Different Kinds of Hydrogen Bonds in Crystal Structures

A special issue of Crystals (ISSN 2073-4352). This special issue belongs to the section "Crystal Engineering".

Deadline for manuscript submissions: 30 June 2024 | Viewed by 10839

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Guest Editor
Department of Physical Chemistry, Faculty of Chemistry, University of Lodz, Pomorska 163/165, 90-236 Lodz, Poland
Interests: electron-density analysis; experiment vs. theory; X-ray single-crystal diffraction; X-ray wavefunction refinement; chemical bonding; hydrogen bonding
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Guest Editor
Department of Physical Chemistry, Faculty of Chemistry, University of Lodz, Pomorska 163/165, 90-236 Lodz, Poland
Interests: hydrogen bond; crystal structure; X-ray diffraction analysis; experimental charge density analysis; QTAIM analysis; structure vs. fluorescent properties
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Hydrogen bonds (HBs) exist everywhere in our lives, from small molecules to macromolecules, whether you notice them or not. Hydrogen bonding in water is still an exciting topic due to the diversity of water molecule clusters; the double-helical structure of DNA is due largely to hydrogen bonding between its base pairs. A hydrogen bond (D−H A, D: donor, A: acceptor) is a special type of electrostatic force attraction that is somewhere between intermolecular or intramolecular, not a covalent bond to a hydrogen atom. It results from the attractive force between a hydrogen atom covalently bonded to a very electronegative atom and another very electronegative atom, such as nitrogen (N), oxygen (O), or fluorine (F). Hydrogen bonds play a crucial role in physical properties as a kind of weak interaction in crystals, such as proton conductivity, deuterium effect, and geometric H/D isotope effects. Taking ferroelectric KH2PO4 as an example, the phase transition temperature of KD2PO4 shows a 107 K upshift after deuteration. Additionally, in some other cases, the physical property exhibits a weak coupling correlation with the deuteration. Therefore, it is vital to understand the function of the hydrogen bond in crystal structures.

The current Special Issue on “Different Kinds of Hydrogen Bonds in Crystal Structures” focuses on the hydrogen bond effect in crystals, with a varied scope of hydrogen bond type, characterization, structure–property relationship, etc.

Dr. Lilianna Checinska
Prof. Dr. Magdalena Małecka
Guest Editors

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Keywords

  • hydrogen bond
  • hydrogen bond type
  • hydrogen bond strength
  • deuterium effect
  • geometric H/D isotope effects
  • proton transfer
  • phase transition
  • ferroelectric
  • hydrogen bond characterization (NMR, IR, and other spectroscopy)
  • X-ray diffraction
  • neutron diffraction

Published Papers (9 papers)

