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Open AccessEditorial

Analysis of Hydrogen Bonds in Crystals

by Sławomir J. Grabowski

Crystals 2016, 6(5), 59; https://doi.org/10.3390/cryst6050059 - 17 May 2016

Cited by 35 | Viewed by 8392

Abstract

The determination of crystal structures provides important information on the geometry of species constituting crystals and on the symmetry relations between them. Additionally, the analysis of crystal structures is so conclusive that it allows us to understand the nature of various interactions. The [...] Read more.

The determination of crystal structures provides important information on the geometry of species constituting crystals and on the symmetry relations between them. Additionally, the analysis of crystal structures is so conclusive that it allows us to understand the nature of various interactions. The hydrogen bond interaction plays a crucial role in crystal engineering and, in general, its important role in numerous chemical, physical and bio-chemical processes was the subject of various studies. That is why numerous important findings on the nature of hydrogen bonds concern crystal structures. This special issue presents studies on hydrogen bonds in crystals, and specific compounds and specific H-bonded patterns existing in crystals are analyzed. However, the characteristics of the H-bond interactions are not only analyzed theoretically; this interaction is compared with other ones that steer the arrangement of molecules in crystals, for example halogen, tetrel or pnicogen bonds. More general findings concerning the influence of the hydrogen bond on the physicochemical properties of matter are also presented. Full article

(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)

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Research

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2051 KiB

Open AccessArticle

Comparisons between Crystallography Data and Theoretical Parameters and the Formation of Intramolecular Hydrogen Bonds: Benznidazole

by Boaz G. Oliveira, Edilson B. Alencar Filho and Mário L. A. A. Vasconcellos

Crystals 2016, 6(5), 56; https://doi.org/10.3390/cryst6050056 - 12 May 2016

Cited by 5 | Viewed by 4613

Abstract

The conformational preferences of benznidazole were examined through the application of DFT, PCM and QTAIM calculations, whose results were compared with crystallography data. The geometries were fully optimized with minimum potential energy surface by means of the Relaxed Potential Energy Surface Scan (RPESS) [...] Read more.

The conformational preferences of benznidazole were examined through the application of DFT, PCM and QTAIM calculations, whose results were compared with crystallography data. The geometries were fully optimized with minimum potential energy surface by means of the Relaxed Potential Energy Surface Scan (RPESS) at AM1, followed by the B3LYP/6-311++G(d,p) theoretical level. As a result, the s-cis conformation (1C) was shown to be more stable (4.78 kcal∙mol⁻¹) than s-trans (1T). The Quantum Theory Atoms in Molecules (QTAIM) was applied in order to characterize the (N–H∙∙∙O=N) and (C–H∙∙∙=N) intramolecular hydrogen bonds. The simulation of solvent effect performed by means of the implicit Polarized Continuum Model (PCM) revealed great results, such as, for instance, that the conformation 1W is more stable (23.17 kcal∙mol⁻¹) in comparison to 1C. Our main goal was stressed in the topological description of intramolecular hydrogen bonds in light of the QTAIM approach, as well as in the solvent simulation to accurately obtain an important conformation of benznidazole. Full article

(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)

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4383 KiB

Open AccessArticle

The Hydrogen Bonded Structures of Two 5-Bromobarbituric Acids and Analysis of Unequal C5–X and C5–X′ Bond Lengths (X = X′ = F, Cl, Br or Me) in 5,5-Disubstituted Barbituric Acids

by Thomas Gelbrich, Doris E. Braun, Stefan Oberparleiter, Herwig Schottenberger and Ulrich J. Griesser

Crystals 2016, 6(4), 47; https://doi.org/10.3390/cryst6040047 - 22 Apr 2016

Cited by 4 | Viewed by 5545

Abstract

The crystal structure of the methanol hemisolvate of 5,5-dibromobarbituric acid (1MH) displays an H-bonded layer structure which is based on N–H∙∙∙O=C, N–H∙∙∙O(MeOH) and (MeOH)O–H∙∙∙O interactions. The barbiturate molecules form an H-bonded substructure which has the fes topology. 5,5′-Methanediylbis(5-bromobarbituric acid) 2, obtained from a [...] Read more.

