Determination of an organic crystal structure with the aid of topochemical and related considerations: correlation of the molecular and crystal structures of α-benzylidene-γ-butyrolactone and 2- benzylidenecyclopentanone with their solid state photoreactivity

The crystal structure of α-benzylidene-γ-butyrolactone 2, can be determined with the aid of atom-atom pairwise energy evaluation procedures, because its (previously reported) solid state photoreactivity coupled with topochemical principles, greatly restricts the number of possible orientations of the molecule in the unit cell. Crystals of lactone 2 are monoclinic with space group P2$_1$/n and with Z = 4, a = 11.014(2), b = 5.959(1), c = 14.286(5), β = 108.05(2). Refinement on 846 non-zero reflections led to an R (reliability) of 0.046. In contrast, the isoelectronic ketone 2-benzylidenecyclopentanone (3) is photostable, and crystallizes in the same space group with Z = 4, a = 7.466(4), b = 6.821(4), c = 19.005(1), β = 94.14(1). The structure of 3 was solved by direct methods and refined on 1037 non-zero reflections to an R of 0.036. The difference between the two structures can be rationalized in terms of intramolecular conformation and weak C-H$\cdots$O hydrogen bonding. Differences in the solid state photoreactivities of the two compounds can be related to the extent of orbital overlap between 'potentially reactive' double bonds on nearest neighbour molecules that are related by inversion. Compound 2 reacts in the solid state topochemically but not topotactically showing directional preference, while 3, which has reduced orbital overlap, is photostable

Strong and weak hydrogen bonds in the protein-ligand interface

The characteristics of NH···O, OH···O, and CH···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 Å radius around the ligand. Notably, NH···O and OH···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 Å 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 CH···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 XH···∏ (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

Strong and weak hydrogen bonds in drug-DNA complexes: a statistical analysis

A statistical analysis of strong and weak hydrogen bonds in the minor groove of DNA was carried out for a set of 70 drug-DNA complexes. The terms "strong" and "weak" pertain to the inherent strengths and weakness of the donor and acceptor fragments rather than to any energy considerations. The dataset was extracted from the protein data bank (PDB). The analysis was performed with an in-house software, hydrogen bond analysis tool (HBAT). In addition to strong hydrogen bonds such as O-H···O and N-H···O, the ubiquitous presence of weak hydrogen bonds such as C-H···O is implicated in molecular recognition. On an average, there are 1.4 weak hydrogen bonds for every strong hydrogen bond. For both categories of interaction, the N(3) of purine and the O(2) of pyrimidine are favoured acceptors. Donor multifurcation is common with the donors generally present in the drug molecules, and shared by hydrogen bond acceptors in the minor groove. Bifurcation and trifurcation are most commonly observed. The metrics for strong hydrogen bonds are consistent with established trends. The geometries are variable for weak hydrogen bonds. A database of recognition geometries for 26 literature amidinium-based inhibitors of Human African Trypanosomes (HAT) was generated with a docking study using seven inhibitors which occur in published crystal structures included in the list of 70 complexes mentioned above, and 19 inhibitors for which the drug-DNA complex crystal structures are unknown. The virtual geometries so generated correlate well with published activities for these 26 inhibitors, justifying our assumption that strong and weak hydrogen bonds are optimized in the active site

Synthon robustness in saccharinate salts of some substituted pyridines

Synthon robustness or lack of structural interference is a sought after goal in crystal engineering. The crystal structures of saccharinate salts 1-6 show the robustness of the newly identified hydrogen bonded synthons I and III

Estudio por GC-MS del aceite de la hoja de Artabotrys odoratissimus

GC-MS study of two fatty oil fractions from Artabotrys odoratissimus (leaves) indicated the presence of fifteen compounds namely, nonanoic acid; methyl phenyl propanoate; decanoic acid; diethyl phthalate; dibutyl phthalate; 2-amino-3-ethyl biphenyl; 5-methyl-9-phenylnonan-3-ol; hexadeca-2,7,11-triene; 2,6-dimethyl-1-phenylhepta-1-one; 2,5-dimethyltetradecahydrophenenthrene; 1-phenylundecane; 1-isopropyl-4,6-dimethyl naphthalene; 5-(2-butyl phenyl)pent-3-en-2-ol; 1-phenyldeca-1-one and 1-phenylundecan-1-one. Some of the compounds are rare occurring and biologically activeEl estudio por GC-MS de dos fracciones del aceite de la hoja de Artabotrys odoratissimus indicó la presencia de quince compuestos tales como: ácido nonanoico; fenil propanoato de metilo; ácido decanoico; ftalato de dietilo; ftalato de dibutilo; 2-amino-3-etil bifenilo; 5-metil-9-fenilnonan-3-ol; hexadeca-2,7,11-trieno; 2,6-dimetil-1-fenilheptan-1-ona; 2,5-dimetiltetradecahidrofenantreno; 1-fenilundecano; 1-isopropil-4,6-dimetil naftaleno; 5-(2-butilfenil)-3-penten-2-ol; 1-fenildecan-1-ona y 1-fenilundecan-1-ona. Algunos de estos compuestos son poco frecuentes y activos biológicamente

Unusually long cooperative chain of seven hydrogen bonds. An alternative packing type for symmetrical phenols

Conformational flexibility in a symmetrical tris-phenol leads to close packed structures that are also characterised by an extended though finite cooperative chain of hydrogen bonds

Crystal engineering in the aminophenols. Novel carborundum network in a supramolecular homologous series

Molecular complexes of 4-(4-aminophenoxy)aniline with a series of diphenols are structurally homologous and adopt the carborundum III topology, which is an unprecedented network for organic solids

Gauche and staggered forms of diethylamine in solvates of 1,5-dichloro-cis-9,10-diethynyl-9,10-dihydroanthracene-9,10-diol. A case of conformational pseudopolymorphism?

Diethylamine has been trapped in its less stable gauche conformation in a solvate of the title diol; the staggered conformation, which is ca. 4 kJ mol-1 more stable, is found in another solvate of the same host

Comparison Between Hydrogen and Halogen Bonds in Complexes of 6-OX-Fulvene with Pnicogen and Chalcogen Electron Donors

Quantum chemical calculations are applied to complexes of 6‐OX‐fulvene (X=H, Cl, Br, I) with ZH3/H2Y (Z=N, P, As, Sb; Y=O, S, Se, Te) to study the competition between the hydrogen bond and the halogen bond. The H‐bond weakens as the base atom grows in size and the associated negative electrostatic potential on the Lewis base atom diminishes. The pattern for the halogen bonds is more complicated. In most cases, the halogen bond is stronger for the heavier halogen atom, and pnicogen electron donors are more strongly bound than chalcogen. Halogen bonds to chalcogen atoms strengthen in the order

Evidence for the characterisation of the C-H …∏ interaction as a weak hydrogen bond: toluene and chlorobenzene solvates of 2,3,7,8-tetraphenyl-1,9,10-anthyridine

The crystal structures of the toluene and chlorobenzene solvates of 2,3,7,8-tetraphenyl-1,9,10-anthyridine are nearly identical save for differences in the mode of solvent inclusion; these differences have an important bearing on the nature of the C-H … ∏ interactions in these structures