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Research

16 pages, 10543 KiB  
Article
Synthesis and Crystal Structure Analysis of Some Aromatic Imines of Syringaldehyde
by Christopher G. Hamaker and Stephan M. Germann
Crystals 2024, 14(1), 99; https://doi.org/10.3390/cryst14010099 - 22 Jan 2024
Cited by 1 | Viewed by 1040
Abstract
A series of syringaldehyde imines with para-substituted anilines have been synthesized in a good yield, and their crystal structures have been analyzed. The orientation of the syringaldehyde hydroxyl group plays in important role in the intermolecular hydrogen-bonding pattern of the molecules. The [...] Read more.
A series of syringaldehyde imines with para-substituted anilines have been synthesized in a good yield, and their crystal structures have been analyzed. The orientation of the syringaldehyde hydroxyl group plays in important role in the intermolecular hydrogen-bonding pattern of the molecules. The O–HN hydrogen bonding interactions primarily determine the three-dimensional packing of the molecules, even though they make up a relatively small percentage of intermolecular interactions in the molecules. The three structures with the p-hydroxy group cis to the imine group give hydrogen-bonded zigzag chains in the monoclinic crystals, while the structure with a trans hydroxy group crystallize in a hexagonal space group (R3¯) and form hydrogen-bonded hexamers. The hexagonal structure also displays BrBr interactions, forming additional hexameric clusters. The analysis of published p-hydroxyphenyl imine crystal structures from the Cambridge Crystallographic Database revealed patterns in the length of the hydrogen bonding interactions based on steric congestion around the hydroxyl group. Full article
(This article belongs to the Special Issue Different Kinds of Hydrogen Bonds in Crystal Structures)
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17 pages, 7028 KiB  
Article
Overlooked Solid State Structure of 1,3-I2C6F4—The Meta-Member of an Iconic Halogen Bond Donors Trio
by Yury V. Torubaev and Ivan V. Skabitsky
Crystals 2023, 13(11), 1555; https://doi.org/10.3390/cryst13111555 - 30 Oct 2023
Cited by 1 | Viewed by 772
Abstract
The solid-state structure of the meta-isomer of diiodotetrafluorobenzene (DITFB), the sole liquid DITFB at 25 °C, is reported. Computational and comparative analyses of its crystal packing have elucidated potential factors contributing to its lower melting point and reduced affinity as a halogen [...] Read more.
The solid-state structure of the meta-isomer of diiodotetrafluorobenzene (DITFB), the sole liquid DITFB at 25 °C, is reported. Computational and comparative analyses of its crystal packing have elucidated potential factors contributing to its lower melting point and reduced affinity as a halogen bond donor conformer as compared to the para-isomer. This discussion also addresses the lower melting points of ortho- and meta-isomers in general. The platelet crystal habit of 1,3-DITFB is examined in relation to its energy framework pattern, proposing a comprehensive and illustrative predictive model for its faster growth in the [001] direction. This growth aligns with the maximum attachment energy. Full article
(This article belongs to the Special Issue Different Kinds of Hydrogen Bonds in Crystal Structures)
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13 pages, 2277 KiB  
Article
Short Fluoroalkanes Suppress a Thermally-Induced Phase Transition in a Layered Organic Crystal
by Christopher E. Marjo, Anne M. Rich, Mohan M. Bhadbhade, Saroj Bhattacharyya, Songyan Yin, David M. Miskovic, Vina R. Aldilla and Naresh Kumar
Crystals 2023, 13(10), 1425; https://doi.org/10.3390/cryst13101425 - 25 Sep 2023
Viewed by 788
Abstract
Ensuring a consistent crystal structure over a wide temperature range can be desirable behaviour in organic devices. This study investigates a layered crystal system formed by hydrogen-bonded chloro-s-triazine rings functionalised with alkyl or fluoroalkyl chains between the layers. When substituted with [...] Read more.
