Characterization of c-h-o hydrogen-bonds on the basis of the charge-density
01 Jun 1995-The Journal of Physical Chemistry (American Chemical Society)-Vol. 99, Iss: 24, pp 9747-9754
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
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.
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.
TL;DR: In this paper, the topological and energetic properties of the electron density distribution ρ(r) of isolated pairwise H⋯F interaction have been theoretically calculated at several geometries and represented against the corresponding internuclear distances.
Abstract: The topological and energetic properties of the electron density distribution ρ(r) of the isolated pairwise H⋯F interaction have been theoretically calculated at several geometries (0.8
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 ...
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
20 Dec 1983
TL;DR: The goal of this series is to pinpoint areas of chemistry where recent progress has outpaced what is covered in any available textbooks, and then seek out and persuade experts in these fields to produce relatively concise but instructive introductions to their fields.
Abstract: New textbooks at all levels of chemistry appear with great regularity. Some fields like basic biochemistry, organic reaction mechanisms, and chemical ther modynamics are well represented by many excellent texts, and new or revised editions are published sufficiently often to keep up with progress in research. However, some areas of chemistry, especially many of those taught at the grad uate level, suffer from a real lack of up-to-date textbooks. The most serious needs occur in fields that are rapidly changing. Textbooks in these subjects usually have to be written by scientists actually involved in the research which is advancing the field. It is not often easy to persuade such individuals to set time aside to help spread the knowledge they have accumulated. Our goal, in this series, is to pinpoint areas of chemistry where recent progress has outpaced what is covered in any available textbooks, and then seek out and persuade experts in these fields to produce relatively concise but instructive introductions to their fields. These should serve the needs of one semester or one quarter graduate courses in chemistry and biochemistry. In some cases the availability of texts in active research areas should help stimulate the creation of new courses. CHARLES R. CANTOR New York Preface This monograph is based on a review on polynucleotide structures written for a book series in 1976."
17 Jul 1991
TL;DR: In this article, the van der Waals Radii cut-off criterion is used to define the strong and weak hydrogen-bond configurations, as well as the relationship between two-center and three-center hydrogen bonds.
Abstract: IA Basic Concepts.- 1 The Importance of Hydrogen Bonds.- 1.1 Historical Perspective.- 1.2 The Importance of Hydrogen Bonds in Biological Structure and Function.- 1.3 The Role of the Water Molecules.- 1.4 Significance of Small Molecule Crystal Structural Studies.- 1.5 The Structural Approach.- 2 Definitions and Concepts.- 2.1 Definition of the Hydrogen Bond - Strong and Weak Bonds.- 2.2 Hydrogen-Bond Configurations: Two- and Three-Center Hydrogen Bonds Bifurcated and Tandem Bonds.- 2.3 Hydrogen Bonds Are Very Different from Covalent Bonds.- 2.4 The van der Waals Radii Cut-Off Criterion Is Not Useful.- 2.5 The Concept of the Hydrogen-Bond Structure.- 2.6 The Importance of ? and ? Cooperativity.- 2.7 Homo-, Anti- and Heterodromic Patterns.- 2.8 Hydrogen Bond Flip-Flop Disorder: Conformational and Configurational.- 2.9 Proton-Deficient Hydrogen Bonds.