The crystal structure of the methanol hemisolvate of 5,5-dibromobarbituric acid (1MH) displays an H-bonded layer structure which is based on N–H∙∙∙O=C, N–H∙∙∙O(MeOH) and (MeOH)O–H∙∙∙O interactions. The barbiturate molecules form an H-bonded substructure which has the fes topology. 5,5′-Methanediylbis(5-bromobarbituric acid) 2, obtained from a solution of 5,5-dibromobarbituric acid in nitromethane, displays a N–H···O=C bonded framework of the sxd type. The conformation of the pyridmidine ring and the lengths of the ring substituent bonds C5–X and C5–X′ in crystal forms of 5,5-dibromobarbituric acid and three closely related analogues (X = X′ = Br, Cl, F, Me) have been investigated. In each case, a conformation close to a C5-endo envelope is correlated with a significant lengthening of the axial C5–X′ in comparison to the equatorial C5–X bond. Isolated molecule geometry optimizations at different levels of theory confirm that the C5-endo envelope is the global conformational energy minimum of 5,5-dihalogenbarbituric acids. The relative lengthening of the axial bond is therefore interpreted as an inherent feature of the preferred envelope conformation of the pyrimidine ring, which minimizes repulsive interactions between the axial substituent and pyrimidine ring atoms. Full article

(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)

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1935 KiB

Open AccessArticle

The Role of Hydrogen Bond in Designing Molecular Optical Materials

by Leonardo H. R. Dos Santos and Piero Macchi

Crystals 2016, 6(4), 43; https://doi.org/10.3390/cryst6040043 - 13 Apr 2016

Cited by 31 | Viewed by 5599

Abstract

In this perspective article, we revise some of the empirical and semi-empirical strategies for predicting how hydrogen bonding affects molecular and atomic polarizabilities in aggregates. We use p-nitroaniline and hydrated oxalic acid as working examples to illustrate the enhancement of donor and [...] Read more.

In this perspective article, we revise some of the empirical and semi-empirical strategies for predicting how hydrogen bonding affects molecular and atomic polarizabilities in aggregates. We use p-nitroaniline and hydrated oxalic acid as working examples to illustrate the enhancement of donor and acceptor functional-group polarizabilities and their anisotropy. This is significant for the evaluation of electrical susceptibilities in crystals; and the properties derived from them like the refractive indices. Full article

(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)

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Open AccessArticle

Isomorphous Crystals from Diynes and Bromodiynes Involved in Hydrogen and Halogen Bonds

by Pierre Baillargeon, Édouard Caron-Duval, Émilie Pellerin, Simon Gagné and Yves L. Dory

Crystals 2016, 6(4), 37; https://doi.org/10.3390/cryst6040037 - 2 Apr 2016

Cited by 5 | Viewed by 7557

Abstract

Isomorphous crystals of two diacetylene derivatives with carbamate functionality (BocNH-CH₂-diyne-X, where X = H or Br) have been obtained. The main feature of these structures is the original 2D arrangement (as supramolecular sheets or walls) in which the H bond and [...] Read more.

Isomorphous crystals of two diacetylene derivatives with carbamate functionality (BocNH-CH₂-diyne-X, where X = H or Br) have been obtained. The main feature of these structures is the original 2D arrangement (as supramolecular sheets or walls) in which the H bond and halogen bond have a prominent effect on the whole architecture. The two diacetylene compounds harbor neighboring carbamate (Boc protected amine) and conjugated alkyne functionalities. They differ only by the nature of the atom located at the penultimate position of the diyne moiety, either a hydrogen atom or a bromine atom. Both of them adopt very similar 2D wall organizations with antiparallel carbamates (as in antiparallel beta pleated sheets). Additional weak interactions inside the same walls between molecular bricks are H bond interactions (diyne-H···O=C) or halogen bond interactions (diyne-Br···O=C), respectively. Based on crystallographic atom coordinates, DFT (B3LYP/6-31++G(d,p)) and DFT (M06-2X/6-31++G(d,p)) calculations were performed on these isostructural crystals to gain insight into the intermolecular interactions. Full article

(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)

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Open AccessArticle

Very Strong Parallel Interactions Between Two Saturated Acyclic Groups Closed with Intramolecular Hydrogen Bonds Forming Hydrogen-Bridged Rings

by Jelena P. Blagojević, Goran V. Janjić and Snežana D. Zarić

Crystals 2016, 6(4), 34; https://doi.org/10.3390/cryst6040034 - 31 Mar 2016

Cited by 5 | Viewed by 5066

Abstract

Saturated acyclic four-atom groups closed with a classic intramolecular hydrogen bond, generating planar five-membered rings (hydrogen-bridged quasi-rings), in which at least one of the ring atoms is bonded to other non-ring atoms that are not in the ring plane and, thus, capable to [...] Read more.

