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

Vanadyl deoxophy lloerythroetioporphyrins (DPEP) and vanadyl etioporphyrins (ETIO) have been identified in Gato Ridge and Boscan petroleum samples using a combination of isobutane chemical ionization and tandem mass spectrometry. In addition, particular porphyrins such as the C30 vanadyl DPEP and ETIO species were identified in a crude oil containing approximately 500 ppm total porphyrins, with only minimal sample clean-up.

The analysis of metalloporphyrins in petroleum using tandem mass spectrometry

The alkenyldiarylmethanes are a class of non-nucleoside reverse transcriptase inhibitors that are currently being developed as potential antivirals for the treatment of HIV infection and AIDS. As part of our continuing investigations on the alkenyldiarylmethanes, a series of thioester analogues were prepared in an effort to improve upon the metabolic stability of the parent lead compound. Hydrolysis of the thioester moieties was consistently observed during ion trap electrospray ionization (ESI) mass spectrometry to the extent that the parent molecular ion was weak in intensity or simply could not be detected. The same hydrolysis observations were also made when the analogues were analyzed by ion trap electron impact (EI) ionization, indicating the hydrolysis event was the result of the ion trap and not ionization technique. Ion-trap-mediated hydrolysis has been observed previously in prior alkenyldiarylmethane studies and prevented characterization of certain intermediates; thus, we wished to investigate whether modifying instrument parameters and protocols affected the instrument-mediated hydrolysis event. Unfortunately, varying the maximum injection time and the number of microscans performed, independent of each other, had little effect on the intensities of the parent ions [MH(+)] or the hydrolysis products] MH(+) -HSCH(3)].

Hydrolysis of thioesters in an ion trap

Mass spectra of substituted dihydrocbalcones

A mass spectral study of selected isopropyl borinic esters

Mass spectrometry is a very valuable analytical tool based on the simple premise of determining the molecular weight of the compound of interest. In fact, mass spectrometry involves the measurement of the mass (m) of a compound as a function of charge (z), m/z. In most mass spectrometer experiments the charge on an ion is one, such that the molecular weight of the ion is equal in value to m/z. Mass spectrometry can be divided into three steps: ionization, mass analysis and detection. Sample introduction is really a distinct component for obtaining quality mass spectra and will be discussed separately.

Karl V. Wood

Papers

The analysis of metalloporphyrins in petroleum using tandem mass spectrometry

Hydrolysis of thioesters in an ion trap

Mass spectra of substituted dihydrocbalcones

A mass spectral study of selected isopropyl borinic esters

Analysis of Phenolic Compounds with Mass Spectrometry