Non-conventional hydrogen bonds
TL;DR: In this paper, the authors define the hydrogen bond as an attractive interaction between two molecular moieties in which at least one of them contains a hydrogen atom that plays a fundamental role.
Abstract: Hydrogen bonds (HBs) are the most important ‘weak’ interactions encountered in solid, liquid and gas phases. The HB can be defined as an attractive interaction between two molecular moieties in which at least one of them contains a hydrogen atom that plays a fundamental role. Classical HBs correspond to those formed by two heteroatoms, A and B, with a hydrogen atom bonded to one of them and located approximately in between (A–H···B). Recently, knowledge of the number of functional groups which act as hydrogen bond donors or acceptors has increased considerably and most of these new groups are discussed.
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TL;DR: The hydrogen bond is the most important of all directional intermolecular interactions, operative in determining molecular conformation, molecular aggregation, and the function of a vast number of chemical systems ranging from inorganic to biological.
Abstract: The hydrogen bond is the most important of all directional intermolecular interactions. It is operative in determining molecular conformation, molecular aggregation, and the function of a vast number of chemical systems ranging from inorganic to biological. Research into hydrogen bonds experienced a stagnant period in the 1980s, but re-opened around 1990, and has been in rapid development since then. In terms of modern concepts, the hydrogen bond is understood as a very broad phenomenon, and it is accepted that there are open borders to other effects. There are dozens of different types of X-H.A hydrogen bonds that occur commonly in the condensed phases, and in addition there are innumerable less common ones. Dissociation energies span more than two orders of magnitude (about 0.2-40 kcal mol(-1)). Within this range, the nature of the interaction is not constant, but its electrostatic, covalent, and dispersion contributions vary in their relative weights. The hydrogen bond has broad transition regions that merge continuously with the covalent bond, the van der Waals interaction, the ionic interaction, and also the cation-pi interaction. All hydrogen bonds can be considered as incipient proton transfer reactions, and for strong hydrogen bonds, this reaction can be in a very advanced state. In this review, a coherent survey is given on all these matters.
5,153 citations
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TL;DR: The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.
Abstract: The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.
2,582 citations
TL;DR: In this paper, the formation of low-barrier hydrogen bonds between ylides and different neutral molecules was studied, and the analysis of the protonation energies and the optimized geometries, interaction energies, and characteristics of the electron density of the complexes showed that these ylsides are very good HB acceptors, forming stable complexes even with weak HB donors.
Abstract: The hydrogen bond (HB) basicity of a series of ylides containing nitrogen, oxygen, or carbon as heavy atoms, as well as the influence of the formation of the HB complexes on their structure, has been studied. In addition, in this paper we propose the formation of some rather strong HBs (that could be considered low-barrier hydrogen bonds, LBHBs) between ylides and different neutral molecules. The ylides chosen for the study were H3N+−N-H, Me3N+−N-H, H2O+−N-H, Me2O+−N-H, H2O+−O-, Me2O+−O-, and Me3N+−C-H2. As HB donors, classical donors such as HF, HCN, and HCCH were used. The analysis of the protonation energies of the ylides and the optimized geometries, interaction energies, and characteristics of the electron density of the complexes shows that these ylides are very good HB acceptors, forming stable complexes even with weak HB donors. With strong donors, when the proton transfer did not take place, very strong HBs were formed with quite large interaction energies and very short HB distances which could ...
1,232 citations
TL;DR: The aim of this Review is to describe the crucial interaction mechanisms in context, and thus classify the entire subject of supramolecular chemistry.
Abstract: Supramolecular chemistry has expanded dramatically in recent years both in terms of potential applications and in its relevance to analogous biological systems. The formation and function of supramolecular complexes occur through a multiplicity of often difficult to differentiate noncovalent forces. The aim of this Review is to describe the crucial interaction mechanisms in context, and thus classify the entire subject. In most cases, organic host-guest complexes have been selected as examples, but biologically relevant problems are also considered. An understanding and quantification of intermolecular interactions is of importance both for the rational planning of new supramolecular systems, including intelligent materials, as well as for developing new biologically active agents.
968 citations
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01 Jan 1990
TL;DR: In this article, the quantum atom and the topology of the charge desnity of a quantum atom are discussed, as well as the mechanics of an atom in a molecule.
Abstract: List of symbols 1. Atoms in chemistry 2. Atoms and the topology of the charge desnity 3. Molecular structure and its change 4. Mathematical models of structural change 5. The quantum atom 6. The mechanics of an atom in a molecule 7. Chemical models and the Laplacian of the charge density 8. The action principle for a quantunm subsystem Appendix - Tables of data Index
11,853 citations
TL;DR: In this paper, a set of criteria are proposed based on the theory of "atoms in molecules" to establish hydrogen bonding, even for multiple interactions involving C-H-O hydrogen bonds.
