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Hydrogen Bonds

A topical collection in Molecules (ISSN 1420-3049). This collection belongs to the section "Computational and Theoretical Chemistry".

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Collection Editor
Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland
Interests: charge-inverted hydrogen bonds; inter- and intramolecular interactions; methods of estimating the interaction energy of intramolecular interactions; steric effects; endohedral chemistry; substituent effects; QTAIM; computational chemistry
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Topical Collection Information

Dear Colleagues,

Hydrogen bonds are, quite rightly, considered the most important type of non-covalent interactions. For example, they have a fundamental impact on the properties of water—the compound that has the most important influence on life processes. Namely, when proclaiming the manifestations of the presence of hydrogen bonds, most often one refers to the exceptionally high boiling point of liquid water compared to its slightly heavier counterpart H2S. Another manifestation of the presence of intermolecular hydrogen bonds is that the density of ice is lesser than the density of liquid water. Consequently, the ice floats on the surface of water, enabling the fish to survive the cold winters. Good solubility of polar substances in water also results from the formation of hydrogen bonds between water molecules and the solute. However, hydrogen bonds are not all about water. Their great importance is also manifested in the case of much larger molecules, such as, e.g., carbohydrates and proteins. It is well known that the helical structure of DNA is due to the presence of intermolecular hydrogen bonds between complementary nitrogen bases (adenine–thymine and cytosine–guanine). Intermolecular hydrogen bonds also affect the so-called protein folding and maintenance of cellulose or polymer chains. As in the case of intermolecular hydrogen bonds, the role of intramolecular hydrogen bonds cannot be overestimated. For example, they can significantly affect the conformational equilibrium (a good example is the keto-enol equilibrium in the gas and liquid phases). Such an equilibrium, in turn, often affects the crystallographic structure of the compound in the solid. A very important effect related to the concept of hydrogen bonding is the effect of proton transfer in the hydrogen bridge X-H···Y with the formation of X··H··Y or X···H-Y. As it most often occurs in the excited state of a system, its study requires different techniques.

The reason for the extraordinary importance of hydrogen bonds in the rich world of various bonds and interactions is their unique location on the strength scale. Namely, on this scale, hydrogen bonds are in the middle, between the weak van der Waals interactions and the stronger covalent bonds. This intermediate strength of hydrogen bonds means that they are created relatively easily and generally in large amounts. Like a glue, they bind individual molecules into dimers, trimers, molecular clusters, or even larger agglomerates. However, the network of hydrogen bonds is dynamic, old bonds are broken and new ones are formed in their place. Therefore, the evolution of such a system is generally described by Molecular Dynamics (MD). A specific property of hydrogen bonds is that, as the smallest among all the elements in the Periodic Table, hydrogen atom allows a relatively close contact of the X and Y atoms in the X-H···Y bridge, most often strongly electronegative and therefore having the same charge sign, acting as a buffer between them.

The aim of this Topical Collection is to bring together scientific articles on various aspects of hydrogen bonding, both inter- and intramolecular. Articles can be based either on experimental research or theoretical calculations or combine both ways of cognition. I hope that the articles collected here will also be a great overview of the multitude of research techniques currently occurring as well as the multiple topics related to the nature of hydrogen bonding and will contribute to an even greater emphasis on its role not only in chemistry, but also in various related sciences. I hope that this Topical Collection will also be a successful continuation of the recent Special Issue on intramolecular hydrogen bonding (see Book and Editorial Molecules 2021, 26(20), 6319), that is extended to intermolecular hydrogen bonds as well.

Dr. Mirosław Jabłoński
Collection Editor

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Related Special Issue

Published Papers (26 papers)

2023

Jump to: 2022, 2021, 2020

3 pages, 198 KiB  
Editorial
Hydrogen Bonds
by Mirosław Jabłoński
Molecules 2023, 28(4), 1616; https://doi.org/10.3390/molecules28041616 - 8 Feb 2023
Cited by 3 | Viewed by 1182
Abstract
The Topical Collection “Hydrogen Bonds” is a continuation of the previous Special Issue “Intramolecular Hydrogen Bonding 2021” [...] Full article