- 2.10 The Excluded Region.- 2.11 The Hydrophobic Effect.- 3 Experimental Studies of Hydrogen Bonding.- 3.1 Infrared Spectroscopy and Gas Electron Diffraction.- 3.2 X-Ray and Neutron Crystal Structure Analysis.- 3.3 Treatment of Hydrogen Atoms in Neutron Diffraction Studies.- 3.4 Charge Density and Hydrogen-Bond Energies.- 3.5 Neutron Powder Diffraction.- 3.6 Solid State NMR Spectroscopy.- 4 Theoretical Calculations of Hydrogen-Bond Geometries.- 4.1 Calculating Hydrogen-Bond Geometries.- 4.2 Ab-Initio Molecular Orbital Methods.- 4.3 Application to Hydrogen-Bonded Complexes.- 4.4 Semi-Empirical Molecular Orbital Methods.- 4.5 Empirical Force Field or Molecular Mechanics Methods.- 5 Effect of Hydrogen Bonding on Molecular Structure.- IB Hydrogen-Bond Geometry.- 6 The Importance of Small Molecule Structural Studies.- 6.1 Problems Associated with the Hydrogen-Bond Geometry.- 6.2 The Hydrogen Bond Can Be Described Statistically.- 6.3 The Problems of Measuring Hydrogen-Bond Lengths and Angles in Small Molecule Crystal Structures.- 7 Metrical Aspects of Two-Center Hydrogen Bonds.- 7.1 The Metrical Properties of O-H *** O Hydrogen Bonds.- 7.1.1 Very Strong and Strong OH *** O Hydrogen Bonds Occur with Oxyanions, Acid Salts, Acid Hydrates, and Carboxylic Acids.- 7.1.2 OH *** O Hydrogen Bonds in the Ices and High Hydrates.- 7.1.3 Carbohydrates Provide the Best Data for OH ... O Hydrogen Bonds: Evidence for the Cooperative Effect.- 7.2 N-H *** O Hydrogen Bonds.- 7.3 N-H *** N Hydrogen Bonds.- 7.4 O-H *** N Hydrogen Bonds.- 7.5 Sequences in Lengths of Two-Center Hydrogen Bonds.- 7.6 H/D Isotope Effect.- 8 Metrical Aspects of Three- and Four-Center Hydrogen Bonds.- 8.1 Three-Center Hydrogen Bonds.- 8.2 Four-Center Hydrogen Bonds.- 9 Intramolecular Hydrogen Bonds.- 10 Weak Hydrogen-Bonding Interactions Formed by C-H Groups as Donors and Aromatic Rings as Acceptors.- 11 Halides and Halogen Atoms as Hydrogen-Bond Acceptors.- 12 Hydrogen-Bond Acceptor Geometries.- II Hydrogen Bonding in Small Biological Molecules.- 13 Hydrogen Bonding in Carbohydrates.- 13.1 Sugar Alcohols (Alditols) as Model Cooperative Hydrogen-Bonded Structures.- 13.2 Influence of Hydrogen Bonding on Configuration and Conformation in Cyclic Monosaccharides.- 13.3 Rules to Describe Hydrogen-Bonding Patterns in Monosaccharides.- 13.4 The Water Molecules Link Hydrogen-Bond Chains into Nets in the Hydrated Monosaccharide Crystal Structures.- 13.5 The Disaccharide Crystal Structures Provide an Important Source of Data About Hydrogen-Bonding Patterns in Polysaccharides.- 13.6 Hydrogen Bonding in the Tri- and Tetrasaccharides Is More Complex and Less Well Defined.- 13.7 The Hydrogen Bonding in Polysaccharide Fiber Structures Is Poorly Defined.- 14 Hydrogen Bonding in Amino Acids and Peptides: Predominance of Zwitterions.- 15 Purines and Pyrimidines.- 15.1 Bases Are Planar and Each Contains Several Different Hydrogen-Bonding Donor and Acceptor Groups.- 15.2 Many Tautomeric Forms Are Feasible But Not Observed.- 15.3 ?-Bond Cooperativity Enhances Hydrogen-Bonding Forces.- 15.4 General, Non-Base-Pairing Hydrogen Bonds.- 16 Base Pairing in the Purine and Pyrimidine Crystal Structures.- 16.1 Base-Pair Configurations with Purine and Pyrimidine Homo-Association.- 16.2 Base-Pair Configurations with Purine-Pyrimidine Hetero-Association: the Watson-Crick Base-Pairs.- 16.3 Base Pairs Can Combine to Form Triplets and Quadruplets.- 17 Hydrogen Bonding in the Crystal Structures of the Nucleosides and Nucleotides.- 17.1 Conformational and Hydrogen-Bonding Characteristics of the Nucleosides and Nucleotides.- 17.2 A Selection of Cyclic Hydrogen-Bonding Patterns Formed in Nucleoside and Nucleotide Crystal Structures.