Photoionization dynamics of glycine adsorbed on a silicon cluster: "on-the-fly" simulations

Dynamics of glycine chemisorbed on the surface of a silicon cluster is studied for a process that involves single-photon ionization, followed by recombination with the electron after a selected time delay. The process is studied by "on-the-fly" molecular dynamics simulations, using the semiempirical parametric method number 3 (PM3) potential energy surface. The system is taken to be in the ground state prior to photoionization, and time delays from 5 to 50 fs before the recombination are considered. The time evolution is computed over 10 ps. The main findings are (1) the positive charge after ionization is initially mostly distributed on the silicon cluster. (2) After ionization the major structural changes are on the silicon cluster. These include Si-Si bond breaking and formation and hydrogen transfer between different silicon atoms. (3) The transient ionization event gives rise to dynamical behavior that depends sensitively on the ion state lifetime. Subsequent to 45 fs evolution in the charged state, the glycine molecule starts to rotate on the silicon cluster. Implications of the results to various processes that are induced by transient transition to a charged state are discussed. These include inelastic tunneling in molecular devices, photochemistry on conducting surfaces, and electron-molecule scattering.     

Vibrational spectroscopy of the G...C base pair: experiment, harmonic and anharmonic calculations, and the nature of the anharmonic couplings

The results of harmonic and anharmonic frequency calculations on a guanine-cytosine complex with an enolic structure (a tautomeric form with cytosine in the enol form and with a hydrogen at the 7-position on guanine) are presented and compared to gas-phase IR-UV double resonance spectral data. Harmonic frequencies were obtained at the RI-MP2/cc-pVDZ, RI-MP2/TZVPP, and semiempirical PM3 levels of electronic structure theory. Anharmonic frequencies were obtained by the CC-VSCF method with improved PM3 potential surfaces; the improved PM3 potential surfaces are obtained from standard PM3 theory by coordinate scaling such that the improved PM3 harmonic frequencies are the same as those computed at the RI-MP2/cc-pVDZ level. Comparison of the data with experimental results indicates that the average absolute percentage deviation for the methods is 2.6% for harmonic RI-MP2/cc-pVDZ (3.0% with the inclusion of a 0.956 scaling factor that compensates for anharmonicity), 2.5% for harmonic RI-MP2/TZVPP (2.9% with a 0.956 anharmonicity factor included), and 2.3% for adapted PM3 CC-VSCF; the empirical scaling factor for the ab initio harmonic calculations improves the stretching frequencies but decreases the accuracy of the other mode frequencies. The agreement with experiment supports the adequacy of the improved PM3 potentials for describing the anharmonic force field of the G...C base pair in the spectroscopically probed region. These results may be useful for the prediction of the pathways of vibrational energy flow upon excitation of this system. The anharmonic calculations indicate that anharmonicity along single mode coordinates can be significant for simple stretching modes. For several other cases, coupling between different vibrational modes provides the main contribution to anharmonicity. Examples of strongly anharmonically coupled modes are the symmetric stretch and group torsion of the hydrogen-bonded NH2 group on guanine, the OH stretch and torsion of the enol group on cytosine, and the NH stretch and NH out-of-plane bend of the non-hydrogen-bonded NH group on guanine.     

Dynamics of Finger Formation in Laplacian Growth Without Surface Tension

We study the dynamics of “finger” formation in Laplacian growth without surface tension in a channel geometry (the Saffman–Taylor problem). We present a pedagogical derivation of the dynamics of the conformal map from a strip in the complex plane to the physical channel. In doing so we pay attention to the boundary conditions (no flux rather than periodic) and derive a field equation of motion for the conformal map. We first consider an explicit analytic class of conformal maps that form a basis for solutions in infinitely long channels, characterized by meromorphic derivatives. The great bulk of these solutions can lose conformality due to finite time singularities. By considerations of the nature of the analyticity of these solutions, we show that those solutions which are free of such singularities inevitably result in a single asymptotic “finger” whose width is determined by initial conditions. This is in contradiction with the experimental results that indicate selection of a finger of width 1/2. In the last part of this paper we show that such a solution might be determined by the boundary conditions of a finite body of fluid, e.g. finiteness can lead to pattern selection.     

Small subgraphs of random regular graphs

The main aim of this short paper is to answer the following question. Given a fixed graph H, for which values of the degree d does a random d-regular graph on n vertices contain a copy of H with probability close to one?     

Crossing numbers of sequences of graphs II: Planar tiles

We describe a method of creating an infinite family of crossing‐critical graphs from a single small planar map, the tile, by gluing together many copies of the tile together in a circular fashion. This method yields all known infinite families of k‐crossing‐critical graphs. Furthermore, the method yields new infinite families, which extend from (4,6) to (3.5,6) the interval of rationals r for which there is, for some k, an infinite sequence of k‐crossing‐critical graphs all having average degree r. © 2003 Wiley Periodicals, Inc. J Graph Theory 42: 332–341, 2003     

Gas permeability and n‐butane solubility of poly(1‐trimethylgermyl‐1‐propyne)

