Encoding and decoding hydrogen-bond patterns of organic compounds
About: This article is published in Accounts of Chemical Research.The article was published on 1990-04-01. It has received 4107 citations till now. The article focuses on the topics: Hydrogen bond.
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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
TL;DR: The ability to prepare structures in the upper part of this range of sizes would open a route to structures comparable in size (and perhaps complementary in function) to those that can be prepared by microlithography and other techniques of microfabrication.
Abstract: Molecular self-assembly is the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by noncovalent bonds. Molecular self-assembly is ubiquitous in biological systems and underlies the formation of a wide variety of complex biological structures. Understanding self-assembly and the associated noncovalent interactions that connect complementary interacting molecular surfaces in biological aggregates is a central concern in structural biochemistry. Self-assembly is also emerging as a new strategy in chemical synthesis, with the potential of generating nonbiological structures with dimensions of 1 to 10(2) nanometers (with molecular weights of 10(4) to 10(10) daltons). Structures in the upper part of this range of sizes are presently inaccessible through chemical synthesis, and the ability to prepare them would open a route to structures comparable in size (and perhaps complementary in function) to those that can be prepared by microlithography and other techniques of microfabrication.
3,119 citations
01 Dec 1991
TL;DR: In this article, self-assembly is defined as the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by noncovalent bonds.
Abstract: Molecular self-assembly is the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by noncovalent bonds. Molecular self-assembly is ubiquitous in biological systems and underlies the formation of a wide variety of complex biological structures. Understanding self-assembly and the associated noncovalent interactions that connect complementary interacting molecular surfaces in biological aggregates is a central concern in structural biochemistry. Self-assembly is also emerging as a new strategy in chemical synthesis, with the potential of generating nonbiological structures with dimensions of 1 to 10(2) nanometers (with molecular weights of 10(4) to 10(10) daltons). Structures in the upper part of this range of sizes are presently inaccessible through chemical synthesis, and the ability to prepare them would open a route to structures comparable in size (and perhaps complementary in function) to those that can be prepared by microlithography and other techniques of microfabrication.
2,591 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
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632 citations
TL;DR: In this article, the packing modes of carboxylic acids are discussed, and the van der Waals distance between carboxyl O atoms appears to be dependent upon their direction of approach.
Abstract: Some features of the packing modes of carboxylic acids are discussed. Monocarboxylic acids R-CO2H, containing residues R, which are either nonchiral or racemic, almost invariably form cyclic hydrogenbonded pairs. If the R group is small, the molecules may interlink by single O H . . . O bonds to form a chain motif in which the O H . . • O(carboxyl) bond is almost linear, the C=O. • • (H)O angle _~ 130 °, and the O-H proton donor lies in the plane of the carbonyl system O = C ( , to which it is hydrogenbonded. Monocarboxylic acids with chiral residues and which are enantiomeric show some tendency to form a hydrogen-bonded chain motif along a twofold screw axis. The angular geometry of this O H . . . O bond shows considerable variation and seems to be dependent upon the van der Waals contacts between the R groups along the hydrogen-bonded chain. Dicarboxylic acids HO2C-R-CO2H form extended chains, the carboxyl groups being interlinked by O H . . . O bonds into cyclic pairs. This arrangement is adopted, almost without exception, for all types of R groups. Carboxylic acids, in which the intramolecular environments of the two carboxyl O atoms are identical, may show orientational disorder of the carboxyl group in the crystal. This depends on the intermolecular environment of the carboxyl dimer. Belonging to this category are p-substituted benzoic acids, which almost invariably adopt the packing motif in which the carboxyl dimers lie side by side with a neighbouring phenyl ring on the same plane and are separated from each other by C H . . O contacts of ~ 3.5 ,~. This arrangement is conducive to disorder of the carboxyl dimer. The benzoic acids, and indeed many planar acids, form stacks in which the direction of offset between the carboxyl groups lies either along the carbonyl C--O bond or the hydroxyl C-OH bond. The carboxyl group in these two stacking types may show disorder of the carboxyl dimer, suggesting that the energy difference between the two stacking types is small. Carboxylic acids also form interplanar contact via an antiparallel arrangement of C-O bonds which may be either C--O or C-OH bonds or a disordered combination thereof. Intramolecular forces probably favour the synplanar C=C-C=O conformation in the ct,fl-unsaturated acids R-CH-CH-CO2H. The antiplanar C=C-C=O form may be induced by intermolecular forces. Orientational disorder between the synand antiplanar C=C-C---O conformations may be induced by the stacking forces of the carboxyl dimers. The observed antiplanar C=C-C=O conformation in a number of acids has been associated with a motif containing a lateral C-H. . .O(carbonyl ) contact _ 3.5 A. The few known crystal structures of carboxylic acids containing an acetylenic C-H proton donor have not shown acetylenic C-H..O(carbonyl ) interactions which are strikingly short. Indeed, but-3-ynoic acid shows only a -C-H. . .C--C contact. The minimum van der Waals distance between carboxyl O atoms appears to be dependent upon their direction of approach. Hydroxyl O atoms which make H 1 contact so that their C-O(H) bonds are almost collinear (C-O. -O-C) , may approach each other to I H within 2.9 A. Carbonyl and hydroxyl O atoms which are arranged so that their electron lone-pair lobes are directed at each other do not make contact less than 3\"5 A.
608 citations
TL;DR: The three-dimensional structure of senkirkine, ClsHnN06, was determined by X-ray crystallography as mentioned in this paper, and the structure was solved by statistical methods.
Abstract: The three-dimensional structure of senkirkine, ClsHnN06, was determined by X-ray crystallography. The substance crystallizes in the orthorhombic space group P212121 with four molecules in a unit cell with dimensions a = 24.601 k 0.002, b = 9.133 f 0.001, and c = 8.708 f 0.001 A. Intensity data were collected with a diffractometer and the structure was solved by statistical methods. Refinement by least squares, which included hydrogen atoms, tonverged at R 0.045 for 2275 observed reflections. The transannular N . . .C distance was found to be 2.292 (4) A. The extent of the partial bond in this and in several other structures is assessed. A correlation is established between the bond number and the frequency of the carbonyl peak in the infrared spectrum. uring the past years the crystal structures of three D alkaloids in which there exists an intramolecular N . . . C=O interaction were determined in these laboratories, viz., protopine, cryptopine, and clivorine. More recently it was suggested4 that such an interaction may be pertinent to the physiological activity of methadone. It seemed desirable, therefore, to obtain additional geometrical information and, if possible, to correlate it to the extensive chemical and spectroscopic (1) S. R. Hall and F. R. Ahmed, Acta Crystallogr., Sect. B, 24, (2) S. R. Hall and F. R. Ahmed, Acta Crystallogr., Sect. B , 24, 346 (3) K . B. Birnbaum, Acta Crystallogr., Secf. B, 28,2825 (1972). (4) H. B. Burgi, J. D. Dunitz, and E. Shefter, Nature (London), New 337(1968).
604 citations