Modification of micro-crystalline graphite and carbon black by acetone, toluene, and phenol.

The chemical interactions of two types of graphite and two types of carbon black (CB) with acetone, toluene, and phenol were studied in order to evaluate the influence of chemical treatment on the structure and morphology of the carbon phases. The experimental treatment of carbon phases was carried out at room temperature for 1 hour. The chemical and phase composition were studied by x-ray photoelectron (XP) and Raman spectroscopies, while the morphology and structure were determined by powder x-ray diffraction, as well as transmission electron microscopy techniques. To shed light on the most probable explanation of the observed results, we performed simulations and calculations of the binding energies of acetone, toluene, and phenol with model carbon phases: a perfect graphene sheet and a defective graphene sheet containing various structural defects (vacancies as well as zigzag and armchair edges). Simulations show that all non-covalent and most covalent coupling reactions are exothermic, with acetone coupling having the higher calorimetric effect. Based on the results of the simulations and the XP spectroscopy measurements, the probable reactions taking place during the respective treatments are outlined. The conducted studies (both theoretical and experimental) show that the treatment of graphite powders and CB with acetone, toluene, or phenol can be used as a preliminary stage of their modification and/or functionalization, including their conversion into graphene-like (defective graphene, reduced graphene oxide, and/or graphene oxide) phases. For example, the treatment of SPHERON 5000 with acetone significantly facilitates their subsequent modification with laser radiation to graphene-like phases.

Dissolution Behavior and Varied Mesoporosity of Zeolites by NH4 F Etching.

The mesopores formation in zeolite crystals has long been considered to occur through the stochastic hydrolysis and removal of framework atoms. Here, we investigate the NH4 F etching of representative small, medium, and large pore zeolites and show that the zeolite dissolution behavior, therefore the mesopore formation probability, is dominated by zeolite architecture at both nano- and sub-nano scales. At the nano-scale, the hidden mosaics of zeolite structure predetermine the spatio-temporal dissolution of the framework, hence the size, shape, location, and orientation of the mesopores. At the sub-nano scale, the intrinsic micropore size and connectivity jointly determine the diffusivity of reactant and dissolved products. As a result, the dissolution propensity varies from removing small framework fragments to consuming nanodomains and up to full digestion of the outmost part of zeolite crystals. The new knowledge will lead to new understanding of zeolite dissolution behavior and new adapted strategies for tailoring hierarchical zeolites.

Sodium and Magnesium Ion Location at the Backbone and at the Nucleobase of RNA: Ab Initio Molecular Dynamics in Water Solution.

The interactions between Na+ or Mg2+ ions with different parts of single-stranded RNA molecules, namely, the oxygen atoms from the phosphate groups or the guanine base, in water solution have been studied using first-principles molecular dynamics. Sodium ions were found to be much more mobile than Mg2+ ions and readily underwent transitions between a state directly bonded to RNA oxygen atoms and a completely solvated state. The inner solvation shell of Na+ ions fluctuated stochastically at a femtosecond timescale coordinating on average 5 oxygen atoms for bonded Na+ ions and 5.5 oxygen atoms for solvated Na+ ions. In contrast, the inner solvation shell of Mg2+ ions was stable in both RNA-bonded and completely solvated states. In both cases, Mg2+ ions coordinated 6 oxygen atoms from the inner solvation shell. Consistent with their stable solvation shells, Mg2+ ions were more effective than Na+ ions in stabilizing the RNA backbone conformation. The exclusion zones between the first and second solvation shells, solvation shell widths, and angles for binding to carbonyl oxygen of guanine for solvated Na+ or Mg2+ ions exhibited a number of quantitative differences when compared with RNA crystallographic data. The presented results support the distinct capacity of Mg2+ ions to support the RNA structure not only in the crystal phase but also in the dynamic water environment both on the side of the phosphate moiety and on the side of the nucleobase.

Density functional study of hydrogen bond formation between methanol and organic molecules containing Cl, F, NH2, OH, and COOH functional groups.