2022

Jump to: 2023, 2021, 2020

16 pages, 3271 KiB  
Article
Exploring the Dynamical Nature of Intermolecular Hydrogen Bonds in Benzamide, Quinoline and Benzoic Acid Derivatives
by Kamil Wojtkowiak and Aneta Jezierska
Molecules 2022, 27(24), 8847; https://doi.org/10.3390/molecules27248847 - 13 Dec 2022
Cited by 3 | Viewed by 1226
Abstract
The hydrogen bonds properties of 2,6-difluorobenzamide, 5-hydroxyquinoline and 4-hydroxybenzoic acid were investigated by Car–Parrinello and path integral molecular dynamics (CPMD and PIMD), respectively. The computations were carried out in vacuo and in the crystalline phase. The studied complexes possess diverse networks of intermolecular [...] Read more.
The hydrogen bonds properties of 2,6-difluorobenzamide, 5-hydroxyquinoline and 4-hydroxybenzoic acid were investigated by Car–Parrinello and path integral molecular dynamics (CPMD and PIMD), respectively. The computations were carried out in vacuo and in the crystalline phase. The studied complexes possess diverse networks of intermolecular hydrogen bonds (N-H…O, O-H…N and O-H…O). The time evolution of hydrogen bridges gave a deeper insight into bonds dynamics, showing that bridged protons are mostly localized on the donor side; however, the proton transfer phenomenon was registered as well. The vibrational features associated with O-H and N-H stretching were analyzed on the basis of the Fourier transform of the atomic velocity autocorrelation function. The spectroscopic effects of hydrogen bond formation were studied. The PIMD revealed quantum effects influencing the hydrogen bridges providing more accurate free energy sampling. It was found that the N…O or O…O interatomic distances decreased (reducing the length of the hydrogen bridge), while the O-H or N-H covalent bond was elongated, which led to the increase in the proton sharing. Furthermore, Quantum Theory of Atoms in Molecules (QTAIM) was used to give insight into electronic structure parameters. Finally, Symmetry-Adapted Perturbation Theory (SAPT) was employed to estimate the energy contributions to the interaction energy of the selected dimers. Full article
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42 pages, 7773 KiB  
Article
Association Complexes of Calix[6]arenes with Amino Acids Explained by Energy-Partitioning Methods
by Emran Masoumifeshani, Michał Chojecki, Dorota Rutkowska-Zbik and Tatiana Korona
Molecules 2022, 27(22), 7938; https://doi.org/10.3390/molecules27227938 - 16 Nov 2022
Cited by 2 | Viewed by 1291
Abstract
Intermolecular complexes with calixarenes are intriguing because of multiple possibilities of noncovalent binding for both polar and nonpolar molecules, including docking in the calixarene cavity. In this contribution calix[6]arenes interacting with amino acids are studied with an additional aim to show that tools [...] Read more.
Intermolecular complexes with calixarenes are intriguing because of multiple possibilities of noncovalent binding for both polar and nonpolar molecules, including docking in the calixarene cavity. In this contribution calix[6]arenes interacting with amino acids are studied with an additional aim to show that tools such as symmetry-adapted perturbation theory (SAPT), functional-group SAPT (F-SAPT), and systematic molecular fragmentation (SMF) methods may provide explanations for different numbers of noncovalent bonds and of their varying strength for various calixarene conformers and guest molecules. The partitioning of the interaction energy provides an easy way to identify hydrogen bonds, including those with unconventional hydrogen acceptors, as well as other noncovalent bonds, and to find repulsive destabilizing interactions between functional groups. Various other features can be explained by energy partitioning, such as the red shift of an IR stretching frequency for some hydroxy groups, which arises from their attraction to the phenyl ring of calixarene. Pairs of hydrogen bonds and other noncovalent bonds of similar magnitude found by F-SAPT explain an increase in the stability of both inclusion and outer complexes. Full article
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16 pages, 3303 KiB  
Article
Intramolecular Interactions in Derivatives of Uracil Tautomers
by Paweł A. Wieczorkiewicz, Tadeusz M. Krygowski and Halina Szatylowicz
Molecules 2022, 27(21), 7240; https://doi.org/10.3390/molecules27217240 - 25 Oct 2022
Cited by 4 | Viewed by 1696
Abstract
The influence of solvents on intramolecular interactions in 5- or 6-substituted nitro and amino derivatives of six tautomeric forms of uracil was investigated. For this purpose, the density functional theory (B97-D3/aug-cc-pVDZ) calculations were performed in ten environments (1 > ε > 109) using [...] Read more.
The influence of solvents on intramolecular interactions in 5- or 6-substituted nitro and amino derivatives of six tautomeric forms of uracil was investigated. For this purpose, the density functional theory (B97-D3/aug-cc-pVDZ) calculations were performed in ten environments (1 > ε > 109) using the polarizable continuum model (PCM) of solvation. The substituents were characterized by electronic (charge of the substituent active region, cSAR) and geometric parameters. Intramolecular interactions between non-covalently bonded atoms were investigated using the theory of atoms in molecules (AIM) and the non-covalent interaction index (NCI) method, which allowed discussion of possible interactions between the substituents and N/NH endocyclic as well as =O/−OH exocyclic groups. The nitro group was more electron-withdrawing in the 5 than in the 6 position, while the opposite effect was observed in the case of electron donation of the amino group. These properties of both groups were enhanced in polar solvents; the enhancement depended on the ortho interactions. Substitution or solvation did not change tautomeric preferences of uracil significantly. However, the formation of a strong NO∙∙∙HO intramolecular hydrogen bond in the 5-NO2 derivative stabilized the dienol tautomer from +17.9 (unsubstituted) to +5.4 kcal/mol (substituted, energy relative to the most stable diketo tautomer). Full article
