Nuclear-spin relaxation in nonrigid molecules: discrete multisite local dynamics combined with anisotropic molecular reorientation

Nuclear-spin relaxation is considered in a molecular system undergoing two types of dynamic processes: asymmetric-top small-step rotational diffusion and discrete multisite local jumps. The two processes are assumed to be uncorrelated. Time correlation functions for relevant rank-two interactions and corresponding spectral density functions are derived for a general relation between the characteristic rate constants. In addition, limiting cases of fast and slow local motions and of some specific jump conditions are also investigated.     

Spin-phonon coupling induced frustration in the exactly solved spin-1/2 Ising model on a decorated planar lattice

Spin-1/2 Ising model with a spin-phonon coupling on decorated planar lattices partially amenable to lattice vibrations is examined using the decoration-iteration transformation and harmonic approximation. It is shown that the magnetoelastic coupling gives rise to an effective antiferromagnetic next-nearest-neighbour interaction, which competes with the nearest-neighbour interaction and is responsible for a frustration of decorating spins. A strong enough spin-phonon coupling consequently leads to an appearance of striking partially ordered and partially disordered phase, where a perfect antiferromagnetic alignment of nodal spins is accompanied with a complete disorder of decorating spins. Thermal dependences of the specific heat are explored in detail.     

On the Finite Spectral Triple of an Almost-Commutative Geometry

In this short communication, we examine the relevance of the signature of the space-time metric in the construction of the product of a pseudo-Riemannian spectral triple with a finite triple describing the internal geometry. We obtain arguments favoring the appearance of SU(2) and U(1) as gage groups in the standard model.     

Asymmetric bioreduction of activated carbon–carbon double bonds using Shewanella yellow enzyme (SYE-4) as novel enoate reductase

Shewanella yellow enzyme (SYE-4), a novel recombinant enoate reductase, was screened against a variety of different substrates bearing an activated double bond, such as unsaturated cyclic ketones, diesters, and substituted imides. Dimethyl- and ethyl esters of 2-methylmaleic acid were selectively reduced to (R)-configured succinic acid derivatives and various N-substituted maleimides furnished the desired (R)-products in up to >99% enantiomeric excess. Naturally occurring (+)-carvone was selectively reduced to (?)-cis-dihydrocarvone and (?)-carvone was converted to the diastereomeric product, respectively. Overall SYE-4 proved to be a useful biocatalyst for the selective reduction of activated CC double bonds and complements the pool of synthetic valuable enoate reductases.     

The Gould-Jacobs Reaction of5-Aminoquinoxaline

 Reaction of 5-aminoquinoxaline with alkoxymethylene derivatives affords the corresponding quinoxalinoaminoethylenes. These undergo a thermal cyclization to yield angularly annelated 10H-pyrido[2,3-f]quinoxalines. The structures of all products were deduced from their IR, UV, mass, ¹H, and ¹³C NMR spectra.     

Large configuration interaction calculations of nuclear spin-spin coupling constants: III. Vibrational effects in ammonia

Large configuration interaction calculations of the proton—proton coupling constant for several geometrical configurations of the ammonia molecules are reported. The analytical expressions for the energy surface and the coupling constant as functions of two cartesian displacement coordinates are fitted to the calculated values. The potential is used for the calculation of the vibrational wavefunctions for ¹⁵NH₃ and ¹⁵ND₃ species and the vibrational averaging of the coupling constant is carried out using these functions. Though the value of the coupling constants shows a very strong geometry dependence, the vibrational corrections are found to be small. A possible correlation of the proton—proton coupling constant with an angular parameter in the NH₂ group in RNH₂ compounds is indicated.     

Hamiltonian replica exchange molecular dynamics using soft-core interactions

To overcome the problem of insufficient conformational sampling within biomolecular simulations, we have developed a novel Hamiltonian replica exchange molecular dynamics (H-REMD) scheme that uses soft-core interactions between those parts of the system that contribute most to high energy barriers. The advantage of this approach over other H-REMD schemes is the possibility to use a relatively small number of replicas with locally larger differences between the individual Hamiltonians. Because soft-core potentials are almost the same as regular ones at longer distances, most of the interactions between atoms of perturbed parts will only be slightly changed. Rather, the strong repulsion between atoms that are close in space, which in many cases results in high energy barriers, is weakened within higher replicas of our proposed scheme. In addition to the soft-core interactions, we proposed to include multiple replicas using the same Hamiltonian/level of softness. We have tested the new protocol on the GTP and 8-Br-GTP molecules, which are known to have high energy barriers between the anti and syn conformation of the base with respect to the sugar moiety. During two 25 ns MD simulations of both systems the transition from the more stable to the less stable (but still experimentally observed) conformation is not seen at all. Also temperature REMD over 50 replicas for 1 ns did not show any transition at room temperature. On the other hand, more than 20 of such transitions are observed in H-REMD using six replicas (at three different Hamiltonians) during 6.8 ns per replica for GTP and 12 replicas (at six different Hamiltonians) during 8.7 ns per replica for 8-Br-GTP. The large increase in sampling efficiency was obtained from an optimized H-REMD scheme involving soft-core potentials, with multiple simulations using the same level of softness. The optimization of the scheme was performed by fast mimicking [J. Hritz and C. Oostenbrink, J. Chem. Phys. 127, 204104 (2007)].     

Characterization of oxidation progress by chemiluminescence: A study of polyethylene with pro-oxidant additives

Non-isothermal chemiluminescence measurements in nitrogen and isothermal measurements in oxygen were used for the evaluation of degradation in pre-oxidized polyethylene either pure or containing Mn-based pro-oxidant additives. The results were compared with infrared spectroscopy data. Chemiluminescence measurements of pure polyethylene and polyethylene with additive made it possible to calculate the set of rate constants, based on the Bolland-Gee oxidation scheme. The oxidation rate constants of polyethylene with additive were significantly higher, while the activation energy of the process appeared lower (65 kJ mol⁻¹), than those of pure polyethylene. The method provides an access to study oxidation processes during the induction period of oxidation when infrared spectroscopy cannot provide sufficient information.     

MALDI-TOF/TOF de novo sequence analysis of 2-D PAGE-separated proteins from Halorhodospira halophila, a bacterium with unsequenced genome

Because protein identifications rely on matches with sequence databases, high-throughput proteomics is currently largely restricted to those species for which comprehensive sequence databases are available. The identification of proteins derived from organisms with unsequenced genomes mainly depends on homology searching. Here, we report the use of a simplified, gel-based, chemical derivatization strategy for de novo sequence analysis using a MALDI-TOF/TOF mass spectrometer. This approach allows the determination of de novo peptide sequences of up to 20 amino acid residues in length. The protocol was applied on a proteomic study of 2-D PAGE-separated proteins from Halorhodospira halophila, an extremophilic eubacterium with yet unsequenced genome. Using three different homology-based search algorithms, we were able to identify more than 30 proteins from this organism using subpicomole quantities of protein.