Ensuring a consistent crystal structure over a wide temperature range can be desirable behaviour in organic devices. This study investigates a layered crystal system formed by hydrogen-bonded chloro-s-triazine rings functionalised with alkyl or fluoroalkyl chains between the layers. When substituted with N-propyl groups (C3), the crystal undergoes a thermally-induced phase transition where the chains are ordered and bent below 170 K and disordered and extended above 175 K. Replacement with fluorinated N-propyl chains (C3-F) produces the same layered crystal but successfully suppresses the phase transition. The hydrocarbon and fluorocarbon analogues were found to be incompatible and unable to form co-crystals from solution or with mechanical mixing. Both effects were ascribed to more attractive C-F…F-C and C-H…F-C interactions in the fluorinated analogue. Long perfluoroalkanes are well known for controlling assembly in the solid state, but this study suggests that short-chain fluoroalkanes can exert strong control over the assembly and stability of an organic crystal. Full article
(This article belongs to the Special Issue Different Kinds of Hydrogen Bonds in Crystal Structures)
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12 pages, 5811 KiB  
Article
Completion of Crystallographic Data for the Series of 4-Halogenated-1H-pyrazoles: Crystal Structure Determination of 4-Iodo-1H-pyrazole and Spectroscopic Comparison
by Kelly L. Rue, Susana Herrera, Indranil Chakraborty, Alexander M. Mebel and Raphael G. Raptis
Crystals 2023, 13(7), 1101; https://doi.org/10.3390/cryst13071101 - 14 Jul 2023
Cited by 1 | Viewed by 916
Abstract
Prior to 2021, 4-bromo-1H-pyrazole (published in 1999) was the only structurally characterized 4-halogenated-1H-pyrazole in the Cambridge Crystallographic Data Center (CCDC). The structures of 4-chloro-1H-pyrazole and 4-fluoro-1H-pyrazole were published in 2021 and 2023, respectively. Herein, we [...] Read more.
Prior to 2021, 4-bromo-1H-pyrazole (published in 1999) was the only structurally characterized 4-halogenated-1H-pyrazole in the Cambridge Crystallographic Data Center (CCDC). The structures of 4-chloro-1H-pyrazole and 4-fluoro-1H-pyrazole were published in 2021 and 2023, respectively. Herein, we report the crystal structure for 4-iodo-1H-pyrazole, completing the crystallographic data for the series of 4-halogenated-1H-pyrazoles. The bromo and chloro analogs are isostructural, forming trimeric H-bonding motifs, whereas the fluoro and iodo analogs form non-isostructural catemers. We also compare the experimental and theoretical (by DFT calculations) IR and 1H NMR spectroscopic data of the four halogenated 4-X-pzH compounds and unsubstituted pyrazole (pzH). An explanation is offered for some counterintuitive structural, infrared, and 1H-NMR spectroscopic data. Full article
(This article belongs to the Special Issue Different Kinds of Hydrogen Bonds in Crystal Structures)
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15 pages, 6845 KiB  
Article
On the Importance of H-Bonding Interactions in the Enclathration of Boric Acids in Na(I) Polymers: Experimental and Theoretical Studies
by Trishnajyoti Baishya, Kamal K. Dutta, Antonio Frontera, Rosa M. Gomila, Miquel Barceló-Oliver and Manjit K. Bhattacharyya
Crystals 2023, 13(6), 895; https://doi.org/10.3390/cryst13060895 - 30 May 2023
Cited by 1 | Viewed by 1117
Abstract
Two Na(I) coordination polymers, namely, {Na(BA)2(μ-H2O)2}n{adp}n (1) and {[Na2(μ-BA)(μ-fum)(μ-H2O)4](BA)}n (2) (where, BA = boric acid, adp = adipic acid, fum = fumarate),were prepared [...] Read more.
Two Na(I) coordination polymers, namely, {Na(BA)2(μ-H2O)2}n{adp}n (1) and {[Na2(μ-BA)(μ-fum)(μ-H2O)4](BA)}n (2) (where, BA = boric acid, adp = adipic acid, fum = fumarate),were prepared and characterized using elemental analysis, TGA, FT-IR, and single-crystal X-ray diffraction techniques. Various unconventional supramolecular interactions, i.e., CH∙∙∙HC and parallel CO∙∙∙CO interactions, stabilize the layered assembly of compound 1. Interesting dual enclathration of BA molecules within the supramolecular host cavities formed by O-H∙∙∙O and C-H∙∙∙C interactions stabilizes the crystal structure of compound 2. The H-bonding interactions in 1 and 2 were further studied theoretically using the quantum theory of atoms in molecules (QTAIM) and the noncovalent interaction plot (NCI Plot) computational tools. The energy of the H-bonds was estimated using the potential energy density at the bond critical points. Theoretical calculations confirmed the presence of O-H∙∙∙O H-bonding interactions in both compounds, forming structure-guiding R22(8) synthons relevant for the stability of the compounds. Full article
(This article belongs to the Special Issue Different Kinds of Hydrogen Bonds in Crystal Structures)
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16 pages, 2508 KiB  
Article