Abstract: It is shown that the total charge density is a valid source to confirm hydrogen bonding without invoking a reference charge density. A set of criteria are proposed based on the theory of “atoms in molecules” to establish hydrogen bonding, even for multiple interactions involving C-H-O hydrogen bonds. These criteria are applied to several van der Waals complexes. Finally a bifurcated intramolecular C-H-O hydrogen bond is predicted in the anti-AIDS drug AZT, which may highlight a crucial feature of the biological activity of a whole class of anti-AIDS drugs. Almost all the methods of physical chemistry, spectroscopy, and diffraction can be used to recognize and study hydrogen bonding.] Each technique focuses on specific properties in order to detect and characterize this phenomenon in its own way. This work is concerned with the manifestation of hydrogen bonding in the charge density obtained from ab initio calculations. Whereas crystallographers have concluded upon hydrogen bonding via purely geometrical criteria, recent deformation density2 studies allow one to observe hydrogen bonding beyond mere ge~metry.~ However, it is not necessary to subtract an arbitrary (promolecular) charge density from the total density to reveal hydrogen bonding, not even in the interpretation of X-ray experiment^.^ Boyd and Choi have shown in two important contribution^^^^ that the theory of “atoms in molecules’’ (AIM)7,8 can be used to characterize hydrogen bonding solely from the (total) charge density for a large set of acceptor molecules, involving HF and HC1 as donors. In a next stage Carroll and Bader performed a more extended analysis on a large set of BASE-HF comple~es.~ This theory has not only provided new insights in conventional intermolecular hydrogenI0.’ ] bonding but has also been successful in intramolecularI33l4 and x-type hydrogen bonds.I5 Drawing from earlier ob~ervations~~~~ ~.’~~~~ and the present work, we formulate eight concerted effects occurring in the charge density which are indicative of hydrogen bonding. All of these effects can be viewed as necessary criteria to conclude that hydrogen bonding is present. By observation one of these conditions has proven to be sufficient as well. This case study on C-H-O interactions shows that this less common type of hydrogen bonding obeys all of the proposed criteria. Moreover, the multiple interactions appearing in the present five examples do not impair the consistency of the global phenomenon of hydrogen bonding as it expresses itself in the charge density. In spite of an early affirmative infrared review,I6 the old controversy on whether C-H-O hydrogen bonds really exist continued for another decade,” but now the dust has settled’* (for an entertaining account of this controversy, see ref 19). The importance of these bonds has been recognized in crystal engineering’9,20 since C-H-O contacts have a determining influence on packing motifs.21
2,654 citations
TL;DR: It is clearly no longer necessary to justify the relevance of C-H’‚‚O hydrogen bonds, so widely invoked are they in small-molecule and biological crystallography and supramolecular synthesis and crystal engineering.
Abstract: The C-H‚‚‚O hydrogen bond is so well-established in structural chemistry that it seems difficult now to believe that when Sutor proposed the existence of this type of hydrogen bond in the early 1960s,1,2 her suggestion was drowned in scepticism, if not outright hostility.3 It was only two decades later, with Taylor and Kennard’s paper, that the subject was properly revived.4 Shortly thereafter, an Account appeared from this laboratory describing the role of the C-H‚‚‚O interaction in crystal engineering.5 Subsequently, one felt confident enough to term these erstwhile “interactions” hydrogen bonds, in a second Account.6 A recent invitation to contribute another Account and the many recent efforts in this direction by my students and postdoctorals have led to the present paper. It is clearly no longer necessary to justify the relevance of C-H‚‚‚O hydrogen bonds, so widely invoked are they in small-molecule and biological crystallography. The presence of O-atoms in a large majority of organic molecules means that this hydrogen bond is widespread, even if not identified in many cases. However, other questions concerning these weak hydrogen bonds could be posed: (1) What is their upper distance limit? (2) Are very short, bent bonds significant? (3) Why do C-H‚‚‚O bonds sometimes disturb the strong O-H‚‚‚O and N-H‚‚‚O network? Alternatively, why do hydrogen bond donors and acceptors not always pair in descending order of strength? (4) How important is cooperativity for weak hydrogen bonds? (5) Are C-H‚‚‚O hydrogen bonds responsible for crystal packing, or are they the forced consequences of packing? (6) Are weak hydrogen bonds robust enough for supramolecular synthesis and crystal engineering? (7) Does the C-H‚‚‚O hydrogen bond have any biological significance? These difficult questions cannot be answered fully. This Account attempts to address some of them, but better answers can only follow from further work.
1,659 citations
TL;DR: The CSD itself acts as a computerized depository for large-volume numerical results for some 30 journals and may conveniently be categorized according to its "dimensionality", as described below and illustrated in Figure 1.
Abstract: ed, together with any associated supplementary (deposited) data. The CSD itself acts as a computerized depository for large-volume numerical results for some 30 journals. A total of 584 primary sources are now referenced in the CSD, of which 74 are regularly scanned in-house to provide ca. 80% of current input. Remaining references are located via a scan of secondary sources, particularly Chemical Abstracts. Each entry in the CSD relates to a specific crystal structure determination of a specific chemical compound. Each entry is identified by a CSD reference code (REFCODE). This consists of eight characters: the first six are alphabetic and identify the chemical compound (initially assigned as a mnemonic of the compound name, now generated automatically for new compounds), the last two characters are digits which trace the publication history and define (a) whether the paper is a republication by the same authors (perhaps reporting an improved coordinate set) or (b) whether the paper is a redetermination by a different set of authors. The information recorded for each entry may conveniently be categorized according to its "dimensionality", as described below and illustrated in Figure 1. 1 D information consists of bibliographic and chemical text strings, together with certain individual numeric items: comBATCH OR VERSION 4 GRAPHICS VERSION 4 GRAPHICS
1,205 citations