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17 pages, 2226 KiB  
Article
A QCT View of the Interplay between Hydrogen Bonds and Aromaticity in Small CHON Derivatives
by Miguel Gallegos, Daniel Barrena-Espés, José Manuel Guevara-Vela, Tomás Rocha-Rinza and Ángel Martín Pendás
Molecules 2022, 27(18), 6039; https://doi.org/10.3390/molecules27186039 - 16 Sep 2022
Cited by 4 | Viewed by 1636
Abstract
The somewhat elusive concept of aromaticity plays an undeniable role in the chemical narrative, often being considered the principal cause of the unusual properties and stability exhibited by certain π skeletons. More recently, the concept of aromaticity has also been utilised to explain [...] Read more.
The somewhat elusive concept of aromaticity plays an undeniable role in the chemical narrative, often being considered the principal cause of the unusual properties and stability exhibited by certain π skeletons. More recently, the concept of aromaticity has also been utilised to explain the modulation of the strength of non-covalent interactions (NCIs), such as hydrogen bonding (HB), paving the way towards the in silico prediction and design of tailor-made interacting systems. In this work, we try to shed light on this area by exploiting real space techniques, such as the Quantum Theory of Atoms in Molecules (QTAIM), the Interacting Quantum Atoms (IQA) approaches along with the electron delocalisation indicators Aromatic Fluctuation (FLU) and Multicenter (MCI) indices. The QTAIM and IQA methods have been proven capable of providing an unbiased and rigorous picture of NCIs in a wide variety of scenarios, whereas the FLU and MCI descriptors have been successfully exploited in the study of diverse aromatic and antiaromatic systems. We used a collection of simple archetypal examples of aromatic, non-aromatic and antiaromatic moieties within organic molecules to examine the changes in π delocalisation and aromaticity induced by the Aromaticity and Antiaromaticity Modulated Hydrogen Bonds (AMHB). We observed fundamental differences in the behaviour of systems containing the HB acceptor within and outside the ring, e.g., a destabilisation of the rings in the former as opposed to a stabilisation of the latter upon the formation of the corresponding molecular clusters. The results of this work provide a physically sound basis to rationalise the strengthening and weakening of AMHBs with respect to suitable non-cyclic non-aromatic references. We also found significant differences in the chemical bonding scenarios of aromatic and antiaromatic systems in the formation of AMHB. Altogether, our investigation provide novel, valuable insights about the complex mutual influence between hydrogen bonds and π systems. Full article
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20 pages, 10507 KiB  
Article
On the Coexistence of the Carbene⋯H-D Hydrogen Bond and Other Accompanying Interactions in Forty Dimers of N-Heterocyclic-Carbenes (I, IMe2, IiPr2, ItBu2, IMes2, IDipp2, IAd2; I = imidazol-2-ylidene) and Some Fundamental Proton Donors (HF, HCN, H2O, MeOH, NH3)
by Mirosław Jabłoński
Molecules 2022, 27(17), 5712; https://doi.org/10.3390/molecules27175712 - 5 Sep 2022
Cited by 6 | Viewed by 2071
Abstract
The subject of research is forty dimers formed by imidazol-2-ylidene (I) or its derivative (IR2) obtained by replacing the hydrogen atoms in both N-H bonds with larger important and popular substituents of increasing complexity (methyl = Me, iso-propyl = i [...] Read more.
The subject of research is forty dimers formed by imidazol-2-ylidene (I) or its derivative (IR2) obtained by replacing the hydrogen atoms in both N-H bonds with larger important and popular substituents of increasing complexity (methyl = Me, iso-propyl = iPr, tert-butyl = tBu, phenyl = Ph, mesityl = Mes, 2,6-diisopropylphenyl = Dipp, 1-adamantyl = Ad) and fundamental proton donor (HD) molecules (HF, HCN, H2O, MeOH, NH3). While the main goal is to characterize the generally dominant C⋯H-D hydrogen bond engaging a carbene carbon atom, an equally important issue is the often omitted analysis of the role of accompanying secondary interactions. Despite the often completely different binding possibilities of the considered carbenes, and especially HD molecules, several general trends are found. Namely, for a given carbene, the dissociation energy values of the IR2HD dimers increase in the following order: NH3< H2O < HCN ≤ MeOH ≪ HF. Importantly, it is found that, for a given HD molecule, IDipp2 forms the strongest dimers. This is attributed to the multiplicity of various interactions accompanying the dominant C⋯H-D hydrogen bond. It is shown that substitution of hydrogen atoms in both N-H bonds of the imidazol-2-ylidene molecule by the investigated groups leads to stronger dimers with HF, HCN, H2O or MeOH. The presented results should contribute to increasing the knowledge about the carbene chemistry and the role of intermolecular interactions, including secondary ones. Full article
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17 pages, 2789 KiB  
Article
High-Density “Windowpane” Coordination Patterns of Water Clusters and Their NBO/NRT Characterization
by Frank Weinhold
Molecules 2022, 27(13), 4218; https://doi.org/10.3390/molecules27134218 - 30 Jun 2022
Cited by 1 | Viewed by 1363
Abstract
Cluster mixture models for liquid water at higher pressures suggest the need for water clusters of higher coordination and density than those commonly based on tetrahedral H-bonding motifs. We show here how proton-ordered water clusters of increased coordination and density can assemble from [...] Read more.
