◽

pp. 140 ◽

Cited By ~ 1

Author(s):

Yu Zhang ◽

Jian-Ge Wang ◽

Weizhou Wang

Keyword(s):

Crystal Structure ◽

Crystal Structures ◽

Quantum Chemical ◽

Halogen Bond ◽

Noncovalent Interactions ◽

Stacking Interactions ◽

Halogen Bonds ◽

Π Stacking ◽

Π Stacking Interaction ◽

Structural Competition

How many strong C−I⋯N halogen bonds can one 1,3,5-trifluoro-2,4,6-triiodobenzene molecule form in a crystal structure? To answer this question, we investigated in detail the noncovalent interactions between 1,3,5-trifluoro-2,4,6-triiodobenzene and a series of 1,10-phenanthroline derivatives by employing a combined theoretical and experimental method. The results of the quantum chemical calculations and crystallographic experiments clearly show that there is a structural competition between a C−I⋯N halogen bond and π⋯π stacking interaction. For example, when there are much stronger π⋯π stacking interactions between two 1,10-phenanthroline derivative molecules or between two 1,3,5-trifluoro-2,4,6-triiodobenzene molecules in the crystal structures, then one 1,3,5-trifluoro-2,4,6-triiodobenzene molecule forms only one C−I⋯N halogen bond with one 1,10-phenanthroline derivative molecule. Another example is when π⋯π stacking interactions in the crystal structures are not much stronger, one 1,3,5-trifluoro-2,4,6-triiodobenzene molecule can form two C−I⋯N halogen bonds with two 1,10-phenanthroline derivative molecules.

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Statistical analysis of noncovalent interactions of anion groups in crystal structures. I. Hydrogen bonding of sulfate anions

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768196003035 ◽

1996 ◽

Vol 52 (4) ◽

pp. 677-684 ◽

Cited By ~ 25

Author(s):

L. Chertanova ◽

C. Pascard

Keyword(s):

Hydrogen Bond ◽

Hydrogen Bonding ◽

Hydrogen Bonds ◽

Small Molecules ◽

Crystal Structures ◽

Noncovalent Interactions ◽

Data Set ◽

Hydrogen Bond Acceptor ◽

Covalently Bonded ◽

Different Types

The hydrogen-bond acceptor characteristics of sulfate dianions are analyzed in crystal structures of small molecules. For 85 anions, neither coordinated to metal ions nor covalently bonded, 697 hydrogen bonds are faund. Of these, 266 (38%) are the O...H—O type and 431 (62%) are the O...H—N type, proportions that correspond well to the stoichiometry of the compounds studied and indicate no preference for a particular donor. The analysis of the data set, after classifying the hydrogen bonds according to the different types of donors, shows that O...H—O bonds are more linear than O...H—N. The anion oxygen–acceptor function is characterized by multiple hydrogen bonding. Only in 56 cases does a sulfate oxygen participate in a single hydrogen bond. In most cases every sulfate oxygen is coordinated by two (187 cases) or three (89 cases) hydrogen bonds. For three H donors, the preferred coordination geometry of the sulfate oxygen is pyramidal. The most frequent coordination around a sulfate dianion is with eight to ten H donors. Thus, sulfate dianions can play a significant cohesive role in molecular aggregation.

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Statistical analysis of noncovalent interactions of anion groups in crystal structures. II. Hydrogen bonding of thiocyanate anions

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768196003011 ◽

1996 ◽

Vol 52 (4) ◽

pp. 685-690 ◽

Cited By ~ 12

Author(s):

L. Tchertanov ◽

C. Pascard

Keyword(s):

Hydrogen Bond ◽

Hydrogen Bonding ◽

Statistical Analysis ◽

Crystal Structures ◽

Solid Angle ◽

Noncovalent Interactions ◽

Spherical Cap ◽

Hydrogen Bond Acceptor ◽

Thiocyanate Anion ◽

Multiple Hydrogen Bonding

The hydrogen-bond acceptor function of the thiocyanate anion is analyzed in 52 crystal structures retrieved from the Cambridge Crystallographic Database. All modes of hydrogen-bond coordination are represented: by the sulfur, by the nitrogen and by the π-system of the anion. The preferred areas for the H donors (D = OH and NH groups) were determined: (a) around sulfur, as a torus centered at the S end, the axis of which is the linear anion, and with an average DSON angle of 99°, and (b) around nitrogen, on a spherical cap delimited by the solid angle, SOND (average = 145°), with the linear anion. The anion-acceptor function is characterized by multiple hydrogen bonding and, in most cases (80%), thiocyanate binds through both acceptor centers (S and N). Important backbonding of sulfur in the thiocyanate anion is structurally evidenced.