The gas permeability and n‐butane solubility in glassy poly(1‐trimethylgermyl‐1‐propyne) (PTMGP) are reported. As synthesized, the PTMGP product contains two fractions: (1) one that is insoluble in toluene and soluble only in carbon disulfide (the toluene‐insoluble polymer) and (2) one that is soluble in both toluene and carbon disulfide (the toluene‐soluble polymer). In as‐cast films, the gas permeability and n‐butane solubility are higher in films prepared from the toluene‐soluble polymer (particularly in those films cast from toluene) than in films prepared from the toluene‐insoluble polymer and increase to a maximum in both fractions after methanol conditioning. For example, in as‐cast films prepared from carbon disulfide, the oxygen permeability at 35 °C is 330 × 10^?10 cm³ (STP) cm/(cm² s cmHg) for the toluene‐soluble polymer and 73 × 10^?10 cm³ (STP) cm/(cm² s cmHg) for the toluene‐insoluble polymer. After these films are conditioned in methanol, the oxygen permeability increases to 5200 × 10^?10 cm³ (STP) cm/(cm² s cmHg) for the toluene‐soluble polymer and 6200 × 10^?10 cm³ (STP) cm/(cm² s cmHg) for the toluene‐insoluble polymer. The rankings of the fractional free volume and nonequilibrium excess free volume in the various PTMGP films are consistent with the measured gas permeability and n‐butane solubility values. Methanol conditioning increases gas permeability and n‐butane solubility of as‐cast PTMGP films, regardless of the polymer fraction type and casting solvent used, and minimizes the permeability and solubility differences between the various films (i.e., the permeability and solubility values of all conditioned PTMGP films are similar). © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2228–2236, 2002     

Evaluation of extraction methods for quantification of aqueous fullerenes in urine

There is a growing concern about the human and environmental health effects of fullerenes (e.g., C(60)) due to their increasing application in research, medicine, and industry. Toxicological and pharmacokinetic research requires standard methods for extraction and detection of fullerenes from biological matrices such as urine. The present study validates the use of liquid-liquid extraction (LLE) and solid-phase extraction (SPE) methods in conjunction with liquid chromatography-mass spectrometry (LC-MS) for the quantitative determination of C(60) in human and synthetic urine as compared with ultrapure water. Glacial acetic acid, which is necessary to prevent emulsions during LLE, inhibited C(60) detection by LC-MS, but this could be mitigated with evaporation. Aqueous C(60) aggregates (nC(60)) were spiked at 180 μg/L into the components of a synthetic urine recipe to determine their individual impacts on extraction and detection. Urea, creatinine, and a complex protein (i.e., gelatin) were found to impair SPE, leading to a low recovery rate of 43 ± 4% for C(60) spiked into human urine. In contrast, C(60) was consistently recovered from synthetic matrices using LLE, and recovery in human urine was 80 ± 6%. These results suggest that LLE combined with LC-MS is suitable for studying the clearance of fullerenes from the body. LLE is a robust technique that holds promise for extracting C(60) from other complex biological matrices (e.g., blood, sweat, amniotic fluid) in toxicological studies, enabling a better understanding of the behavior of fullerenes in human and animal systems and facilitating a more comprehensive risk evaluation of fullerenes.     

A conjecture of Erd?s on graph Ramsey numbers

The Ramsey number r(G) of a graph G is the minimum N such that every red–blue coloring of the edges of the complete graph on N vertices contains a monochromatic copy of G. Determining or estimating these numbers is one of the central problems in combinatorics.One of the oldest results in Ramsey Theory, proved by Erd?s and Szekeres in 1935, asserts that the Ramsey number of the complete graph with m edges is at most . Motivated by this estimate Erd?s conjectured, more than a quarter century ago, that there is an absolute constant c such that for any graph G with m edges and no isolated vertices. In this short note we prove this conjecture.     

Prediction of a linear polymer made of xenon and carbon

Electronic structure calculations predict the existence of a novel type of a chemically bound noble gas compound. The predicted species is an extended linear and periodic polymer, made of the repeat unit -(XeCC)-, where CC is the acetylenic group. The polymer has a strong partly ionic nature, with positive partial charge on the xenon atoms and a negative one on the CC groups. High energy barriers are found for the removal of a Xe atom from the chain, indicating high stability. This is the first polymer with a noble-gas-containing building block.     

Cr(VI) adsorption mechanism on rice husk ash burned at low temperature by method of IR spectra

Boehm titration method was used to analyze functional groups on cell surface of rice husk ash burned at low temperature in the present paper. Effects of initial pH value and temperature on Cr(VI) adsorption were studied, adsorption capacity was tested with the help of kinetic models and adsorption isotherms, instruments of Fourier transform infrared spectroscopy(FTIR) and scanning electron microscope (SEM) were used to check characteristics and adsorption mechanism of Cr(VI). The results indicated that optimal removing rate was achieved at initial pH value 5, and pH values of aqueous solution changed little be fore and after adsorption process. The adsorbent of rice husk ash could remove Cr(VI) effectively, and the maximum removing rate could be 95% with Cr(VI) concentration 20 mg x L(-1) and achieve 1-2 level of state standard(GB8978-1996). The adsorption process fits pseudo-second-order kinetic model and Langmuir isotherm better, the maximum adsorption capacity of Cr(VI) was 3.2776 mg x g(-1). Results of FTIR showed that amide II band, Si--O--Si, O--Si--O were important for Cr(VI) removal. SEM micrographs revealed that series of needle-shaped precipitation appeared on cell surface, and inorganic precipitation mechanism and redox mechanism might work in the test. As a kind of low cost adsorbent, rice husk ash can be applied to remove heavy metals in environment with great potential.