Saturated acyclic four-atom groups closed with a classic intramolecular hydrogen bond, generating planar five-membered rings (hydrogen-bridged quasi-rings), in which at least one of the ring atoms is bonded to other non-ring atoms that are not in the ring plane and, thus, capable to form intermolecular interactions, were studied in this work, in order to find the preferred mutual positions of these species in crystals and evaluate strength of intermolecular interactions. We studied parallel interactions of these rings by analysing crystal structures in the Cambridge Structural Database (CSD) and by quantum chemical calculations. The rings can have one hydrogen atom out of the ring plane that can form hydrogen bonds between two parallel rings. Hence, in these systems with parallel rings, two types of hydrogen bonds can be present, one in the ring, and the other one between two parallel rings. The CSD search showed that 27% of the rings in the crystal structures form parallel interactions. The calculations at very accurate CCSD(T)/CBS level revealed strong interactions, in model systems of thiosemicarbazide, semicarbazide and glycolamide dimers the energies are −9.68, −7.12 and −4.25 kcal/mol. The hydrogen bonds between rings, as well as dispersion interactions contribute to the strong interaction energies. Full article

(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)

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6633 KiB

Open AccessArticle

Theoretical Studies on Hydrogen Bonds in Anions Encapsulated by an Azamacrocyclic Receptor

by Jing Wang, Jiande Gu, Md. Alamgir Hossain and Jerzy Leszczynski

Crystals 2016, 6(3), 31; https://doi.org/10.3390/cryst6030031 - 22 Mar 2016

Cited by 2 | Viewed by 4461

Abstract

Hydrogen bonds in two halides encapsulated by an azamacrocyclic receptor were studied in detail by the density functional theory (DFT) approaches at B3LYP/6-311++G(d,p) and M06-2X/6-311++G(d,p) levels. The atoms in molecules (AIM) theory and the electron density difference maps were applied for characterizing the [...] Read more.

Hydrogen bonds in two halides encapsulated by an azamacrocyclic receptor were studied in detail by the density functional theory (DFT) approaches at B3LYP/6-311++G(d,p) and M06-2X/6-311++G(d,p) levels. The atoms in molecules (AIM) theory and the electron density difference maps were applied for characterizing the hydrogen bond patterns. The results suggest that the fluoride complex has a unique binding pattern which shows a hydrogen bond augmented with ionic bond characteristics. Full article

(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)

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Open AccessArticle

Effect of Intra- and Intermolecular Interactions on the Properties of para-Substituted Nitrobenzene Derivatives

by Halina Szatylowicz, Olga A. Stasyuk, Célia Fonseca Guerra and Tadeusz M. Krygowski

Crystals 2016, 6(3), 29; https://doi.org/10.3390/cryst6030029 - 18 Mar 2016

Cited by 21 | Viewed by 6844

Abstract

To study the influence of intra- and intermolecular interactions on properties of the nitro group in para-substituted nitrobenzene derivatives, two sources of data were used: (i) Cambridge Structural Database and (ii) quantum chemistry modeling. In the latter case, “pure” intramolecular interactions were [...] Read more.

To study the influence of intra- and intermolecular interactions on properties of the nitro group in para-substituted nitrobenzene derivatives, two sources of data were used: (i) Cambridge Structural Database and (ii) quantum chemistry modeling. In the latter case, “pure” intramolecular interactions were simulated by gradual rotation of the nitro group in para-nitroaniline, whereas H-bond formation at the amino group allowed the intermolecular interactions to be accounted for. BLYP functional with dispersion correction and TZ2P basis set (ADF program) were used to perform all calculations. It was found that properties of the nitro group dramatically depend on both its orientation with respect to the benzene ring as well as on the substituent in the para-position. The nitro group lies in the plane of the benzene ring for only a small number of molecules, whereas the mean value of the twist angle is 7.3 deg, mostly due to intermolecular interactions in the crystals. This distortion from planarity and the nature of para-substituent influence the aromaticity of the ring (described by HOMA index) and properties of the nitro group due to electronic effects. The results obtained by QM calculations fully coincide with observations found for the data set of crystal structures. Full article

(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)

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Open AccessArticle

Non-Covalent Interactions in Hydrogen Storage Materials LiN(CH₃)₂BH₃ and KN(CH₃)₂BH₃

by Filip Sagan, Radosław Filas and Mariusz P. Mitoraj

Crystals 2016, 6(3), 28; https://doi.org/10.3390/cryst6030028 - 18 Mar 2016

Cited by 28 | Viewed by 8203

Abstract

In the present work, an in-depth, qualitative and quantitative description of non-covalent interactions in the hydrogen storage materials LiN(CH₃)₂BH₃ and KN(CH₃)₂BH₃ was performed by means of the charge and energy decomposition method (ETS-NOCV) [...] Read more.

