Left-right noncommutative Poisson algebras

The notions of left-right noncommutative Poisson algebra (NP^lr-algebra) and left-right algebra with bracket AWB^lr are introduced. These algebras are special cases of NLP-algebras and algebras with bracket AWB, respectively, studied earlier. An NP^lr-algebra is a noncommutative analogue of the classical Poisson algebra. Properties of these new algebras are studied. In the categories AWB^lr and NP^lr-algebras the notions of actions, representations, centers, actors and crossed modules are described as special cases of the corresponding wellknown notions in categories of groups with operations. The cohomologies of NP^lr-algebras and AWB^lr (resp. of NP^r-algebras and AWB^r) are defined and the relations between them and the Hochschild, Quillen and Leibniz cohomologies are detected. The cases P is a free AWB^r, the Hochschild or/and Leibniz cohomological dimension of P is ≤ n are considered separately, exhibiting interesting possibilities of representations of the new cohomologies by the well-known ones and relations between the corresponding cohomological dimensions.     

Ball-and-socket stacking of supercharged geodesic polyarenes: bonding by interstitial lithium ions

Unprecedented supramolecular stacks of highly reduced geodesic pi-systems were prepared by the reduction of the derivatized fullerenes Me(5)C(60)H and Ph(5)C(60)H and corannulene with lithium metal (R(5)C(60)(5)(-)/Cor(4)(-)/9Li(+)). The host--guest assemblies form because of the enhanced electrostatic interactions between the lithium cations and the anionic moieties, in addition to the structural compatibility between the curved hydrocarbons. The high stability of these new supramolecular assemblies (heterodimers) enables the introduction of another organization motif to the system. This is achieved by using tethered corannulenes as host molecules, which leads to the formation of tethered bis-heterodimers ((Me(5)C(60)(5)(-)/Cor(4)(-))(2)(CH(2))(8)/18Li(+)).     

Fidelity discrimination in DNA polymerase beta: differing closing profiles for a mismatched (G:A) versus matched (G:C) base pair

Understanding fidelity-the faithful replication or repair of DNA by polymerases-requires tracking of the structural and energetic changes involved, including the elusive transient intermediates, for nucleotide incorporation at the template/primer DNA junction. We report, using path sampling simulations and a reaction network model, strikingly different transition states in DNA polymerase beta's conformational closing for correct dCTP versus incorrect dATP incoming nucleotide opposite a template G. The cascade of transition states leads to differing active-site assembly processes toward the "two-metal-ion catalysis" geometry. We demonstrate that these context-specific pathways imply different selection processes: while active-site assembly occurs more rapidly with the correct nucleotide and leads to primer extension, the enzyme remains open longer, has a more transient closed state, and forms product more slowly when an incorrect nucleotide is present. Our results also suggest that the rate-limiting step in pol beta's conformational closing is not identical to that for overall nucleotide insertion and that the rate-limiting step in the overall nucleotide incorporation process for matched as well as mismatched systems occurs after the closing conformational change.     

Current-induced rotation of helical molecular wires

We show that electric current running through a nanojunction with a biased helical molecule can induce unidirectional rotation of the molecular component. In an electric field, conduction electrons injected into the molecule are accelerated along the helical path going through its body, thereby gaining directed angular momentum. Conservation laws require that an angular momentum of the same size but opposite sense is imparted to the rigid-body rotation of the helix. We describe the angular momentum exchange processes that underlie the operation of the nanorotor, discuss factors limiting its efficiency, and propose potential applications.     

Conformational transition pathway of polymerase beta/DNA upon binding correct incoming substrate

