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A series of sodium and magnesium complexes with α-diimine ligands, [Na2(LiPr)(Et2O)]2 (1, LiPr = [(2,6-iPr2C6H3)N(Me)C]2), [Na2(LMes)(solv)2]2 (LMes = [(2,4,6-Me3C6H3)N(Me)C]2, 2a, solv = Et2O; 2b, solv = THF), [Na4(LEt)2]n (3, LEt = [(2,6-Et2C6H3)N(Me)C]2), and [Mg(LMes)(THF)3] (4), have been synthesized by reduction of the diimine ligands with sodium or magnesium metal. Single-crystal X-ray diffraction analysis revealed that the sodium complexes have a 2:1 [Na2L] unit that aggregates to dimeric (1, 2a, 2b) or polymeric (3) structures, while the magnesium complex (4) shows a monomeric 1:1 structure. In all compounds 1−4, the ligand is doubly reduced to a dianion. The two Na+ ions in 1, 2a, 2b, and 3 show different coordination modes, one of which is chelated by the N donors of a ligand with supplementary Na−C bonds to the phenyl ring of another ligand within the [Na2L]2 dimer, while the other is bonded by the central C2N2 core of the ligand and solvent molecules (1, 2a, and 2b). Compound 3 displays a nov...

The heterometallic binuclear cyclopentadienylironnickel carbonyl compounds Cp2FeNi(CO)n (n =3 , 2, 1; Cp =η 5 -C5H5) have been studied by density functional theory (BP86) for comparison with the isoelectronic homometallic dicobalt derivatives Cp2Co2(CO)n. The FeNi tricarbonyl is shown to be the doubly bridged isomer Cp2Fe(CO)Ni(µ-CO)2 with an Fe– Ni distance of 2.455 A (BP86), in accord with experiment and in contrast to Cp2Co2(CO)3 where singly and triply bridged but not doubly bridged isomers are found. The dicarbonyl compounds Cp2FeNi(µ-CO)2 and Cp2Co2(µ-CO)2 both have analogous doubly bridged structures with M=M distances around 2.35 A, suggesting formal M=M double bonds. The monocarbonyl compounds have analogous singly bridged axial structures Cp2FeNi(µ-CO) and Cp2Co2(µ-CO) with

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.

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.

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.

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.