In the present work, an in-depth, qualitative and quantitative description of non-covalent interactions in the hydrogen storage materials LiN(CH₃)₂BH₃ and KN(CH₃)₂BH₃ was performed by means of the charge and energy decomposition method (ETS-NOCV) as well as the Interacting Quantum Atoms (IQA) approach. It was determined that both crystals are stabilized by electrostatically dominated intra- and intermolecular M∙∙∙H–B interactions (M = Li, K). For LiN(CH₃)₂BH₃ the intramolecular charge transfer appeared (B–H→Li) to be more pronounced compared with the corresponding intermolecular contribution. We clarified for the first time, based on the ETS-NOCV and IQA methods, that homopolar BH∙∙∙HB interactions in LiN(CH₃)₂BH₃ can be considered as destabilizing (due to the dominance of repulsion caused by negatively charged borane units), despite the fact that some charge delocalization within BH∙∙∙HB contacts is enforced (which explains H∙∙∙H bond critical points found from the QTAIM method). Interestingly, quite similar (to BH∙∙∙HB) intermolecular homopolar dihydrogen bonds CH∙∙∙HC appared to significantly stabilize both crystals—the ETS-NOCV scheme allowed us to conclude that CH∙∙∙HC interactions are dispersion dominated, however, the electrostatic and σ/σ*(C–H) charge transfer contributions are also important. These interactions appeared to be more pronounced in KN(CH₃)₂BH₃ compared with LiN(CH₃)₂BH₃. Full article

(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)

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3460 KiB

Open AccessArticle

RCH₃···O Interactions in Biological Systems: Are They Trifurcated H-Bonds or Noncovalent Carbon Bonds?

by Antonio Bauzá and Antonio Frontera

Crystals 2016, 6(3), 26; https://doi.org/10.3390/cryst6030026 - 17 Mar 2016

Cited by 68 | Viewed by 7626

Abstract

In this manuscript, we combine high-level ab initio calculations on some model systems (XCH₃ σ-hole/H-bond donors) and a Protein Data Bank (PDB) survey to distinguish between trifurcated H-bonds and noncovalent carbon bonds in XCH₃···O complexes (X = any atom or [...] Read more.

In this manuscript, we combine high-level ab initio calculations on some model systems (XCH₃ σ-hole/H-bond donors) and a Protein Data Bank (PDB) survey to distinguish between trifurcated H-bonds and noncovalent carbon bonds in XCH₃···O complexes (X = any atom or group). Recently, it has been demonstrated both experimentally and theoretically the importance of noncovalent carbon bonds in the solid state. When an electron-rich atom interacts with a methyl group, the role of the methyl group is commonly viewed as a weak H-bond donor. However, if the electron-rich atom is located equidistant from the three H atoms, the directionality of each individual H-bond in the trifurcated binding mode is poor. Therefore, the XCH₃···O interaction could be also defined as a tetrel bond (C···O interaction). In this manuscript, we shed light into this matter and demonstrate the importance of XCH₃···O noncovalent carbon bonding interactions in two relevant protein-substrate complexes retrieved from the PDB. Full article

(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)

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1520 KiB

Open AccessCommunication

A Cadmium Anionic 1-D Coordination Polymer {[Cd(H₂O)₆][Cd₂(atr)₂(μ₂-btc)₂(H₂O)₄] 2H₂O}_n within a 3-D Supramolecular Charge-Assisted Hydrogen-Bonded and π-Stacking Network

by Anas Tahli, Ümit Köc, Reda F. M. Elshaarawy, Anna Christin Kautz and Christoph Janiak

Crystals 2016, 6(3), 23; https://doi.org/10.3390/cryst6030023 - 2 Mar 2016

Cited by 13 | Viewed by 6174

Abstract

The hydrothermal reaction of 4,4′-bis(1,2,4-triazol-4-yl) (btr) and benzene-1,3,5-tricarboxylic acid (H₃btc) with Cd(OAc)₂·2H₂O at 125 °C in situ forms 4-amino-1,2,4-triazole (atr) from btr, which crystallizes to a mixed-ligand, poly-anionic chain of [Cd₂(atr)₂(µ₂-btc) [...] Read more.

