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Gautam R Desiraju

Publications and source records attributed to Gautam R Desiraju.

At least 19 recordsLinked to original sources
PubMed2007

Strong and weak hydrogen bonds in the protein-ligand interface.

The characteristics of N--H...O, O--H...O, and C--H...O hydrogen bonds and other weak intermolecular interactions are analyzed in a large and diverse group of 251 protein-ligand complexes using a new computer program that was developed in-house for this purpose. The interactions examined in the present study are those which occur in the active sites, defined here as a sphere of 10 A radius around the ligand. Notably, N--H...O and O--H...O bonds tend towards linearity. Multifurcated interactions are especially common, especially multifurcated acceptors, and the average degree of furcation is 2.6 hydrogen bonds per furcated acceptor. A significant aspect of this study is that we have been able to assess the reliability of hydrogen bond geometry as a function of crystallographic resolution. Thresholds of 2.3 and 2.0 A are established for strong and weak hydrogen bonds, below which hydrogen bond geometries may be safely considered for detailed analysis. Interactions involving water as donor or acceptor, and C--H...O bonds with Gly and Tyr as donors are ubiquitous in the active site. A similar trend was observed in an external test set of 233 protein-ligand complexes belonging to the kinase family. Weaker interactions like X--H...pi (X = C, N, O) and those involving halogen atoms as electrophiles or nucleophiles have also been studied. We conclude that the strong and weak hydrogen bonds are ubiquitous in protein-ligand recognition, and that with suitable computational tools very large numbers of strong and weak intermolecular interactions in the ligand-protein interface may be analyzed reliably. Results confirm earlier trends reported previously by us but the extended nature of the present data set mean that the observed trends are more reliable.

Binding Sites↗
PubMed2006

Form I of desloratadine, a tricyclic antihistamine.

The title compound [systematic name: 8-chloro-11-(piperidin-4-ylidene)-6,11-dihydro-5H-benzo[4,5]cyclohepta[2,1-b]pyridine], C19H19ClN2, was crystallized from ethyl acetate. The interesting feature of the reported structure is that it does not contain any strong hydrogen bonds, although the molecule contains a secondary NH group, which is a good hydrogen-bond donor.

Crystallography, X-Ray↗
PubMed2006

Solid-state architecture of saccharin salts of some diamines.

Hydrazinium saccharinate, N2H5+.C7H4NO3S-, crystallizes in a 1:1 ratio, while ethylenediaminium bis(saccharinate), C2H10N2(2+).2C7H4NO3S-, and butane-1,4-diaminium bis(saccharinate), C4H14N2(2+).2C7H4NO3S-, form in a 1:2 cation-anion stoichiometry. The structures contain many strong hydrogen bonds of the N+-H...N-, N+-H...O, N-H...O and N-H...N types, with auxiliary C-H...O interactions.

Amines↗
PubMed2006

Isostructurality, polymorphism and mechanical properties of some hexahalogenated benzenes: the nature of halogen...halogen interactions.

The nature of intermolecular interactions between halogen atoms, X...X (X = Cl, Br, I), continues to be of topical interest because these interactions may be used as design elements in crystal engineering. Hexahalogenated benzenes (C6Cl(6-n)Br(n), C6Cl(6-n)I(n), C6Br(6-n)I(n)) crystallise in two main packing modes, which take the monoclinic space group P2(1)/n and the triclinic space group P1. The former, which is isostructural to C6Cl6, is more common. For molecules that lack inversion symmetry, adoption of this monoclinic structure would necessarily lead to crystallographic disorder. In C6Cl6, the planar molecules form Cl...Cl contacts and also pi...pi stacking interactions. When crystals of C6Cl6 are compressed mechanically along their needle length, that is, [010], a bending deformation takes place, because of the stronger interactions in the stacking direction. Further compression propagates consecutively in a snakelike motion through the crystal, similar to what has been suggested for the motion of dislocations. The bending of C6Cl6 crystals is related to the weakness of the Cl...Cl interactions compared with the stronger pi...pi stacking interactions. The triclinic packing is less common and is restricted to molecules that have a symmetrical (1,3,5- and 2,4,6-) halogen substitution pattern. This packing type is characterised by specific, polarisation-induced X...X interactions that result in threefold-symmetrical X3 synthons, especially when X = I; this leads to a layered pseudohexagonal structure in which successive planar layers are inversion related and stacked so that bumps in one layer fit into the hollows of the next in a space-filling manner. The triclinic crystals shear on application of a mechanical stress only along the plane of deformation. This shearing arises from the sliding of layers against one another. Nonspecificity of the weak interlayer interactions here is demonstrated by the structure of twinned crystals of these compounds. One of the compounds studied (1,3,5-tribromo-2,4,6-triiodobenzene) is dimorphic, adopting both the monoclinic and triclinic structures, and the reasons for polymorphism are suggested. To summarise, both chemical and geometrical models need to be considered for X...X interactions in hexahalogenated benzenes. The X...X interactions in the monoclinic group are nonspecific, whereas in the triclinic group some X...X interactions are anisotropic, chemically specific and crystal-structure directing.