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Crystal structures, packing features, Hirshfeld surface analyses and DFT calculations of hydrogen-bond energy of two homologous 8a-aryl-2,3,4,7,8,8a-hexahydropyrrolo[1,2-a]pyrimidin-6(1H)-ones

Acta Crystallographica Section C Structural Chemistry ◽

10.1107/s2053229620005409 ◽

2020 ◽

Vol 76 (5) ◽

pp. 483-489 ◽

Cited By ~ 1

Author(s):

Vyacheslav S. Grinev ◽

Elena I. Linkova ◽

Mikhail N. Krainov ◽

Maksim V. Dmitriev ◽

Alevtina Yu. Yegorova

Keyword(s):

Hydrogen Bond ◽

Hydrogen Bonds ◽

Dft Calculations ◽

Crystal Structures ◽

Bond Energy ◽

Crystal Packing ◽

Noncovalent Interactions ◽

Hirshfeld Surface ◽

Hydrogen Bond Energy ◽

Bicyclic Lactams

The crystal structures and packing features of two homologous Meyer's bicyclic lactams with fused pyrrolidone and medium-sized perhydropyrimidine rings, namely, 8a-phenyl-2,3,4,7,8,8a-hexahydropyrrolo[1,2-a]pyrimidin-6(1H)-one, C13H16N2O (1), and 8a-(4-methylphenyl)-2,3,4,7,8,8a-hexahydropyrrolo[1,2-a]pyrimidin-6(1H)-one, C14H18N2O (2), were elucidated, and Hirshfeld surface plots were calculated and drawn for visualization and a deeper analysis of the intermolecular noncovalent interactions. Molecules of 1 and 2 are weakly linked by intermolecular C=O...H—N hydrogen bonds into chains, which are in turn weakly linked by other C=O...H—Car interactions. The steric volume of the substituent significantly affects the crystal packing pattern.

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Advancing the use of Voronoi–Dirichlet polyhedra to describe interactions in organic molecular crystal structures by the example of galunisertib polymorphs

CrystEngComm ◽

10.1039/d0ce01535k ◽

2021 ◽

Author(s):

Viktor N. Serezhkin ◽

Anton V. Savchenkov

Keyword(s):

Crystal Structures ◽

Molecular Crystal ◽

Noncovalent Interactions ◽

Organic Molecular Crystal ◽

Universal Approach ◽

Structure Properties

The universal approach for studying structure/properties relationships shows that every polymorph of galunisertib is characterized with unique noncovalent interactions.

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Halides of Macrocyclic Silver(II) Complexes: Crystal Structures with Hydrogen Bond Network and Reaction Kinetics of the Decomposition

Inorganica Chimica Acta ◽

10.1016/j.ica.2021.120431 ◽

2021 ◽

pp. 120431

Author(s):

Akinori Honda ◽

Shunta Kakihara ◽

Shuhei Ichimura ◽

Kazuaki Tomono ◽

Mina Matsushita ◽

...

Keyword(s):

Hydrogen Bond ◽

Reaction Kinetics ◽

Crystal Structures ◽

Hydrogen Bond Network ◽

Bond Network ◽

Kinetics Of

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The Face-to-Face σ-Hole···σ-Hole Stacking Interactions: Structures, Energies, and Nature

Crystals ◽

10.3390/cryst11080877 ◽

2021 ◽

Vol 11 (8) ◽

pp. 877

Author(s):

Yu Zhang ◽

Weizhou Wang

Keyword(s):

Quantum Chemical ◽

Noncovalent Interactions ◽

Electrostatic Energy ◽

Stacking Interactions ◽

Energy Component ◽

Stacking Interaction ◽

Face To Face ◽

The Face ◽

Π Stacking Interaction ◽

Induction Energy

The existence of the π···π stacking interaction is well-known. Similarly, it is reasonable to assume the existence of the σ-hole···σ-hole stacking interaction. In this work, the structures, energies, and nature of the face-to-face σ-hole···σ-hole stacking interactions in the crystal structures have been investigated in detail by the quantum chemical calculations. The calculated results clearly show that the face-to-face σ-hole···σ-hole stacking interactions exist and have unique properties, although their strengths are not very significant. The energy component analysis reveals that, unlike many other dispersion-dominated noncovalent interactions in which the induction energies always play minor roles for their stabilities, for the face-to-face σ-hole···σ-hole stacking interaction the contribution of the induction energy to the total attractive energy is close to or even larger than that of the electrostatic energy. The structures, energies, and nature of the face-to-face σ-hole···σ-hole stacking interactions confined in small spaces have also been theoretically simulated. One of the important findings is that encapsulation of the complex bound by the face-to-face σ-hole···σ-hole stacking interaction can tune the electronic properties of the container.

