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Ab initio molecular orbital theory (Moller-Plesset theory to full fourth order and a series of extended basis sets) is used to compute total atomization energies for the complete series of AH/sub n/ hydrides (A = Li to Cl). These data are used in combination with generally accepted experimental data on isolated atoms to predict ideal gas heats of formation at 298.15 K for these molecules. Comparisons with high-quality experimental data indicates that, for hydrides, this level of theory has an error level of about +/-2 kcal mol/sup -1/. For several of these hydrides, there are no experimentally determined heats of formation. The authors predict ..delta..H/sub f//sup 0//sub 298/ values (in kcal mol/sup -1/) for BeH/sub 2/ (39.5), MgH/sub 2/ (38.6), AlH/sub 2/ (64.0), PH (59.2), and PH/sub 2/ (34.8). The authors computed heats of formation call into question the experimental heats of formation of BH/sub 2/ and SiH/sub 2/. 23 references, 4 tables.

The low-lying singlet and triplet states of H 2 CBe and HCBeH are examined using ab inito molecular orbital theory. In agreement with earlier results, the lowest-lying structure of H 2 CBe has C 2v symmetry and is a triplet with one π electron ( 3 B 1 ). The results presented here suggest that the lowest-energy singlet structure is the ( 1 B 1 ) open-shell singlet, also with C 2v symmetry, at least 2.5 kcal/mol higher in energy. The singlet C 2v structure with two π electrons ( 1 A 1 ) is 15.9 kcal/mol higher than 3 B 1 . All of these structures are bound with respect to the ground state of methylene and the beryllium atom. In HCBeH, linear equilibrium geometries are found for the triplet ( 3 Σ) and singlet ( 1 Δ) states. The triplet is more stable than the singlet ( 1 Δ) by 35.4 kcal/mol, and is only 2.9 kcal/mol higher in energy than triplet H 2 CBe. Since the transition structure connecting these two triplet molecules is found to be 50.2 kcal/mol higher in energy than H 2 CBe, both triplet equilibrium species might exist independently. The harmonic vibrational frequencies of all structures are also reported.

The potential energy surface of the singlet carbenoid CH 2 FLi has been examined using ab initio methods including electron correlation and zero-point energy corrections. The three non-tetrahedral structures found earlier are confirmed to be minima, but only the lowest energy structure 1 should be experimentally observable. Two other local minima, 2 and 3 , should rearrange to 1 with minimal activation. On the other hand, 1 should be quite rigid configurationally. This structure is predicted to be stable with respect to separated singlet methylene and lithium fluoride monomer by 49.3 kcal/mol, though the reaction of two molecules of 1 to form ethylene and two lithium fluoride monomers is exothermic by 98 kcal/mol.

Activation of amino acids appears to have played a crucial role in prebiotic peptide bond formation. As a model of this process in living systems, phosphates have been used as amino acid activators. The possible role of clay and other minerals has also been investigated. We are presently using ab initio methods to investigate the activation of amino acids by these agents, as an initial step in peptide bond formation. A model of this activation process is described by the reaction: ZCH2COOH + XO4Hn+1 --> ZCH2COOXO3Hn + H2O. The first step in such an investigation, reported here, was to determine the lowest energy structures of a suitable set of reactions. As initial models of amino acids, Z was chosen to be H and NH2, corresponding to acetic acid and glycine, respectively, XO4Hn+1 = H3PO4 represents a phosphate group, while Si(OH)4 describes an edge tetrahedral site of a clay mineral. Al(OH)4- was also included to represent tetrahedral edge site where the silicon is replaced by an aluminum. Finally, to complete the series XO4Hn+1, H2SO4 was added to the set of reactants. All species were optimized using the STO-3G and STO-3G* basis sets. For H3PO4 and Al(OH)4-, STO-3G* full optimizations were not possible. In these cases, certain torsional angles were optimized separately, then held at the optimized value, while the rest of the bond lengths and angles were optimized. All structures were compared to other calculations and to experimental geometries when available.

The NCI Retrovirus Integration Database is a MySql-based relational database created for storing and retrieving comprehensive information about retroviral integration sites, primarily, but not exclusively, HIV-1. The database is accessible to the public for submission or extraction of data originating from experiments aimed at collecting information related to retroviral integration sites including: the site of integration into the host genome, the virus family and subtype, the origin of the sample, gene exons/introns associated with integration, and proviral orientation. Information about the references from which the data were collected is also stored in the database. Tools are built into the website that can be used to map the integration sites to UCSC genome browser, to plot the integration site patterns on a chromosome, and to display provirus LTRs in their inserted genome sequence. The website is robust, user friendly, and allows users to query the database and analyze the data dynamically. Availability: https://rid.ncifcrf.gov; or http://home.ncifcrf.gov/hivdrp/resources.htm.

DNA sequence motifs with the ability to form non-B (non-canonical) structures have been linked to a variety of regulatory and pathological processes. Although the exact mechanism is unknown, recent work has provided significant evidence that non-B DNA structures may play a role in DNA instability and mutagenesis, leading to both DNA rearrangements and increased mutational rates, which are hallmarks of cancer. We have developed algorithms to identify a wide variety of non-B-DNA-forming motifs, including G-quadruplex-forming repeats, direct repeats and slipped motifs, inverted repeats and cruciform motifs, mirror repeats and triplex motifs, and A-phased repeats. After identifying these motifs in the mammalian reference genomes of human, mouse, chimpanzee, macaque, cow, dog, rat and platypus, the data were made publicly available in non-B DB [1]. However, it soon became apparent that it was not feasible to annotate the ever-growing list of genomic data and that it would be more effective to provide researchers with a systematic tool to predict these motifs in their own genomic data. Thus, the non-B DNA Motif Search Tool (nBMST) was created, and it is freely available online [2]. nBMST is a web interface that enables researchers to interactively submit any DNA sequence for searching for non-B DNA motifs. Once a user submits one or more DNA sequences in FASTA format, nBMST returns a comprehensive results page that contains the following: downloadable files in both a tab-delimited format and a generic feature format (GFF); a visualization, including PNG images; and a dynamic genome browser created using the Generic Genome Browser (GBrowse) [3] (version 2.0). Currently, nBMST allows file sizes of up to 20 MB of DNA sequence to be uploaded and stores the results for registered users for up to six months. In summary, the purpose of nBMST is to help provide insight into the involvement of alternative DNA conformations in cancer and other diseases, as well as into other potential biological functions.