Cluster mixture models for liquid water at higher pressures suggest the need for water clusters of higher coordination and density than those commonly based on tetrahedral H-bonding motifs. We show here how proton-ordered water clusters of increased coordination and density can assemble from a starting cyclic tetramer or twisted bicyclic (Möbius-like) heptamer to form extended Aufbau sequences of stable two-, three-, and four-coordinate “windowpane” motifs. Such windowpane clusters exhibit sharply reduced (~90°) bond angles that differ appreciably from the tetrahedral angles of idealized crystalline ice Ih. Computed free energy and natural resonance theory (NRT) bond orders provide quantitative descriptors for the relative stabilities of clusters and strengths of individual coordinative linkages. The unity and consistency of NRT description is demonstrated to extend from familiar supra-integer bonds of the molecular regime to the near-zero bond orders of the weakest linkages in the present H-bond clusters. Our results serve to confirm that H-bonding exemplifies resonance–covalent (fractional) bonding in the sub-integer range and to further discount the dichotomous conceptions of “electrostatics” for intermolecular bonding vs. “covalency” for intramolecular bonding that still pervade much of freshman-level pedagogy and force-field methodology. Full article
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13 pages, 3456 KiB  
Article
Simultaneous Estimation of Two Coupled Hydrogen Bond Geometries from Pairs of Entangled NMR Parameters: The Test Case of 4-Hydroxypyridine Anion
by Elena Yu. Tupikina, Mark V. Sigalov and Peter M. Tolstoy
Molecules 2022, 27(12), 3923; https://doi.org/10.3390/molecules27123923 - 18 Jun 2022
Cited by 3 | Viewed by 1315
Abstract
The computational method for estimating the geometry of two coupled hydrogen bonds with geometries close to linear using a pair of spectral NMR parameters was proposed. The method was developed based on the quantum-chemical investigation of 61 complexes with two hydrogen bonds formed [...] Read more.
The computational method for estimating the geometry of two coupled hydrogen bonds with geometries close to linear using a pair of spectral NMR parameters was proposed. The method was developed based on the quantum-chemical investigation of 61 complexes with two hydrogen bonds formed by oxygen and nitrogen atoms of the 4-hydroxypyridine anion with OH groups of substituted methanols. The main idea of the method is as follows: from the NMR chemical shifts of nuclei of atoms forming the 4-hydroxylpyridine anion, we select such pairs, whose values can be used for simultaneous determination of the geometry of two hydrogen bonds, despite the fact that every NMR parameter is sensitive to the geometry of each of the hydrogen bonds. For these parameters, two-dimensional maps of dependencies of NMR chemical shifts on interatomic distances in two hydrogen bonds were constructed. It is shown that, in addition to chemical shifts of the nitrogen atom and quaternary carbon, which are experimentally difficult to obtain, chemical shifts of the carbons and protons of the CH groups can be used. The performance of the proposed method was evaluated computationally as well on three additional complexes with substituted alcohols. It was found that, for all considered cases, hydrogen bond geometries estimated using two-dimensional correlations differed from those directly calculated by quantum-chemical methods by not more than 0.04 Å. Full article
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19 pages, 6296 KiB  
Article
Theoretical Studies on the Structure and Intramolecular Interactions of Fagopyrins—Natural Photosensitizers of Fagopyrum
by Sebastian Szymański and Irena Majerz
Molecules 2022, 27(12), 3689; https://doi.org/10.3390/molecules27123689 - 8 Jun 2022
Cited by 6 | Viewed by 1396
Abstract
Compounds characterized by a double-anthrone moiety are found in many plant species. One of them are fagopyrins—naturally occurring photosensitizers of Fagopyrum. The photosensitizing properties of fagopyrins are related to the selective absorption of light, which is a direct result of their spatial [...] Read more.
Compounds characterized by a double-anthrone moiety are found in many plant species. One of them are fagopyrins—naturally occurring photosensitizers of Fagopyrum. The photosensitizing properties of fagopyrins are related to the selective absorption of light, which is a direct result of their spatial and electronic structure and many intramolecular interactions. The nature of the interactions varies in different parts of the molecule. The aim of this study is to determine the structure and intramolecular interactions of fagopyrin molecules. For this purpose, in silico calculations were used to perform geometry optimization in the gas phase. QTAIM and NCI analysis suggest the formation of the possible conformers in the fagopyrin molecules. The presence of a strong OHO hydrogen bond was shown in the anthrone moiety of fagopyrin. The minimum energy difference for selected conformers of fagopyrins was 1.1 kcal∙mol−1, which suggested that the fagopyrin structure may exist in a different conformation in plant material. Similar interactions were observed in previously studied structures of hypericin and sennidin; however, only fagopyrin showed the possibility of brake the strong OHO hydrogen bond in favor of forming a new OHN hydrogen bond. Full article
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19 pages, 5764 KiB  
Review
Isotope Effects on Chemical Shifts in the Study of Hydrogen Bonds in Small Molecules
by Poul Erik Hansen
Molecules 2022, 27(8), 2405; https://doi.org/10.3390/molecules27082405 - 8 Apr 2022
Cited by 5 | Viewed by 1779
Abstract
This review is giving a short introduction to the techniques used to investigate isotope effects on NMR chemical shifts. The review is discussing how isotope effects on chemical shifts can be used to elucidate the importance of either intra- or intermolecular hydrogen bonding [...] Read more.