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Crystal-to-Crystal Transformation from K2[Co(C2O4)2(H2O)2]·4H2O to K2[Co(μ-C2O4)(C2O4)]

Magnetochemistry ◽

10.3390/magnetochemistry7060077 ◽

2021 ◽

Vol 7 (6) ◽

pp. 77

Author(s):

Bin Zhang ◽

Yan Zhang ◽

Guangcai Chang ◽

Zheming Wang ◽

Daoben Zhu

Keyword(s):

Hydrogen Bond ◽

Physical Properties ◽

Crystal Structures ◽

Molecular Crystal ◽

Trigonal Prism ◽

Space Group ◽

Cell Parameters ◽

Oxalate Anion ◽

Crystal Transformation ◽

Antiferromagnetic Ordering

Crystal-to-crystal transformation is a path to obtain crystals with different crystal structures and physical properties. K2[Co(C2O4)2(H2O)2]·4H2O (1) is obtained from K2C2O4·2H2O, CoCl2·6H2O in H2O with a yield of 60%. It is crystallized in the triclinic with space group P1 and cell parameters: a = 7.684(1) Å, b = 9.011(1) Å, c = 10.874(1) Å, α = 72.151(2)°, β = 70.278(2)°, γ = 80.430(2)°, V = 670.0(1) Å3, Z = 2 at 100 K. 1 is composed of K+, mononuclear anion [Co(C2O4)2(H2O)22−] and H2O. Co2+ is coordinated by two bidentated oxalate anion and two H2O in an octahedron environment. There is a hydrogen bond between mononuclear anion [Co(C2O4)2(H2O)22−] and H2O. K2[Co(μ-C2O4)(C2O4)] (2) is obtained from 1 by dehydration. The cell parameters of 2 are a = 8.460(5) Å, b = 6.906 (4) Å, c = 14.657(8) Å, β = 93.11(1)°, V = 855.0(8) Å3 at 100 K, with space group in P2/c. It is composed of K+ and zigzag [Co(μ-C2O4)(C2O42−]n chain. Co2+ is coordinated by two bisbendentate oxalate and one bidentated oxalate anion in trigonal-prism. 1 is an antiferromagnetic molecular crystal. The antiferromagnetic ordering at 8.2 K is observed in 2.

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Cyclisierung von Di(tert-butyl-methyl)ketazin zu 1,2-Diaza-3-bora- und 1,2-Diaza-3-sila-cyclopent-5-enen / Cyclization of Di(tert-butyl-methyl)ketazine to 1,2-Diaza-3-bora- and 1,2-Diaza-3-sila-cyclopent-5-enes

Zeitschrift für Naturforschung B ◽

10.1515/znb-2006-1013 ◽

2006 ◽

Vol 61 (10) ◽

pp. 1261-1274 ◽

Cited By ~ 5

Author(s):

Florian Armbruster ◽

Nina Armbruster ◽

Uwe Klingebiel ◽

Mathias Noltemeyer ◽

Stefan Schmatz

Keyword(s):

Crystal Structures ◽

Quantum Chemical Calculations ◽

Chlorine Atom ◽

Quantum Chemical ◽

Membered Ring ◽

Substitution Product ◽

Tert Butyl ◽

Isomeric Structures

The results of quantum chemical calculations on lithium ketazides suggest mainly four isomeric structures with different modes of lithium coordination (A-D). A monolithium ketazide thf-adduct (1) was isolated supporting the results of the quantum chemical calculations. In reactions of the lithiated di(tert-butyl-methyl)ketazine with BCl3 and Cl2BPh, 1,2-aza-azonia-3-borata-cyclopent-5-enes (2, 3) were isolated. Substitution of a chlorine atom of 2 and 3 with t-BuLi leads to the formation of derivatives 4 and 5. HCl elimination from 2 with Et3N gives - via a diazaboracyclopentene (6) - a bicyclus 7. In the reaction of the dilithiated ketazine with F2BN(SiMe3)2, the diaza-boracyclopentene 8 is obtained while with Cl4Si, F3SiN(SiMe3)2, and Cl2SiMe2 the diazasilacyclopentenes 9 - 11 are generated. SiF4 reacts with the dilithium ketazide to give a spirocyclus (12). The monolithium ketazide and Cl2SiMe2 react at 30 °C to give a four-membered ring isomer of the substitution product which is formed via a 1,3-chlorine shift from silicon to carbon (13). A tetrameric silanolate was isolated as a by-product in this reaction. It gives evidence for the structure of lithium ketazide A. Crystal structures of 5, 7, 10, and 14 are reported.

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