Aqua ions-graphene interfacial and confinement behavior: insights from isobaric-isothermal molecular dynamics

We carry out a systematic microstructural characterization of the solid-fluid interface (SFI) of water and simple metal chloride aqueous solutions in contact with a free-standing plate or with two such plates separated by an interplate distance 0 ≤ h (?) ≤ 30 at ambient conditions via isothermal-isobaric molecular dynamics. With this characterization, we target the interrogation of the system in search for answers to fundamental questions regarding the structure of the "external" and "internal" (confined) SFIs, the effect of the differential hydration behavior among species, and its link to species expulsion from confinement. For water at ambient conditions, we found that the structure of the "external" SFIs is independent of the interplate distance h in the range 0 ≤ h (?) ≤ 30, that is, the absence of wall-mediated correlation effects between "external" and "internal" SFIs, and that for h < 9 ? the slit-pores dewet. Moreover, we observed a selective expulsion of ions caused by the differential hydration between the anion and the cations with a consequent charging of the slit-pore. All these observations were interpreted in terms of the axial profiles for precisely defined order parameters, including tetrahedral configuration, hydrogen bonding, and species coordination numbers.     

X-ray structure analysis and the intervalent electron transfer in organic mixed-valence crystals with bridged aromatic cation radicals

X-ray crystallography identifies the aromatic donor group D = 2,5-dimethoxy-4-methylphenyl to be a suitable redox center for the construction of organic mixed-valence crystals owing to its large structural change attendant upon 1e oxidation to the cation-radical (D*(+)). The combination of cyclic voltammetry, dynamic ESR line broadening, and electronic (NIR) spectroscopy allows the intervalence electron transfer between the redox centers in the mixed-valence system D-br-D*(+) [where br can be an aliphatic trimethylene or an aromatic (poly)phenylene bridge] to be probed quantitatively. Independent measures of the electronic coupling matrix element (H) for D/D*(+) electron exchange via Mulliken-Hush theory accord with the X-ray crystallographic data-both sufficient to consistently identify the various D-br-D*(+) according to the Robin-Day classification. Thus, the directly coupled biaryl D-D*(+) is a completely delocalized cation in class III with the charge distributed equally over both redox centers. The trimethylene- and biphenylene-bridged cations D(CH(2))(3)D*(+) and D(ph)(2)D*(+) with highly localized charge distributions are prototypical class II systems involving moderately coupled redox centers with H approximately equal to 400 cm(-1). The borderline region between class II/III is occupied by the phenylene-bridged cation D(ph)D*(+); and the X-ray, CV, and NIR analyses yield ambivalent H values (which we believe to be) largely a result of an unusually asymmetric (20/80) charge distribution that is polarized between the D/D*(+) redox centers.     

Activation volume measurement for C[bond]H activation. Evidence for associative benzene substitution at a platinum(II) center

The reaction of the platinum(II) methyl cation [(N-N)Pt(CH(3))(solv)](+) (N-N = ArN[double bond]C(Me)C(Me)[double bond]NAr, Ar = 2,6-(CH(3))(2)C(6)H(3), solv = H(2)O (1a) or TFE = CF(3)CH(2)OH (1b)) with benzene in TFE/H(2)O solutions cleanly affords the platinum(II) phenyl cation [(N-N)Pt(C(6)H(5))(solv)](+) (2). High-pressure kinetic studies were performed to resolve the mechanism for the entrance of benzene into the coordination sphere. The pressure dependence of the overall second-order rate constant for the reaction resulted in Delta V(++) = -(14.3 +/- 0.6) cm(3) mol(-1). Since the overall second order rate constant k = K(eq)k(2), Delta V(++) = Delta V degrees (K(eq)) + Delta V(++)(k(2)). The thermodynamic parameters for the equilibrium constant between 1a and 1b, K(eq) = [1b][H(2)O]/[1a][TFE] = 8.4 x 10(-4) at 25 degrees C, were found to be Delta H degrees = 13.6 +/- 0.5 kJ mol(-1), Delta S degrees = -10.4 +/- 1.4 J K(-1) mol(-1), and Delta V degrees = -4.8 +/- 0.7 cm(3) mol(-1). Thus DeltaV(++)(k(2)) for the activation of benzene by the TFE solvento complex equals -9.5 +/- 1.3 cm(3) mol(-1). This significantly negative activation volume, along with the negative activation entropy for the coordination of benzene, clearly supports the operation of an associative mechanism.     

Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations

A protocol is described for the treatment of molecular polarization in force field calculations. The resulting model is consistent in that both inter- and intramolecular polarization are handled within a single scheme. An analytical formula for removing intramolecular polarization from a set of atomic multipoles for an arbitrary static structure or conformation is given. With the help of the intramolecular polarization, these permanent atomic multipoles can then be applied in modeling alternative conformations of a molecule. Equipped with this simple technique, one can derive transferable electrostatic parameters for peptides and proteins using flexible model compounds such as dipeptides. The proposed procedure is tested for its ability to describe the electrostatic potential around various configurations of the N-methylacetamide dimer. The effect of different intramolecular polarization schemes on the accuracy of a force field model of the electrostatic potential of alanine dipeptide is investigated. A group-based scheme for including direct intramolecular polarization is shown to be most successful in accounting for the conformational dependence of electrostatic potentials.     

Electron tunneling through sensitizer wires bound to proteins

We report a quantitative theoretical analysis of long-range electron transfer through sensitizer wires bound in the active-site channel of cytochrome P450cam. Each sensitizer wire consists of a substrate group with high binding affinity for the enzyme active site connected to a ruthenium-diimine through a bridging aliphatic or aromatic chain. Experiments have revealed a dramatic dependence of electron transfer rates on the chemical composition of both the bridging group and the substrate. Using combined molecular dynamics simulations and electronic coupling calculations, we show that electron tunneling through perfluorinated aromatic bridges is promoted by enhanced superexchange coupling through virtual reduced states. In contrast, electron flow through aliphatic bridges occurs by hole-mediated superexchange. We have found that a small number of wire conformations with strong donor–acceptor couplings can account for the observed electron tunneling rates for sensitizer wires terminated with either ethylbenzene or adamantane. In these instances, the rate is dependent not only on electronic coupling of the donor and acceptor but also on the nuclear motion of the sensitizer wire, necessitating the calculation of average rates over the course of a molecular dynamics simulation. These calculations along with related recent findings have made it possible to analyze the results of many other sensitizer-wire experiments that in turn point to new directions in our attempts to observe reactive intermediates in the catalytic cycles of P450 and other heme enzymes.     

Anodic stripping electrochemical analysis of metal nanoparticles

Traditional anodic stripping voltammetry (ASV) involves electrodeposition (reduction) of metal ions from solution over some time scale onto a working electrode followed by stripping (oxidation) of the deposited metal in a second step, where the stripping potential and quantity of charge passed provide information about the metal identity and solution concentration, respectively. ASV has recently been extended to the analysis of metal nanoparticles (NPs), which have grown popular because of their fascinating properties tunable by size, shape, and composition. There is a need for improved methods of NP analysis, and because metal NPs can be oxidized to metal ions, ASV is a logical choice. Early studies involved metal NPs as tags for the detection of biomolecules. More recently, anodic stripping has been used to directly analyze the physical, chemical, and structural properties of metal NPs. This review highlights the stripping analysis of NP assemblies on macroelectrodes, individual NPs in solution during collisions with a microelectrode, and a single NP attached to an electrode. A surprising amount of information can be learned from this very simple, low-cost technique.     

Communication: Phase incremented echo train acquisition in NMR spectroscopy

We present an improved and general approach for implementing echo train acquisition (ETA) in magnetic resonance spectroscopy, particularly where the conventional approach of Carr-Purcell-Meiboom-Gill (CPMG) acquisition would produce numerous artifacts. Generally, adding ETA to any N-dimensional experiment creates an N + 1 dimensional experiment, with an additional dimension associated with the echo count, n, or an evolution time that is an integer multiple of the spacing between echo maxima. Here we present a modified approach, called phase incremented echo train acquisition (PIETA), where the phase of the mixing pulse and every other refocusing pulse, φ(P), is incremented as a single variable, creating an additional phase dimension in what becomes an N + 2 dimensional experiment. A Fourier transform with respect to the PIETA phase, φ(P), converts the φ(P) dimension into a Δp dimension where desired signals can be easily separated from undesired coherence transfer pathway signals, thereby avoiding cumbersome or intractable phase cycling schemes where the receiver phase must follow a master equation. This simple modification eliminates numerous artifacts present in NMR experiments employing CPMG acquisition and allows "single-scan" measurements of transverse relaxation and J-couplings. Additionally, unlike CPMG, we show how PIETA can be appended to experiments with phase modulated signals after the mixing pulse.     

An integrated chemical biology approach provides insight into cdk2 functional redundancy and inhibitor sensitivity

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Highlights? Demonstration that Cdk2 is rate-limiting for DNA replication due to insufficient Cdk1 activity ? A simple bioinformatic approach to design inhibitor resistant mutations in kinases ? Demonstration of distinct binding modes and selectivity of Cdk inhibitors ? Identification of kinetic and structural mechanisms of inhibitor resistance