Various hydrogen-bonded complexes of methanol with different proton accepting and proton donating molecules containing Cl, F, NH(2), OH, OR, and COOH functional groups have been modeled using DFT with hybrid B3LYP and M05-2X functionals. The latter functional was found to provide more accurate estimates of the structural and thermodynamic parameters of the complexes of halides, amines, and alcohols. The characteristics of these complexes are influenced not only by the principle hydrogen bond of the methanol OH with the proton acceptor heteroatom, but also by additional hydrogen bonds of a C-H moiety with methanol oxygen as a proton acceptor. The contribution of the former hydrogen bond in the total binding enthalpy increases in the order chlorides < fluorides < alcohols < amines, while the contribution of the second type of hydrogen bond increases in the reverse order. A general correlation was found between the binding enthalpy of the complex and the electrostatic potential at the hydrogen center participating in the formation of the hydrogen bond. The calculated binding enthalpies of different complexes were used to clarify which functional groups can potentially form a hydrogen bond to the 2'-OH hydroxyl group in ribose, which is strong enough to block it from participation in the intramolecular catalytic activation of the peptide bond synthesis. Such blocking could result in inhibition of the protein biosynthesis in the living cell if the corresponding group is delivered as a part of a drug molecule in the vicinity of the active site in the ribosome. According to our results, such activity can be accomplished by secondary or tertiary amines, alkoxy groups, deprotonated carboxyl groups, and aliphatic fluorides, but not by the other modeled functional groups.

Computational capacity of pyramidal neurons in the cerebral cortex.

The electric activities of cortical pyramidal neurons are supported by structurally stable, morphologically complex axo-dendritic trees. Anatomical differences between axons and dendrites in regard to their length or caliber reflect the underlying functional specializations, for input or output of neural information, respectively. For a proper assessment of the computational capacity of pyramidal neurons, we have analyzed an extensive dataset of three-dimensional digital reconstructions from the NeuroMorpho.Org database, and quantified basic dendritic or axonal morphometric measures in different regions and layers of the mouse, rat or human cerebral cortex. Physical estimates of the total number and type of ions involved in neuronal electric spiking based on the obtained morphometric data, combined with energetics of neurotransmitter release and signaling fueled by glucose consumed by the active brain, support highly efficient cerebral computation performed at the thermodynamically allowed Landauer limit for implementation of irreversible logical operations. Individual proton tunneling events in voltage-sensing S4 protein α-helices of Na+, K+ or Ca2+ ion channels are ideally suited to serve as single Landauer elementary logical operations that are then amplified by selective ionic currents traversing the open channel pores. This miniaturization of computational gating allows the execution of over 1.2 zetta logical operations per second in the human cerebral cortex without combusting the brain by the released heat.

Interaction of Na+, K+, Mg2+ and Ca2+ counter cations with RNA.

Alkaline and alkaline earth ions, namely Na+, K+, Mg2+ and Ca2+, are critical for the stability, proper folding and functioning of RNA. Moreover, those metal ions help to facilitate macromolecular interactions as well as the formation of supramolecular structures (e.g. the ribosome and the ribozymes). Therefore, identifying the interactions between ions and nucleic acids is a key to the better comprehension of the physical nature and biological functions of those biomolecules. The scope of this review is to highlight the preferential location and binding sites of alkaline and alkaline earth metal ions compensating the negatively charged backbone of nucleic acids and interacting with other electronegative centers, focusing on RNA. We summarize experimental studies from X-ray crystallography and spectroscopic analysis (infrared, Raman and NMR spectroscopies). Computational results obtained with classical and ab initio methods are presented afterwards.

Hydrogen Atom Transfer from Water or Alcohols Activated by Presolvated Electrons.

High-energy irradiation of protic solvents can transiently introduce excess electrons that are implicated in a diverse range of reductive processes. Here we report the evolution of electron solvation in water and in alcohols following photodetachment from aqueous hydroxide or the corresponding alkoxides studied by two- and three-pulse femtosecond spectroscopy and ab initio molecular dynamic simulations. The experiments reveal an ultrafast recombination channel of the excess electrons. Through the calculations this channel emerges as an H-atom transfer process to the hydroxyl or alkoxy radical species from neighboring solvent molecules, which are activated as the presolvated electron occupies their antibonding orbitals. The initially low activation barrier in the early stages of electron solvation was found to increase (from 12 to 44 kJ/mol in water) as full solvation proceeded.