Vibrational spectroscopy of the G...C base pair: experiment, harmonic and anharmonic calculations, and the nature of the anharmonic couplings

The results of harmonic and anharmonic frequency calculations on a guanine-cytosine complex with an enolic structure (a tautomeric form with cytosine in the enol form and with a hydrogen at the 7-position on guanine) are presented and compared to gas-phase IR-UV double resonance spectral data. Harmonic frequencies were obtained at the RI-MP2/cc-pVDZ, RI-MP2/TZVPP, and semiempirical PM3 levels of electronic structure theory. Anharmonic frequencies were obtained by the CC-VSCF method with improved PM3 potential surfaces; the improved PM3 potential surfaces are obtained from standard PM3 theory by coordinate scaling such that the improved PM3 harmonic frequencies are the same as those computed at the RI-MP2/cc-pVDZ level. Comparison of the data with experimental results indicates that the average absolute percentage deviation for the methods is 2.6% for harmonic RI-MP2/cc-pVDZ (3.0% with the inclusion of a 0.956 scaling factor that compensates for anharmonicity), 2.5% for harmonic RI-MP2/TZVPP (2.9% with a 0.956 anharmonicity factor included), and 2.3% for adapted PM3 CC-VSCF; the empirical scaling factor for the ab initio harmonic calculations improves the stretching frequencies but decreases the accuracy of the other mode frequencies. The agreement with experiment supports the adequacy of the improved PM3 potentials for describing the anharmonic force field of the G...C base pair in the spectroscopically probed region. These results may be useful for the prediction of the pathways of vibrational energy flow upon excitation of this system. The anharmonic calculations indicate that anharmonicity along single mode coordinates can be significant for simple stretching modes. For several other cases, coupling between different vibrational modes provides the main contribution to anharmonicity. Examples of strongly anharmonically coupled modes are the symmetric stretch and group torsion of the hydrogen-bonded NH2 group on guanine, the OH stretch and torsion of the enol group on cytosine, and the NH stretch and NH out-of-plane bend of the non-hydrogen-bonded NH group on guanine.     

Further solvent-free reactions of ferrocenylaldehydes: Synthesis of 1,1′-ferrocenyldiimines and ferrocenylacrylonitriles

Grinding of 1,1′-ferrocenedicarboxaldehyde with a 2.2 molar equivalent of an aromatic amine in a solvent-free environment provided excellent yields of 1,1′-ferrocenyldiimines. After mixing the aldehyde and amines, a gum or melt formed which eventually solidified to the product. An analytically pure sample of the product was obtained by cold recrystallization. Grinding of ferrocenecarboxaldehyde and 4-substituted phenylacetonitriles under solvent-free conditions provided good yields of the corresponding ferrocenylacrylonitriles. The yield in this reaction was very low when the substituent group para to the acetonitrile group was electron-donating.     

Structural basis for recognition of bacterial cell wall teichoic acid by pseudo-symmetric SH3b-like repeats of a viral peptidoglycan hydrolase

Endolysins are bacteriophage-encoded peptidoglycan hydrolases targeting the cell wall of host bacteria via their cell wall-binding domains (CBDs). The molecular basis for selective recognition of surface carbohydrate ligands by CBDs remains elusive. Here, we describe, in atomic detail, the interaction between the Listeria phage endolysin domain CBD500 and its cell wall teichoic acid (WTA) ligands. We show that 3′O-acetylated GlcNAc residues integrated into the WTA polymer chain are the key epitope recognized by a CBD binding cavity located at the interface of tandem copies of beta-barrel, pseudo-symmetric SH3b-like repeats. This cavity consists of multiple aromatic residues making extensive interactions with two GlcNAc acetyl groups via hydrogen bonds and van der Waals contacts, while permitting the docking of the diastereomorphic ligands. Our multidisciplinary approach tackled an extremely challenging protein–glycopolymer complex and delineated a previously unknown recognition mechanism by which a phage endolysin specifically recognizes and targets WTA, suggesting an adaptable model for regulation of endolysin specificity.

Combining genetic, biochemical and computational approaches, we elucidated the molecular mechanisms underlying the recognition of Listeria wall teichoic acid by bacteriophage-encoded SH3b repeats.     

Simplified time-dependent self-consistent field approximation for intramolecular dynamics

The time-dependent Hartree approximation is applied to intramolecular dynamics of polyatomics with smooth, locally quadratic potential surfaces. It is shown that the full quantum solution is obtained from a certain single self-consistent trajectory. An extremely simple model results, pertinent to intramolecular energy transfer, vibrational lineshapes and unimolecular decay.     

Chains of reinsurance

A one-dimensional, hierarchical system of reinsurance is considered. A member of the chain is in direct contact with only two other members: the one from which coverage is bought and the one to which coverage is sold. Exceptions are the first link (which does not sell any reinsurance coverage) and the last link (which does not buy any). The problem is to find the values of the quotas and the loadings that are optimal in some sense. Assuming exponential utility functions and a normal distribution for the claims, an explicit solution is found for two versions of the model.     

Dissociation dynamics of Ar3 in the time-dependent self-consistent field (TDSCF) approximation

The TDSCF approximation is applied to dissociation of Ar₃, which exhibits strong-coupling behavior (efficient internal energy transfer). The TDSCF results are in excellent agreement with those of exact classical dynamics. Combined with earlier findings for weak-coupling cases, this suggests validity of TDSCF for dissociation at all coupling strengths.     

On the numerical evaluation of the distribution of aggregate claims and its stop-loss premiums

The paper develops a method for the numerical evaluation of the distribution of aggregate claims and its stop-loss premiums.     

Characterization of rodlike aggregates generated from a cationic surfactant and a polymerizable counterion

The polymerization of elongated micellar structures offers a novel approach to the production of high-aspect-ratio, water-soluble amphiphilic nanorods. A cationic surfactant with a vinyl-containing counterion, cetyltrimethylammonium 4-vinylbenzoate, has been synthesized and polymerized to produce high-aspect-ratio nanoparticles which are insensitive to changes in solution conditions. Aggregates are polymerized over a range of initiator concentrations allowing for control of the product length. Small-angle neutron scattering and light scattering are used to characterize the dimensions of the polymerized aggregates, showing them to have a fixed radius of 2 nm and contour lengths varying from 96 to 340 nm. Proton NMR verifies the chemical structure and provides insight into the mobility of the aggregate components. Finally, gel permeation chromatography of the polymer extracted from the aggregates indicates that the polymerization reaction controls the aggregate dimensions.     

Robust Algorithms for the Stable Set Problem

The stable set problem is to find in a simple graph a maximum subset of pairwise non-adjacent vertices. The problem is known to be NP-hard in general and can be solved in polynomial time on some special classes, like cographs or claw-free graphs. Usually, efficient algorithms assume membership of a given graph in a special class. Robust algorithms apply to any graph G and either solve the problem for G or find in it special forbidden configurations. In the present paper we describe several efficient robust algorithms, extending some known results.