π-Hole Triel Bonds between TrPhX2 (Tr = B, Al, Ga; X = F, Cl, Br, CH3, OH) and (BH)2(NHC)2 (NHC = Nitrogen-Heterocyclic Carbene)
by Sean A. C. McDowell, Zhihao Niu and Qingzhong Li
Crystals 2023, 13(6), 872; https://doi.org/10.3390/cryst13060872 - 26 May 2023
Viewed by 840
Abstract
The π-hole triel bond formed by (BH)2(NHC)2 (NHC denotes nitrogen-heterocyclic carbene) and TrPhX2 (Tr = B, Al, and Ga; X = F, Cl, Br, CH3, and OH) was investigated computationally, with the B=B bond in (BH)2 [...] Read more.
The π-hole triel bond formed by (BH)2(NHC)2 (NHC denotes nitrogen-heterocyclic carbene) and TrPhX2 (Tr = B, Al, and Ga; X = F, Cl, Br, CH3, and OH) was investigated computationally, with the B=B bond in (BH)2(NHC)2 being the electron donor. A large interaction energy ensures that the complex is quite stable. When the substituent X in the electron acceptor is fixed, the magnitude of the interaction energy varies with the identity of the Tr atom. When Tr is Al or Ga, the interaction energy is stronger than when it is B. With an increase in the electron-withdrawing ability of the substituents, the interaction energy shows distinct changes. When Tr is B or Al, the interaction energy varies as TrPhBr2 > TrPhCl2 > TrPhF2, which is different from the order of their positive electrostatic potentials. When Tr = Ga, the interaction energy hardly changes with an increase in the electronegativity of the halogen atoms. For CH3 and OH substitution, larger interaction energies were obtained, with the interaction energy for the OH substituent being the largest. The main interactions in these systems are a triel bond and an X· ·H hydrogen bond. When the substituents are fixed, the interaction energy of the triel bond increases in the order AlPhX2 < GaPhX2 < BPhX2, which is different from the order of the positive electrostatic potentials on the Tr atom in TrPhX2. When X is a halogen atom, the interaction energy of the triel bond decreases in the order Br > Cl > F, which is opposite to the trend for the positive electrostatic potentials on Tr in TrPhX2. In most complexes, the interaction energy for the hydrogen bond is less than that for the triel bond; there is no hydrogen bond in the methyl-substituted complex. In general, the interaction energy of the hydrogen bonds increases with an increase in the electronegativity of the halogen atoms. Full article
(This article belongs to the Special Issue Different Kinds of Hydrogen Bonds in Crystal Structures)
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15 pages, 4357 KiB  
Article
The Cobalt(II) Oxidotellurate(IV) Hydroxides Co2(TeO3)(OH)2 and Co15(TeO3)14(OH)2
by Felix Eder, Matthias Weil, Prativa Pramanik and Roland Mathieu
Crystals 2023, 13(2), 176; https://doi.org/10.3390/cryst13020176 - 19 Jan 2023
Cited by 1 | Viewed by 1504
Abstract
Previously unknown Co2(TeO3)(OH)2 and Co15(TeO3)14(OH)2 were obtained under mild hydrothermal reaction conditions (210 °C, autogenous pressure) from alkaline solutions. Their crystal structures were determined from single-crystal X-ray diffraction data. Co2 [...] Read more.
Previously unknown Co2(TeO3)(OH)2 and Co15(TeO3)14(OH)2 were obtained under mild hydrothermal reaction conditions (210 °C, autogenous pressure) from alkaline solutions. Their crystal structures were determined from single-crystal X-ray diffraction data. Co2(TeO3)(OH)2 (Z = 2, P1¯, a = 5.8898(5), b = 5.9508(5), c = 6.8168(5) Å, α = 101.539(2), β = 100.036(2), γ = 104.347(2)°, 2120 independent reflections, 79 parameters, R[F2 > 2σ(F2)] = 0.017) crystallizes in a unique structure comprised of undulating 2[Co2(OH)6/3O3/3O2/2O1/1]4− layers. Adjacent layers are linked by TeIV atoms along the [001] stacking direction. Co2(TeO3)(OH)2 is stable up to 450 °C and decomposes under the release of water into Co6Te5O16 and CoO. Magnetic measurements of Co2(TeO3)(OH)2 showed antiferromagnetic ordering at ≈ 70 K. The crystal structure of Co15(TeO3)14(OH)2 (Z = 3, R3¯, a = 11.6453(2), c = 27.3540(5) Å, 3476 independent reflections, 112 parameters, R[F2 > 2σ(F2)] = 0.026) is isotypic with Co15(TeO3)14F2. A quantitative structural comparison revealed that the main structural difference between the two phases is connected with the replacement of F by OH, whereas the remaining part of the three-periodic network defined by [CoO6], [CoO5(OH)], [CoO5] and [TeO3] polyhedra is nearly unaffected. Consequently, the magnetic properties of the two phases are similar, namely being antiferromagnetic at low temperatures. Full article