- 17.3 General Hydrogen-Bonding Patterns in Nucleoside and Nucleotide Crystal Structures.- III Hydrogen Bonding in Biological Macromolecules.- 18 O-H *** O Hydrogen Bonding in Crystal Structures of Cyclic and Linear Oligoamyloses: Cyclodextrins, Maltotriose, and Maltohexaose.- 18.1 The Cyclodextrins and Their Inclusion Complexes.- 18.2 Crystal Packing Patterns of Cyclodextrins Are Determined by Hydrogen Bonding.- 18.3 Cyclodextrins as Model Compounds to Study Hydrogen-Bonding Networks.- 18.4 Cooperative, Homodromic, and Antidromic Hydrogen-Bonding Patterns in the ?-Cyclodextrin Hydrates.- 18.5 Homodromic and Antidromic O-H *** O Hydrogen-Bonding Systems Analyzed Theoretically.- 18.6 Intramolecular Hydrogen Bonds in the ?-Cyclodextrin Molecule are Variable - the Induced-Fit Hypothesis.- 18.7 Flip-Flop Hydrogen Bonds in ?-Cyclodextrin * 11 H2O.- 18.8 From Flip-Flop Disorder to Ordered Homodromic Arrangements at Low lbmperature: The Importance of the Cooperative Effect.- 18.9 Maltohexaose Polyiodide and Maltotriose - Double and Single Left-Handed Helices With and Without Intramolecular O(2) *** O(3?) Hydrogen Bonds.- 19 Hydrogen Bonding in Proteins.- 19.1 Geometry of Secondary-Structure Elements: Helix, Pleated Sheet, and Turn.- 19.2 Hydrogen-Bond Analysis in Protein Crystal Structures.- 19.3 Hydrogen-Bonding Patterns in the Secondary Structure Elements.- 19.4 Hydrogen-Bonding Patterns Involving Side-Chains.- 19.5 Internal Water Molecules as Integral Part of Protein Structures.- 19.6 Metrical Analysis of Hydrogen Bonds in Proteins.- 19.7 Nonsecondary-Structure Hydrogen-Bond Geometry Between Main-Chains, Side-Chains and Water Molecules.- 19.8 Three-Center (Bifurcated) Bonds in Proteins.- 19.9 Neutron Diffraction Studies on Proteins Give Insight into Local Hydrogen-Bonding Flexibility.- 19.10 Site-Directed Mutagenesis Gives New Insight into Protein Thermal Stability and Strength of Hydrogen Bonds.- 20 The Role of Hydrogen Bonding in the Structure and Function of the Nucleic Acids.- 20.1 Hydrogen Bonding in Nucleic Acids is Essential for Life.- 20.2 The Structure of DNA and RNA Double Helices is Determined by Watson-Crick Base-Pair Geometry.- 20.3 Systematic and Accidental Base-Pair Mismatches: "Wobbling" and Mutations.- 20.4 Noncomplementary Base Pairs Have a Structural Role in tRNA.- 20.5 Homopolynucleotide Complexes Are Stabilized by a Variety of Base-Base Hydrogen Bonds - Three-Center (Bifurcated) Hydrogen Bonds in A-Tracts.- 20.6 Specific Protein-Nucleic Acid Recognition Involves Hydrogen Bonding.- IV Hydrogen Bonding by the Water Molecule.- 21 Hydrogen-Bonding Patterns in Water, Ices, the Hydrate Inclusion Compounds, and the Hydrate Layer Structures.- 21.1 Liquid Water and the Ices.- 21.2 The Hydrate Inclusion Compounds.- 21.3 Hydrate Layer Structures.- 22 Hydrates of Small Biological Molecules: Carbohydrates, Amino Acids, Peptides, Purines, Pyrimidines, Nucleosides and Nucleotides.- 23 Hydration of Proteins.- 23.1 Characterization of "Bound Water" at Protein Surfaces - the First Hydration Shell.- 23.2 Sites of Hydration in Proteins.- 23.3 Metrics of Water Hydrogen Bonding to Proteins.- 23.4 Ordered Water Molecules at Protein Surfaces - Clusters and Pentagons.- 24 Hydration of Nucleic Acids.- 24.1 Two Water Layers Around the DNA Double Helix.- 24.2 Crystallographically Determined Hydration Sites in A-, B-, Z-DNA. A Statistical Analysis.- 24.3 Hydration Motifs in Double Helical Nucleic Acids.- 24.3.1 Sequence-Independent Motifs.- 24.3.2 Sequence-Dependent Motifs.- 24.4 DNA Hydration and Structural Transitions Are Correlated: Some Hypotheses.- 25 The Role of Three-Center Hydrogen Bonds in the Dynamics of Hydration and of Structure Transition.- References.- Refcodes.
05 Nov 2011