Automated annotation of chemical names in the literature with tunable accuracy.

BACKGROUND: A significant portion of the biomedical and chemical literature refers to small molecules. The accurate identification and annotation of compound name that are relevant to the topic of the given literature can establish links between scientific publications and various chemical and life science databases. Manual annotation is the preferred method for these works because well-trained indexers can understand the paper topics as well as recognize key terms. However, considering the hundreds of thousands of new papers published annually, an automatic annotation system with high precision and relevance can be a useful complement to manual annotation. RESULTS: An automated chemical name annotation system, MeSH Automated Annotations (MAA), was developed to annotate small molecule names in scientific abstracts with tunable accuracy. This system aims to reproduce the MeSH term annotations on biomedical and chemical literature that would be created by indexers. When comparing automated free text matching to those indexed manually of 26 thousand MEDLINE abstracts, more than 40% of the annotations were false-positive (FP) cases. To reduce the FP rate, MAA incorporated several filters to remove "incorrect" annotations caused by nonspecific, partial, and low relevance chemical names. In part, relevance was measured by the position of the chemical name in the text. Tunable accuracy was obtained by adding or restricting the sections of the text scanned for chemical names. The best precision obtained was 96% with a 28% recall rate. The best performance of MAA, as measured with the F statistic was 66%, which favorably compares to other chemical name annotation systems. CONCLUSIONS: Accurate chemical name annotation can help researchers not only identify important chemical names in abstracts, but also match unindexed and unstructured abstracts to chemical records. The current work is tested against MEDLINE, but the algorithm is not specific to this corpus and it is possible that the algorithm can be applied to papers from chemical physics, material, polymer and environmental science, as well as patents, biological assay descriptions and other textual data.

The protonated guanine-cytosine base pair.

Protonated base pairs were recently implicated in the context of DNA proton transfer and charge migration. The effects of protonating different sites of the guanine-cytosine (GC) base pair are studied here by using the DZP++ B3LYP density functional method. Optimized structures for the protonated GC base pair are compared with those of parent GC and the neutral hydrogenated GC radical (GCH). Proton and hydrogen-atom additions significantly disturb the structure of the GC base pair. However, the structural perturbations arising from protonation are often less than those arising from hydrogenation of GC. Protonation of the GC base pair causes significant strengthening of the interstrand hydrogen bonds and a concomitant increase in the base dissociation energies. The adiabatic ionization potentials (AIPs), vertical ionization potentials (VIPs), and proton affinities (PAs) for the different protonation sites of the GC base pair are predicted. The N7 site of guanine is the preferred site for protonation of the GC base pair.

Chromium carbonyl nitrosyls: comparison with isoelectronic manganese carbonyl derivatives.

Density functional methods indicate that the global minimum for Cr2(NO)2(CO)8 is a staggered D4d structure in accord with experiment and analogous to the isoelectronic Mn2(CO)10. For the unsaturated Cr2(NO)2(CO)n derivatives the lowest energy structures are very different from the lowest energy structures for the isoelectronic Mn2(CO)n+2 derivatives. Thus the global minimum for Cr2(NO)2(CO)7 is an unbridged structure with a Cr(NO)(CO)4 fragment linked to a Cr(NO)(CO)3 fragment through a Cr=Cr double bond. For Cr2(NO)2(CO)6 the global minimum is a structure with two bridging CO groups, whereas the global minimum for Mn2(CO)8 is an unbridged structure. For Cr2(NO)2(CO)5 both NO groups are bridging NO groups with one of them having a short enough Cr-O distance to be considered a formal five-electron donor eta2-mu-NO group. Thus the isoelectronic substitution of NO for CO with a necessary adjustment in the central metal atom can lead to significant shifts in the relative energies of various structural types of metal carbonyl nitrosyls, particularly for unsaturated molecules. For the mononuclear Cr(NO)2(CO)3 the theoretical structure differs from that deduced from matrix isolation experiments. Moreover, the nu(CO) and nu(NO) vibrational frequencies predicted here for Cr(NO)2(CO)3 correspond more closely with the unassigned species labeled "Cr(NO)(CO)x" in the experiments rather than the species claimed to be Cr(NO)2(CO)3.

Molecular Structures and Energetics Associated with Hydrogen Atom Addition to the Guanine-Cytosine Base Pair.

The radicals generated by hydrogen-atom addition to the Watson-Crick guanine-cytosine (G-C) DNA base pair were studied theoretically using an approach that has proved effective in predicting molecular structures and energetics. All optimized structures were confirmed to be minima via vibrational frequency analysis. The dissociation energies of the base-pair radicals are predicted and compared with that of the neutral G-C base pair. The lowest-energy base-pair radical is that with the hydrogen atom attached to the C8 position of guanine, resulting in the nitrogen radical designated G(C8)-C. In this, the most favorable radical, the G-C pair C8 [Formula: see text] N7 distance of 1.310 Å increases to 1.453 Å when the π bond is broken upon hydrogen-atom addition. This radical has a dissociation energy of 28 kcal/mol, which may be compared with 27 kcal/mol for neutral G-C. The other (GC + H)(•) radical dissociation energies range downward to 8 kcal/mol. Significant structural changes were observed when the hydrogen was added to the sites where the interstrand hydrogen bonds are formed. For example, "butterfly"-shape structures were found when the hydrogen atom was added to the C4 or C5 sites of guanine. The formation of radical G(C2)-C may cause a single-strand break because of significant strain in the closely stacked base pairs. Radical G(C8)-C is of biological importance because it may be an intermediate in the formation of 8-oxo guanine.

Successive attachment of electrons to protonated Guanine: (G+H)* radicals and (G+H)- anions.

The structures, energetics, and vibrational frequencies of nine hydrogenated 9H-keto-guanine radicals (G+H)(*) and closed-shell anions (G+H)(-) are predicted using the carefully calibrated (Chem. Rev. 2002, 102, 231) B3LYP density functional method in conjunction with a DZP++ basis set. These radical and anionic species come from consecutive electron attachment to the corresponding protonated (G+H)(+) cations in low pH environments. The (G+H)(+) cations are studied using the same level of theory. The proton affinity (PA) of guanine computed in this research (228.1 kcal/mol) is within 0.7 kcal/mol of the latest experiment value. The radicals range over 41 kcal/mol in relative energy, with radical r1, in which H is attached at the C8 site of guanine, having the lowest energy. The lowest energy anion is a2, derived by hydride ion attachment at the C2 site of guanine. No stable N2-site hydride should exist in the gas phase. Structure a9 was predicted to be dissociative in this research. The theoretical adiabatic electron affinities (AEA), vertical electron affinities, and vertical detachment energies were computed, with AEAs ranging from 0.07 to 3.12 eV for the nine radicals.