Computational models for proton transfer in biological systems

A computational scheme based on a “mixed basis set” approach is applied to the study of the structure and the energetics in proton transfer systems. Five hydrogen-bonded systems of the type (CH₃H_nA ‥ H ‥ BH_mCH₃)⁺, where A and B can be N, O, or S, have been investigated with various minimal and extended basis sets. Calculations with the extended basis set yield double-well potential energy curves, which the minimal basis set is unable to reproduce. Calculations with the mixed basis set, constructed from an extended basis set on the atoms engaged in the hydrogen transfer part and a minimal basis set on the rest of the molecule, give predictions of geometries, potential energy curves, and relative energies similar to the results from the extended basis set. Inclusion of polarization functions in the mixed basis set becomes essential in systems that contain third row atoms. This scheme should become useful in studies of large molecules in which different parts can be represented at different levels of computational complexity.     

Synthesis of functionalized vinylgermanes through a new ruthenium-catalyzed coupling reaction

Vinyl-substituted germanes react stereo- and regioselectively with olefins in the presence of complexes containing Ru-H and Ru-Ge bonds with the formation of functionalized vinylgermanes that cannot be synthesized by olefin cross-metathesis procedures. The reaction opens a new catalytic route for preparation of a class of organogermanes that are potent organometallic reagents for organic synthesis because they show very low toxicity and could replace organotin compounds. The mechanism of this new catalytic route was proven to involve an interesting insertion of the vinylgermane into the Ru-H bond and beta-Ge transfer to the metal with elimination of ethylene and generation of an Ru-Ge bond, followed by insertion of the alkene into the Ru-Ge bond and beta-H transfer to the metal to eliminate the substituted vinylgermane.     

Theoretical calculations of homoconjugation equilibrium constants in systems modeling acid-base interactions in side chains of biomolecules using the potential of mean force

The potentials of mean force (PMFs) were determined for systems forming cationic and anionic homocomplexes composed of acetic acid, phenol, isopropylamine, n-butylamine, imidazole, and 4(5)-methylimidazole, and their conjugated bases or acids, respectively, in three solvents with different polarity and hydrogen-bonding propensity: acetonitrile (AN), dimethyl sulfoxide (DMSO), and water (H(2)O). For each pair and each solvent a series of umbrella-sampling molecular dynamics simulations with the AMBER force field, explicit solvent, and counterions added to maintain a zero net charge of a system were carried out and the PMF was calculated by using the Weighted Histogram Analysis Method (WHAM). Subsequently, homoconjugation-equilibrium constants were calculated by numerical integration of the respective PMF profiles. In all cases but imidazole stable homocomplexes were found to form in solution, which was manifested as the presence of contact minima corresponding to hydrogen-bonded species in the PMF curves. The calculated homoconjugation constants were found to be greater for complexes with the OHO bridge (acetic acid and phenol) than with the NHN bridge and they were found to decrease with increasing polarity and hydrogen-bonding propensity of the solvent (i.e., in the series AN > DMSO > H(2)O), both facts being in agreement with the available experimental data. It was also found that interactions with counterions are manifested as the broadening of the contact minimum or appearance of additional minima in the PMF profiles of the acetic acid-acetate, phenol/phenolate system in acetonitrile, and the 4(5)-methylimidazole/4(5)-methylimidzole cation conjugated base system in dimethyl sulfoxide.     

Protonated serine octamer cluster: structure elucidation by gas-phase H/D exchange reactions

The H/D exchange kinetics of the protonated serine octamer was investigated by both flow-tube and FT-ICR experiments. The exchange was observed to be bimodal in agreement with previous observations. Quantitative analysis of the experimental results led to site-specific H/D exchange rate constants on the basis of which the structures of both ion populations were deduced. We observe the two separate conformers exchanging 33 hydrogens each-in an independent manner and at different rates. This result was achieved through a probabilistic algorithm that groups together equivalent hydrogen atoms having equal rate constants. The slower exchanging population A is assigned an all-zwitterionic structure. Its faster exchanging counterpart B is assigned an all-neutral structure. Population A was found to be more stable toward collision-induced activation than population B. All of these findings are consistent with previous experimental results, thus comprising a self-consistent picture of the protonated serine octamer and its gas-phase properties.     

Supramolecular synthons based on N-H...N and C-H...O hydrogen bonds. Crystal engineering of a helical structure with 5,5-diethylbarbituric acid

5,5-Diethylbarbituric acid is a convenient molecular precursor for a newly identified N-H...N/C-H...O synthon, which is robust enough for the design of a helix architecture.     

Decompositions of a complete multidigraph into nonhamiltonian paths

For n ≥ 3, the complete n‐vertex multidigraph with any fixed multiplicity of edges is proved to be decomposable into nonhamiltonian (directed) paths of arbitrarily prescribed lengths (≤ n ? 2) provided that the lengths sum up to the size of the multidigraph. © 2005 Wiley Periodicals, Inc. J Graph Theory     

Isolation of isomers based on hydrogen/deuterium exchange in the gas phase

A method to isolate isomers in a Fourier transform ion cyclotron resonance mass spectrometer on the basis of their different hydrogen/deuterium exchange rates has been developed and applied to the protonated serine octamer cluster. Isolation allows interrogation of each isomer by infrared multi-photon dissociation to determine any differences in the building blocks that form these clusters. The experimental results strongly support previous assignments of an all-zwitterion structure to the slower-exchanging isomer and an all-neutral structure to its faster- exchanging counterpart.