Journal Article↗
PubMed2006

Five varieties of hydrogen bond in 1-formyl-3-thiosemicarbazide: an electron density study.

In an attempt to investigate the putative S-H...N hydrogen bond, we have studied the title compound, 1-formyl-3-thiosemicarbazide, which was revealed in a CSD search as a crystal structure which might show such an interaction. However, a redetermination of the structure at room temperature and careful analysis showed that the earlier study [Saxena et al. (1991). Acta Cryst. C47, 2374-2376] on which the CSD search was based was in error and that the possibility of an S-H...N hydrogen bond is negated. The presence of five other varieties of hydrogen bond (N-H...O, N-H...S, N-H...N, C-H...O, C-H...S) in the crystal packing prompted us to redirect our efforts and to undertake a study of the charge-density distribution at 90 K. The topological analysis of these five varieties of hydrogen bond was carried out with Bader's quantum theory of ;atoms in molecules' and by applying Koch-Popelier's criteria. The analysis reveals that the hydrogen-bond strength is highest for N-H...O and lowest for C-H...S with N-H...S, N-H...N and C-H...O forming the middle order.

Journal Article↗
PubMed2005

Crystal structure prediction of aminols: advantages of a supramolecular synthon approach with experimental structures.

The supramolecular synthon approach to crystal structure prediction (CSP) takes into account the complexities inherent in crystallization. The synthon is a kinetically favored unit, and through analysis of commonly occurring synthons in a group of related compounds, kinetic factors are implicitly invoked. The working assumption is that while the experimental structure need not be at the global minimum, it will appear somewhere in a list of computationally generated structures so that it can be suitably identified and ranked upward using synthon information. These ideas are illustrated with a set of aminophenols, or aminols. In the first stage, a training database is created of the 10 isomeric methylaminophenols. The crystal structures of these compounds were determined. The prototypes 2-, 3-, and 4-aminophenols were also included in the training database. Small and large synthons in these 13 crystal structures were then identified. Small synthons are of high topological but low geometrical value and are used in negative screens to eliminate computationally derived structures that are chemically unreasonable. Large synthons are more restrictive geometrically and are used in positive screens ranking upward predicted structures that contain these more well-defined patterns. In the second stage, these screens are applied to CSP of nine new aminols carried out in 14 space groups. In each space group, up to 10 lowest energy structures were analyzed with respect to their synthon content. The results are encouraging, and the predictions were classified as good, unclear, or bad. Two predictions were verified with actual crystal structure determinations.

Journal Article↗
PubMed2005

C-H...O and other weak hydrogen bonds. From crystal engineering to virtual screening.

Hydrogen bonds, X-H...A, formed by weak donors (X = C) and acceptors (A = pi system) were generally dismissed as being of little consequence before and even during the 1970s. This situation changed in the early 1980s, and during the two following decades they were implicated as being significant in many small molecule crystal structures, and also in solution. Today, knowledge gained about these interactions is being used to understand the structure of biomolecules with implications for structure based drug design.

Crystallization↗