This review is giving a short introduction to the techniques used to investigate isotope effects on NMR chemical shifts. The review is discussing how isotope effects on chemical shifts can be used to elucidate the importance of either intra- or intermolecular hydrogen bonding in ionic liquids, of ammonium ions in a confined space, how isotope effects can help define dimers, trimers, etc., how isotope effects can lead to structural parameters such as distances and give information about ion pairing. Tautomerism is by advantage investigated by isotope effects on chemical shifts both in symmetric and asymmetric systems. The relationship between hydrogen bond energies and two-bond deuterium isotope effects on chemical shifts is described. Finally, theoretical calculations to obtain isotope effects on chemical shifts are looked into. Full article
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12 pages, 1637 KiB  
Article
The Role of Hydrogen Bonds in Interactions between [PdCl4]2− Dianions in Crystal
by Rafał Wysokiński, Wiktor Zierkiewicz, Mariusz Michalczyk, Thierry Maris and Steve Scheiner
Molecules 2022, 27(7), 2144; https://doi.org/10.3390/molecules27072144 - 26 Mar 2022
Cited by 6 | Viewed by 2053
Abstract
[PdCl4]2− dianions are oriented within a crystal in such a way that a Cl of one unit approaches the Pd of another from directly above. Quantum calculations find this interaction to be highly repulsive with a large positive interaction energy. [...] Read more.
[PdCl4]2− dianions are oriented within a crystal in such a way that a Cl of one unit approaches the Pd of another from directly above. Quantum calculations find this interaction to be highly repulsive with a large positive interaction energy. The placement of neutral ligands in their vicinity reduces the repulsion, but the interaction remains highly endothermic. When the ligands acquire a unit positive charge, the electrostatic component and the full interaction energy become quite negative, signalling an exothermic association. Raising the charge on these counterions to +2 has little further stabilizing effect, and in fact reduces the electrostatic attraction. The ability of the counterions to promote the interaction is attributed in part to the H-bonds which they form with both dianions, acting as a sort of glue. Full article
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14 pages, 3919 KiB  
Article
Hydrogen Bonds with Fluorine in Ligand–Protein Complexes-the PDB Analysis and Energy Calculations
by Wojciech Pietruś, Rafał Kafel, Andrzej J. Bojarski and Rafał Kurczab
Molecules 2022, 27(3), 1005; https://doi.org/10.3390/molecules27031005 - 2 Feb 2022
Cited by 15 | Viewed by 2881
Abstract
Fluorine is a common substituent in medicinal chemistry and is found in up to 50% of the most profitable drugs. In this study, a statistical analysis of the nature, geometry, and frequency of hydrogen bonds (HBs) formed between the aromatic and aliphatic C–F [...] Read more.
Fluorine is a common substituent in medicinal chemistry and is found in up to 50% of the most profitable drugs. In this study, a statistical analysis of the nature, geometry, and frequency of hydrogen bonds (HBs) formed between the aromatic and aliphatic C–F groups of small molecules and biological targets found in the Protein Data Bank (PDB) repository was presented. Interaction energies were calculated for those complexes using three different approaches. The obtained results indicated that the interaction energy of F-containing HBs is determined by the donor–acceptor distance and not by the angles. Moreover, no significant relationship between the energies of HBs with fluorine and the donor type was found, implying that fluorine is a weak HB acceptor for all types of HB donors. However, the statistical analysis of the PDB repository revealed that the most populated geometric parameters of HBs did not match the calculated energetic optima. In a nutshell, HBs containing fluorine are forced to form due to the stronger ligand–receptor neighboring interactions, which make fluorine the “donor’s last resort”. Full article
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12 pages, 3618 KiB  
Article
Hydrogen Bonding and Polymorphism of Amino Alcohol Salts with Quinaldinate: Structural Study
by Nina Podjed and Barbara Modec
Molecules 2022, 27(3), 996; https://doi.org/10.3390/molecules27030996 - 1 Feb 2022
Cited by 2 | Viewed by 1626
Abstract
Three amino alcohols, 3-amino-1-propanol (abbreviated as 3a1pOH), 2-amino-1-butanol (2a1bOH), and 2-amino-2-methyl-1-propanol (2a2m1pOH), were reacted with quinoline-2-carboxylic acid, known as quinaldinic acid. This combination yielded three salts, (3a1pOHH)quin (1, 3a1pOHH+ = protonated 3-amino-1-propanol, quin = anion of quinaldinic acid), (2a1bOHH)quin [...] Read more.
Three amino alcohols, 3-amino-1-propanol (abbreviated as 3a1pOH), 2-amino-1-butanol (2a1bOH), and 2-amino-2-methyl-1-propanol (2a2m1pOH), were reacted with quinoline-2-carboxylic acid, known as quinaldinic acid. This combination yielded three salts, (3a1pOHH)quin (1, 3a1pOHH+ = protonated 3-amino-1-propanol, quin = anion of quinaldinic acid), (2a1bOHH)quin (2, 2a1bOHH+ = protonated 2-amino-1-butanol), and (2a2m1pOHH)quin (3, 2a2m1pOHH+ = protonated 2-amino-2-methyl-1-propanol). The 2-amino-1-butanol and 2-amino-2-methyl-1-propanol systems produced two polymorphs each, labeled 2a/2b and 3a/3b, respectively. The compounds were characterized by X-ray structure analysis on single-crystal. The crystal structures of all consisted of protonated amino alcohols with NH3+ moiety and quinaldinate anions with carboxylate moiety. The used amino alcohols contained one OH and one NH2 functional group, both prone to participate in hydrogen bonding. Therefore, similar connectivity patterns were expected. This proved to be true to some extent as all structures contained the NH3+∙∙∙OOC heterosynthon. Nevertheless, different hydrogen bonding and π∙∙∙π stacking interactions were observed, leading to distinct connectivity motifs. The largest difference in hydrogen bonding occurred between polymorphs 3a and 3b, as they had only one heterosynton in common. Full article
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2021

