Molecular structure does not easily identify the intricate noncovalent interactions that govern many areas of biology and chemistry, including design of new materials and drugs. We develop an approach to detect noncovalent interactions in real space, based on the electron density and its derivatives. Our approach reveals the underlying chemistry that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids. Most importantly, the method, requiring only knowledge of the atomic coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of nonbonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands.

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Revealing noncovalent interactions.

Roles of glycine betaine and proline in improving plant abiotic stress resistance

Noncovalent interactions hold the key to understanding many chemical, biological, and technological problems. Describing these noncovalent interactions accurately, including their positions in real space, constitutes a first step in the process of decoupling the complex balance of forces that define noncovalent interactions. Because of the size of macromolecules, the most common approach has been to assign van der Waals interactions (vdW), steric clashes (SC), and hydrogen bonds (HBs) based on pairwise distances between atoms according to their vdW radii. We recently developed an alternative perspective, derived from the electronic density: the non-covalent interactions (NCI) index [J. Am. Chem. Soc. 2010, 132, 6498]. This index has the dual advantages of being generally transferable to diverse chemical applications and being very fast to compute, since it can be calculated from promolecular densities. Thus, NCI analysis is applicable to large systems, including proteins and DNA, where analysis of noncova...

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NCIPLOT: A Program for Plotting Noncovalent Interaction Regions

Arbuscular mycorrhizal (AM) fungi form mutualistic, symbiotic associations with the roots of more than 80% of land plants. The fungi are incapable of completing their life cycle in the absence of a host root. Their spores can germinate and grow in the absence of a host, but their hyphal growth is very limited. Little is known about the molecular mechanisms that govern signalling and recognition between AM fungi and their host plants. In one of the first stages of host recognition, the hyphae of AM fungi show extensive branching in the vicinity of host roots before formation of the appressorium, the structure used to penetrate the plant root. Host roots are known to release signalling molecules that trigger hyphal branching, but these branching factors have not been isolated. Here we have isolated a branching factor from the root exudates of Lotus japonicus and used spectroscopic analysis and chemical synthesis to identify it as a strigolactone, 5-deoxy-strigol. Strigolactones are a group of sesquiterpene lactones, previously isolated as seed-germination stimulants for the parasitic weeds Striga and Orobanche. The natural strigolactones 5-deoxy-strigol, sorgolactone and strigol, and a synthetic analogue, GR24, induced extensive hyphal branching in germinating spores of the AM fungus Gigaspora margarita at very low concentrations.

Plant sesquiterpenes induce hyphal branching in arbuscular mycorrhizal fungi

http://nhjy.hzau.edu.cn/kech/ssyy/qysd/njsl/21.pdf

Potential biochemical indicators of salinity tolerance in plants

Mass spectrometric investigation of silver ion promoted carbon-carbon bond scission

Further fractionation of the EtOH extract of the bark of Annona bullata Rich. (Annonaceae) has led to the isolation of a new nonadjacent bis-tetrahydrofuran acetogenin, bullatalicinone, and the known adjacent bis-tetrahydrofuran acetogenin, squamocin. These two compounds showed potent and selective cytotoxicities for certain human tumor cell lines. Their structures have been elucidated by chemical and spectral methods. Bullatalicinone is the methylketo-lactone derivative of bullatalicin which we found previously in this plant.

Bullatalicinone, a new potent bioactive acetogenin, and squamocin from annona bullata (Annonaceae)

A dramatic source temperature effect is observed in the low collision energy collision-induced dissociation spectra of molecular ions derived via 70 eV electron bombardment of 2-pentanone and via charge exchange. The observation cannot simply be attibuted to the increased thermal energy of the 2-pentanone molecular ions. A number of factors appear to contribute to the observed results, (i) the increase, with temperature, in the ratio of the concentration of enol to keto neutral molecules, (ii) temperature effects on the Franck-Condon factors which control the yields and internal energies of the keto and enol molecular ions, (iii) differences in the relative stabilities of the keto and enol molecular ions, (iv) temperature effects on the equilibrium between the isomeric molecular ions. This last item is probably most important, with the concentration of 






being most significant. These data highlight the role that ion source temperature can play as a variable in elucidating ion structure problems.

The effect of ion source temperature on the fragmentation of 2-pentanone

Electrospray ionization (ESI) mass spectrometry was employed to obtain both molecular weight confirmation and structural information for a series of novel alkenyldiarylmethane (ADAM) analogs. The mass spectral data were intended for use during the structure elucidation of ester hydrolysis products formed during an in vitro metabolism study of a series of novel ADAM analogs. The data on the precursor molecules show the presence of the molecular ion peak, [M+H]+, as well as a peak consistent with the hydrolysis product of the original ester ([MH-ROH+H2O]+). However, chemical ionization mass spectrometry, elemental analysis and 1H NMR data indicated the presence of only the intact diester compounds, suggesting that the formation of the hydrolysis product was an instrumental artifact, i.e., in-beam hydrolysis during ESI or a result of longer ion residence times of the ion trap mass analyzer. Copyright © 2003 John Wiley & Sons, Ltd.

Karl V. Wood

Papers

Mass spectrometric investigation of silver ion promoted carbon-carbon bond scission

Bullatalicinone, a new potent bioactive acetogenin, and squamocin from annona bullata (Annonaceae)

The effect of ion source temperature on the fragmentation of 2-pentanone

The ‘apparent’ hydrolysis of alkyl esters during electrospray ionization

A fungitoxic phenolic compound in Hydrilla verticillata