The hydrothermal reaction of 4,4′-bis(1,2,4-triazol-4-yl) (btr) and benzene-1,3,5-tricarboxylic acid (H₃btc) with Cd(OAc)₂·2H₂O at 125 °C in situ forms 4-amino-1,2,4-triazole (atr) from btr, which crystallizes to a mixed-ligand, poly-anionic chain of [Cd₂(atr)₂(µ₂-btc)₂(H₂O)₄]^2–. Together with a hexaaquacadmium(II) cation and water molecules the anionic coordination-polymeric forms a 3-D supramolecular network of hexaaquacadmium(II)-catena-[bis(4-amino-1,2,4-triazole)tetraaquabis(benzene-1,3,5-tricarboxylato)dicadmate(II)] dihydrate, 1-D-{[Cd(H₂O)₆][Cd₂(atr)₂(µ₂-btc)₂(H₂O)₄] 2H₂O}_n which is based on hydrogen bonds (in part charge-assisted) and π–π interactions. Full article

(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)

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1980 KiB

Open AccessFeature PaperArticle

Charge-Assisted Hydrogen-Bonded Networks of NH₄⁺ and [Co(NH₃)₆]³⁺ with the New Linker Anion of 4-Phosphono-Biphenyl-4′-Carboxylic Acid

by Christian Heering, Bahareh Nateghi and Christoph Janiak

Crystals 2016, 6(3), 22; https://doi.org/10.3390/cryst6030022 - 24 Feb 2016

Cited by 11 | Viewed by 9528

Abstract

The new linker molecule 4-phosphono-biphenyl-4′-carboxylic acid (H₂O₃P-(C₆H₄)₂-COOH, H₃BPPA) has been structurally elucidated in hydrogen-bonded networks with the ammonium cation NH₄(H₂BPPA)(H₃BPPA) (1) and the [...] Read more.

The new linker molecule 4-phosphono-biphenyl-4′-carboxylic acid (H₂O₃P-(C₆H₄)₂-COOH, H₃BPPA) has been structurally elucidated in hydrogen-bonded networks with the ammonium cation NH₄(H₂BPPA)(H₃BPPA) (1) and the hexaamminecobalt(III) cation [Co(NH₃)₆](BPPA)·4H₂O (2). The protic O-H and N-H hydrogen atoms were found and refined in the low-temperature single-crystal X-ray structures. The hydrogen bonds in both structures are so-called charge-assisted; that is, the H-bond donor and/or acceptor carry positive and/or negative ionic charges, respectively. The H-bonded network in 1 consists of one formally mono-deprotonated 4-phosphonato-biphenyl-4′-carboxylic acid group; that is, a H₂BPPA⁻ anion and a neutral H₃BPPA molecule, which together form a 3D hydrogen-bonded network. However, an almost symmetric resonance-assisted hydrogen bond (RAHB) bond [O···H = 1.17 (3) and 1.26 (3) Å, O···H···O = 180 (3)°] signals charge delocalization between the formal H₂BPPA⁻ anion and the formally neutral H₃BPPA molecule. Hence, the anion in 1 is better formulated as [H₂BPPA···H···H₂BPPA]⁻. In the H-bonded network of 2 the 4-phosphonato-biphenyl-4′-carboxylic acid is triply deprotonated, BPPA³⁻. The [Co(NH₃)₆]³⁺ cation is embedded between H-bond acceptor groups, –COO⁻ and –PO₃⁻ and H₂O molecules. The incorporation of sixteen H₂O molecules per unit cell makes 2 an analogue of the well-studied guanidinium sulfonate frameworks. Full article

(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)

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Open AccessArticle

H₂XP:OH₂ Complexes: Hydrogen vs. Pnicogen Bonds

by Ibon Alkorta, Janet E. Del Bene and Jose Elguero

Crystals 2016, 6(2), 19; https://doi.org/10.3390/cryst6020019 - 2 Feb 2016

Cited by 20 | Viewed by 5765

Abstract

A search of the Cambridge Structural Database (CSD) was carried out for phosphine-water and arsine-water complexes in which water is either the proton donor in hydrogen-bonded complexes, or the electron-pair donor in pnicogen-bonded complexes. The range of experimental P-O distances in the phosphine [...] Read more.

