First-order model potential for optical dipole transitions: Application to the lithium isoelectronic sequence

We have constructed two first-order model potentials which were designed to yield dipole transition moments, and have applied them to the lithium isoelectronic sequence. The models contain two or three adjustable parameters, chosen so as to reproduce selected transition moment data on a single ion of the sequence. With negligible computational effort, they both yield other transition moments of high accuracy.     

Erratum to “The primes contain arbitrarily long polynomial progressions”

In our previous paper “The primes contain arbitrarily long polynomial progressions” [Acta Math., 201 (2008), 213–305] there were some minor errors in our definition of the polynomial forms and polynomial correlation conditions, which is unreasonably strong as written due to the overly loose bound on the degree of the polynomials involved. In this erratum we repair this issue by capping the degree of the polynomials more strongly, and adjusting some other relevant components of the argument accordingly.     

Water perturbed by cellophane: comparison of its physicochemical properties with those of water perturbed with cotton wool or Nafion

We present experimental data on water repetitively brought in contact with cellophane. Although this hydrophilic polymer is insoluble in water, repetitively immersing it in water changes the liquid’s properties. We compare the physicochemical properties of the water left over after removing the cellophane to those of previously published data on water repetitively brought in contact with other in water insoluble polymers (cotton wool or Nafion). Some of the properties are similar. All the properties considerably differ from those of the Milli-Q^® water used. On lyophilizing these waters, solid residues remain. The residues are soluble in water. The chemical nature of the residues differs from that of the perturbing polymers.

     

Receiver-amplifier, self-immolative dendritic device

Self-immolative dendrimers disassemble through a domino-like chain fragmentation initiated by a single cleavage at the dendrimer core. We have designed and synthesized dendritic molecules that resemble dendritic architectures present in nature. The unique design allows a cleavage signal received by any one of the multiple triggers on one side of the dendrimer to be transferred convergently to a focal point. The signal is divergently amplified through to the other side of the dendrimer, reporter units are released, and fluorescence is emitted. During signal propagation, the dendritic molecule disassembles in a self-immolative manner into small fragments. These compounds are the longest dendritic system ever reported to disassemble through sequential self-immolative reactions. The synthesized dendritic molecules have an architecture and signal-conducting activity related to that of neurons.     

DNA polymerase beta catalysis: are different mechanisms possible?

DNA polymerases are crucial constituents of the complex cellular machinery for replicating and repairing DNA. Discerning mechanistic pathways of DNA polymerase on the atomic level is important for revealing the origin of fidelity discrimination. Mammalian DNA polymerase beta (pol beta), a small (39 kDa) member of the X-family, represents an excellent model system to investigate polymerase mechanisms. Here, we explore several feasible low-energy pathways of the nucleotide transfer reaction of pol beta for correct (according to Watson-Crick hydrogen bonding) G:C basepairing versus the incorrect G:G case within a consistent theoretical framework. We use mixed quantum mechanics/molecular mechanics (QM/MM) techniques in a constrained energy minimization protocol to effectively model not only the reactive core but also the influence of the rest of the enzymatic environment and explicit solvent on the reaction. The postulated pathways involve initial proton abstraction from the terminal DNA primer O3'H group, nucleophilic attack that extends the DNA primer chain, and elimination of pyrophosphate. In particular, we analyze several possible routes for the initial deprotonation step: (i) direct transfer to a phosphate oxygen O(Palpha) of the incoming nucleotide, (ii) direct transfer to an active site Asp group, and (iii) transfer to explicit water molecules. We find that the most probable initial step corresponds to step (iii), involving initial deprotonation to water, which is followed by proton migration to active site Asp residues, and finally to the leaving pyrophosphate group, with an activation energy of about 15 kcal/mol. We argue that initial deprotonation steps (i) and (ii) are less likely as they are at least 7 and 11 kcal/mol, respectively, higher in energy. Overall, the rate-determining step for both the correct and the incorrect nucleotide cases is the initial deprotonation in concert with nucleophilic attack at the phosphate center; however, the activation energy we obtain for the mismatched G:G case is 5 kcal/mol higher than that of the matched G:C complex, due to active site structural distortions. Taken together, our results support other reported mechanisms and help define a framework for interpreting nucleotide specificity differences across polymerase families, in terms of the concept of active site preorganization or the so-called "pre-chemistry avenue".     

Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo

We develop an "end-transfer configurational bias Monte Carlo" method for efficient thermodynamic sampling of complex biopolymers and assess its performance on a mesoscale model of chromatin (oligonucleosome) at different salt conditions compared to other Monte Carlo moves. Our method extends traditional configurational bias by deleting a repeating motif (monomer) from one end of the biopolymer and regrowing it at the opposite end using the standard Rosenbluth scheme. The method's sampling efficiency compared to local moves, pivot rotations, and standard configurational bias is assessed by parameters relating to translational, rotational, and internal degrees of freedom of the oligonucleosome. Our results show that the end-transfer method is superior in sampling every degree of freedom of the oligonucleosomes over other methods at high salt concentrations (weak electrostatics) but worse than the pivot rotations in terms of sampling internal and rotational sampling at low-to-moderate salt concentrations (strong electrostatics). Under all conditions investigated, however, the end-transfer method is several orders of magnitude more efficient than the standard configurational bias approach. This is because the characteristic sampling time of the innermost oligonucleosome motif scales quadratically with the length of the oligonucleosomes for the end-transfer method while it scales exponentially for the traditional configurational-bias method. Thus, the method we propose can significantly improve performance for global biomolecular applications, especially in condensed systems with weak nonbonded interactions and may be combined with local enhancements to improve local sampling.     

Mechanism of reaction of alkyl radicals with (Ni(II)L)2+ complexes in aqueous solutions

The reactions of methyl radicals, CH(3), with the macrocyclic complexes Ni(II)L(1-5) (L(1-5) = cyclam derivatives, vide infra) and Ni(II)edta in aqueous solutions were studied. Methyl radicals react with all these nickel complexes, forming intermediates with Ni(III)-C sigma-bonds. The L(m)Ni(III)-CH(3) complexes are formed in equilibria processes with relatively fast forward rate constants of k(f) > 1 x 10(8) M(-1) s(-1) (except in the case of NiL(2)-trans I cyclam, where the reaction is slower). In all cases the decomposition of the transient complexes occurs via the homolytic cleavage of the metal-carbon sigma-bond. When the homolysis is relatively slow, an isomerisation process of the transient is also observed with the exception of NiL(2), where no isomerisation was observed. The results suggest that the strength of the Ni(III)-CH(3)sigma-bond is mainly affected by steric hindrance.     

Formation of amphiphile self-assembly phases in protic ionic liquids

A range of protic ionic liquids (PILs) have been identified as being capable of supporting the self-assembly of the nonionic surfactants myverol 18-99 K (predominantly monoolein) and phytantriol. PIL-surfactant penetration scans have provided a high throughput technique to determine which lyotropic liquid crystalline phases were formed in the 40 PIL-surfactant systems investigated. Lamellar, inverse hexagonal, and bicontinuous cubic phases that are stable in excess PIL have been observed in surfactant-PIL systems. The studied PILs possess a wide range of solvent properties, including surface tension and viscosity. The nature of the formed amphiphile self-assembly phases is discussed in terms of the PIL structure and solvent properties.     

Effect of protic ionic liquids (PILs) on the formation of non-ionic dodecyl poly(ethylene oxide) surfactant self-assembly structures and the effect of these surfactants on the nanostructure of PILs

The ability of a series of non-ionic dodecyl poly(ethylene oxide) surfactants to form micelles in a variety of protic ionic liquids (PILs) was investigated using small and wide angle X-ray scattering (SAXS/WAXS). The C(12)E(n) surfactants with n = 3-8 were examined in PILs which contained either an ethyl, diethyl, triethyl, butyl, pentyl, ethanol or pentanol-ammonium cation in conjunction with either a nitrate or formate anion. The ability of the PILs to support micelles of these surfactants was highly dependent on their liquid nanostructure. The PILs containing hydroxyl groups on the cations were not nanostructured and had very low surfactant solubility (<1 wt%). The highly nanostructured PILs with butylammonium or pentylammonium cations contain large non-polar domains, and had excellent surfactant solubility, but due to the greater hydrocarbon solubility they had insufficient drive from the "solvophobic effect" to enable micelle formation. The PILs of ethylammonium nitrate (EAN), propylammonium nitrate (PAN), diethylammonium formate (DEAF) and triethylammonium formate (TEAF) had smaller non-polar domains, and all supported micelle formation below 20 wt% surfactant. The critical micelle concentration (CMC) of surfactants in EAN were two orders of magnitude greater than in water. The minimum molecular areas of the poly(ethylene oxide) head groups at the air/ionic liquid interface, A(min), were significantly larger in EAN than in water. The SAXS patterns from the micelles present in EAN fitted well to ellipsoids, whereas the micelles present in PAN fitted well to spheres. The nanostructure of select PILs was also influenced by the presence of surfactants.     

Incomplete Relative Semi-Abelian Categories

We propose relative (to a distinguished class E of epimorphisms) versions of the so-called old and new style axioms for semi-abelian categories, and prove the equivalence of these two sets of axioms. The same results were obtained before under much stronger completeness/cocompleteness assumptions. One of obvious purposes of such a generalization is to include the trivial case of E being the class of all isomorphisms when the ground category is an arbitrary pointed category.