Jump to: 2023, 2022, 2020

3 pages, 183 KiB  
Editorial
Intramolecular Hydrogen Bonding 2021
by Mirosław Jabłoński
Molecules 2021, 26(20), 6319; https://doi.org/10.3390/molecules26206319 - 19 Oct 2021
Cited by 5 | Viewed by 2119
Abstract
Undoubtedly, hydrogen bonds occupy a leading place in the rich world of intermolecular interactions [...] Full article
25 pages, 8159 KiB  
Article
Naphthazarin Derivatives in the Light of Intra- and Intermolecular Forces
by Karol Kułacz, Michał Pocheć, Aneta Jezierska and Jarosław J. Panek
Molecules 2021, 26(18), 5642; https://doi.org/10.3390/molecules26185642 - 17 Sep 2021
Cited by 6 | Viewed by 2217
Abstract
Our long-term investigations have been devoted the characterization of intramolecular hydrogen bonds in cyclic compounds. Our previous work covers naphthazarin, the parent compound of two systems discussed in the current work: 2,3-dimethylnaphthazarin (1) and 2,3-dimethoxy-6-methylnaphthazarin (2). Intramolecular hydrogen bonds [...] Read more.
Our long-term investigations have been devoted the characterization of intramolecular hydrogen bonds in cyclic compounds. Our previous work covers naphthazarin, the parent compound of two systems discussed in the current work: 2,3-dimethylnaphthazarin (1) and 2,3-dimethoxy-6-methylnaphthazarin (2). Intramolecular hydrogen bonds and substituent effects in these compounds were analyzed on the basis of Density Functional Theory (DFT), Møller–Plesset second-order perturbation theory (MP2), Coupled Clusters with Singles and Doubles (CCSD) and Car-Parrinello Molecular Dynamics (CPMD). The simulations were carried out in the gas and crystalline phases. The nuclear quantum effects were incorporated a posteriori using the snapshots taken from ab initio trajectories. Further, they were used to solve a vibrational Schrödinger equation. The proton reaction path was studied using B3LYP, ωB97XD and PBE functionals with a 6-311++G(2d,2p) basis set. Two energy minima (deep and shallow) were found, indicating that the proton transfer phenomena could occur in the electronic ground state. Next, the electronic structure and topology were examined in the molecular and proton transferred (PT) forms. The Atoms In Molecules (AIM) theory was employed for this purpose. It was found that the hydrogen bond is stronger in the proton transferred (PT) forms. In order to estimate the dimers’ stabilization and forces responsible for it, the Symmetry-Adapted Perturbation Theory (SAPT) was applied. The energy decomposition revealed that dispersion is the primary factor stabilizing the dimeric forms and crystal structure of both compounds. The CPMD results showed that the proton transfer phenomena occurred in both studied compounds, as well as in both phases. In the case of compound 2, the proton transfer events are more frequent in the solid state, indicating an influence of the environmental effects on the bridged proton dynamics. Finally, the vibrational signatures were computed for both compounds using the CPMD trajectories. The Fourier transformation of the autocorrelation function of atomic velocity was applied to obtain the power spectra. The IR spectra show very broad absorption regions between 700 cm1–1700 cm1 and 2300 cm1–3400 cm1 in the gas phase and 600 cm1–1800 cm1 and 2200 cm1–3400 cm1 in the solid state for compound 1. The absorption regions for compound 2 were found as follows: 700 cm1–1700 cm1 and 2300 cm1–3300 cm1 for the gas phase and one broad absorption region in the solid state between 700 cm1 and 3100 cm1. The obtained spectroscopic features confirmed a strong mobility of the bridged protons. The inclusion of nuclear quantum effects showed a stronger delocalization of the bridged protons. Full article
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16 pages, 926 KiB  
Review
Modern Theoretical Approaches to Modeling the Excited-State Intramolecular Proton Transfer: An Overview
by Joanna Jankowska and Andrzej L. Sobolewski
Molecules 2021, 26(17), 5140; https://doi.org/10.3390/molecules26175140 - 25 Aug 2021
Cited by 28 | Viewed by 3894
Abstract
The excited-state intramolecular proton transfer (ESIPT) phenomenon is nowadays widely acknowledged to play a crucial role in many photobiological and photochemical processes. It is an extremely fast transformation, often taking place at sub-100 fs timescales. While its experimental characterization can be highly challenging, [...] Read more.
The excited-state intramolecular proton transfer (ESIPT) phenomenon is nowadays widely acknowledged to play a crucial role in many photobiological and photochemical processes. It is an extremely fast transformation, often taking place at sub-100 fs timescales. While its experimental characterization can be highly challenging, a rich manifold of theoretical approaches at different levels is nowadays available to support and guide experimental investigations. In this perspective, we summarize the state-of-the-art quantum-chemical methods, as well as molecular- and quantum-dynamics tools successfully applied in ESIPT process studies, focusing on a critical comparison of their specific properties. Full article
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13 pages, 2749 KiB  
Article
Spectroscopic Identification of Hydrogen Bond Vibrations and Quasi-Isostructural Polymorphism in N-Salicylideneaniline
by Łukasz Hetmańczyk, Eugene A. Goremychkin, Janusz Waliszewski, Mikhail V. Vener, Paweł Lipkowski, Peter M. Tolstoy and Aleksander Filarowski
Molecules 2021, 26(16), 5043; https://doi.org/10.3390/molecules26165043 - 20 Aug 2021
Cited by 8 | Viewed by 2432
Abstract
The ortho-hydroxy aryl Schiff base 2-[(E)-(phenylimino)methyl]phenol and its deutero-derivative have been studied by the inelastic incoherent neutron scattering (IINS), infrared (IR) and Raman experimental methods, as well as by Density Functional Theory (DFT) and Density-Functional Perturbation Theory (DFPT) simulations. The assignments of [...] Read more.
The ortho-hydroxy aryl Schiff base 2-[(E)-(phenylimino)methyl]phenol and its deutero-derivative have been studied by the inelastic incoherent neutron scattering (IINS), infrared (IR) and Raman experimental methods, as well as by Density Functional Theory (DFT) and Density-Functional Perturbation Theory (DFPT) simulations. The assignments of vibrational modes within the 3500–50 cm−1 spectral region made it possible to state that the strong hydrogen bond in the studied compound can be classified as the so-called quasi-aromatic bond. The isotopic substitution supplemented by the results of DFT calculations allowed us to identify vibrational bands associated with all five major hydrogen bond vibrations. Quasi-isostructural polymorphism of 2-[(E)-(phenylimino)methyl]phenol (SA) and 2-[(E)-(phenyl-D5-imino)methyl]phenol (SA-C6D5) has been studied by powder X-ray diffraction in the 20–320 K temperature range. Full article
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11 pages, 414 KiB  
Article
On the Relationship between Hydrogen Bond Strength and the Formation Energy in Resonance-Assisted Hydrogen Bonds
by José Manuel Guevara-Vela, Miguel Gallegos, Mónica A. Valentín-Rodríguez, Aurora Costales, Tomás Rocha-Rinza and Ángel Martín Pendás
Molecules 2021, 26(14), 4196; https://doi.org/10.3390/molecules26144196 - 10 Jul 2021
Cited by 17 | Viewed by 2462
Abstract
Resonance-assisted hydrogen bonds (RAHB) are intramolecular contacts that are characterised by being particularly energetic. This fact is often attributed to the delocalisation of π electrons in the system. In the present article, we assess this thesis via the examination of the effect of [...] Read more.