A search of the Cambridge Structural Database (CSD) was carried out for phosphine-water and arsine-water complexes in which water is either the proton donor in hydrogen-bonded complexes, or the electron-pair donor in pnicogen-bonded complexes. The range of experimental P-O distances in the phosphine complexes is consistent with the results of ab initio MP2/aug’-cc-pVTZ calculations carried out on complexes H₂XP:OH₂, for X = NC, F, Cl, CN, OH, CCH, H, and CH₃. Only hydrogen-bonded complexes are found on the H₂(CH₃)P:HOH and H₃P:HOH potential surfaces, while only pnicogen-bonded complexes exist on H₂(NC)P:OH₂, H₂FP:OH₂, H₂(CN)P:OH₂, and H₂(OH)P:OH₂ surfaces. Both hydrogen-bonded and pnicogen-bonded complexes are found on the H₂ClP:OH₂ and H₂(CCH)P:OH₂ surfaces, with the pnicogen-bonded complexes more stable than the corresponding hydrogen-bonded complexes. The more electronegative substituents prefer to form pnicogen-bonded complexes, while the more electropositive substituents form hydrogen-bonded complexes. The H₂XP:OH₂ complexes are characterized in terms of their structures, binding energies, charge-transfer energies, and spin-spin coupling constants ^2hJ(O-P), ^1hJ(H-P), and ¹J(O-H) across hydrogen bonds, and ^1pJ(P-O) across pnicogen bonds. Full article

(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)

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Open AccessArticle

Constructor Graphs as Useful Tools for the Classification of Hydrogen Bonded Solids: The Case Study of the Cationic (Dimethylphosphoryl)methanaminium (dpmaH⁺) Tecton

by Guido J. Reiss

Crystals 2016, 6(1), 6; https://doi.org/10.3390/cryst6010006 - 31 Dec 2015

Cited by 3 | Viewed by 5721

Abstract

The structural chemistry of a series of dpmaH (dpmaH = (dimethylphosphoryl)methanaminium) salts has been investigated using constructor graph representations to visualize structural dependencies, covering the majority of known dpmaH salts. It is shown that the structurally related α-aminomethylphosphinic acid [...] Read more.

The structural chemistry of a series of dpmaH (dpmaH = (dimethylphosphoryl)methanaminium) salts has been investigated using constructor graph representations to visualize structural dependencies, covering the majority of known dpmaH salts. It is shown that the structurally related α-aminomethylphosphinic acid can be integrated in the systematology of the dpmaH salts. Those dpmaH salts with counter anions that are weak hydrogen bond acceptors (ClO₄⁻, SnCl₆²⁻, IrCl₆²⁻,I⁻) tend to form head-to-tail hydrogen bonded moieties purely consisting of dpmaH⁺ cations as the primarily structural motif. In structures with weak to very weak hydrogen bonds between the dpmaH⁺ cations and the counter anions, the anions fill the gaps in the structures. In salts with medium to strong hydrogen bond acceptor counter ions (Cl⁻, NO₃⁻, PdCl₄²⁻), the predominant structural motif is a double head-to-tail hydrogen bonded (dpmaH⁺)₂ dimer. These dimeric units form further NH···X hydrogen bonds to neighboring counter anions X, which results in one-dimensional and two-dimensional architectures. Full article

(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)

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Open AccessArticle

[FHF]⁻—The Strongest Hydrogen Bond under the Influence of External Interactions

by Sławomir J. Grabowski

Crystals 2016, 6(1), 3; https://doi.org/10.3390/cryst6010003 - 25 Dec 2015

Cited by 30 | Viewed by 8090

Abstract

A search through the Cambridge Structural Database (CSD) for crystal structures containing the [FHF]⁻ anion was carried out. Forty five hydrogen bifluoride structures were found mainly with the H-atom moved from the mid-point of the F…F distance. However several [FHF]⁻ systems [...] Read more.