The closing conformational transition of wild-type polymerase beta bound to DNA template/primer before the chemical step (nucleotidyl transfer reaction) is simulated using the stochastic difference equation (in length version, "SDEL") algorithm that approximates long-time dynamics. The order of the events and the intermediate states during pol beta's closing pathway are identified and compared to a separate study of pol beta using transition path sampling (TPS) (Radhakrishnan, R.; Schlick, T. Proc. Natl. Acad. Sci. USA 2004, 101, 5970-5975). Results highlight the cooperative and subtle conformational changes in the pol beta active site upon binding the correct substrate that may help explain DNA replication and repair fidelity. These changes involve key residues that differentiate the open from the closed conformation (Asp192, Arg258, Phe272), as well as residues contacting the DNA template/primer strand near the active site (Tyr271, Arg283, Thr292, Tyr296) and residues contacting the beta and gamma phosphates of the incoming nucleotide (Ser180, Arg183, Gly189). This study compliments experimental observations by providing detailed atomistic views of the intermediates along the polymerase closing pathway and by suggesting additional key residues that regulate events prior to or during the chemical reaction. We also show general agreement between two sampling methods (the stochastic difference equation and transition path sampling) and identify methodological challenges involved in the former method relevant to large-scale biomolecular applications. Specifically, SDEL is very quick relative to TPS for obtaining an approximate path of medium resolution and providing qualitative information on the sequence of events; however, associated free energies are likely very costly to obtain because this will require both successful further refinement of the path segments close to the bottlenecks and large computational time.     

Ionic liquids as amphiphile self-assembly media

In recent years, the number of non-aqueous solvents which mediate hydrocarbon-solvent interactions and promote the self-assembly of amphiphiles has been markedly increased by the reporting of over 30 ionic liquids which possess this previously unusual solvent characteristic. This new situation allows a different exploration of the molecular "solvophobic effect" and tests the current understanding of amphiphile self-assembly. Interestingly, both protic and aprotic ionic liquids support amphiphile self-assembly, indicating that it is not required for the solvents to be able to form a hydrogen bonded network. Here, the use of ionic liquids as amphiphile self-assembly media is reviewed, including micelle and liquid crystalline mesophase formation, their use as a solvent phase in microemulsions and emulsions, and the emerging field of nanostructured inorganic materials synthesis. Surfactants, lipids and block co-polymers are the focus amphiphile classes in this critical review (174 references).     

Intense laser alignment in dissipative media as a route to solvent dynamics

We extend the concept of alignment by short intense pulses to dissipative environments within a density matrix formalism and illustrate the application of this method as a probe of the dissipative properties of dense media. In particular, we propose a means of disentangling rotational population relaxation from decoherence effects via strong laser alignment. We illustrate also the possibility of suppressing rotational relaxation to prolong the alignment lifetime through choice of the field parameters. Implications to several disciplines and a number of potential applications are proposed.     

Encoding and Processing of Alphanumeric Information by Chemical Mixtures

A novel infochemical device that is based on ¹H NMR readout of chemical information is presented. This chemical encoding system utilizes two measurable parameters of homogeneous mixtures, chemical shift and peak integration, for three different applications: 1) a text‐encoding device that is based on spectral representation of a sequence of symbols, 2) encoding of 21‐digit binary numbers, each represented by an NMR spectrum, and their algebraic manipulations, such as addition and subtraction, and 3) encoding of 21‐digit decimal numbers. The first application enables molecular information storage and encryption. The relative concentration of each component, as measured by the relevant peak integration, can represent a symbol. The second application of this system, in addition to its obvious memory capability, enables mathematical operations. The NMR spectrum of a given mixture represents a 21‐digit binary number where each of the peaks encodes for a specific digit. In any of the input mixtures (numbers) each compound is either present or absent, representing either 1 or 0, respectively. We used the various binary numbers to carry out addition operations by combining two or more solutions (numbers). Subtraction operations were also preformed by digital processing of the information. The third application is the representation of decimal numbers. As before, each of the peaks encodes for a specific digit. In any of the input mixtures each compound is present in one of 10 different relative concentrations, representing the 10 digits of a decimal number.     

Calorimetric and spectrophotometric investigation of PLGA nanoparticles and their complex with DNA

The calorimetric investigation of non-coated and chitosan-coated PLGA nanoparticles (NP) shows that at initial temperatures of heating particle swelling takes place what results in an internal architectural change at lower than physiological temperature. It has shown that the temperature of NP tightness perturbing depends on solvent polarity: as more polar is the solvent more stable are particles. The break of existing bonds in NP shell is accompanied with heat absorption peak which undergoes significant changes depending on heating rate. In the wide pH 2–8 interval in transition temperature no changes occurred. The obtained results show that such NP could be used in acidic area for drug transfer, which gives possibility to take medicine orally. It was shown that DNA attaches only to chitosan-coated NP. The optimal ratio for DNA loading onto the NP was found to be 7:1 (W_NP/W_DNA).