Resonance-assisted hydrogen bonds (RAHB) are intramolecular contacts that are characterised by being particularly energetic. This fact is often attributed to the delocalisation of π electrons in the system. In the present article, we assess this thesis via the examination of the effect of electron-withdrawing and electron-donating groups, namely −F, −Cl, −Br, −CF3, −N(CH3)2, −OCH3, −NHCOCH3 on the strength of the RAHB in malondialdehyde by using the Quantum Theory of Atoms in Molecules (QTAIM) and the Interacting Quantum Atoms (IQA) analyses. We show that the influence of the investigated substituents on the strength of the investigated RAHBs depends largely on its position within the π skeleton. We also examine the relationship between the formation energy of the RAHB and the hydrogen bond interaction energy as defined by the IQA method of wave function analysis. We demonstrate that these substituents can have different effects on the formation and interaction energies, casting doubts regarding the use of different parameters as indicators of the RAHB formation energies. Finally, we also demonstrate how the energy density can offer an estimation of the IQA interaction energy, and therefore of the HB strength, at a reduced computational cost for these important interactions. We expected that the results reported herein will provide a valuable understanding in the assessment of the energetics of RAHB and other intramolecular interactions. Full article
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15 pages, 3287 KiB  
Article
Perturbating Intramolecular Hydrogen Bonds through Substituent Effects or Non-Covalent Interactions
by Al Mokhtar Lamsabhi, Otilia Mó and Manuel Yáñez
Molecules 2021, 26(12), 3556; https://doi.org/10.3390/molecules26123556 - 10 Jun 2021
Cited by 7 | Viewed by 2283
Abstract
An analysis of the effects induced by F, Cl, and Br-substituents at the α-position of both, the hydroxyl or the amino group for a series of amino-alcohols, HOCH2(CH2)nCH2NH2 (n = 0–5) on the [...] Read more.
An analysis of the effects induced by F, Cl, and Br-substituents at the α-position of both, the hydroxyl or the amino group for a series of amino-alcohols, HOCH2(CH2)nCH2NH2 (n = 0–5) on the strength and characteristics of their OH···N or NH···O intramolecular hydrogen bonds (IMHBs) was carried out through the use of high-level G4 ab initio calculations. For the parent unsubstituted amino-alcohols, it is found that the strength of the OH···N IMHB goes through a maximum for n = 2, as revealed by the use of appropriate isodesmic reactions, natural bond orbital (NBO) analysis and atoms in molecules (AIM), and non-covalent interaction (NCI) procedures. The corresponding infrared (IR) spectra also reflect the same trends. When the α-position to the hydroxyl group is substituted by halogen atoms, the OH···N IMHB significantly reinforces following the trend H < F < Cl < Br. Conversely, when the substitution takes place at the α-position with respect to the amino group, the result is a weakening of the OH···N IMHB. A totally different scenario is found when the amino-alcohols HOCH2(CH2)nCH2NH2 (n = 0–3) interact with BeF2. Although the presence of the beryllium derivative dramatically increases the strength of the IMHBs, the possibility for the beryllium atom to interact simultaneously with the O and the N atoms of the amino-alcohol leads to the global minimum of the potential energy surface, with the result that the IMHBs are replaced by two beryllium bonds. Full article
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19 pages, 5385 KiB  
Article
A Family of Ethyl N-Salicylideneglycinate Dyes Stabilized by Intramolecular Hydrogen Bonding: Photophysical Properties and Computational Study
by Larisa E. Alkhimova, Maria G. Babashkina and Damir A. Safin
Molecules 2021, 26(11), 3112; https://doi.org/10.3390/molecules26113112 - 23 May 2021
Cited by 5 | Viewed by 2142
Abstract
In this work we report solvatochromic and luminescent properties of ethyl N-salicylideneglycinate (1), ethyl N-(5-methoxysalicylidene)glycinate (2), ethyl N-(5-bromosalicylidene)glycinate (3), and ethyl N-(5-nitrosalicylidene)glycinate (4) dyes. 14 correspond to a class [...] Read more.
In this work we report solvatochromic and luminescent properties of ethyl N-salicylideneglycinate (1), ethyl N-(5-methoxysalicylidene)glycinate (2), ethyl N-(5-bromosalicylidene)glycinate (3), and ethyl N-(5-nitrosalicylidene)glycinate (4) dyes. 14 correspond to a class of N-salicylidene aniline derivatives, whose photophysical properties are dictated by the intramolecular proton transfer between the OH-function and the imine N-atom, affording tautomerization between the enol-imine and keto-enamine forms. Photophysical properties of 14 were studied in different pure non-polar and (a)protic polar solvents as well as upon gradual addition of NEt3, NaOH, and CH3SO3H. The DFT calculations were performed to verify the structures of 14 as well as their electronic and optical properties. Full article
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11 pages, 2437 KiB  
Article
Polymorphism and Conformational Equilibrium of Nitro-Acetophenone in Solid State and under Matrix Conditions
by Łukasz Hetmańczyk, Przemysław Szklarz, Agnieszka Kwocz, Maria Wierzejewska, Magdalena Pagacz-Kostrzewa, Mikhail Ya. Melnikov, Peter M. Tolstoy and Aleksander Filarowski
Molecules 2021, 26(11), 3109; https://doi.org/10.3390/molecules26113109 - 22 May 2021
Cited by 6 | Viewed by 2435
Abstract
Conformational and polymorphic states in the nitro-derivative of o-hydroxy acetophenone have been studied by experimental and theoretical methods. The potential energy curves for the rotation of the nitro group and isomerization of the hydroxyl group have been calculated by density functional theory [...] Read more.
Conformational and polymorphic states in the nitro-derivative of o-hydroxy acetophenone have been studied by experimental and theoretical methods. The potential energy curves for the rotation of the nitro group and isomerization of the hydroxyl group have been calculated by density functional theory (DFT) to estimate the barriers of the conformational changes. Two polymorphic forms of the studied compound were obtained by the slow and fast evaporation of polar and non-polar solutions, respectively. Both of the polymorphs were investigated by Infrared-Red (IR) and Raman spectroscopy, Incoherent Inelastic Neutron Scattering (IINS), X-ray diffraction, nuclear quadrupole resonance spectroscopy (NQR), differential scanning calorimetry (DSC) and density functional theory (DFT) methods. In one of the polymorphs, the existence of a phase transition was shown. The position of the nitro group and its impact on the crystal cell of the studied compound were analyzed. The conformational equilibrium determined by the reorientation of the hydroxyl group was observed under argon matrix isolation. An analysis of vibrational spectra was achieved for the interpretation of conformational equilibrium. The infrared spectra were measured in a wide temperature range to reveal the spectral bands that were the most sensitive to the phase transition and conformational equilibrium. The results showed the interrelations between intramolecular processes and macroscopic phenomena in the studied compound. Full article
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12 pages, 2067 KiB  
Article
Perturbing the O–HO Hydrogen Bond in 1-oxo-3-hydroxy-2-propene
by Ibon Alkorta, José Elguero and Janet E. Del Bene
Molecules 2021, 26(11), 3086; https://doi.org/10.3390/molecules26113086 - 21 May 2021
Cited by 2 | Viewed by 1782
Abstract
Ab initio MP2/aug’-cc-pVTZ calculations have been carried out to identify and characterize equilibrium structures and transition structures on the 1-oxo-3-hydroxy-2-propene: Lewis acid potential energy surfaces, with the acids LiH, LiF, BeH2, and BeF2. Two equilibrium structures, one with the [...] Read more.