(This article belongs to the Special Issue Different Kinds of Hydrogen Bonds in Crystal Structures)
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13 pages, 4427 KiB  
Article
Hydrogen-Bonded Chain of Rings Motif in N-(4-Methoxyphenyl)piperazin-1-ium Salts with Benzoate Anions: Supramolecular Assemblies and Their Energy Frameworks
by Prabhakar Priyanka, Bidarur K. Jayanna, Thayamma R. Divakara, Gejjalagere P. Suresha, Vinaya, Yeriyur B. Basavaraju, Hemmige S. Yathirajan, Sean R. Parkin and Lilianna Chęcińska
Crystals 2022, 12(12), 1807; https://doi.org/10.3390/cryst12121807 - 12 Dec 2022
Cited by 2 | Viewed by 1669
Abstract
The crystal structures of three salts, namely N-(4-methoxyphenyl)piperazin-1-ium ethoxybenzoate monohydrate (I), N-(4-methoxyphenyl)piperazin-1-ium methoxybenzoate monohydrate (II) and N-(4-methoxyphenyl)piperazin-1-ium hydroxybenzoate monohydrate (III), have been determined and compared. In each of them, the ionic components and the water molecules are linked by a [...] Read more.
The crystal structures of three salts, namely N-(4-methoxyphenyl)piperazin-1-ium ethoxybenzoate monohydrate (I), N-(4-methoxyphenyl)piperazin-1-ium methoxybenzoate monohydrate (II) and N-(4-methoxyphenyl)piperazin-1-ium hydroxybenzoate monohydrate (III), have been determined and compared. In each of them, the ionic components and the water molecules are linked by a combination of N—H···O and O—H···O hydrogen bonds to form infinite chains of edge-fused centrosymmetric rings running parallel to the [100] direction. The C—H···O, C—H···π(arene) interactions and O—H···O in (III) are responsible for the further propagation of the aforementioned chains into di-periodic layers or tri-periodic networks. From an energetic point of view, all structures are primarily di-periodic; the very strong ionic interactions determine the periodicity. For comparison purposes, quantum chemical calculations were performed to show the difference between the ionic and neutral components. The energy of the hydrogen-bonded ring motifs was also estimated. Full article
(This article belongs to the Special Issue Different Kinds of Hydrogen Bonds in Crystal Structures)
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14 pages, 4181 KiB  
Article
Hydrogen Bonding in Crystals of Pyrrol-2-yl Chloromethyl Ketone Derivatives and Methyl Pyrrole-2-Carboxylate
by Małgorzata Domagała, Alina T. Dubis, Sławomir Wojtulewski, Manfred Zabel and Arno Pfitzner
Crystals 2022, 12(11), 1523; https://doi.org/10.3390/cryst12111523 - 26 Oct 2022
Cited by 1 | Viewed by 1519
Abstract
The crystal and molecular structure of three derivatives of carbonyl 2-substituted pyrroles was determined by the single crystal X-ray diffraction. There are 2,2-dichloro-1-(1-methyl-1H-pyrrol-2-yl)ethan-1-one (I), 2-chloro-1-(1H-pyrrol-2-yl)ethan-1-one (II) and methyl 1H-pyrrole-2-carboxylate (III). All [...] Read more.
The crystal and molecular structure of three derivatives of carbonyl 2-substituted pyrroles was determined by the single crystal X-ray diffraction. There are 2,2-dichloro-1-(1-methyl-1H-pyrrol-2-yl)ethan-1-one (I), 2-chloro-1-(1H-pyrrol-2-yl)ethan-1-one (II) and methyl 1H-pyrrole-2-carboxylate (III). All compounds crystallize with one molecule in the asymmetric unit in P212121 for I and II, and P21/c group for III. Despite the similar structures of the investigated compounds, the hydrogen bonds formed in their crystal structures adopt different H-bond motifs. In structure I, the dimers R12(5) and R21(7) form a chain along the b-axis, while in structures II and III, chain C(5) structural motifs are formed. The single point calculations at a ωB97XD/6-311++G(d,p) level of theory indicate that systems with N-H⋯O bonds have greater interaction energies (are more stable) compared with systems featuring C-H⋯O/Cl bonds. A descriptive Hirshfeld analysis showed that the greatest differences are visible for the H⋯H interactions. These H⋯H interactions predominate in structure III, accounting for 45% of the intermolecular interactions, while in structures I and II, they account for only 25%. Although compounds I-II contain Cl-atoms, the percentage of Cl⋯Cl interactions is rather low. In structure with two Cl-atoms (I), the contribution of the Cl⋯Cl contacts is 8.7% and for II, the contribution accounts for only 0.4% of the interactions. Full article
(This article belongs to the Special Issue Different Kinds of Hydrogen Bonds in Crystal Structures)
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