A search through the Cambridge Structural Database (CSD) for crystal structures containing the [FHF]⁻ anion was carried out. Forty five hydrogen bifluoride structures were found mainly with the H-atom moved from the mid-point of the F…F distance. However several [FHF]⁻ systems characterized by D_∞h symmetry were found, the same as this anion possesses in the gas phase. The analysis of CSD results as well as the analysis of results of ab initio calculations on the complexes of [FHF]⁻ with Lewis acid moieties show that the movement of the H-atom from the central position depends on the strength of interaction of this anion with external species. The analysis of the electron charge density distribution in complexes of [FHF]⁻ was performed with the use of the Quantum Theory of Atoms in Molecules (QTAIM) approach and the Natural Bond Orbitals (NBO) method. Full article

(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)

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Open AccessArticle

Structural Elucidation of α-Cyclodextrin-Succinic Acid Pseudo Dodecahydrate: Expanding the Packing Types of α-Cyclodextrin Inclusion Complexes

by Sofiane Saouane and Francesca P. A. Fabbiani

Crystals 2016, 6(1), 2; https://doi.org/10.3390/cryst6010002 - 24 Dec 2015

Cited by 5 | Viewed by 8866

Abstract

This paper reports a new packing type of α-cyclodextrin inclusion complexes, obtained here with succinic acid under low-temperature crystallization conditions. The structure of the 1:1 complex is characterized by heavy disorder of the guest, the solvent, and part of the host. The crystal [...] Read more.

This paper reports a new packing type of α-cyclodextrin inclusion complexes, obtained here with succinic acid under low-temperature crystallization conditions. The structure of the 1:1 complex is characterized by heavy disorder of the guest, the solvent, and part of the host. The crystal packing belongs to the known channel-type structure; the basic structural unit is composed of cyclodextrin trimers, as opposed to the known isolated molecular or dimeric constructs, packed along the c-axis. Each trimer is made of crystallographically independent molecules assembled in a stacked vase-like cluster. A multi-temperature single-crystal X-ray diffraction analysis reveals the presence of dynamic disorder. Full article

(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)

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785 KiB

Open AccessArticle

Diffusivity and Mobility of Adsorbed Water Layers at TiO₂ Rutile and Anatase Interfaces

by Niall J. English

Crystals 2016, 6(1), 1; https://doi.org/10.3390/cryst6010001 - 22 Dec 2015

Cited by 15 | Viewed by 4895

Abstract

Molecular-dynamics simulations have been carried out to study diffusion of water molecules adsorbed to anatase-(101) and rutile-(110) interfaces at room temperature (300 K). The mean squared displacement (MSD) of the adsorbed water layers were determined to estimate self-diffusivity therein, and the mobility of [...] Read more.

Molecular-dynamics simulations have been carried out to study diffusion of water molecules adsorbed to anatase-(101) and rutile-(110) interfaces at room temperature (300 K). The mean squared displacement (MSD) of the adsorbed water layers were determined to estimate self-diffusivity therein, and the mobility of these various layers was gauged in terms of the “swopping” of water molecules between them. Diffusivity was substantially higher within the adsorbed monolayer at the anatase-(101) surface, whilst the anatase-(101) surface’s more open access facilitates easier contact of adsorbed water molecules with those beyond the first layer, increasing the level of dynamical inter-layer exchange and mobility of the various layers. It is hypothesised that enhanced ease of access of water to the anatase-(101) surface helps to rationalise experimental observations of its comparatively greater photo-activity. Full article

(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)

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Dissection of the Factors Affecting Formation of a CH∙∙∙O H-Bond. A Case Study

by Steve Scheiner

Crystals 2015, 5(3), 327-345; https://doi.org/10.3390/cryst5030327 - 25 Aug 2015

Cited by 16 | Viewed by 5534

Abstract

Quantum calculations are used to examine how various constituent components of a large molecule contribute to the formation of an internal CH∙∙∙O H-bond. Such a bond is present in the interaction between two amide units, connected together by a series of functional groups. [...] Read more.

Quantum calculations are used to examine how various constituent components of a large molecule contribute to the formation of an internal CH∙∙∙O H-bond. Such a bond is present in the interaction between two amide units, connected together by a series of functional groups. Each group is removed one at a time, so as to monitor the effect of each upon the H-bond, and thereby learn the bare essentials that are necessary for its formation, as well as how its presence affects the overall molecular structure. Also studied is the perturbation caused by change in the length of the aliphatic chain connecting the two amide groups. The energy of the CH∙∙∙O H-bond is calculated directly, as is the rigidity of the entire molecular framework. Full article

(This article belongs to the Special Issue Analysis of Hydrogen Bonds in Crystals)

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