Ab initio MP2/aug’-cc-pVTZ calculations have been carried out to identify and characterize equilibrium structures and transition structures on the 1-oxo-3-hydroxy-2-propene: Lewis acid potential energy surfaces, with the acids LiH, LiF, BeH2, and BeF2. Two equilibrium structures, one with the acid interacting with the C=O group and the other with the interaction occurring at the O–H group, exist on all surfaces. These structures are separated by transition structures that present the barriers to the interconversion of the two equilibrium structures. The structures with the acid interacting at the C=O group have the greater binding energies. Since the barriers to convert the structures with interaction occurring at the O–H group are small, only the isomers with interaction occurring at the C=O group could be experimentally observed, even at low temperatures. Charge-transfer energies were computed for equilibrium structures, and EOM-CCSD spin–spin coupling constants 2hJ(O–O), 1hJ(H–O), and 1J(O–H) were computed for equilibrium and transition structures. These coupling constants exhibit a second-order dependence on the corresponding distances, with very high correlation coefficients. Full article
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21 pages, 3212 KiB  
Review
Molecular Tailoring Approach for the Estimation of Intramolecular Hydrogen Bond Energy
by Milind M. Deshmukh and Shridhar R. Gadre
Molecules 2021, 26(10), 2928; https://doi.org/10.3390/molecules26102928 - 14 May 2021
Cited by 30 | Viewed by 3056
Abstract
Hydrogen bonds (HBs) play a crucial role in many physicochemical and biological processes. Theoretical methods can reliably estimate the intermolecular HB energies. However, the methods for the quantification of intramolecular HB (IHB) energy available in the literature are mostly empirical or indirect and [...] Read more.
Hydrogen bonds (HBs) play a crucial role in many physicochemical and biological processes. Theoretical methods can reliably estimate the intermolecular HB energies. However, the methods for the quantification of intramolecular HB (IHB) energy available in the literature are mostly empirical or indirect and limited only to evaluating the energy of a single HB. During the past decade, the authors have developed a direct procedure for the IHB energy estimation based on the molecular tailoring approach (MTA), a fragmentation method. This MTA-based method can yield a reliable estimate of individual IHB energy in a system containing multiple H-bonds. After explaining and illustrating the methodology of MTA, we present its use for the IHB energy estimation in molecules and clusters. We also discuss the use of this method by other researchers as a standard, state-of-the-art method for estimating IHB energy as well as those of other noncovalent interactions. Full article
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19 pages, 3843 KiB  
Article
Focal Point Evaluation of Energies for Tautomers and Isomers for 3-hydroxy-2-butenamide: Evaluation of Competing Internal Hydrogen Bonds of Types -OH…O=, -OH…N, -NH…O=, and CH…X (X=O and N)
by Zikri Altun, Erdi Ata Bleda and Carl Trindle
Molecules 2021, 26(9), 2623; https://doi.org/10.3390/molecules26092623 - 30 Apr 2021
Cited by 4 | Viewed by 2336
Abstract
The title compound is a small molecule with many structural variations; it can illustrate a variety of internal hydrogen bonds, among other noncovalent interactions. Here we examine structures displaying hydrogen bonding between carbonyl oxygen and hydroxyl H; between carbonyl oxygen and amino H; [...] Read more.
The title compound is a small molecule with many structural variations; it can illustrate a variety of internal hydrogen bonds, among other noncovalent interactions. Here we examine structures displaying hydrogen bonding between carbonyl oxygen and hydroxyl H; between carbonyl oxygen and amino H; hydroxyl H and amino N; hydroxyl O and amino H. We also consider H-bonding in its tautomer 2-oxopropanamide. By extrapolation algorithms applied to Hartree-Fock and correlation energies as estimated in HF, MP2, and CCSD calculations using the cc-pVNZ correlation-consistent basis sets (N = 2, 3, and 4) we obtain reliable relative energies of the isomeric forms. Assuming that such energy differences may be attributed to the presence of the various types of hydrogen bonding, we attempt to infer relative strengths of types of H-bonding. The Atoms in Molecules theory of Bader and the Local Vibrational Modes analysis of Cremer and Kraka are applied to this task. Hydrogen bonds are ranked by relative strength as measured by local stretching force constants, with the stronger =O…HO- > NH…O= > -OH…N well separated from a cluster > NH…O= ≈ >NH…OH ≈ CH…O= of comparable and intermediate strength. Weaker but still significant interactions are of type CH…N which is stronger than CH…OH. Full article
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22 pages, 5329 KiB  
Review
A Spectroscopic Overview of Intramolecular Hydrogen Bonds of NH…O,S,N Type
by Poul Erik Hansen
Molecules 2021, 26(9), 2409; https://doi.org/10.3390/molecules26092409 - 21 Apr 2021
Cited by 15 | Viewed by 3533
Abstract
Intramolecular NH…O,S,N interactions in non-tautomeric systems are reviewed in a broad range of compounds covering a variety of NH donors and hydrogen bond acceptors. 1H chemical shifts of NH donors are good tools to study intramolecular hydrogen bonding. However in some cases [...] Read more.
Intramolecular NH…O,S,N interactions in non-tautomeric systems are reviewed in a broad range of compounds covering a variety of NH donors and hydrogen bond acceptors. 1H chemical shifts of NH donors are good tools to study intramolecular hydrogen bonding. However in some cases they have to be corrected for ring current effects. Deuterium isotope effects on 13C and 15N chemical shifts and primary isotope effects are usually used to judge the strength of hydrogen bonds. Primary isotope effects are investigated in a new range of magnitudes. Isotope ratios of NH stretching frequencies, νNH/ND, are revisited. Hydrogen bond energies are reviewed and two-bond deuterium isotope effects on 13C chemical shifts are investigated as a possible means of estimating hydrogen bond energies. Full article
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2020

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37 pages, 2395 KiB  
Review
A Critical Overview of Current Theoretical Methods of Estimating the Energy of Intramolecular Interactions
by Mirosław Jabłoński
Molecules 2020, 25(23), 5512; https://doi.org/10.3390/molecules25235512 - 25 Nov 2020
Cited by 50 | Viewed by 3170
Abstract
This article is probably the first such comprehensive review of theoretical methods for estimating the energy of intramolecular hydrogen bonds or other interactions that are frequently the subject of scientific research. Rather than on a plethora of numerical data, the main focus is [...] Read more.
This article is probably the first such comprehensive review of theoretical methods for estimating the energy of intramolecular hydrogen bonds or other interactions that are frequently the subject of scientific research. Rather than on a plethora of numerical data, the main focus is on discussing the theoretical rationale of each method. Additionally, attention is paid to the fact that it is very often possible to use several variants of a particular method. Both of the methods themselves and their variants often give wide ranges of the obtained estimates. Attention is drawn to the fact that the applicability of a particular method may be significantly limited by various factors that disturb the reliability of the estimation, such as considerable structural changes or new important interactions in the reference system. Full article
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